Dernières modifications :

Tagmentation.
diff --git a/biblio/21143862.mdwn b/biblio/21143862.mdwn
new file mode 100644
index 00000000..968690eb
--- /dev/null
+++ b/biblio/21143862.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition."]]
+[[!tag transposase]]
+
+Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J.
+
+Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
+
+Genome Biol. 2010;11(12):R119. doi: 10.1186/gb-2010-11-12-r119
+
+[[!pmid 21143862 desc="Tn5 tagmentation: in vitro transposase-catalyzed adaptor insertion."]]
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index 4e839843..0075de9f 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -2,6 +2,9 @@
 
 _work in progress_
 
+ - Tn5 tagmentation (“in vitro transposase-catalyzed adaptor insertion”):
+   [[Adey and coll., 2010|biblio/21143862]].
+
  - Method to produce Tn5 in a laboratory: [[Picelli and coll., 2014|biblio/25079858]].
 
  - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is

transposase
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index 4101ec2a..4e839843 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -7,4 +7,6 @@ _work in progress_
  - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is
    not efficient on hyperbranched DNA ([[Gole and coll., 2013|biblio/24213699]]).
 
+ - Tn5 still binds after ligating its payload ([[Amini and coll., 2014|biblio/25326703]]).
+
 [[!inline pages="tagged(transposase)" limit=0]]

updated PO files
diff --git "a/Debian/debi\303\242neries/X61.en.po" "b/Debian/debi\303\242neries/X61.en.po"
new file mode 100644
index 00000000..c8c1078d
--- /dev/null
+++ "b/Debian/debi\303\242neries/X61.en.po"
@@ -0,0 +1,49 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2020-09-21 01:43+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Merci, VAIO\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'utilise tous les jours un VAIO Pro 13 mk2 acheté il y a 5 ans avec 3 ans "
+"de guarantie.  Cela faisait quelques mois que j'avais remarqué que quelque "
+"chose enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré "
+"au point qu'il a doublé d'épaisseur.  Après avoir appelé le service "
+"après-vente de VAIO, quelqu'un est passé le prendre pour faire une "
+"estimation du coût de la réparation.  Et ensuite on nous a annoncé que ça "
+"serait gratuit.  Le voici de retour dans mes mains en moins de deux "
+"semaines.  Bravo VAIO !"
+msgstr ""

transposase
diff --git a/biblio/31988135.mdwn b/biblio/31988135.mdwn
index 962a94a6..4e62598f 100644
--- a/biblio/31988135.mdwn
+++ b/biblio/31988135.mdwn
@@ -7,4 +7,4 @@ Proc Natl Acad Sci U S A. 2020 Jan 27. pii: 201919800. doi:10.1073/pnas.19198001
 
 RNA sequencing by direct tagmentation of RNA/DNA hybrids.
 
-[[!pmid 31988135 desc="Impact on size profile is much harder to notice compared with DNA/DNA tagmentation (Figs S9 and S10)."]]
+[[!pmid 31988135 desc="Sequencing HEteRo RNA-DNA-hYbrid (SHERRY).  Impact on size profile is much harder to notice compared with DNA/DNA tagmentation (Figs S9 and S10)."]]
diff --git a/tags/transposase.mdwn b/tags/transposase.mdwn
index f8db17c5..4101ec2a 100644
--- a/tags/transposase.mdwn
+++ b/tags/transposase.mdwn
@@ -1,4 +1,10 @@
 [[!meta title="pages tagged transposase"]]
 
-[[!inline pages="tagged(transposase)" actions="no" archive="yes"
-feedshow=10]]
+_work in progress_
+
+ - Method to produce Tn5 in a laboratory: [[Picelli and coll., 2014|biblio/25079858]].
+
+ - Tn5 can tagment RNA/DNA hybrids ([[Di and coll., 2020|biblio/31988135]]),  but it is
+   not efficient on hyperbranched DNA ([[Gole and coll., 2013|biblio/24213699]]).
+
+[[!inline pages="tagged(transposase)" limit=0]]

Café hier.
diff --git a/biblio/32669707.mdwn b/biblio/32669707.mdwn
new file mode 100644
index 00000000..c315b18a
--- /dev/null
+++ b/biblio/32669707.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nucleolar RNA polymerase II drives ribosome biogenesis."]]
+[[!tag transcription ribosome nucleolus]]
+
+Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K.
+
+Nature. 2020 Sep;585(7824):298-302. doi: 10.1038/s41586-020-2497-0
+
+Nucleolar RNA polymerase II drives ribosome biogenesis.
+
+[[!pmid 32669707 desc="Active (S2p) Pol II is enriched at InterGenic Spacer (IGS) regions.  Pol II inhibition with α-amanitin (AMN) or flavopiridol for 30 min was sufficient to disrupt rRNA processing.  IGS noncoding RNAs (ncRNAs) decreased in abundance following Pol I inhibition and increased with Pol II inhibition.  Double inhibition decreased their abundance.  Pol I transcribed sense intergenic ncRNAs (sincRNAs) and Pol II antisense intergenic ncRNAs (asincRNAs)."]]

Café
diff --git a/biblio/32211845.mdwn b/biblio/32211845.mdwn
new file mode 100644
index 00000000..be4874ee
--- /dev/null
+++ b/biblio/32211845.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata."]]
+[[!tag Oikopleura]]
+
+DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. 
+
+Genome Biol Evol. 2020 Jun 1;12(6):948-964. doi:10.1093/gbe/evaa060
+
+Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata.
+
+[[!pmid 32211845 desc="210 single-copy orthogroups from 37 tunicates + 10 outgroups.  Questions the annotation (gene name) of the Hox genes in Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 66ac8c68..bf2df3f6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -40,8 +40,10 @@ Phylogeny
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
  - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]]),
    on 798 genes in 28 species ([[Kocot and coll., 2018|biblio/29330139]]),
-   and 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
-   show that Oikopleuridae is sister to all other tunicates.
+   258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]]),
+   and 210 single-copy orthogroups from 37 tunicates + 10 outgroups
+   [[DeBiasse and coll., 2020|biblio/32211845]] show that appendicularians are
+   sister to all other tunicates.
  - “The difference between coding sequences was considerably higher in
    comparisons between strains of different oceans than within the Bergen gene
    pool.  We ignore whether and how Oikopleura dioica is subdivided into multiple

Café
diff --git a/biblio/29330139.mdwn b/biblio/29330139.mdwn
new file mode 100644
index 00000000..79ea63b7
--- /dev/null
+++ b/biblio/29330139.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Phylogenomics offers resolution of major tunicate relationships."]]
+[[!tag Oikopleura tunicate evolution]]
+
+Kocot KM, Tassia MG, Halanych KM, Swalla BJ.
+
+Mol Phylogenet Evol. 2018 Apr;121:166-173. doi:10.1016/j.ympev.2018.01.005
+
+Phylogenomics offers resolution of major tunicate relationships.
+
+[[!pmid 29330139 desc="A matrix of 798 genes totaling 254,865 amino acid positions places appendicularians as the sister group to all other tunicates."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ce6665c1..66ac8c68 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -38,8 +38,9 @@ Phylogeny
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
- - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
-   and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
+ - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]]),
+   on 798 genes in 28 species ([[Kocot and coll., 2018|biblio/29330139]]),
+   and 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
    show that Oikopleuridae is sister to all other tunicates.
  - “The difference between coding sequences was considerably higher in
    comparisons between strains of different oceans than within the Bergen gene

Shasta
diff --git a/biblio/32686750.mdwn b/biblio/32686750.mdwn
new file mode 100644
index 00000000..5b53d3c0
--- /dev/null
+++ b/biblio/32686750.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes."]]
+[[!tag assembly method software]]
+
+Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B.
+
+Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi:10.1038/s41587-020-0503-6
+
+Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
+
+[[!pmid 32686750 desc="Runs in memory (no disk IO) and requires terabyte amounts for human genome.  Designed for Nanopore data.  Reads are run length encoded before assembling.  Assemblies are more fragmented, but with less disagreements to the reference.  The estimated cost of running is lower than for competitors."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 259f50eb..6ff69435 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -15,6 +15,14 @@ contings and increase their accuracy.  (The predecessor of Flye, ABruijn, was
 reported by [[Istace and coll. (2017)|biblio/28369459]] to be able to assemble
 mitochondrial genomes, unlike Canu and other assemblers.)
 
+The Shasta assembler [[Shafin and coll., 2020|biblio/32686750]] is designed for
+Nanopore data. Reads are run length encoded before assembly, to mitigate the
+impact of errors in homopolymer tracts.  The assembly runs entirely in memory;
+it needs terabyte amounts for a human genome, but as a consequence it runs
+fast. Shasta assemblies tend to be more fragmented, but have less disagreement
+with the reference.  Shasta also comes with polishing modules similar to Racon
+and Medaka, but also  to be faster. 
+
 After assembly, the contigs can be further polished with Racon ([[Vaser, Sović,
 Nagarajan and Šikić, 2017|biblio/28100585]]).
 

Ptitdéj
diff --git a/biblio/32500941.mdwn b/biblio/32500941.mdwn
new file mode 100644
index 00000000..c27da783
--- /dev/null
+++ b/biblio/32500941.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Highly active rubiscos discovered by systematic interrogation of natural sequence diversity."]]
+[[!tag screen]]
+
+Davidi D, Shamshoum M, Guo Z, Bar-On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller-Cajar O, Milo R.
+
+EMBO J. 2020 Jun 5:e104081. doi:10.15252/embj.2019104081
+
+Highly active rubiscos discovered by systematic interrogation of natural sequence diversity.
+
+[[!pmid 32500941 desc="A faster enzyme was found, but its specificity to CO2 is lower."]]

creating tag page tags/COVID-19
diff --git a/tags/COVID-19.mdwn b/tags/COVID-19.mdwn
new file mode 100644
index 00000000..87e460c2
--- /dev/null
+++ b/tags/COVID-19.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged COVID-19"]]
+
+[[!inline pages="tagged(COVID-19)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/SARS-CoV-2
diff --git a/tags/SARS-CoV-2.mdwn b/tags/SARS-CoV-2.mdwn
new file mode 100644
index 00000000..f3dce043
--- /dev/null
+++ b/tags/SARS-CoV-2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged SARS-CoV-2"]]
+
+[[!inline pages="tagged(SARS-CoV-2)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32868442.mdwn b/biblio/32868442.mdwn
new file mode 100644
index 00000000..6ddf9c9a
--- /dev/null
+++ b/biblio/32868442.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid isothermal amplification and portable detection system for SARS-CoV-2."]]
+[[!tag SARS-CoV-2 COVID-19 microfluidic isothermal]]
+
+Ganguli A, Mostafa A, Berger J, Aydin MY, Sun F, Ramirez SAS, Valera E, Cunningham BT, King WP, Bashir R.
+
+Proc Natl Acad Sci U S A. 2020 Aug 31:202014739. doi:10.1073/pnas.2014739117
+
+Rapid isothermal amplification and portable detection system for SARS-CoV-2.
+
+[[!pmid 32868442 desc="RT-LAMP assay on gene N.  Amplification in a microfluidic device.  LEDs (λpeak = 485 nm, XPEBBL, Cree) used to excite the EvaGreen fluorescent dye.  Signal read on a smartphone camera after going through a custom long-pass filter.]]

Café
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
index 1cda6a7d..6dc18731 100644
--- a/tags/automation.mdwn
+++ b/tags/automation.mdwn
@@ -1,4 +1,9 @@
 [[!meta title="pages tagged automation"]]
 
-[[!inline pages="tagged(automation)" actions="no" archive="yes"
-feedshow=10]]
+“Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery” ([[Kitano 2016|biblio/AI_37_2642]]).
+
+“A mobile robotic chemist” ([[Burger and coll., 2020|biblio/32641813]]).
+
+The use of laboratory automation in synthetic biology studied by a sociologist: [[Meckin 2020|biblio/32904024]].
+
+[[!inline pages="tagged(automation)" limit=0]]

Café
diff --git a/biblio/32904024.mdwn b/biblio/32904024.mdwn
new file mode 100644
index 00000000..981c1018
--- /dev/null
+++ b/biblio/32904024.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience."]]
+[[!tag automation]]
+
+Meckin R.
+
+Sci Technol Human Values. 2020 Nov;45(6):1220-1241. doi:10.1177/0162243919893757
+
+Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience.
+
+[[!pmid 32904024 desc="Synthetic biologists studied by a sociologist."]]

Café
diff --git a/biblio/32817535.mdwn b/biblio/32817535.mdwn
new file mode 100644
index 00000000..2aef39ef
--- /dev/null
+++ b/biblio/32817535.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Vianna JA, Fernandes FAN, Frugone MJ, Figueiró HV, Pertierra LR, Noll D, Bi K, Wang-Claypool CY, Lowther A, Parker P, Le Bohec C, Bonadonna F, Wienecke B, Pistorius P, Steinfurth A, Burridge CP, Dantas GPM, Poulin E, Simison WB, Henderson J, Eizirik E, Nery MF, Bowie RCK."]]
+[[!tag genome]]
+
+Vianna JA, Fernandes FAN, Frugone MJ, Figueiró HV, Pertierra LR, Noll D, Bi K, Wang-Claypool CY, Lowther A, Parker P, Le Bohec C, Bonadonna F, Wienecke B, Pistorius P, Steinfurth A, Burridge CP, Dantas GPM, Poulin E, Simison WB, Henderson J, Eizirik E, Nery MF, Bowie RCK.
+
+Genome-wide analyses reveal drivers of penguin diversification.
+
+Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22303-22310. doi:10.1073/pnas.2006659117
+
+[[!pmid 32817535 desc="Assemblies guided by the reference empreor penguin genome."]]

Add tag.
diff --git a/biblio/17333540.mdwn b/biblio/17333540.mdwn
index 56ea8e2e..24076ba1 100644
--- a/biblio/17333540.mdwn
+++ b/biblio/17333540.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica."]]
-[[!tag Oikopleura histone telomere H3S28p]]
+[[!tag Oikopleura histone telomere H3S28p H3S31p]]
 
 Chromosome Res. 2007;15(2):189-201. doi:10.1007/s10577-006-1112-z
 

Café
diff --git a/biblio/12453460.mdwn b/biblio/12453460.mdwn
new file mode 100644
index 00000000..a646de14
--- /dev/null
+++ b/biblio/12453460.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Patterning through differential endoreduplication in epithelial organogenesis of the chordate, Oikopleura dioica."]]
+[[!tag Oikopleura cell_cycle]]
+
+Ganot P, Thompson EM.
+
+Patterning through differential endoreduplication in epithelial organogenesis of the chordate, _Oikopleura dioica_.
+
+Dev Biol. 2002 Dec 1;252(1):59-71. doi:10.1006/dbio.2002.0834
+
+[[!pmid 12453460 desc="In the epithelial cells, “endoreduplication begins before tailshift and stops during gamete differentiation.”  “Endocycles are asynchronous within a given field of oikoplastic cells, but the replication pattern is bilaterally symmetrical.”  “In mature animals, final ploidy levels ranged from a low of 34 C in chain of pearl nuclei to 1300 C in giant Eisen nuclei.”  Cells with higher ploidy had shorter gap phases."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f3ed4dc6..ce6665c1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -392,6 +392,10 @@ Development
    ([[Bassham and Postlethwait (2000)|biblio/10753519]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
+ - Epithelial cells divide by mitosis during embryogenesis.  Once the final number
+   of cells is produce, they grow by endomitosis, with final ploidy ranging between
+   ~30 to ~1300 C. Cells with higher ploidy have shorter gap phases.  Endomitoses
+   stop when gamete differentiation starts.  [[Ganot and Thompson, 2002|biblio/12453460]]
  - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations
    of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
    ([[Spada and coll., 2007|biblio/17288541]]).

Published.
diff --git a/biblio/10.1101_831495.mdwn b/biblio/32788667.mdwn
similarity index 50%
rename from biblio/10.1101_831495.mdwn
rename to biblio/32788667.mdwn
index b21a6829..7bd4e28c 100644
--- a/biblio/10.1101_831495.mdwn
+++ b/biblio/32788667.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="High throughput, error corrected Nanopore single cell transcriptome sequencing"]]
-[[!tag bioRxiv Nanopore single_cell]]
+[[!tag Nanopore single_cell]]
 
 Kevin Lebrigand, Virginie Magnone, Pascal Barbry and Rainer Waldmann
 
-Posted November 05, 2019
+Nat Commun. 2020 Aug 12;11(1):4025. doi:10.1038/s41467-020-17800-6.
 
 High throughput, error corrected Nanopore single cell transcriptome sequencing
 
-[[!doi 10.1101/831495 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]
+[[!pmid 32788667 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]

Café
diff --git a/biblio/10.1101_2020.03.10.985549.mdwn b/biblio/10.1101_2020.03.10.985549.mdwn
new file mode 100644
index 00000000..791bf8ac
--- /dev/null
+++ b/biblio/10.1101_2020.03.10.985549.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants"]]
+[[!tag bioRxiv genome]]
+
+Jing Xia, Aarthi Venkat, Karine Le Roch, Ferhat Ay and Jon P. Boyle
+
+bioRxiv 2020.03.10.985549; doi:https://doi.org/10.1101/2020.03.10.985549
+
+Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.
+
+[[!doi 10.1101/2020.03.10.985549 desc="Long-read sequencing leads to revision of the karyotype."]]

Centromeres.
diff --git a/biblio/23832878.mdwn b/biblio/23832878.mdwn
new file mode 100644
index 00000000..e7c17334
--- /dev/null
+++ b/biblio/23832878.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry."]]
+[[!tag cell_cycle centromere microscopy]]
+
+Amakawa G, Ikemoto K, Ito H, Furuya T, Sasaki K.
+
+J Histochem Cytochem. 2013 Oct;61(10):699-705. doi:10.1369/0022155413498754
+
+Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry.
+
+[[!pmid 23832878 desc="Fluorescence in situ hybridization (FISH) using chromosome enumeration DNA probes (CEPs) labeling centromeric regions.  The intensity of the staining increases as the cell progresses in the cell cycle.  On the published pictures, it is rare to be able to resolve the centromeric regions of the sister chromatids."]]
diff --git a/tags/centromere.mdwn b/tags/centromere.mdwn
index 40284a22..6a3d6ca9 100644
--- a/tags/centromere.mdwn
+++ b/tags/centromere.mdwn
@@ -2,17 +2,27 @@
 
 _Work in progress_
 
+## Sequence
+
  - Brute-force analysis to find the most abundant large tandem repeat can find
    centromeres ([[Melters and coll., 2013|biblio/23363705]]).
- - In medaka, study of homologous pairs of centromeres suggest that the
-   acrocentric ones evolve slower ([[Ichikawa and coll., 2017|biblio/29184138]]).
+ - In the three-spine stickleback, the centromere sequence of chrX differs from
+   the one of chrY ([[Peichel and coll., 2020|biblio/32684159]]).
+
+## Visualisation
+
  - In Oikopleura (and many others) H3S28p marks mitotic centromeres [[Fent and
    coll., 2019|biblio/31306061]].
+ - Centromeric regions of sister chromatids are rarely resolved in FISH.  Instead,
+   the intensity of the spot increases ([[Amakawa and coll., 2013|biblio/23832878]]).
+
+## Evolution
+
+ - In medaka, study of homologous pairs of centromeres suggest that the
+   acrocentric ones evolve slower ([[Ichikawa and coll., 2017|biblio/29184138]]).
  - Centromere breakage and inactivation in yeast: [[Sankaranarayanan and coll.,
    2020|biblio/31958060]].
  - Centromere relocation to a transcribed region in yeast, detected by ChIP of
    centromeric H3 [[Ola and coll., 2020|biblio/32424070]].
- - In the three-spine stickleback, the centromere sequence of chrX differs from
-   the one of chrY ([[Peichel and coll., 2020|biblio/32684159]]).
 
 [[!inline pages="tagged(centromere)" limit="0"]]

Café
diff --git a/biblio/32313176.mdwn b/biblio/32313176.mdwn
new file mode 100644
index 00000000..614e184a
--- /dev/null
+++ b/biblio/32313176.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Deeply conserved synteny resolves early events in vertebrate evolution."]]
+[[!tag evolution synteny chromosome]]
+
+Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS.
+
+Nat Ecol Evol. 2020 Jun;4(6):820-830. doi:10.1038/s41559-020-1156-z
+
+Deeply conserved synteny resolves early events in vertebrate evolution.
+
+[[!pmid 32313176 desc="Most of the 19 amphioxus (lancelet) chromosomes directly correspond to one of the 17 ancestral chordate linkage groups.  Pattern of paralogue elimination show that autotetraploidy was followed by allotetraploidy in bony vertebrates."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 9bd08b3a..364c601e 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -9,7 +9,8 @@ were enriched near CTCF-binding events.
 distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
-The ancestral chordate has 17 chromosomes according to [[Putnam and coll, 2008|biblio/18563158]].
+The ancestral chordate has 17 chromosomes according to amphioxus assemblies of
+[[Putnam and coll, 2008|biblio/18563158]] and [[Simakov and coll., 2020|biblio/32313176]].
 
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 

Café
diff --git a/biblio/32845085.mdwn b/biblio/32845085.mdwn
new file mode 100644
index 00000000..1449e819
--- /dev/null
+++ b/biblio/32845085.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SBML Level 3: an extensible format for the exchange and reuse of biological models."]]
+[[!tag software systems_biology]]
+
+Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members.
+
+Mol Syst Biol. 2020 Aug;16(8):e9110. doi:10.15252/msb.20199110
+
+SBML Level 3: an extensible format for the exchange and reuse of biological models.
+
+[[!pmid  32845085 desc="Modularisation of SBML."]]

Café
diff --git a/biblio/25940625.mdwn b/biblio/25940625.mdwn
new file mode 100644
index 00000000..4e6edbf0
--- /dev/null
+++ b/biblio/25940625.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Accurate identification of centromere locations in yeast genomes using Hi-C."]]
+[[!tag assembly software]]
+
+Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS.
+
+Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi:10.1093/nar/gkv424.
+
+Accurate identification of centromere locations in yeast genomes using Hi-C.
+
+[[!pmid 25940625 desc="Tested on yeast and Plasmodium falciparium.  First, detects regions enriched in Hi-C contacts.  Then, prioritises local maxima enriched in trans-contacts."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index b999bbb0..259f50eb 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -51,6 +51,9 @@ that most contact points are due to local (same-chromosome) proximity.  Version
 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll.,
 2019|biblio/31433799]]).
 
+The Hi-C data can also be used to call the location of centromeres ([[Varoquaux
+and coll., 2015|biblio/25940625]], Marie-Nelly and coll., 2014(not read)).
+
 Assemblies can be aligned with [[last-dotplot|LAST]] or, for SVG export and
 interactive browsing with D-GENIES ([[Cabanettes and Klopp
 2018|biblio/29888139]]).

creating tag page tags/synthetic
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
new file mode 100644
index 00000000..0f4fd49c
--- /dev/null
+++ b/tags/synthetic.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged synthetic"]]
+
+[[!inline pages="tagged(synthetic)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32791980.mdwn b/biblio/32791980.mdwn
new file mode 100644
index 00000000..c1f0bb10
--- /dev/null
+++ b/biblio/32791980.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Sc3.0: revamping and minimizing the yeast genome"]]
+[[!tag yeast synthetic]]
+
+Dai J, Boeke JD, Luo Z, Jiang S, Cai Y.
+
+Genome Biol. 2020 Aug 13;21(1):205. doi:10.1186/s13059-020-02130-z
+
+Sc3.0: revamping and minimizing the yeast genome
+
+[[!pmid 32791980 desc="Proposes to build a core “essential gene array (eArray)” as a centromeric chromosome that can be linearised to serve as a base to build more complex genomes."]]
diff --git a/tags/synthethic.mdwn b/tags/synthethic.mdwn
index 9ec53efc..d8a82e40 100644
--- a/tags/synthethic.mdwn
+++ b/tags/synthethic.mdwn
@@ -1,4 +1,7 @@
 [[!meta title="pages tagged synthethic"]]
 
-[[!inline pages="tagged(synthethic)" actions="no" archive="yes"
-feedshow=10]]
+_in progress_
+
+Sc3.0 roadmap: [[Dai and coll., 2020|32791980]].
+
+[[!inline pages="tagged(synthethic)" limit=0]]

Café
diff --git a/biblio/1465136.mdwn b/biblio/1465136.mdwn
new file mode 100644
index 00000000..1039f0b1
--- /dev/null
+++ b/biblio/1465136.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells."]]
+[[!tag trans-splicing]]
+
+Bruzik JP, Maniatis T.
+
+Nature. 1992 Dec 17;360(6405):692-5. doi:10.1038/360692a0
+
+Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells.
+
+[[!pmid 1465136 desc="Trans-splicing in vivo in COS cells and in vitro in HeLa cell extracts, using splice leaders and actin genes from C. elegans and Leptomonas colosoma, and also using an adenoviral RNA as acceptor."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 7ded5bdd..0a750e29 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -1,5 +1,8 @@
 [[!meta title="pages tagged trans-splicing"]]
 
+Trans-spplicing of a splice leader from a nematode and a trypanosome was shown
+to be possible in COS cells and HeLa cell extracts by [[Bruzik and Maniatis, 1992|biblio/1465136]].
+
 Trans-splicing was discovered in tunicates by [[Vandenberghe, Meedel and Hastings, 2001|biblio/11159910]].
 
 The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).

Café
diff --git a/biblio/32763167.mdwn b/biblio/32763167.mdwn
new file mode 100644
index 00000000..8ae9cd71
--- /dev/null
+++ b/biblio/32763167.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes."]]
+[[!tag genome evolution mutation]]
+
+Bourguignon T, Kinjo Y, Villa-Martín P, Coleman NV, Tang Q, Arab DA, Wang Z, Tokuda G, Hongoh Y, Ohkuma M, Ho SYW, Pigolotti S, Lo N.
+
+Curr Biol. 2020 Jul 29:S0960-9822(20)31026-5. doi:10.1016/j.cub.2020.07.034
+
+Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes.
+
+[[!pmid 32763167 desc="”gene-loss rate strongly correlated with synonymous substitution rate”"]]

updated PO files
diff --git "a/Debian/debi\303\242neries/VAIO.en.po" "b/Debian/debi\303\242neries/VAIO.en.po"
index 82de0f0e..ee54a5db 100644
--- "a/Debian/debi\303\242neries/VAIO.en.po"
+++ "b/Debian/debi\303\242neries/VAIO.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2020-08-09 01:03+0000\n"
+"POT-Creation-Date: 2020-08-09 01:08+0000\n"
 "PO-Revision-Date: 2020-08-09 10:07+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
@@ -43,14 +43,13 @@ msgid ""
 "chose enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré "
 "au point qu'il a doublé d'épaisseur.  Après avoir appelé le service après-"
 "vente de VAIO, quelqu'un est passé le prendre pour faire une estimation du "
-"coût de la réparation.  Et ensuite on nous a annoncé que ça serait "
-"gratuit.  Le voici de retour dans mes mains en moins de deux semaines.  "
-"Bravo VAIO !"
+"coût de la réparation.  Et ensuite on nous a annoncé que ça serait gratuit.  "
+"Le voici de retour dans mes mains en moins de deux semaines.  Bravo VAIO !"
 msgstr ""
 "I use everyday a VAIO Pro mk2 that I bought 5 years ago with 3 years of "
 "warranty. It has been a few months that I was noticing that something was "
-"slowly inflating inside.  In July, things accelerated to the point that "
-"its thickness had doubled.  After we called the customer service of VAIO, "
-"somebody came to pick up the laptop in order to make a cost estimate.  "
-"Then we learned on the phone that it would be free.  It is back in my "
-"hands in less than two weeks.  Bravo VAIO !"
+"slowly inflating inside.  In July, things accelerated to the point that its "
+"thickness had doubled.  After we called the customer service of VAIO, "
+"somebody came to pick up the laptop in order to make a cost estimate.  Then "
+"we learned on the phone that it would be free.  It is back in my hands in "
+"less than two weeks.  Bravo VAIO !"

Bravo VAIO
diff --git "a/Debian/debi\303\242neries/VAIO.en.po" "b/Debian/debi\303\242neries/VAIO.en.po"
index c48f50f2..82de0f0e 100644
--- "a/Debian/debi\303\242neries/VAIO.en.po"
+++ "b/Debian/debi\303\242neries/VAIO.en.po"
@@ -3,47 +3,54 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2020-08-09 01:03+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2020-08-09 10:07+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Merci, VAIO\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Thank you, VAIO\"]]\n"
 
 #. type: Plain text
 msgid ""
 "J'utilise tous les jours un VAIO Pro 13 mk2 acheté il y a 5 ans avec 3 ans "
 "de guarantie.  Cela faisait quelques mois que j'avais remarqué que quelque "
 "chose enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré "
-"au point qu'il a doublé d'épaisseur.  Après avoir appelé le service "
-"après-vente de VAIO, quelqu'un est passé le prendre pour faire une "
-"estimation du coût de la réparation.  Et ensuite on nous a annoncé que ça "
-"serait gratuit.  Le voici de retour dans mes mains en moins de deux "
-"semaines.  Bravo VAIO !"
+"au point qu'il a doublé d'épaisseur.  Après avoir appelé le service après-"
+"vente de VAIO, quelqu'un est passé le prendre pour faire une estimation du "
+"coût de la réparation.  Et ensuite on nous a annoncé que ça serait "
+"gratuit.  Le voici de retour dans mes mains en moins de deux semaines.  "
+"Bravo VAIO !"
 msgstr ""
+"I use everyday a VAIO Pro mk2 that I bought 5 years ago with 3 years of "
+"warranty. It has been a few months that I was noticing that something was "
+"slowly inflating inside.  In July, things accelerated to the point that "
+"its thickness had doubled.  After we called the customer service of VAIO, "
+"somebody came to pick up the laptop in order to make a cost estimate.  "
+"Then we learned on the phone that it would be free.  It is back in my "
+"hands in less than two weeks.  Bravo VAIO !"

updated PO files
diff --git "a/Debian/debi\303\242neries/VAIO.en.po" "b/Debian/debi\303\242neries/VAIO.en.po"
new file mode 100644
index 00000000..c48f50f2
--- /dev/null
+++ "b/Debian/debi\303\242neries/VAIO.en.po"
@@ -0,0 +1,49 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2020-08-09 01:03+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 09 Aug 2020 10:01:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Merci, VAIO\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'utilise tous les jours un VAIO Pro 13 mk2 acheté il y a 5 ans avec 3 ans "
+"de guarantie.  Cela faisait quelques mois que j'avais remarqué que quelque "
+"chose enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré "
+"au point qu'il a doublé d'épaisseur.  Après avoir appelé le service "
+"après-vente de VAIO, quelqu'un est passé le prendre pour faire une "
+"estimation du coût de la réparation.  Et ensuite on nous a annoncé que ça "
+"serait gratuit.  Le voici de retour dans mes mains en moins de deux "
+"semaines.  Bravo VAIO !"
+msgstr ""

Merci VAIO
diff --git "a/Debian/debi\303\242neries/VAIO.mdwn" "b/Debian/debi\303\242neries/VAIO.mdwn"
new file mode 100644
index 00000000..ff14577b
--- /dev/null
+++ "b/Debian/debi\303\242neries/VAIO.mdwn"
@@ -0,0 +1,13 @@
+[[!meta date="Sun, 09 Aug 2020 10:01:20 +0900"]]
+[[!meta updated="Sun, 09 Aug 2020 10:01:20 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Merci, VAIO"]]
+
+J'utilise tous les jours un VAIO Pro 13 mk2 acheté il y a 5 ans avec 3 ans de
+guarantie.  Cela faisait quelques mois que j'avais remarqué que quelque chose
+enflait lentement à l'intérieur.  Et en juillet, tout s'est accéléré au point
+qu'il a doublé d'épaisseur.  Après avoir appelé le service après-vente de VAIO,
+quelqu'un est passé le prendre pour faire une estimation du coût de la
+réparation.  Et ensuite on nous a annoncé que ça serait gratuit.  Le voici de
+retour dans mes mains en moins de deux semaines.  Bravo VAIO !

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Local changes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index d9f40bf1..5b7046df 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -219,6 +219,7 @@ Genes and pathways
  - Two connexins, CxA and CxB are expressed during embyogenesis ([[Mikhaleva,
    Tolstenkov and Glover 2019|biblio/30905687]]).
  - Piwi ([[Henriet and coll., 2015|biblio/25779047]]).
+ - Metallothioneins _OdMT1_ and _OdMT2_ [[Calatayud and coll., 2018|biblio/30284576]].
 
 ### Lost
 

creating tag page tags/robot
diff --git a/tags/robot.mdwn b/tags/robot.mdwn
new file mode 100644
index 00000000..e671a3a9
--- /dev/null
+++ b/tags/robot.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged robot"]]
+
+[[!inline pages="tagged(robot)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32641813.mdwn b/biblio/32641813.mdwn
index 01f15e5b..d216d919 100644
--- a/biblio/32641813.mdwn
+++ b/biblio/32641813.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A mobile robotic chemist."]]
-[[!tag automation]]
+[[!tag robot automation]]
 
 A mobile robotic chemist.
 
diff --git a/biblio/32661153.mdwn b/biblio/32661153.mdwn
new file mode 100644
index 00000000..caea9011
--- /dev/null
+++ b/biblio/32661153.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An artificial aquatic polyp that wirelessly attracts, grasps, and releases objects."]]
+[[!tag robot]]
+
+Pilz da Cunha M, Kandail HS, den Toonder JMJ, Schenning APHJ.
+
+Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17571-17577. doi: 10.1073/pnas.2004748117
+
+An artificial aquatic polyp that wirelessly attracts, grasps, and releases objects.
+
+[[!pmid 32661153 desc="A magnetic PDMS stem rotates to create a water flow.  When a liquid droplet comes near, UV light is sent to induce folding of liquid cristal polymer arms."]]

Café
diff --git a/biblio/32632238.mdwn b/biblio/32632238.mdwn
new file mode 100644
index 00000000..ce790110
--- /dev/null
+++ b/biblio/32632238.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="ZipSeq: barcoding for real-time mapping of single cell transcriptomes."]]
+[[!tag single_cell method]]
+
+Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF.
+
+Nat Methods. 2020 Aug;17(8):833-843. doi:10.1038/s41592-020-0880-2
+
+ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
+
+[[!pmid 32632238 desc="Bind antibodies with conjugated oligonucleotides to the cell.  Uncage one strand in regions of interest and hybdidise to a specific barclde.  Repeat for other ROIs.  Dissociate and single-cell sequence."]]

cleanup
diff --git a/biblio/To_Do b/biblio/To_Do
index 071d9e24..1bf865e9 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -257,15 +257,9 @@ Tags are also frequently found in the CDS, but rarely in the 3'UTR. Tag number i
 15893974 [enhancers] [not read]
 vent2 and id3 regulator elements identified by xenopus-human comparisons.
 
-15923379 [enzymes]
-50 residues were mutated and tested for complementation in a Trl1 null yeast strain.
-
 15782219 [miRNA]
 Small RNA viruses and retroviruses do not seem to encode miRNAs. Some viral miRNAs are transcribed through a polIII tRNA promoter.
 
-15815676 [misc]
-A badly writtem MTA can be worse than non MTA at all.
-
 15937218 [miRNA]
 Repeat Associated siRNA (rasiRNA) were detected in zebrafish.
 
@@ -335,18 +329,12 @@ Out of 126 ultraconserved elements in a melanogaster / A. Gambiae comparison, on
 12429865 [tags]
 Provides an easy access to various statistical tests.
 
-16059932 [enhancers] [not read]
-Small human-fugu conserved sequences (max 24 bp) in the promoter and intron 1 of a non-TF gene.
-
 15339345 [tags]
 Usage of "Bayes Error Rate" instead of a cutoff on p-values. R packaged available under GPL.
 
 16103215 [misc]
 Supports the idea that the only function of some RNA is to have been transcribed.
 
-16077029 [misc]
-Suppressive PCR allows the use of one gene-specific primer, and one random primer. Asymetric cloning is the second safeguard against background.
-
 16049110 [enhancers]
 The minimal promoter used here is from GATA2 and may cause a bias towards enhancers of developmental regulators.
 
@@ -377,9 +365,6 @@ Single-tube nested PCR using two different annealing temperatures.
 11574151 [neurogenin]
 Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafish ngn1 is).
 
-16280998 [patents]
-Perpetual-motion machines are not patentable.
-
 16224006 [IP]
 20 % of the human coding genome is patented.
 
@@ -425,9 +410,6 @@ This miRNA is localised with its target in the synapto-dendritic compartment.
 16458883 [enhancers]
 The first enhancer conserved from insects to vertebrates.
 
-16465154 [IP]
-In the US, one can not be inventor on a patent if he has not made an intellectual contribution.
-
 16408288 [enhancers]
 Not read. Sox 2 enhancers conserved in vertebrates.
 
@@ -443,9 +425,6 @@ Proposing a distributed research system similar to distributed computing, and di
 16336043 [misc]
 The human faeces might be a vector of infections plant RNA viruses.
 
-16489339 [tags]
-Protocol with random primers
-
 16495311 [enhancers]
 Not read. Enhancers of Krox-20, conserved between chicken and mouse.
 

Café
diff --git a/biblio/32747824.mdwn b/biblio/32747824.mdwn
new file mode 100644
index 00000000..58e6f0a1
--- /dev/null
+++ b/biblio/32747824.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes."]]
+[[!tag HPV]]
+
+Gagliardi, A., Porter, V. L., Zong, Z., Bowlby, R., Titmuss, E., Namirembe, C., Griner, N. B., Petrello, H., Bowen, J., Chan, S. K., Culibrk, L., Darragh, T. M., Stoler, M. H., Wright, T. C., Gesuwan, P., Dyer, M. A., Ma, Y., Mungall, K. L., Jones, S., Nakisige, C., … Marra, M. A. 
+
+Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes.
+
+Nature genetics, 52(8), 800–810. 2020 DOI:10.1038/s41588-020-0673-7
+
+[[!pmid 32747824 desc="“SMGs [significantly mutated genes] included [PIK3CA] FAT1, KMT2D, FBXW7, CASP8, MAPK1 and ZNF750.”  “High-risk HPV-16 (clade A9), HPV-18 and HPV-45 (clade A7) were the most abundant”.  ”KLF12, TP63, RAD51B and MYC were among 16 genes that were the closest in proximity to an integration event in multiple samples”.  “ERVs [...] expression was significantly higher in integrated samples and was also positively correlated with the number of HPV insertions within the event.”  “The absence of E2 expression in the A7-enriched cluster supports the current understanding that tumors with HPV-18 (clade A7) are always associated with integration, which leads to loss of E2 expression.”  “Conversely, only about 76% of cervical tumors with HPV-16 (clade A9) show evidence of HPV integration, supporting the presumed presence of episomal HPV DNA due to the persistent expression of the E2 gene observed in our samples.”"]]

mosquito
diff --git a/biblio/28336562.mdwn b/biblio/28336562.mdwn
index dc4d22b7..f24a9326 100644
--- a/biblio/28336562.mdwn
+++ b/biblio/28336562.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds."]]
-[[!tag centromere chromosome muller_element]]
+[[!tag mosquito centromere chromosome muller_element]]
 
 Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL.
 

creating tag page tags/fish
diff --git a/tags/fish.mdwn b/tags/fish.mdwn
new file mode 100644
index 00000000..d8bc26a7
--- /dev/null
+++ b/tags/fish.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged fish"]]
+
+[[!inline pages="tagged(fish)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/32684159.mdwn b/biblio/32684159.mdwn
new file mode 100644
index 00000000..155fdca4
--- /dev/null
+++ b/biblio/32684159.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution"]]
+[[!tag fish genome chromosome structure centromere]]
+
+Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA.
+
+Genome Biol. 2020 Jul 19;21(1):177. doi:10.1186/s13059-020-02097-x
+
+Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution.
+
+[[!pmid 32684159 desc="“debris” fragments wrongly identified by 3D-DNA were added back to the assembly.  Centromere of chrY different from the one of chrX."]]
diff --git a/tags/centromere.mdwn b/tags/centromere.mdwn
index e24282ed..40284a22 100644
--- a/tags/centromere.mdwn
+++ b/tags/centromere.mdwn
@@ -12,5 +12,7 @@ _Work in progress_
    2020|biblio/31958060]].
  - Centromere relocation to a transcribed region in yeast, detected by ChIP of
    centromeric H3 [[Ola and coll., 2020|biblio/32424070]].
+ - In the three-spine stickleback, the centromere sequence of chrX differs from
+   the one of chrY ([[Peichel and coll., 2020|biblio/32684159]]).
 
 [[!inline pages="tagged(centromere)" limit="0"]]

Café
diff --git a/biblio/32663838.mdwn b/biblio/32663838.mdwn
new file mode 100644
index 00000000..b63ec297
--- /dev/null
+++ b/biblio/32663838.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Telomere-to-telomere assembly of a complete human X chromosome."]]
+[[!tag chromosome structure]]
+
+Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Lindsay TAG, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM.
+
+Nature. 2020 Jul 14. doi: 10.1038/s41586-020-2547-7.
+
+Telomere-to-telomere assembly of a complete human X chromosome.
+
+[[!pmid  32663838 desc="The Hi-C contact map of the human X chromosome shows that its long arm is divided in two large areas that have reduced interactions with each other."]]

creating tag page tags/supergene
diff --git a/tags/supergene.mdwn b/tags/supergene.mdwn
new file mode 100644
index 00000000..bbef001f
--- /dev/null
+++ b/tags/supergene.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged supergene"]]
+
+[[!inline pages="tagged(supergene)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/23334415.mdwn b/biblio/23334415.mdwn
new file mode 100644
index 00000000..248cbabb
--- /dev/null
+++ b/biblio/23334415.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A Y-like social chromosome causes alternative colony organization in fire ants."]]
+[[!tag chromosome variants supergene]]
+
+Wang J, Wurm Y, Nipitwattanaphon M, Riba-Grognuz O, Huang YC, Shoemaker D, Keller L.
+
+Nature. 2013 Jan 31;493(7434):664-8. doi:10.1038/nature11832
+
+A Y-like social chromosome causes alternative colony organization in fire ants.
+
+[[!pmid 23334415 desc="“The lack of recombination over more than half of the two heteromorphic social chromosomes can be explained by at least one large inversion of around 9 megabases, and this absence of recombination has led to the accumulation of deleterious mutations, including repetitive elements in the non-recombining region of Sb compared with the homologous region of SB.”"]]

Cleanup
diff --git a/biblio/12711698.mdwn b/biblio/12711698.mdwn
new file mode 100644
index 00000000..aeaffaec
--- /dev/null
+++ b/biblio/12711698.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new strategy to amplify degraded RNA from small tissue samples for microarray studies."]]
+[[!tag reverse_transcription amplification]]
+
+Xiang CC, Chen M, Ma L, Phan QN, Inman JM, Kozhich OA, Brownstein MJ.
+
+Nucleic Acids Res. 2003 May 1;31(9):e53. doi:10.1093/nar/gng053
+
+A new strategy to amplify degraded RNA from small tissue samples for microarray studies.
+
+[[!pmid 12711698 desc="Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones)."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index de0a3f83..071d9e24 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -20,12 +20,6 @@ Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subseq
 12161654 [misc]
 Fluorescent bar-coded oligos to monitor transcription in vivo.
 
-10499525 [single cell]
-Single cell RT-PCR.
-
-12711698 [amplification] [tracked]
-Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones).
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 

Café
diff --git a/biblio/32677034.mdwn b/biblio/32677034.mdwn
new file mode 100644
index 00000000..0ce22483
--- /dev/null
+++ b/biblio/32677034.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A genome database for a Japanese population of the larvacean Oikopleura dioica."]]
+[[!tag Oikopleura genome OIST]]
+
+Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA.
+
+A genome database for a Japanese population of the larvacean Oikopleura dioica.
+
+Dev Growth Differ. 2020 Jul 16. doi:10.1111/dgd.12689
+
+[[!pmid 32677034 desc="The OSKA2016 genome."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index a5d46cb7..f2b6fe29 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -81,6 +81,8 @@ Genome
    ([[Denoeud et al., 2010|biblio/21097902]]).  In 2019, it is the smallest
    sequenced chordate genome, but some [[nematodes|nematode]] have been found
    with smaller genomes.
+ - The OSAKA2016 genome assembly (PacBio) from the North Pacific species is ~65 Mb-long
+   [[Wang and coll., 2020|biblio/32677034]].
  - Other oikopleuid genomes have been sequenced by [[Naville and coll. (2019)|biblio/30880010]]:
    small genomes are also found in _O. longicauda_ (131 Mbp) and _F. borealis_ (91 Mbp).
    There is an apparent correlation between organism size and genome size:

Cleanup
diff --git a/biblio/10537171.mdwn b/biblio/10537171.mdwn
new file mode 100644
index 00000000..9a64beb6
--- /dev/null
+++ b/biblio/10537171.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single cell reverse transcription-polymerase chain reaction analysis of rat supraoptic magnocellular neurons: neuropeptide phenotypes and high voltage-gated calcium channel subtypes."]]
+[[!tag single_cell]]
+
+Glasgow E, Kusano K, Chin H, Mezey E, Young WS 3rd, Gainer H.
+
+Endocrinology. 1999 Nov;140(11):5391-401. doi:10.1210/endo.140.11.7136
+
+Single cell reverse transcription-polymerase chain reaction analysis of rat supraoptic magnocellular neurons: neuropeptide phenotypes and high voltage-gated calcium channel subtypes
+
+[[!pmid 10537171 desc="cDNA synthesis primed with random hexamers."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 17806808..de0a3f83 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -11,9 +11,6 @@ PATRICIA J. WITTKOPP, BELINDA K. HAERUM & ANDREW G. CLARK
 http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020178
 ggcacgcga/cc => C-box for dro hairy.
 
-10537171
-Full in situ random priming cDNA synthesis
-
 12593794 [general]
 Noise due to RNA extraction is 40 times greater than noise due to replicate hybridisation
 

Café
diff --git a/biblio/10.1126_sciadv.aaz9037.mdwn b/biblio/10.1126_sciadv.aaz9037.mdwn
new file mode 100644
index 00000000..9824d716
--- /dev/null
+++ b/biblio/10.1126_sciadv.aaz9037.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ocean currents promote rare species diversity in protists"]]
+[[!tag speciation]]
+
+Paula Villa Martín, Aleš Buček, Thomas Bourguignon and Simone Pigolotti
+
+Science Advances  15 Jul 2020 Vol. 6, no. 29, eaaz9037 doi:10.1126/sciadv.aaz9037
+
+Ocean currents promote rare species diversity in protists
+
+[[!doi 10.1126/sciadv.aaz9037 desc="The model runs backwards in time and merge individuals in species if they can be traced to a common geographical origin.  Ocean currents increase species diversity by limiting mixture."]]

Café
diff --git a/biblio/31036053.mdwn b/biblio/31036053.mdwn
new file mode 100644
index 00000000..f1b6c7c3
--- /dev/null
+++ b/biblio/31036053.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""]]
+[[!tag sequence_tag bias]]
+
+Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification.
+
+Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB.
+
+Genome Biol. 2019 Apr 29;20(1):85. doi:10.1186/s13059-019-1691-6
+
+[[!pmid 31036053 desc="Sequencing templates already containing full Illumina adapters are cleaved from plasmids with a type IIS enzyme that generates blunt ends.  Comparison between fixed-length and variable-length payloads allowed to study the size bias in Illumina sequencers.  NextSeq > iSeq > MiSeq > NovaSeq.  A freeze-thaw cycle reduced the prevalence of the smallest templates (~150 bp)."]]

Café
diff --git a/biblio/32619237.mdwn b/biblio/32619237.mdwn
new file mode 100644
index 00000000..62de0252
--- /dev/null
+++ b/biblio/32619237.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-
+associated core promoter regulation."]]
+[[!tag CAGE zebrafish cell_cycle promoter]]
+
+Nucleic Acids Res. 2020 Jul 3:gkaa563. doi:10.1093/nar/gkaa563
+
+Wragg JW, Roos L, Vucenovic D, Cvetesic N, Lenhard B, Müller F.
+
+Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-
+associated core promoter regulation.
+
+[[!pmid 32619237 desc="“TATA-box enrichment in genes upregulated in G1 (∼30 bp upstream of the TSS), but no enrichment in WW dinucleotide frequency between the G1 and S/G2/M differentially expressed gene sets.”  “Four TATA-divergent poly-W pentamers (TTAAA, TAAAT, TTTAA, AATAA) were significantly enriched (P < 0.001–0.01) in the promoters of genes upregulated in S/G2/M cells.”  “TATA-box utilization is highly enriched in sharp promoters over other behaviours, interestingly however this is only true in the gene set upregulated in G1. In the S/G2/M upregulated gene set promoter shape was only weakly associated with TATA utilization.”"]]

Suppressive PCR.
diff --git a/biblio/7731798.mdwn b/biblio/7731798.mdwn
index 78722dac..bf12e97c 100644
--- a/biblio/7731798.mdwn
+++ b/biblio/7731798.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="An improved PCR method for walking in uncloned genomic DNA."]]
-[[!tag method library]]
+[[!tag method amplification library]]
 
 Nucleic Acids Res. 1995 Mar 25;23(6):1087-8.
 
diff --git a/tags/amplification.mdwn b/tags/amplification.mdwn
index c2e5833a..f5162ec2 100644
--- a/tags/amplification.mdwn
+++ b/tags/amplification.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged amplification"]]
 
-[[!inline pages="tagged(amplification)" actions="no" archive="yes"
-feedshow=10]]
+_work in progress..._
+
+‘Suppression PCR’ was first published in English in [[Siebert and coll.,
+1995|biblio/7731798]].  Figure 1B shows a ‘panhandle’ structure.
+
+[[!inline pages="tagged(amplification)" limit=0]]

Post-caféwq
diff --git a/biblio/32494014.mdwn b/biblio/32494014.mdwn
new file mode 100644
index 00000000..ef51a344
--- /dev/null
+++ b/biblio/32494014.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Insights into variation in meiosis from 31,228 human sperm genomes."]]
+[[!tag recombination meiosis single_cell]]
+
+Bell AD, Mello CJ, Nemesh J, Brumbaugh SA, Wysoker A, McCarroll SA.
+
+Nature. 2020 Jul;583(7815):259-264. doi:10.1038/s41586-020-2347-0
+
+Insights into variation in meiosis from 31,228 human sperm genomes.
+
+[[!pmid 32494014 desc="“We identified 813,122 crossovers in the 31,228 gamete genomes.” “Gametes with fewer crossovers in half of their genome tended to have fewer crossovers in the other half of their genome.” “Large concentrations of crossovers in distal regions.” “The sex chromosomes and acrocentric chromosomes had the highest rates of aneuploidy.”"]]

Cleanup
diff --git a/biblio/1557406.mdwn b/biblio/1557406.mdwn
new file mode 100644
index 00000000..5af7cc0c
--- /dev/null
+++ b/biblio/1557406.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Analysis of gene expression in single live neurons."]]
+[[!tag amplification]]
+
+Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P.
+
+Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):3010-4. doi:10.1073/pnas.89.7.3010
+
+Analysis of gene expression in single live neurons.
+
+[[!pmid 1557406  desc="Adds a second round of amplification."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 99956f1d..17806808 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -4,12 +4,6 @@ Nature 430, 85 - 88 (01 July 2004); doi:10.1038/nature02698
 Evolutionary changes in cis and trans gene regulation 
 PATRICIA J. WITTKOPP, BELINDA K. HAERUM & ANDREW G. CLARK 
 
-1557406
-Adds a second round of amplification
-
-11687821
-Review citing the 2 upper articles
-
 12172558
 * Says that exponential (65+25 cycles) is more faithful than linear.
 * Limits [dNTP] to produce only 3' cDNA that are a few hundrer base pairs long.

Café
diff --git a/biblio/32641813.mdwn b/biblio/32641813.mdwn
new file mode 100644
index 00000000..01f15e5b
--- /dev/null
+++ b/biblio/32641813.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A mobile robotic chemist."]]
+[[!tag automation]]
+
+A mobile robotic chemist.
+
+Nature. 2020 Jul;583(7815):237-241. doi:10.1038/s41586-020-2442-2
+
+Burger B, Maffettone PM, Gusev VV, Aitchison CM, Bai Y, Wang X, Li X, Alston BM, Li B, Clowes R, Rankin N, Harris B, Sprick RS, Cooper AI.
+
+[[!pmid 32641813 desc="“The robot uses laser scanning and touch feedback, rather than a vision system. It can therefore operate in complete darkness, if needed.“  “The robot operated autonomously over eight days, performing 688 experiments within a ten-variable experimental space, driven by a batched Bayesian search algorithm.”"]]

Lab culture.
diff --git a/biblio/32628172.mdwn b/biblio/32628172.mdwn
new file mode 100644
index 00000000..3c26b82d
--- /dev/null
+++ b/biblio/32628172.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica."]]
+[[!tag OIST Oikopleura]]
+
+Masunaga A, Liu AW, Tan Y, Scott A, Luscombe NM.
+
+J Vis Exp. 2020 Jun 16;(160). doi:10.3791/61279
+
+Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica.
+
+[[!pmid 32628172 desc="OISTs culture protocol."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 23aec410..a5d46cb7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -603,6 +603,10 @@ Culture protocols (incomplete list):
    helicoidal paddle to stir the culture.
  - Tested once in Ctenophore tubes ([[Patry, Bubel, Hansen and Knowles,
    2020|biblio/32292660]]).
+ - Nishida lab protocol: [[Nishida 2008|biblio/18494706]].
+ - Thompson lab protocol: [[Bouquet and coll., 2009|biblio/19461862]].
+ - Cañestro lab protocol: [[Martí-Solans and coll., 2015|biblio/25044679]].
+ - OIST's culture protocol: [[Masunaga and coll., 2020|biblio/32628172]].
 
 Food tested in laboratory (totally incomplete list):
 

Syntax
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index c6bd41c7..78a4581f 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -12,6 +12,6 @@ and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
 diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
 D. silvestris diverged 5.1 My ago.
 
-See also [[muller_elements]].
+See also [[Muller elements|muller_element]].
 
 [[!inline pages="tagged(Drosophila)" limit=0]]

Move text
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index bbf30799..c6bd41c7 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -12,7 +12,6 @@ and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
 diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
 D. silvestris diverged 5.1 My ago.
 
-_D. bifasciata_ (and other Drosophila) have large and highly repetitive
-pericentric regions [[Bracewell and coll., 2020|biblio/31969429]]
+See also [[muller_elements]].
 
 [[!inline pages="tagged(Drosophila)" limit=0]]
diff --git a/tags/muller_element.mdwn b/tags/muller_element.mdwn
index b1d29765..dad30cae 100644
--- a/tags/muller_element.mdwn
+++ b/tags/muller_element.mdwn
@@ -12,4 +12,7 @@ species, and few contacts between both arms of the same chromosome ([[Dudchenko
 and coll., 2017|biblio/28336562]]).  Note that the chromosomes of Aedes aegypti
 are significantly larger than what is usually found in Drosophila.
 
+_D. bifasciata_ (and other Drosophila) have large and highly repetitive
+pericentric regions [[Bracewell and coll., 2020|biblio/31969429]].
+
 [[!inline pages="tagged(muller_element)" limit=0]]

cleanup
diff --git a/biblio/16790564.mdwn b/biblio/16790564.mdwn
index cb8160df..cc605a75 100644
--- a/biblio/16790564.mdwn
+++ b/biblio/16790564.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Primer Extension Enrichment Reaction (PEER): A New Subtraction Method for Identification of Genetic Differences Between Biological Specimens"]]
-[[!tag method protocol]]
+[[!tag method library]]
 
 Ganova-Raeva L, Zhang X, Cao F, Fields H, Khudyakov Y.
 
diff --git a/biblio/31969429.mdwn b/biblio/31969429.mdwn
index f48e4619..c2452220 100644
--- a/biblio/31969429.mdwn
+++ b/biblio/31969429.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Chromosome-Level Assembly of _Drosophila bifasciata_ Reveals Important Karyotypic Transition of the X Chromosome."]]
-[[!tag Hi-C Drosophila genome]]
+[[!tag Drosophila centromere chromosome muller_element]]
 
 Bracewell R, Tran A, Chatla K, Bachtrog D.
 
diff --git a/tags/Hi-C.mdwn b/tags/Hi-C.mdwn
deleted file mode 100644
index a68fe3b5..00000000
--- a/tags/Hi-C.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Hi-C"]]
-
-[[!inline pages="tagged(Hi-C)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/products.mdwn b/tags/products.mdwn
deleted file mode 100644
index fb0cb13f..00000000
--- a/tags/products.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged products"]]
-
-[[!inline pages="tagged(products)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/Hi-C
diff --git a/tags/Hi-C.mdwn b/tags/Hi-C.mdwn
new file mode 100644
index 00000000..a68fe3b5
--- /dev/null
+++ b/tags/Hi-C.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Hi-C"]]
+
+[[!inline pages="tagged(Hi-C)" actions="no" archive="yes"
+feedshow=10]]

Cleanup
diff --git a/biblio/16790564.mdwn b/biblio/16790564.mdwn
new file mode 100644
index 00000000..cb8160df
--- /dev/null
+++ b/biblio/16790564.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Primer Extension Enrichment Reaction (PEER): A New Subtraction Method for Identification of Genetic Differences Between Biological Specimens"]]
+[[!tag method protocol]]
+
+Ganova-Raeva L, Zhang X, Cao F, Fields H, Khudyakov Y.
+
+Nucleic Acids Res. 2006 Jun 21;34(11):e76. doi: 10.1093/nar/gkl391
+
+Primer Extension Enrichment Reaction (PEER): A New Subtraction Method for Identification of Genetic Differences Between Biological Specimens
+
+[[!pmid 16790564 desc="Generates primers by MmeI cleavage of cDNA extremities, and inactivates those which are complementary to the driver library by extending them with ddNTP"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8021e42b..99956f1d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -512,9 +512,6 @@ rasiRNA, the drosophila piRNA, are 5'P and one of their 2' or 3' is not OH. They
 16778056 [small RNAs]
 Its neighbors got pseudogenized too in humans.
 
-16790564 [protocols]
-Generates primers by MmeI cleavage of cDNA extremities, and inactivates those which are complementary to the driver library by extending them with ddNTP.
-
 16822854 [protocols]
 The fluorophore and the quencher are separated by the strand-displacement activity of the enzyme.
 
@@ -833,9 +830,6 @@ Evidence for complex polyA minus mRNA.
 18836037 [misc]
 [not read] Having a binding site is not always essential.
 
-18829718 [enzymes]
-[not read]De-adenylates at 35 ℃, and circularises at 65 ℃.
-
 18988746 [genome]
 [not read] Many chromosomal aberrations in ES cells.
 

Café
diff --git a/biblio/31969429.mdwn b/biblio/31969429.mdwn
new file mode 100644
index 00000000..f48e4619
--- /dev/null
+++ b/biblio/31969429.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-Level Assembly of _Drosophila bifasciata_ Reveals Important Karyotypic Transition of the X Chromosome."]]
+[[!tag Hi-C Drosophila genome]]
+
+Bracewell R, Tran A, Chatla K, Bachtrog D.
+
+G3 (Bethesda). 2020 Mar 5;10(3):891-897. doi:10.1534/g3.119.400922
+
+Chromosome-Level Assembly of _Drosophila bifasciata_ Reveals Important Karyotypic Transition of the X Chromosome.
+
+[[!pmid 31969429 desc="Chromosome arms do not interact much with each other.  Large and highly repetitive pericentric regions in which it is hard to map the Hi-C reads."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 5d7fe7f3..bbf30799 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -12,4 +12,7 @@ and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
 diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
 D. silvestris diverged 5.1 My ago.
 
+_D. bifasciata_ (and other Drosophila) have large and highly repetitive
+pericentric regions [[Bracewell and coll., 2020|biblio/31969429]]
+
 [[!inline pages="tagged(Drosophila)" limit=0]]

Cleanup
diff --git a/biblio/8474458.mdwn b/biblio/8474458.mdwn
new file mode 100644
index 00000000..3881a3d6
--- /dev/null
+++ b/biblio/8474458.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Olf-1-binding Site: Characterization of an Olfactory Neuron-Specific Promoter Motif"]]
+[[!tag olfaction Olf-1]]
+
+Kudrycki K, Stein-Izsak C, Behn C, Grillo M, Akeson R, Margolis FL.
+
+Mol Cell Biol. 1993 May;13(5):3002-14. doi:10.1128/mcb.13.5.3002
+
+Olf-1-binding Site: Characterization of an Olfactory Neuron-Specific Promoter Motif
+
+[[!pmid 8474458 desc="The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 310367d3..8021e42b 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -722,15 +722,6 @@ Provides a R library
 9151732 [olfactory]
 [not read] Primary paper for O/E-2 and O/E-3 and their binding capacities.
 
-14656972 [olfactory]
-[not read] Six promoters from a OR gene family, the analysis of conserved motifs, bandshifts and yeast one-hybrid.
-
-8474458 [olfactory]
-[not read] "The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG."
-
-10395892 [misc]
-[not read] Review on the "Kozak" sequence.
-
 17010214 [olfactory]
 Primary paper for CLICs (clusters in conservation).
 

Café
diff --git a/biblio/18563158.mdwn b/biblio/18563158.mdwn
new file mode 100644
index 00000000..44150dc8
--- /dev/null
+++ b/biblio/18563158.mdwn
@@ -0,0 +1,18 @@
+[[!meta title="The amphioxus genome and the evolution of the chordate karyotype."]]
+[[!tag chromosome synteny]]
+
+Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T,
+Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I,
+Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka
+J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K,
+Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T,
+Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar
+DS.
+
+Nature. 2008 Jun 19;453(7198):1064-71. doi:10.1038/nature06967
+
+The amphioxus genome and the evolution of the chordate karyotype.
+
+[[!pmid 18563158 desc="17 ancestral chordate chromosomes."]]
+
+“We estimate that the haploid amphioxus genome contains 21,900 protein-coding loci. [...] The observed heterozygosity shows correlations at short distances that decay on scales greater than ∼1 kb, indicating extensive recombination in the population. [...] Wwe reconstructed the gene complements of 17 linkage groups (that is, proto-chromosomes) of the last common chordate ancestor. [...] This analysis shows that most of the human genome (112 segments spanning 2.68 Gb, or 95% of the euchromatic genome) was affected by large-scale duplication events on the vertebrate stem before the bony vertebrate radiation (that is, the teleost/tetrapod split), and that nearly all of the ancient chordate chromosomes were quadruplicated. [...] Allowing for a range of nearly parsimonious reconstructions of 2R, we estimate that the bony vertebrate ancestor had between 37 and 49 chromosomes.”
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 83c8fa61..9bd08b3a 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -9,6 +9,8 @@ were enriched near CTCF-binding events.
 distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
+The ancestral chordate has 17 chromosomes according to [[Putnam and coll, 2008|biblio/18563158]].
+
 The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
 
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints

Cleanup todo list.
diff --git a/biblio/18829718.mdwn b/biblio/18829718.mdwn
index 13248de7..27e6bd1d 100644
--- a/biblio/18829718.mdwn
+++ b/biblio/18829718.mdwn
@@ -7,4 +7,4 @@ Nucleic Acids Res. 2008 Nov;36(19):6218-27. doi:10.1093/nar/gkn602
 
 Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA.
 
-[[!pmid 18829718 desc="Used in the NEB's 5´ DNA Adenylation Kit.  Lacks specificity for RNA and DNA."]]
+[[!pmid 18829718 desc="Used in the NEB's 5´ DNA Adenylation Kit.  Lacks specificity for RNA and DNA.  Optimal at 65 °C, inactivated at 75 °C, and mostly adenylylating at 37 °C."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index eedb614f..310367d3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -839,9 +839,6 @@ Another histone modification to take into account.
 527589 [transcription]
 Evidence for complex polyA minus mRNA.
 
-18829718 [enzymes]
-Optimal at 65 ℃, inactivated at 75 ℃, and mostly adenylylating at 37 ℃.
-
 18836037 [misc]
 [not read] Having a binding site is not always essential.
 

Cleanup old tags.
diff --git a/biblio/24097351.mdwn b/biblio/24097351.mdwn
index b574cfae..902652fe 100644
--- a/biblio/24097351.mdwn
+++ b/biblio/24097351.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Spatial organization within a niche as a determinant of stem-cell fate."]]
-[[!tag stem_cell niche hair]]
+[[!tag stem_cell hair]]
 
 Rompolas P, Mesa KR, Greco V.
 
diff --git a/tags/niche.mdwn b/tags/niche.mdwn
deleted file mode 100644
index a8553fa4..00000000
--- a/tags/niche.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged niche"]]
-
-[[!inline pages="tagged(niche)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/30333059.mdwn b/biblio/30333059.mdwn
index d321efe2..fc327c70 100644
--- a/biblio/30333059.mdwn
+++ b/biblio/30333059.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Chromosome evolution at the origin of the ancestral vertebrate genome."]]
-[[!tag chromosome evolution]]
+[[!tag synteny chromosome evolution]]
 
 Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H.
 

creating tag page tags/breakpoint
diff --git a/tags/breakpoint.mdwn b/tags/breakpoint.mdwn
new file mode 100644
index 00000000..8c230a4f
--- /dev/null
+++ b/tags/breakpoint.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged breakpoint"]]
+
+[[!inline pages="tagged(breakpoint)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/25801028.mdwn b/biblio/25801028.mdwn
new file mode 100644
index 00000000..e0b046ef
--- /dev/null
+++ b/biblio/25801028.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="The 3D organization of chromatin explains evolutionary fragile genomic regions."]]
+[[!tag chromosome breakpoint synteny]]
+
+Berthelot C, Muffato M, Abecassis J, Roest Crollius H.
+
+Cell Rep. 2015 Mar 24;10(11):1913-24. doi: 10.1016/j.celrep.2015.02.046
+
+The 3D organization of chromatin explains evolutionary fragile genomic regions.
+
+[[!pmid 25801028 desc="Explains the power law distribution of breakpoints in mammals and yeast with chromosome contacts (Hi-C) and open chromatin (ENCODE)."]]
+
+“We [...] reconstruct the ancestral gene order in the 95-million-year-old ancestral genome of Boreoeutheria, the last common ancestor of primates, rodents, and laurasiatherians. [...] This reconstructed genome was further annotated with respect to its intergenic regions [...] their lengths, GC content and their proportion of conserved non-coding sequence as defined by GERP. [...] We then identified evolutionary rearrangement breakpoints that have occurred in the human, mouse, dog, cow, and horse lineages. [...] We identified a total of 751 breakpoints, 20 of which correspond to independent breakpoint reuse. [...] The identified breakpoints show the typical characteristics of rearrangement breakpoints; i.e., they occur in GC-rich, gene-dense regions possessing lower proportions of conserved non-coding sequence. [...] Breakpoint events per intergene increase as a power law of intergene length rather than a proportionality law. [...] Ancestral intergenes with high CNE content have been disrupted by significantly fewer breakpoints than intergenes of similar length with lower CNE content. [...] Rpeated elements and recombination frequencies are distributed radically differently from breakpoints, eliminating them as potential candidates to explain the breakpoint pattern. [...] The density of open chromatin is similar to the pattern of breakpoints with the proportion of DNA in an open state decreasing as intergene size increases. [...] Simulating inversions in the human genome according to contact probability [...] rearrangements were allowed to occur only between open chromatin regions, using chromatin state profiles for different cell types published by the ENCODE consortium.  Under this model, the simulated average number of breakpoints per intergene closely reproduces the relationship with intergene length observed in real data.”
diff --git a/tags/chromosome.mdwn b/tags/chromosome.mdwn
index 9c9cf0d3..74f69441 100644
--- a/tags/chromosome.mdwn
+++ b/tags/chromosome.mdwn
@@ -1,7 +1,3 @@
 [[!meta title="pages tagged chromosome"]]
 
-... _in progress_ ...
-
- - The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
-
 [[!inline pages="tagged(chromosome)" limit=0]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 4ece1256..83c8fa61 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -5,6 +5,12 @@ breakpoints (~30 per Gb), associated with segmental duplication or Alu element
 enrichment.  They often bore signatures of non-homology based mechanisms, and
 were enriched near CTCF-binding events.
 
+[[Berthelot and coll. (2015)|biblio/25801028]] show that breakpoint
+distribution follows a power law and explain it with a model that requires
+breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
+
+The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
+
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons

Café
diff --git a/biblio/30333059.mdwn b/biblio/30333059.mdwn
new file mode 100644
index 00000000..d321efe2
--- /dev/null
+++ b/biblio/30333059.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome evolution at the origin of the ancestral vertebrate genome."]]
+[[!tag chromosome evolution]]
+
+Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H.
+
+Genome Biol. 2018 Oct 17;19(1):166. doi:10.1186/s13059-018-1559-1
+
+Chromosome evolution at the origin of the ancestral vertebrate genome.
+
+[[!pmid 30333059 desc="“The pre-1R karyotype comprised 17 chromosomes, duplicated into 34 chromosomes after the first WGD and followed by seven fusions. The resulting 27 chromosomes were duplicated in the second WGD leading to 54 Vertebrata chromosomes, at the origin of the approximately 60,000 extant species of vertebrates.” “The 54 chromosomes in the post-2R Vertebrata led to a Euteleostomi karyotype of 50 chromosomes (4 fusions) and to an Amniota karyotype of 49 chromosomes.”  “The structure of the 17 pre-1R chromosomes is still strikingly apparent in the human genome, with some chromosomes almost entirely composed of genes from a single pre-1R chromosome (e.g., chromosomes 14 and 15).“  “We note that although all chromosome tetrads corresponding to pre-1R chromosomes are complete (i.e., are composed of 4 CARs), the 49 reconstructed Amniota chromosomes display large differences in gene numbers: the largest contains 862 genes (chromosome 37) and the smallest only 16 genes (chromosome 49). This could reflect either a more intense process of gene inactivation and loss on chromosomes with fewer genes, or a more intense rate of rearrangement on those chromosomes, leading to greater difficulties in reconstructing them.“"]]
diff --git a/tags/chromosome.mdwn b/tags/chromosome.mdwn
index c857eb30..9c9cf0d3 100644
--- a/tags/chromosome.mdwn
+++ b/tags/chromosome.mdwn
@@ -1,4 +1,7 @@
 [[!meta title="pages tagged chromosome"]]
 
-[[!inline pages="tagged(chromosome)" actions="no" archive="yes"
-feedshow=10]]
+... _in progress_ ...
+
+ - The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]].
+
+[[!inline pages="tagged(chromosome)" limit=0]]

Generation time
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 83c32ac4..23aec410 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -338,6 +338,8 @@ Development
    at 15 °C ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).  Note that
    culture conditions might differ.  ~1 day generation time reported in microcosms
    at 29°C in Jamaica ([[Hopcroft and Roff, 1995|biblio/10.1093_plankt_17.2.205]]).
+   ~1.2 day generation in the Seto inland sea ([[Uye and Ichino,
+   1995|biblio/10.1016_0022-0981_95_00004-B]]).
  - Increased food abundance increases egg number but does not change diameter nor
    generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
    Food reduction before day 4 causes growth arrest (GA), in which all cell cycles

Café
diff --git a/biblio/10.1093_plankt_17.2.205.mdwn b/biblio/10.1093_plankt_17.2.205.mdwn
new file mode 100644
index 00000000..30153144
--- /dev/null
+++ b/biblio/10.1093_plankt_17.2.205.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Zooplankton growth rates: extraordinary production by the larvacean Oikopleura dioica in tropical waters"]]
+[[!tag Oikopleura]]
+
+Russell R. Hopcroft, John C. Roff
+
+Journal of Plankton Research, Volume 17, Issue 2, February 1995, Pages 205–220, https://doi.org/10.1093/plankt/17.2.205
+
+Zooplankton growth rates: extraordinary production by the larvacean Oikopleura dioica in tropical waters
+
+[[!doi 10.1093/plankt/17.2.205 desc="Generation time of ~1 day for O. dioica in Jamaica at 29°C."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8634c0d0..83c32ac4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -336,7 +336,8 @@ Development
    h at 14.2 °C and 120 ± 6 h at 17.2 °C ([[Bouquet and coll.,
    2018|biblio/29298334]]), and 132 ± 13 h (5.5 d) at 20 °C and 159 ± 20 h (6.9 d)
    at 15 °C ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).  Note that
-   culture conditions might differ.
+   culture conditions might differ.  ~1 day generation time reported in microcosms
+   at 29°C in Jamaica ([[Hopcroft and Roff, 1995|biblio/10.1093_plankt_17.2.205]]).
  - Increased food abundance increases egg number but does not change diameter nor
    generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
    Food reduction before day 4 causes growth arrest (GA), in which all cell cycles
@@ -571,8 +572,8 @@ Ecology
  - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
    presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
    2009|biblio/10.1007_978-1-4020-8278-8_41]]).
- - Jamaica, where it was less abundant than _O. longicauda_ ([[Hopcroft and
-   Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
+ - Jamaica, where it was less abundant than _O. longicauda_ ([[Hopcroft and Roff,
+   1995|biblio/10.1093_plankt_17.2.205]], [[Hopcroft and Roff, 1998|biblio/10.1093_plankt_20.3.557]]).
  - South Atlantic: found all year near Mar del Plata in 2000—1, where it was
    most abundant in summer ([[Viñas and coll.,
    2013|biblio/10.1080_17451000.2012.745003]]), Caravelas river estuary and

Café
diff --git a/biblio/32513727.mdwn b/biblio/32513727.mdwn
new file mode 100644
index 00000000..f40cba48
--- /dev/null
+++ b/biblio/32513727.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Elimination of rNMPs from mitochondrial DNA has no effect on its stability."]]
+[[!tag mitochondrion]]
+
+Elimination of rNMPs from mitochondrial DNA has no effect on its stability.
+
+Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):14306-14313
+
+Wanrooij PH, Tran P, Thompson LJ, Carvalho G, Sharma S, Kreisel K, Navarrete C, Feldberg AL, Watt DL, Nilsson AK, Engqvist MKM, Clausen AR, Chabes A.
+
+[[!pmid 32513727 desc="In mouse, mitochondrial DNA strands have a few (usually ~10 or less) ribonucleotides misincorporated into them.  Their number correlate with the ration between rNTPs and dNTPs.  Reducing misincorporation did not have obvious benefits for the animals. "]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 355dde86..318a642c 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -87,4 +87,7 @@ Mitochondria can be lost in eukaryotes, be them monocellular ([[Karnkowska and
 coll., 2019|biblio/31387118]]), or multicellular ([[Yahalomi and coll.,
 2020|biblio/32094163]]).
 
+Mitochondrial DNA has a few rNTP misincorporated, but they do not seem to be
+detrimental ([[Wanrooij and coll., 2020|biblio/32513727]]).
+
 [[!inline pages="tagged(mitochondrion)" limit=0]]

Café
diff --git a/biblio/32205368.mdwn b/biblio/32205368.mdwn
new file mode 100644
index 00000000..4ac75659
--- /dev/null
+++ b/biblio/32205368.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics."]]
+[[!tag Oikopleura eDNA]]
+
+Vorobev A, Dupouy M, Carradec Q, Delmont TO, Annamalé A, Wincker P, Pelletier E.
+
+Genome Res. 2020 Apr;30(4):647-659. doi:10.1101/gr.253070.119
+
+Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.
+
+[[!pmid 32205368 desc="Metagenomics-based transcriptomes (MGTs): metatranscriptomic-based unigenes of the MATOU-v1 catalog detected by metagenomic reads mapping in at least three different Tara Oceans samples and displaying no more than 90% of their total genomic occurrence signal in a single sample, grouped based on the covariation of their genomic abundance across the samples, with a minimum of 500 unigenes per group.  Oikopleuridae detected (Figure 1)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 10221c2c..8634c0d0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -589,7 +589,7 @@ Ecology
    (with oral gland cells and ~8 to 14 subchordal cells).
  - Indian ocean near Australia: detected in eDNA sequencing of 18S rRNA
    ([[Berry and coll., 2019|biblio/30735490]])
-
+ - TARA Oceans ([[Vorobev and coll., 2020|biblio/32205368]]).
 
 Laboratory culture
 ------------------
diff --git a/tags/eDNA.mdwn b/tags/eDNA.mdwn
index 8187c113..289530cb 100644
--- a/tags/eDNA.mdwn
+++ b/tags/eDNA.mdwn
@@ -4,5 +4,6 @@
    [[Berry and coll., 2019|biblio/30735490]].
  - Oikopleura 18S detected in at least one MiSeq run from
    [[Djurhuus and coll. 2020|biblio/31937756]]
+ - Oikopleuridae detected in TARA Oceans ([[Vorobev and coll., 2020|biblio/32205368]]).
 
 [[!inline pages="tagged(eDNA)" limit=0]]

Café
diff --git a/biblio/32152607.mdwn b/biblio/32152607.mdwn
new file mode 100644
index 00000000..b424203c
--- /dev/null
+++ b/biblio/32152607.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An open-source drug discovery platform enables ultra-large virtual screens."]]
+[[!tag method drug]]
+
+Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H.
+
+Nature. 2020 Apr;580(7805):663-668. doi:10.1038/s41586-020-2117-z
+
+An open-source drug discovery platform enables ultra-large virtual screens.
+
+[[!pmid 32152607 desc="“VirtualFlow can dock 1 billion compounds in approximately 2 weeks when leveraging 10,000 CPU cores simultaneously.”"]]

Café
diff --git a/biblio/15343333.mdwn b/biblio/15343333.mdwn
new file mode 100644
index 00000000..1ff1dba8
--- /dev/null
+++ b/biblio/15343333.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D.
+
+Nature. 2004 Sep 2;431(7004):67-71. doi:10.1038/nature02709
+
+Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica.
+
+[[!pmid 15343333 desc="No BAC clone was found with more than one _Hox_ gene."]]
diff --git a/biblio/32349121.mdwn b/biblio/32349121.mdwn
new file mode 100644
index 00000000..721dfe9a
--- /dev/null
+++ b/biblio/32349121.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Massively multiplexed nucleic acid detection with Cas13."]]
+[[!tag emulsion HPV method]]
+
+Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC.
+
+Nature. 2020 Jun;582(7811):277-282. doi:10.1038/s41586-020-2279-8
+
+Massively multiplexed nucleic acid detection with Cas13.
+
+[[!pmid 32349121 desc="1050 color codes using 4 fluorophores."]]

Typo
diff --git a/biblio/30988468.mdwn b/biblio/30988468.mdwn
index c4af398a..8ca592ae 100644
--- a/biblio/30988468.mdwn
+++ b/biblio/30988468.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase.]]
+[[!meta title="Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase."]]
 [[!tag enzyme method]]
 
 Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M.

Cafə
diff --git a/biblio/30988468.mdwn b/biblio/30988468.mdwn
new file mode 100644
index 00000000..c4af398a
--- /dev/null
+++ b/biblio/30988468.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase.]]
+[[!tag enzyme method]]
+
+Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M.
+
+Nat Methods. 2019 May;16(5):437-445. doi:10.1038/s41592-019-0370-6.
+
+Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase.
+
+[[!pmid 30988468 desc="TRAID-seq (tethered rNTase activity identified by high-throughput sequencing). “Enzymes were fused to MS2 coat protein (MS2) and coexpressed in yeast with a reporter RNA bearing high-affinity MS2-binding sites. Interaction of MS2 with its binding sites tethered the fusion protein to the RNA23 and circumvented the activity of proteins that might bring the rNTase to its endogenous substrates.” Final substrate: “ tRNASer(AGA), in which the 4-bp variable arm was replaced by a single MS2-binding site”.  Problem with background polyadenlyation in previous attempt with RNase P–derived RNA.  “CeMUT-2 added tails with a 1:1 ratio of uridines to guanosines.”  These might form a hairpin to prime RdRP.  “CeNPOL-1 added tails composed of random combinations of all four nucleotides.”"]]

PNAS
diff --git a/biblio/32487729.mdwn b/biblio/32487729.mdwn
new file mode 100644
index 00000000..77471995
--- /dev/null
+++ b/biblio/32487729.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes."]]
+[[!tag olfaction mutation]]
+
+Rausell A, Luo Y, Lopez M, Seeleuthner Y, Rapaport F, Favier A, Stenson PD, Cooper DN, Patin E, Casanova JL, Quintana-Murci L, Abel L.
+
+Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes.
+
+Proc Natl Acad Sci U S A. 2020 Jun 2:201917993.doi: 10.1073/pnas.1917993117
+
+[[!pmid 32487729 desc="“The set of 166 dispensable genes was enriched in olfactory receptor genes (41 genes).”"]]

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 89c46e7b..1788c12c 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-16 01:15+0000\n"
+"POT-Creation-Date: 2020-06-16 01:18+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -102,8 +102,8 @@ msgstr ""
 #. type: Plain text
 msgid ""
 "I joined OIST in 2018, to study **the genetic structure and population "
-"variations** of an animal plankton, Oikopleura dioica, that has a genome 50 "
-"time more compact than the human one, which empowers us to sequence at "
+"variations** of an animal plankton, _Oikopleura dioica_, that has a genome "
+"50 time more compact than the human one, which empowers us to sequence at "
 "chromosomal resolution many individual sampled from all over the World."
 msgstr ""
 
@@ -113,6 +113,7 @@ msgid ""
 "project, by **packaging bioinformatics tools**, which are redistributed in "
 "Debian ([Möller and coll., 2010](https://pubmed.gov/21210984)) and its "
 "derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my "
-"contributions and other activities as a RIKEN researcher, I use the GPG key "
-"number B3443334. My ORCID ID is 0000-0001-7410-6295."
+"contributions and other activities as a OIST researcher, I use the GPG key "
+"number AE57EADA9D77898C5B064F15A59E8B5A44E7EABC. My ORCID ID is "
+"[0000-0001-7410-6295](https://orcid.org/0000-0001-7410-6295)."
 msgstr ""

ORCID, etc.
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 8d78cffb..41a4ad95 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -65,7 +65,7 @@ this promoter-centric work, I have also explored the huge repertoire of the **T
 cell antigen receptors**.
 
 I joined OIST in 2018, to study **the genetic structure and population
-variations** of an animal plankton, Oikopleura dioica, that has a genome
+variations** of an animal plankton, _Oikopleura dioica_, that has a genome
 50 time more compact than the human one, which empowers us to sequence
 at chromosomal resolution many individual sampled from all over the
 World.
@@ -74,5 +74,6 @@ I am also a **Free Software** enthusiast, and contribute to the Debian Med
 project, by **packaging bioinformatics tools**, which are redistributed in
 Debian ([Möller and coll., 2010](https://pubmed.gov/21210984)) and its
 derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my
-contributions and other activities as a RIKEN researcher, I use the GPG key
-number B3443334. My ORCID ID is 0000-0001-7410-6295.
+contributions and other activities as a OIST researcher, I use the GPG key
+number AE57EADA9D77898C5B064F15A59E8B5A44E7EABC. My ORCID ID is
+[0000-0001-7410-6295](https://orcid.org/0000-0001-7410-6295).

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 38eefe8e..89c46e7b 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-15 08:46+0000\n"
+"POT-Creation-Date: 2020-06-16 01:15+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -88,13 +88,15 @@ msgstr ""
 msgid ""
 "Together with my colleagues at RIKEN and collaborators in the field of "
 "neuroscience, I have applied nanoCAGE to the study of single neuron cell "
-"types, for instance the **olfactory neurons** ([Plessy et al., 2012), or in "
-"dopaminergic cells, where we could demonstrate the expression of haemoglobin "
-"in the midbrain (Biagioli et al., 2009). We are also exploring the sub-"
-"cellular localisation of RNA in **Purkinje neurons** (Kratz et al., 2014), "
-"and neurogenesis in the mouse olfactory epithelium using single-cell CAGE "
-"and ATAC-seq techniques. In parallel with this promoter-centric work, I have "
-"also explored the huge repertoire of the **T cell antigen receptors**."
+"types, for instance the **olfactory neurons** ([Plessy and coll., 2012]"
+"(https://pubmed.gov/22194471)), or in dopaminergic cells, where we could "
+"demonstrate the expression of haemoglobin in the midbrain ([Biagioli and "
+"coll., 2009](https://pubmed.gov/19717439)). We are also exploring the sub-"
+"cellular localisation of RNA in **Purkinje neurons** ([Kratz and coll., 2014]"
+"(https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory "
+"epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with "
+"this promoter-centric work, I have also explored the huge repertoire of the "
+"**T cell antigen receptors**."
 msgstr ""
 
 #. type: Plain text
@@ -109,8 +111,8 @@ msgstr ""
 msgid ""
 "I am also a **Free Software** enthusiast, and contribute to the Debian Med "
 "project, by **packaging bioinformatics tools**, which are redistributed in "
-"Debian (Möller et al., 2010) and its derivatives such as Ubuntu and "
-"(cloud)Bio-Linux. For digital signature of my contributions and other "
-"activities as a RIKEN researcher, I use the GPG key number B3443334. My "
-"ORCID ID is 0000-0001-7410-6295."
+"Debian ([Möller and coll., 2010](https://pubmed.gov/21210984)) and its "
+"derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my "
+"contributions and other activities as a RIKEN researcher, I use the GPG key "
+"number B3443334. My ORCID ID is 0000-0001-7410-6295."
 msgstr ""

Plus de PubMed
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index e3efec94..8d78cffb 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -53,15 +53,16 @@ development and analysis, I have been a **member of the FANTOM consortium**
 since FANTOM3.
 
 Together with my colleagues at RIKEN and collaborators in the field of
-neuroscience, I have applied nanoCAGE to the study of single neuron
-cell types, for instance the **olfactory neurons** ([Plessy et al., 2012),
-or in dopaminergic cells, where we could demonstrate the expression of
-haemoglobin in the midbrain (Biagioli et al., 2009). We are also
-exploring the sub-cellular localisation of RNA in **Purkinje neurons**
-(Kratz et al., 2014), and neurogenesis in the mouse olfactory
-epithelium using single-cell CAGE and ATAC-seq techniques. In parallel
-with this promoter-centric work, I have also explored the huge
-repertoire of the **T cell antigen receptors**.
+neuroscience, I have applied nanoCAGE to the study of single neuron cell types,
+for instance the **olfactory neurons** ([Plessy and coll.,
+2012](https://pubmed.gov/22194471)), or in dopaminergic cells, where we could
+demonstrate the expression of haemoglobin in the midbrain ([Biagioli and coll.,
+2009](https://pubmed.gov/19717439)). We are also exploring the sub-cellular
+localisation of RNA in **Purkinje neurons** ([Kratz and coll.,
+2014](https://pubmed.gov/24904046)), and neurogenesis in the mouse olfactory
+epithelium using single-cell CAGE and ATAC-seq techniques. In parallel with
+this promoter-centric work, I have also explored the huge repertoire of the **T
+cell antigen receptors**.
 
 I joined OIST in 2018, to study **the genetic structure and population
 variations** of an animal plankton, Oikopleura dioica, that has a genome
@@ -71,7 +72,7 @@ World.
 
 I am also a **Free Software** enthusiast, and contribute to the Debian Med
 project, by **packaging bioinformatics tools**, which are redistributed in
-Debian (Möller et al., 2010) and its derivatives such as Ubuntu and
-(cloud)Bio-Linux. For digital signature of my contributions and other
-activities as a RIKEN researcher, I use the GPG key number
-B3443334. My ORCID ID is 0000-0001-7410-6295.
+Debian ([Möller and coll., 2010](https://pubmed.gov/21210984)) and its
+derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my
+contributions and other activities as a RIKEN researcher, I use the GPG key
+number B3443334. My ORCID ID is 0000-0001-7410-6295.

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 1cf95c10..38eefe8e 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-15 07:55+0000\n"
+"POT-Creation-Date: 2020-06-15 08:46+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -58,25 +58,28 @@ msgid ""
 "On April 2013, I started a new development cycle as the leader of the "
 "Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, "
 "Division of Genomics Technology, to expand this work on single cells "
-"following a **population transcriptomics** approach (Plessy et al., 2013) "
-"focused on sampling the largest possible number of cells. In our ongoing "
-"developments, we have reached **single-cell and single molecule resolution** "
-"through the introduction of transposase fragmentation and unique molecular "
-"identifiers (Poulain et al., 2017). The protocol exists in two versions, one "
-"for FACS-isolated cells, and one for the Fluidigm C1 platform (Kouno et al., "
-"2019)."
+"following a **population transcriptomics** approach ([Plessy and coll., 2013]"
+"(https://pubmed.gov/23281054)) focused on sampling the largest possible "
+"number of cells. In our ongoing developments, we have reached **single-cell "
+"and single molecule resolution** through the introduction of transposase "
+"fragmentation and unique molecular identifiers ([Poulain and coll., 2017]"
+"(https://pubmed.gov/28349422)). The protocol exists in two versions, one for "
+"FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll., "
+"2019](https://pubmed.gov/30664627))."
 msgstr ""
 
 #. type: Plain text
 msgid ""
 "I have complemented my work on CAGE with the development of a gene-centred "
-"technique for detecting promoters, termed Deep-RACE (Olivarius et al., 2009, "
-"Plessy et al., 2012), which we used to validate our discovery of the "
-"pervasive expression of retrotransposons detected by CAGE (Faulkner et al., "
-"2009). To study transcription start activity at nucleotide resolution in "
-"zebrafish transfected with chimeric transgenes containing a copy of an "
-"endogenous promoter, I combined Deep-RACE, CAGE and paired-end sequencing in "
-"a technology that we called “Single-Locus CAGE” (Haberle et al., 2014). With "
+"technique for detecting promoters, termed Deep-RACE ([Olivarius and coll., "
+"2009](https://pubmed.gov/19317658), [Plessy and coll., 2012](http://dx.doi."
+"org/10.1002/9783527644582.ch4)), which we used to validate our discovery of "
+"the pervasive expression of retrotransposons detected by CAGE ([Faulkner and "
+"coll., 2009](https://pubmed.gov/19377475)). To study transcription start "
+"activity at nucleotide resolution in zebrafish transfected with chimeric "
+"transgenes containing a copy of an endogenous promoter, I combined Deep-"
+"RACE, CAGE and paired-end sequencing in a technology that we called “Single-"
+"Locus CAGE” ([Haberle and coll., 2014](https://pubmed.gov/24531765)). With "
 "my contributions related to CAGE development and analysis, I have been a "
 "**member of the FANTOM consortium** since FANTOM3."
 msgstr ""
@@ -85,7 +88,7 @@ msgstr ""
 msgid ""
 "Together with my colleagues at RIKEN and collaborators in the field of "
 "neuroscience, I have applied nanoCAGE to the study of single neuron cell "
-"types, for instance the **olfactory neurons** (Plessy et al., 2012), or in "
+"types, for instance the **olfactory neurons** ([Plessy et al., 2012), or in "
 "dopaminergic cells, where we could demonstrate the expression of haemoglobin "
 "in the midbrain (Biagioli et al., 2009). We are also exploring the sub-"
 "cellular localisation of RNA in **Purkinje neurons** (Kratz et al., 2014), "

More links
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 80ab04d2..e3efec94 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -26,32 +26,35 @@ artefacts and unwanted sequences generated by ribosomal RNAs using
 low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and
 coll., 2016](https://pubmed.gov/27071605)).
 
-On April 2013, I started a new development cycle as the leader of the
-Genomics Miniaturization Technology Unit at RIKEN Center for Life
-Sciences, Division of Genomics Technology, to expand this work on
-single cells following a **population transcriptomics** approach (Plessy
-et al., 2013) focused on sampling the largest possible number of
-cells. In our ongoing developments, we have reached **single-cell and
+On April 2013, I started a new development cycle as the leader of the Genomics
+Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of
+Genomics Technology, to expand this work on single cells following a
+**population transcriptomics** approach ([Plessy and coll.,
+2013](https://pubmed.gov/23281054)) focused on sampling the largest possible
+number of cells. In our ongoing developments, we have reached **single-cell and
 single molecule resolution** through the introduction of transposase
-fragmentation and unique molecular identifiers (Poulain et al.,
-2017). The protocol exists in two versions, one for FACS-isolated
-cells, and one for the Fluidigm C1 platform (Kouno et al., 2019).
+fragmentation and unique molecular identifiers ([Poulain and coll.,
+2017](https://pubmed.gov/28349422)). The protocol exists in two versions, one
+for FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll.,
+2019](https://pubmed.gov/30664627)).
 
-I have complemented my work on CAGE with the development of a
-gene-centred technique for detecting promoters, termed Deep-RACE
-(Olivarius et al., 2009, Plessy et al., 2012), which we used to
-validate our discovery of the pervasive expression of retrotransposons
-detected by CAGE (Faulkner et al., 2009). To study transcription start
-activity at nucleotide resolution in zebrafish transfected with
-chimeric transgenes containing a copy of an endogenous promoter, I
-combined Deep-RACE, CAGE and paired-end sequencing in a technology
-that we called “Single-Locus CAGE” (Haberle et al., 2014). With my
-contributions related to CAGE development and analysis, I have been a
-**member of the FANTOM consortium** since FANTOM3.
+I have complemented my work on CAGE with the development of a gene-centred
+technique for detecting promoters, termed Deep-RACE ([Olivarius and coll.,
+2009](https://pubmed.gov/19317658), [Plessy and coll.,
+2012](http://dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate
+our discovery of the pervasive expression of retrotransposons detected by CAGE
+([Faulkner and coll., 2009](https://pubmed.gov/19377475)). To study
+transcription start activity at nucleotide resolution in zebrafish transfected
+with chimeric transgenes containing a copy of an endogenous promoter, I
+combined Deep-RACE, CAGE and paired-end sequencing in a technology that we
+called “Single-Locus CAGE” ([Haberle and coll.,
+2014](https://pubmed.gov/24531765)). With my contributions related to CAGE
+development and analysis, I have been a **member of the FANTOM consortium**
+since FANTOM3.
 
 Together with my colleagues at RIKEN and collaborators in the field of
 neuroscience, I have applied nanoCAGE to the study of single neuron
-cell types, for instance the **olfactory neurons** (Plessy et al., 2012),
+cell types, for instance the **olfactory neurons** ([Plessy et al., 2012),
 or in dopaminergic cells, where we could demonstrate the expression of
 haemoglobin in the midbrain (Biagioli et al., 2009). We are also
 exploring the sub-cellular localisation of RNA in **Purkinje neurons**

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 20b07d75..1cf95c10 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-15 07:48+0000\n"
+"POT-Creation-Date: 2020-06-15 07:55+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -26,27 +26,31 @@ msgid ""
 "My training as a researcher started with **developmental genetics in "
 "drosophila and zebrafish**, where I studied the activity of transcription "
 "enhancers ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their "
-"evolutionary conservation (Plessy et al., 2005). This gave me a strong "
-"interest for whole-transcriptome analysis and technology. For that purpose, "
-"I have joined RIKEN in 2004, where have worked on high-throughput methods "
-"for **profiling promoters and inferring gene networks**, and in particular "
-"on CAGE (Cap Analysis Gene Expression)."
+"evolutionary conservation ([Plessy and coll., 2005](https://pubmed."
+"gov/15797614)). This gave me a strong interest for whole-transcriptome "
+"analysis and technology. For that purpose, I have joined RIKEN in 2004, "
+"where have worked on high-throughput methods for **profiling promoters and "
+"inferring gene networks**, and in particular on CAGE (Cap Analysis Gene "
+"Expression)."
 msgstr ""
 
 #. type: Plain text
 msgid ""
 "I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to "
-"analyse small samples yielding only nanograms of RNA (Plessy et al., 2010). "
-"In the same manuscript, we also introduced its paired-end variant, "
-"**CAGEscan**, which we use to **associate novel promoters with "
-"annotations**. Since then, we have kept improving or expanding these "
-"techniques, by updating the protocol (Salimullah et al., 2011), reducing the "
-"sequence bias introduced by the molecular barcodes (Tang et al., 2013), "
-"combining multiple cap-enrichment steps (Batut et al., 2013), benchmarking "
-"the use of locked nucleic acids for template switching (Harbers et al., "
-"2013), and reducing the number of primer artefacts and unwanted sequences "
-"generated by ribosomal RNAs using low-complexity “pseudo-random” reverse-"
-"transcription primers (Arnaud et al., 2016)."
+"analyse small samples yielding only nanograms of RNA ([Plessy and coll., "
+"2010](https://pubmed.gov/20543846)). In the same manuscript, we also "
+"introduced its paired-end variant, **CAGEscan**, which we use to **associate "
+"novel promoters with annotations**. Since then, we have kept improving or "
+"expanding these techniques, by updating the protocol ([Salimullah and coll., "
+"2011](https://pubmed.gov/21205859)), reducing the sequence bias introduced "
+"by the molecular barcodes ([Tang and coll., 2013](https://pubmed."
+"gov/23180801)), combining multiple cap-enrichment steps ([Batut and coll., "
+"2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic "
+"acids for template switching ([Harbers and coll., 2013](https://pubmed."
+"gov/24079827)), and reducing the number of primer artefacts and unwanted "
+"sequences generated by ribosomal RNAs using low-complexity “pseudo-random” "
+"reverse-transcription primers ([Arnaud and coll., 2016](https://pubmed."
+"gov/27071605))."
 msgstr ""
 
 #. type: Plain text

Liens
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 1e386c0d..80ab04d2 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -1,29 +1,30 @@
 Charles Plessy, open-source biologist
 -------------------------------------
 
-My training as a researcher started with **developmental genetics in
-drosophila and zebrafish**, where I studied the activity of
-transcription enhancers ([Blader and coll.,
-2003](https://pubmed.gov/12559493)) and their evolutionary
-conservation (Plessy et al., 2005). This gave me a strong interest for
-whole-transcriptome analysis and technology. For that purpose, I have
-joined RIKEN in 2004, where have worked on high-throughput methods for
-**profiling promoters and inferring gene networks**, and in particular on
-CAGE (Cap Analysis Gene Expression).
+My training as a researcher started with **developmental genetics in drosophila
+and zebrafish**, where I studied the activity of transcription enhancers
+([Blader and coll., 2003](https://pubmed.gov/12559493)) and their evolutionary
+conservation ([Plessy and coll., 2005](https://pubmed.gov/15797614)). This gave
+me a strong interest for whole-transcriptome analysis and technology. For that
+purpose, I have joined RIKEN in 2004, where have worked on high-throughput
+methods for **profiling promoters and inferring gene networks**, and in
+particular on CAGE (Cap Analysis Gene Expression).
 
 I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to
-analyse small samples yielding only nanograms of RNA (Plessy et al.,
-2010). In the same manuscript, we also introduced its paired-end
-variant, **CAGEscan**, which we use to **associate novel promoters with
-annotations**. Since then, we have kept improving or expanding these
-techniques, by updating the protocol (Salimullah et al., 2011),
-reducing the sequence bias introduced by the molecular barcodes (Tang
-et al., 2013), combining multiple cap-enrichment steps (Batut et al.,
-2013), benchmarking the use of locked nucleic acids for template
-switching (Harbers et al., 2013), and reducing the number of primer
+analyse small samples yielding only nanograms of RNA ([Plessy and coll.,
+2010](https://pubmed.gov/20543846)). In the same manuscript, we also introduced
+its paired-end variant, **CAGEscan**, which we use to **associate novel
+promoters with annotations**. Since then, we have kept improving or expanding
+these techniques, by updating the protocol ([Salimullah and coll.,
+2011](https://pubmed.gov/21205859)), reducing the sequence bias introduced by
+the molecular barcodes ([Tang and coll., 2013](https://pubmed.gov/23180801)),
+combining multiple cap-enrichment steps ([Batut and coll.,
+2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic
+acids for template switching ([Harbers and coll.,
+2013](https://pubmed.gov/24079827)), and reducing the number of primer
 artefacts and unwanted sequences generated by ribosomal RNAs using
-low-complexity “pseudo-random” reverse-transcription primers (Arnaud
-et al., 2016).
+low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and
+coll., 2016](https://pubmed.gov/27071605)).
 
 On April 2013, I started a new development cycle as the leader of the
 Genomics Miniaturization Technology Unit at RIKEN Center for Life

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 16ff1771..20b07d75 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-15 07:45+0000\n"
+"POT-Creation-Date: 2020-06-15 07:48+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -23,30 +23,30 @@ msgstr ""
 
 #. type: Plain text
 msgid ""
-"My training as a researcher started with developmental genetics in "
-"drosophila and zebrafish, where I studied the activity of transcription "
+"My training as a researcher started with **developmental genetics in "
+"drosophila and zebrafish**, where I studied the activity of transcription "
 "enhancers ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their "
 "evolutionary conservation (Plessy et al., 2005). This gave me a strong "
 "interest for whole-transcriptome analysis and technology. For that purpose, "
 "I have joined RIKEN in 2004, where have worked on high-throughput methods "
-"for profiling promoters and inferring gene networks, and in particular on "
-"CAGE (Cap Analysis Gene Expression)."
+"for **profiling promoters and inferring gene networks**, and in particular "
+"on CAGE (Cap Analysis Gene Expression)."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"I have developed a miniaturized version of CAGE, termed nanoCAGE, to analyse "
-"small samples yielding only nanograms of RNA (Plessy et al., 2010). In the "
-"same manuscript, we also introduced its paired-end variant, CAGEscan, which "
-"we use to associate novel promoters with annotations. Since then, we have "
-"kept improving or expanding these techniques, by updating the protocol "
-"(Salimullah et al., 2011), reducing the sequence bias introduced by the "
-"molecular barcodes (Tang et al., 2013), combining multiple cap-enrichment "
-"steps (Batut et al., 2013), benchmarking the use of locked nucleic acids for "
-"template switching (Harbers et al., 2013), and reducing the number of primer "
-"artefacts and unwanted sequences generated by ribosomal RNAs using low-"
-"complexity “pseudo-random” reverse-transcription primers (Arnaud et al., "
-"2016)."
+"I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to "
+"analyse small samples yielding only nanograms of RNA (Plessy et al., 2010). "
+"In the same manuscript, we also introduced its paired-end variant, "
+"**CAGEscan**, which we use to **associate novel promoters with "
+"annotations**. Since then, we have kept improving or expanding these "
+"techniques, by updating the protocol (Salimullah et al., 2011), reducing the "
+"sequence bias introduced by the molecular barcodes (Tang et al., 2013), "
+"combining multiple cap-enrichment steps (Batut et al., 2013), benchmarking "
+"the use of locked nucleic acids for template switching (Harbers et al., "
+"2013), and reducing the number of primer artefacts and unwanted sequences "
+"generated by ribosomal RNAs using low-complexity “pseudo-random” reverse-"
+"transcription primers (Arnaud et al., 2016)."
 msgstr ""
 
 #. type: Plain text
@@ -54,9 +54,9 @@ msgid ""
 "On April 2013, I started a new development cycle as the leader of the "
 "Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, "
 "Division of Genomics Technology, to expand this work on single cells "
-"following a population transcriptomics approach (Plessy et al., 2013) "
+"following a **population transcriptomics** approach (Plessy et al., 2013) "
 "focused on sampling the largest possible number of cells. In our ongoing "
-"developments, we have reached single-cell and single molecule resolution "
+"developments, we have reached **single-cell and single molecule resolution** "
 "through the introduction of transposase fragmentation and unique molecular "
 "identifiers (Poulain et al., 2017). The protocol exists in two versions, one "
 "for FACS-isolated cells, and one for the Fluidigm C1 platform (Kouno et al., "
@@ -74,34 +74,34 @@ msgid ""
 "endogenous promoter, I combined Deep-RACE, CAGE and paired-end sequencing in "
 "a technology that we called “Single-Locus CAGE” (Haberle et al., 2014). With "
 "my contributions related to CAGE development and analysis, I have been a "
-"member of the FANTOM consortium since FANTOM3."
+"**member of the FANTOM consortium** since FANTOM3."
 msgstr ""
 
 #. type: Plain text
 msgid ""
 "Together with my colleagues at RIKEN and collaborators in the field of "
 "neuroscience, I have applied nanoCAGE to the study of single neuron cell "
-"types, for instance the olfactory neurons (Plessy et al., 2012), or in "
+"types, for instance the **olfactory neurons** (Plessy et al., 2012), or in "
 "dopaminergic cells, where we could demonstrate the expression of haemoglobin "
 "in the midbrain (Biagioli et al., 2009). We are also exploring the sub-"
-"cellular localisation of RNA in Purkinje neurons (Kratz et al., 2014), and "
-"neurogenesis in the mouse olfactory epithelium using single-cell CAGE and "
-"ATAC-seq techniques. In parallel with this promoter-centric work, I have "
-"also explored the huge repertoire of the T cell antigen receptors."
+"cellular localisation of RNA in **Purkinje neurons** (Kratz et al., 2014), "
+"and neurogenesis in the mouse olfactory epithelium using single-cell CAGE "
+"and ATAC-seq techniques. In parallel with this promoter-centric work, I have "
+"also explored the huge repertoire of the **T cell antigen receptors**."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"I joined OIST in 2018, to study the genetic structure and population "
-"variations of an animal plankton, Oikopleura dioica, that has a genome 50 "
+"I joined OIST in 2018, to study **the genetic structure and population "
+"variations** of an animal plankton, Oikopleura dioica, that has a genome 50 "
 "time more compact than the human one, which empowers us to sequence at "
 "chromosomal resolution many individual sampled from all over the World."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"I am also a Free Software enthusiast, and contribute to the Debian Med "
-"project, by packaging bioinformatics tools, which are redistributed in "
+"I am also a **Free Software** enthusiast, and contribute to the Debian Med "
+"project, by **packaging bioinformatics tools**, which are redistributed in "
 "Debian (Möller et al., 2010) and its derivatives such as Ubuntu and "
 "(cloud)Bio-Linux. For digital signature of my contributions and other "
 "activities as a RIKEN researcher, I use the GPG key number B3443334. My "

Bold
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 86511230..1e386c0d 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -1,21 +1,21 @@
 Charles Plessy, open-source biologist
 -------------------------------------
 
-My training as a researcher started with developmental genetics in
-drosophila and zebrafish, where I studied the activity of
+My training as a researcher started with **developmental genetics in
+drosophila and zebrafish**, where I studied the activity of
 transcription enhancers ([Blader and coll.,
 2003](https://pubmed.gov/12559493)) and their evolutionary
 conservation (Plessy et al., 2005). This gave me a strong interest for
 whole-transcriptome analysis and technology. For that purpose, I have
 joined RIKEN in 2004, where have worked on high-throughput methods for
-profiling promoters and inferring gene networks, and in particular on
+**profiling promoters and inferring gene networks**, and in particular on
 CAGE (Cap Analysis Gene Expression).
 
-I have developed a miniaturized version of CAGE, termed nanoCAGE, to
+I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to
 analyse small samples yielding only nanograms of RNA (Plessy et al.,
 2010). In the same manuscript, we also introduced its paired-end
-variant, CAGEscan, which we use to associate novel promoters with
-annotations. Since then, we have kept improving or expanding these
+variant, **CAGEscan**, which we use to **associate novel promoters with
+annotations**. Since then, we have kept improving or expanding these
 techniques, by updating the protocol (Salimullah et al., 2011),
 reducing the sequence bias introduced by the molecular barcodes (Tang
 et al., 2013), combining multiple cap-enrichment steps (Batut et al.,
@@ -28,10 +28,10 @@ et al., 2016).
 On April 2013, I started a new development cycle as the leader of the
 Genomics Miniaturization Technology Unit at RIKEN Center for Life
 Sciences, Division of Genomics Technology, to expand this work on
-single cells following a population transcriptomics approach (Plessy
+single cells following a **population transcriptomics** approach (Plessy
 et al., 2013) focused on sampling the largest possible number of
-cells. In our ongoing developments, we have reached single-cell and
-single molecule resolution through the introduction of transposase
+cells. In our ongoing developments, we have reached **single-cell and
+single molecule resolution** through the introduction of transposase
 fragmentation and unique molecular identifiers (Poulain et al.,
 2017). The protocol exists in two versions, one for FACS-isolated
 cells, and one for the Fluidigm C1 platform (Kouno et al., 2019).
@@ -46,27 +46,27 @@ chimeric transgenes containing a copy of an endogenous promoter, I
 combined Deep-RACE, CAGE and paired-end sequencing in a technology
 that we called “Single-Locus CAGE” (Haberle et al., 2014). With my
 contributions related to CAGE development and analysis, I have been a
-member of the FANTOM consortium since FANTOM3.
+**member of the FANTOM consortium** since FANTOM3.
 
 Together with my colleagues at RIKEN and collaborators in the field of
 neuroscience, I have applied nanoCAGE to the study of single neuron
-cell types, for instance the olfactory neurons (Plessy et al., 2012),
+cell types, for instance the **olfactory neurons** (Plessy et al., 2012),
 or in dopaminergic cells, where we could demonstrate the expression of
 haemoglobin in the midbrain (Biagioli et al., 2009). We are also
-exploring the sub-cellular localisation of RNA in Purkinje neurons
+exploring the sub-cellular localisation of RNA in **Purkinje neurons**
 (Kratz et al., 2014), and neurogenesis in the mouse olfactory
 epithelium using single-cell CAGE and ATAC-seq techniques. In parallel
 with this promoter-centric work, I have also explored the huge
-repertoire of the T cell antigen receptors.
+repertoire of the **T cell antigen receptors**.
 
-I joined OIST in 2018, to study the genetic structure and population
-variations of an animal plankton, Oikopleura dioica, that has a genome
+I joined OIST in 2018, to study **the genetic structure and population
+variations** of an animal plankton, Oikopleura dioica, that has a genome
 50 time more compact than the human one, which empowers us to sequence
 at chromosomal resolution many individual sampled from all over the
 World.
 
-I am also a Free Software enthusiast, and contribute to the Debian Med
-project, by packaging bioinformatics tools, which are redistributed in
+I am also a **Free Software** enthusiast, and contribute to the Debian Med
+project, by **packaging bioinformatics tools**, which are redistributed in
 Debian (Möller et al., 2010) and its derivatives such as Ubuntu and
 (cloud)Bio-Linux. For digital signature of my contributions and other
 activities as a RIKEN researcher, I use the GPG key number

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
index 9a9a3dce..16ff1771 100644
--- a/open-source-biologist.en.po
+++ b/open-source-biologist.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2020-06-15 07:41+0000\n"
+"POT-Creation-Date: 2020-06-15 07:45+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -16,16 +16,21 @@ msgstr ""
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 
+#. type: Title -
+#, no-wrap
+msgid "Charles Plessy, open-source biologist"
+msgstr ""
+
 #. type: Plain text
 msgid ""
 "My training as a researcher started with developmental genetics in "
 "drosophila and zebrafish, where I studied the activity of transcription "
-"enhancers (Blader et al., 2003) and their evolutionary conservation (Plessy "
-"et al., 2005). This gave me a strong interest for whole-transcriptome "
-"analysis and technology. For that purpose, I have joined RIKEN in 2004, "
-"where have worked on high-throughput methods for profiling promoters and "
-"inferring gene networks, and in particular on CAGE (Cap Analysis Gene "
-"Expression)."
+"enhancers ([Blader and coll., 2003](https://pubmed.gov/12559493)) and their "
+"evolutionary conservation (Plessy et al., 2005). This gave me a strong "
+"interest for whole-transcriptome analysis and technology. For that purpose, "
+"I have joined RIKEN in 2004, where have worked on high-throughput methods "
+"for profiling promoters and inferring gene networks, and in particular on "
+"CAGE (Cap Analysis Gene Expression)."
 msgstr ""
 
 #. type: Plain text
@@ -39,8 +44,8 @@ msgid ""
 "molecular barcodes (Tang et al., 2013), combining multiple cap-enrichment "
 "steps (Batut et al., 2013), benchmarking the use of locked nucleic acids for "
 "template switching (Harbers et al., 2013), and reducing the number of primer "
-"artefacts and unwanted sequences generated by ribosomal RNAs using "
-"low-complexity “pseudo-random” reverse-transcription primers (Arnaud et al., "
+"artefacts and unwanted sequences generated by ribosomal RNAs using low-"
+"complexity “pseudo-random” reverse-transcription primers (Arnaud et al., "
 "2016)."
 msgstr ""
 
@@ -78,10 +83,10 @@ msgid ""
 "neuroscience, I have applied nanoCAGE to the study of single neuron cell "
 "types, for instance the olfactory neurons (Plessy et al., 2012), or in "
 "dopaminergic cells, where we could demonstrate the expression of haemoglobin "
-"in the midbrain (Biagioli et al., 2009). We are also exploring the "
-"sub-cellular localisation of RNA in Purkinje neurons (Kratz et al., 2014), "
-"and neurogenesis in the mouse olfactory epithelium using single-cell CAGE "
-"and ATAC-seq techniques. In parallel with this promoter-centric work, I have "
+"in the midbrain (Biagioli et al., 2009). We are also exploring the sub-"
+"cellular localisation of RNA in Purkinje neurons (Kratz et al., 2014), and "
+"neurogenesis in the mouse olfactory epithelium using single-cell CAGE and "
+"ATAC-seq techniques. In parallel with this promoter-centric work, I have "
 "also explored the huge repertoire of the T cell antigen receptors."
 msgstr ""
 

Link
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
index 44cb7d05..86511230 100644
--- a/open-source-biologist.mdwn
+++ b/open-source-biologist.mdwn
@@ -1,6 +1,10 @@
+Charles Plessy, open-source biologist
+-------------------------------------
+
 My training as a researcher started with developmental genetics in
 drosophila and zebrafish, where I studied the activity of
-transcription enhancers (Blader et al., 2003) and their evolutionary
+transcription enhancers ([Blader and coll.,
+2003](https://pubmed.gov/12559493)) and their evolutionary
 conservation (Plessy et al., 2005). This gave me a strong interest for
 whole-transcriptome analysis and technology. For that purpose, I have
 joined RIKEN in 2004, where have worked on high-throughput methods for

updated PO files
diff --git a/open-source-biologist.en.po b/open-source-biologist.en.po
new file mode 100644
index 00000000..9a9a3dce
--- /dev/null
+++ b/open-source-biologist.en.po
@@ -0,0 +1,104 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2020-06-15 07:41+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+msgid ""
+"My training as a researcher started with developmental genetics in "
+"drosophila and zebrafish, where I studied the activity of transcription "
+"enhancers (Blader et al., 2003) and their evolutionary conservation (Plessy "
+"et al., 2005). This gave me a strong interest for whole-transcriptome "
+"analysis and technology. For that purpose, I have joined RIKEN in 2004, "
+"where have worked on high-throughput methods for profiling promoters and "
+"inferring gene networks, and in particular on CAGE (Cap Analysis Gene "
+"Expression)."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"I have developed a miniaturized version of CAGE, termed nanoCAGE, to analyse "
+"small samples yielding only nanograms of RNA (Plessy et al., 2010). In the "
+"same manuscript, we also introduced its paired-end variant, CAGEscan, which "
+"we use to associate novel promoters with annotations. Since then, we have "
+"kept improving or expanding these techniques, by updating the protocol "
+"(Salimullah et al., 2011), reducing the sequence bias introduced by the "
+"molecular barcodes (Tang et al., 2013), combining multiple cap-enrichment "
+"steps (Batut et al., 2013), benchmarking the use of locked nucleic acids for "
+"template switching (Harbers et al., 2013), and reducing the number of primer "
+"artefacts and unwanted sequences generated by ribosomal RNAs using "
+"low-complexity “pseudo-random” reverse-transcription primers (Arnaud et al., "
+"2016)."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"On April 2013, I started a new development cycle as the leader of the "
+"Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, "
+"Division of Genomics Technology, to expand this work on single cells "
+"following a population transcriptomics approach (Plessy et al., 2013) "
+"focused on sampling the largest possible number of cells. In our ongoing "
+"developments, we have reached single-cell and single molecule resolution "
+"through the introduction of transposase fragmentation and unique molecular "
+"identifiers (Poulain et al., 2017). The protocol exists in two versions, one "
+"for FACS-isolated cells, and one for the Fluidigm C1 platform (Kouno et al., "
+"2019)."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"I have complemented my work on CAGE with the development of a gene-centred "
+"technique for detecting promoters, termed Deep-RACE (Olivarius et al., 2009, "
+"Plessy et al., 2012), which we used to validate our discovery of the "
+"pervasive expression of retrotransposons detected by CAGE (Faulkner et al., "
+"2009). To study transcription start activity at nucleotide resolution in "
+"zebrafish transfected with chimeric transgenes containing a copy of an "
+"endogenous promoter, I combined Deep-RACE, CAGE and paired-end sequencing in "
+"a technology that we called “Single-Locus CAGE” (Haberle et al., 2014). With "
+"my contributions related to CAGE development and analysis, I have been a "
+"member of the FANTOM consortium since FANTOM3."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Together with my colleagues at RIKEN and collaborators in the field of "
+"neuroscience, I have applied nanoCAGE to the study of single neuron cell "
+"types, for instance the olfactory neurons (Plessy et al., 2012), or in "
+"dopaminergic cells, where we could demonstrate the expression of haemoglobin "
+"in the midbrain (Biagioli et al., 2009). We are also exploring the "
+"sub-cellular localisation of RNA in Purkinje neurons (Kratz et al., 2014), "
+"and neurogenesis in the mouse olfactory epithelium using single-cell CAGE "
+"and ATAC-seq techniques. In parallel with this promoter-centric work, I have "
+"also explored the huge repertoire of the T cell antigen receptors."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"I joined OIST in 2018, to study the genetic structure and population "
+"variations of an animal plankton, Oikopleura dioica, that has a genome 50 "
+"time more compact than the human one, which empowers us to sequence at "
+"chromosomal resolution many individual sampled from all over the World."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"I am also a Free Software enthusiast, and contribute to the Debian Med "
+"project, by packaging bioinformatics tools, which are redistributed in "
+"Debian (Möller et al., 2010) and its derivatives such as Ubuntu and "
+"(cloud)Bio-Linux. For digital signature of my contributions and other "
+"activities as a RIKEN researcher, I use the GPG key number B3443334. My "
+"ORCID ID is 0000-0001-7410-6295."
+msgstr ""

CV en ligne.
diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn
new file mode 100644
index 00000000..44cb7d05
--- /dev/null
+++ b/open-source-biologist.mdwn
@@ -0,0 +1,69 @@
+My training as a researcher started with developmental genetics in
+drosophila and zebrafish, where I studied the activity of
+transcription enhancers (Blader et al., 2003) and their evolutionary
+conservation (Plessy et al., 2005). This gave me a strong interest for
+whole-transcriptome analysis and technology. For that purpose, I have
+joined RIKEN in 2004, where have worked on high-throughput methods for
+profiling promoters and inferring gene networks, and in particular on
+CAGE (Cap Analysis Gene Expression).
+
+I have developed a miniaturized version of CAGE, termed nanoCAGE, to
+analyse small samples yielding only nanograms of RNA (Plessy et al.,
+2010). In the same manuscript, we also introduced its paired-end
+variant, CAGEscan, which we use to associate novel promoters with
+annotations. Since then, we have kept improving or expanding these
+techniques, by updating the protocol (Salimullah et al., 2011),
+reducing the sequence bias introduced by the molecular barcodes (Tang
+et al., 2013), combining multiple cap-enrichment steps (Batut et al.,
+2013), benchmarking the use of locked nucleic acids for template
+switching (Harbers et al., 2013), and reducing the number of primer
+artefacts and unwanted sequences generated by ribosomal RNAs using
+low-complexity “pseudo-random” reverse-transcription primers (Arnaud
+et al., 2016).
+
+On April 2013, I started a new development cycle as the leader of the
+Genomics Miniaturization Technology Unit at RIKEN Center for Life
+Sciences, Division of Genomics Technology, to expand this work on
+single cells following a population transcriptomics approach (Plessy
+et al., 2013) focused on sampling the largest possible number of
+cells. In our ongoing developments, we have reached single-cell and
+single molecule resolution through the introduction of transposase
+fragmentation and unique molecular identifiers (Poulain et al.,
+2017). The protocol exists in two versions, one for FACS-isolated
+cells, and one for the Fluidigm C1 platform (Kouno et al., 2019).
+
+I have complemented my work on CAGE with the development of a
+gene-centred technique for detecting promoters, termed Deep-RACE
+(Olivarius et al., 2009, Plessy et al., 2012), which we used to
+validate our discovery of the pervasive expression of retrotransposons
+detected by CAGE (Faulkner et al., 2009). To study transcription start
+activity at nucleotide resolution in zebrafish transfected with
+chimeric transgenes containing a copy of an endogenous promoter, I
+combined Deep-RACE, CAGE and paired-end sequencing in a technology
+that we called “Single-Locus CAGE” (Haberle et al., 2014). With my
+contributions related to CAGE development and analysis, I have been a
+member of the FANTOM consortium since FANTOM3.
+
+Together with my colleagues at RIKEN and collaborators in the field of
+neuroscience, I have applied nanoCAGE to the study of single neuron
+cell types, for instance the olfactory neurons (Plessy et al., 2012),
+or in dopaminergic cells, where we could demonstrate the expression of
+haemoglobin in the midbrain (Biagioli et al., 2009). We are also
+exploring the sub-cellular localisation of RNA in Purkinje neurons
+(Kratz et al., 2014), and neurogenesis in the mouse olfactory
+epithelium using single-cell CAGE and ATAC-seq techniques. In parallel
+with this promoter-centric work, I have also explored the huge
+repertoire of the T cell antigen receptors.
+
+I joined OIST in 2018, to study the genetic structure and population
+variations of an animal plankton, Oikopleura dioica, that has a genome
+50 time more compact than the human one, which empowers us to sequence
+at chromosomal resolution many individual sampled from all over the
+World.
+
+I am also a Free Software enthusiast, and contribute to the Debian Med
+project, by packaging bioinformatics tools, which are redistributed in
+Debian (Möller et al., 2010) and its derivatives such as Ubuntu and
+(cloud)Bio-Linux. For digital signature of my contributions and other
+activities as a RIKEN researcher, I use the GPG key number
+B3443334. My ORCID ID is 0000-0001-7410-6295.

Hox
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e42bd2a1..10221c2c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -201,6 +201,7 @@ Genes and pathways
  - Defensome genes such as dehydrogenases and  (Glutamate-cysteine ligase modifier subunit; Gclm)
    are activated by polyunsaturated aldehydes produced by diatoms
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
+ - The _Hox_ cluster has been split up in Oikopleura ([[Seo and coll., 2004|biblio/15343333]]).
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
    Illustrating how diverged are the sequences, earlier attempts to clone Hox genes yielded
    only a single clone ([[Holland and coll. 1994|biblio/7579513]]).