Dernières modifications :

Found what "Fol, 1872" stands for.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5af5724..80701f1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -18,7 +18,8 @@ Some links:
  - Oikopleura Histone Database: <http://apps.cbu.uib.no/oikohistonedb>
  - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
  - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/> ([[Danks et al., 2013|biblio/23185044]])
-
+ - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
+   ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
 
 Phylogeny
 ---------

Avant café
diff --git a/biblio/30217597.mdwn b/biblio/30217597.mdwn
new file mode 100644
index 0000000..4700286
--- /dev/null
+++ b/biblio/30217597.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors."]]
+[[!tag Oikopleura]]
+
+Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D.
+
+Dev Biol. 2018 Sep 11. pii: S0012-1606(18)30157-X. doi:10.1016/j.ydbio.2018.09.006
+
+Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors.
+
+[[!pmid 30217597 desc="The tandem-duplicated propA and probB genes participate to the development of the house secreting epitelium and control (directly or indirectly) oik41a."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b026220..5af5724 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -153,6 +153,9 @@ Development
    who noted that it is exceptional in invertebrates, and hypothethise that it may
    be caused by neofunctionalisation (house production, ...) or by the small size of
    the genome (doubling the genes would then double the amount of regulatory sequences).
+ - The tandem _propA_ and _propB_ genes control directly or indirectly _oik41a_
+   and proper development of the house-secreting epithelium ([[Mikhaleva et
+   al., 2018|biblio/30217597]]).
 
 
 Physiology

schpoump
diff --git a/biblio/22343429.mdwn b/biblio/22343429.mdwn
new file mode 100644
index 0000000..893e24b
--- /dev/null
+++ b/biblio/22343429.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research."]]
+[[!tag method nucleus]]
+
+Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, Zhang HB.
+
+Nat Protoc. 2012 Feb 16;7(3):467-78. doi:10.1038/nprot.2011.455
+
+Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research.
+
+[[!pmid 22343429 desc="Method to produce low melting agarose plugs or beads."]]

Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro.
diff --git a/biblio/26579937.mdwn b/biblio/26579937.mdwn
new file mode 100644
index 0000000..e316361
--- /dev/null
+++ b/biblio/26579937.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro."]]
+[[!tag CRISPR not_read]]
+
+Hinz JM, Laughery MF, Wyrick JJ.
+
+J Biol Chem. 2016 Nov 25;291(48):24851-24856 doi:10.1074/jbc.C116.758706
+
+Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro.
+
+[[!pmid 26579937 desc="Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro."]]

Debranched.
diff --git a/biblio/24213699.mdwn b/biblio/24213699.mdwn
index 7ddff5e..041b09a 100644
--- a/biblio/24213699.mdwn
+++ b/biblio/24213699.mdwn
@@ -7,4 +7,4 @@ Nat Biotechnol. 2013 Dec;31(12):1126-32. doi: 10.1038/nbt.2720
 
 Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.
 
-[[!pmid 24213699 desc="Tn5 is not efficient on hyperbranched DNA"]]
+[[!pmid 24213699 desc="Tn5 is not efficient on hyperbranched DNA.  Random hexamers and DNA polymerase I were used to debranch the DNA."]]

Old
diff --git a/biblio/28973477.mdwn b/biblio/28973477.mdwn
new file mode 100644
index 0000000..43763bb
--- /dev/null
+++ b/biblio/28973477.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Self-biotinylation of DNA G-quadruplexes via intrinsic peroxidase activity."]]
+[[!tag method structure]]
+
+Nucleic Acids Res. 2017 Sep 29;45(17):9813-9822. doi:10.1093/nar/gkx765
+
+Einarson OJ, Sen D.
+
+Self-biotinylation of DNA G-quadruplexes via intrinsic peroxidase activity.
+
+[[!pmid 28973477 desc="Could it be turned into a single-cell method ?"]]

Correct tag.
diff --git a/biblio/30154186.mdwn b/biblio/30154186.mdwn
index fe84ccf..896ea95 100644
--- a/biblio/30154186.mdwn
+++ b/biblio/30154186.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler"]]
-[[!tag method sequence_tag nucleus]]
+[[!tag method sequence_tags nucleus]]
 
 J Cell Biol. 2018 Aug 28. pii: jcb.201807108. doi:10.1083/jcb.201807108
 

Prevent smiley.
diff --git a/biblio/30154186.mdwn b/biblio/30154186.mdwn
index ecbc8a1..fe84ccf 100644
--- a/biblio/30154186.mdwn
+++ b/biblio/30154186.mdwn
@@ -7,4 +7,4 @@ Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel
 
 Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler 
 
-[[!pmid 30154186 desc="Tyramide free radicals can label DNA directly.  In TSA-Seq (Tyramide Signal Amplification-Sequencing), HRP is targeted on proteins of interest, biotinylated TSA labels neighboring DNA, and biotin-DNA complexes are purified and sequenced.  Distances between chromosome domains and nuclear speckles is reproducible across experiments. Between peripheral lamina (marked by lamin A and B) and nuclear speckles (marked by SON), an increasing gradient of transcriptional activity is clearly visible."]]
+[[!pmid 30154186 desc="Tyramide free radicals can label DNA directly.  In TSA-Seq (Tyramide Signal Amplification-Sequencing), HRP is targeted on proteins of interest, biotinylated TSA labels neighboring DNA, and biotin-DNA complexes are purified and sequenced.  Distances between chromosome domains and nuclear speckles is reproducible across experiments. Between peripheral lamina, marked by lamin A and B, and nuclear speckles (marked by SON), an increasing gradient of transcriptional activity is clearly visible."]]

Old.
diff --git a/biblio/30154186.mdwn b/biblio/30154186.mdwn
new file mode 100644
index 0000000..ecbc8a1
--- /dev/null
+++ b/biblio/30154186.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler"]]
+[[!tag method sequence_tag nucleus]]
+
+J Cell Biol. 2018 Aug 28. pii: jcb.201807108. doi:10.1083/jcb.201807108
+
+Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS.
+
+Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler 
+
+[[!pmid 30154186 desc="Tyramide free radicals can label DNA directly.  In TSA-Seq (Tyramide Signal Amplification-Sequencing), HRP is targeted on proteins of interest, biotinylated TSA labels neighboring DNA, and biotin-DNA complexes are purified and sequenced.  Distances between chromosome domains and nuclear speckles is reproducible across experiments. Between peripheral lamina (marked by lamin A and B) and nuclear speckles (marked by SON), an increasing gradient of transcriptional activity is clearly visible."]]

Old
diff --git a/biblio/29895867.mdwn b/biblio/29895867.mdwn
new file mode 100644
index 0000000..179f50f
--- /dev/null
+++ b/biblio/29895867.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="A photoelectrochemical platform for the capture and release of rare single cells."]]
+[[!tag single_cell microfluidic]]
+
+Parker SG, Yang Y, Ciampi S, Gupta B, Kimpton K, Mansfeld FM, Kavallaris M,
+Gaus K, Gooding JJ.
+
+Nat Commun. 2018 Jun 12;9(1):2288. doi:10.1038/s41467-018-04701-y
+
+A photoelectrochemical platform for the capture and release of rare single cells.
+
+[[!pmid 29895867 desc="Cells captured by an antibody by an electrochemically cleavable linker."]]

Normalisation.
diff --git a/biblio/21596820.mdwn b/biblio/21596820.mdwn
index 340bdb9..47716c3 100644
--- a/biblio/21596820.mdwn
+++ b/biblio/21596820.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Unamplified cap analysis of gene expression on a single-molecule sequencer."]]
-[[!tag CAGE Helicos sequence_tag method]]
+[[!tag CAGE Helicos sequence_tags method]]
 
 Genome Res. 2011 Jul;21(7):1150-9. doi:10.1101/gr.115469.110
 
diff --git a/tags/sequence_tag.mdwn b/tags/sequence_tag.mdwn
deleted file mode 100644
index 244d1cd..0000000
--- a/tags/sequence_tag.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged sequence tag"]]
-
-[[!inline pages="tagged(sequence_tag)" actions="no" archive="yes"
-feedshow=10]]

Old
diff --git a/biblio/28973448.mdwn b/biblio/28973448.mdwn
new file mode 100644
index 0000000..6fafeed
--- /dev/null
+++ b/biblio/28973448.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers."]]
+[[!tag sequence_tags epigenetic method]]
+
+Nucleic Acids Res. 2017 Sep 29;45(17):e153. doi:10.1093/nar/gkx648
+
+Zarnegar MA, Reinitz F, Newman AM, Clarke MF.
+
+Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers.
+
+[[!pmid 28973448 desc="Proximity ligation between DNA ends and antibody-linked adaptors."]]

Café
diff --git a/biblio/17829536.mdwn b/biblio/17829536.mdwn
new file mode 100644
index 0000000..d70c5ed
--- /dev/null
+++ b/biblio/17829536.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Zooplankton Species Groups in the North Pacific"]]
+[[!tag richness statistics]]
+
+Science. 1963 May 3;140(3566):453-60 doi:10.1126/science.140.3566.453
+
+Fager EW, McGowan JA.
+
+Zooplankton Species Groups in the North Pacific
+
+[[!pmid 17829536 desc="Fager & McGowan index of affinity: [J/√(Na.Nb)] - 1/2√Nb, where J is number of joined occurences and Na and Nb are the number of occurences of a and b respectively.  Nb is chosen to be greater or equal to Na.  Scores higher than 0.5 denote affinity.  The paper then explores the geographical distribution of groups of species, where all species in the same group have affinity for each other."]]

Splice leader sequence.
diff --git a/biblio/15314184.mdwn b/biblio/15314184.mdwn
index 2ca7c3e..b45e7b3 100644
--- a/biblio/15314184.mdwn
+++ b/biblio/15314184.mdwn
@@ -7,4 +7,4 @@ Mol Cell Biol. 2004 Sep;24(17):7795-805. doi:10.1128/MCB.24.17.7795-7805.2004
 
 Spliced-Leader RNA trans Splicing in a Chordate, Oikopleura dioica, with a Compact Genome.
 
-[[!pmid 15314184 desc="5′ splice leader (SL) found in 90/158 ESTs containing a start codon.  The SL RNA is found downstream of the 5S RNA in at least 40 occurences, and aproximately 2/3 of all the 5S rRNA genes.  O. doica is the first chordate where gene operons have been described."]]
+[[!pmid 15314184 desc="5′ splice leader (SL) found in 90/158 ESTs containing a start codon.  The SL RNA is found downstream of the 5S RNA in at least 40 occurences, and aproximately 2/3 of all the 5S rRNA genes.  Its sequence is ACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG. O. doica is the first chordate where gene operons have been described."]]

Old
diff --git a/biblio/29320473.mdwn b/biblio/29320473.mdwn
new file mode 100644
index 0000000..e7a9587
--- /dev/null
+++ b/biblio/29320473.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Systems of mechanized and reactive droplets powered by multi-responsive surfactants."]]
+[[!tag emulsion]]
+
+Nature. 2018 Jan 18;553(7688):313-318. doi:10.1038/nature25137
+
+Yang Z, Wei J, Sobolev YI, Grzybowski BA.
+
+Systems of mechanized and reactive droplets powered by multi-responsive surfactants.
+
+[[!pmid 29320473 desc="New amphiphilic surfactants containing gold, iron oxide or lead sulfide were used to create droplets that aggregate in magnetic fields, translate or rotate under laser illumination, and weld together electric fields. Combining these three manipulations allowed for the creation of complex structures used as microreactors for chemical reactions between reagents brought by individual droplets."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index b72e5ee..dc83bbe 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -21,4 +21,8 @@ Different kinds of surfactants:
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
  - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]
 
+Reactive droplets:
+
+ - Illumination changing magnetic or electric properties of droplets ([[Yang et al., 2018|biblio/29320473]]).
+
 [[!inline pages="tagged(emulsion)" actions="no" limit=0]]

Link to BOLD.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index a21d1f5..b026220 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -191,5 +191,7 @@ Ecology
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
  - It was already reported to be frequent in Japanese waters [[in 1907 by T. Aida|biblio/AA0069577]].
+ - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)
+   database of DNA barcodes.
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Tiling.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b16538d..a21d1f5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -17,7 +17,7 @@ Some links:
 
  - Oikopleura Histone Database: <http://apps.cbu.uib.no/oikohistonedb>
  - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
- - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
+ - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/> ([[Danks et al., 2013|biblio/23185044]])
 
 
 Phylogeny
@@ -131,6 +131,7 @@ Transcriptome
    by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  Larger introns tend
    to be older, and among the large introns, the older contain repeat elements less frequently
    than the newer ([[Denoeud et al., 2010|biblio/21097902]]). 
+ - 12 developmental stages were studied with tiling arrays by [[Danks et al., 2013|biblio/23185044]].
 
 
 Tools

Tiling array.
diff --git a/biblio/23185044.mdwn b/biblio/23185044.mdwn
new file mode 100644
index 0000000..b5e9c64
--- /dev/null
+++ b/biblio/23185044.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Nucleic Acids Res. 2013 Jan;41(Database issue):D845-53. doi:10.1093/nar/gks1159
+
+Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni H, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM, Manak JR.
+
+OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.
+
+[[!pmid 23185044 desc="Tiling array expression data for 12 developmental stages."]]

Café.
diff --git a/biblio/1929090.mdwn b/biblio/1929090.mdwn
new file mode 100644
index 0000000..48feb89
--- /dev/null
+++ b/biblio/1929090.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The Seasonal Distribution of the Appendicularia in the Region of San Diego, California"]]
+[[!tag Oikopleura]]
+
+Ecology Vol. 3, No. 1 (Jan., 1922), pp. 55-64
+
+Christine E. Essenberg
+
+The Seasonal Distribution of the Appendicularia in the Region of San Diego, California
+
+[[!doi 10.2307/1929090 desc="Higher abundances of O. dioica in cool temperatures during winter."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index a27282b..b16538d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -183,6 +183,9 @@ Ecology
 
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).
+ - In California, _O. dioica_ was reported by C. Essenberg
+   ([[1922|biblio/1929090]]) to be rare in summer's warm (> 20ºC) waters and
+   more abundant in winter's cool (13~16 ºC) waters.
  - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).

Methylation.
diff --git a/biblio/28115992.mdwn b/biblio/28115992.mdwn
index 3a7c736..8c32193 100644
--- a/biblio/28115992.mdwn
+++ b/biblio/28115992.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Sex-specific chromatin landscapes in an ultra-compact chordate genome."]]
-[[!tag Oikopleura epigenetic]]
+[[!tag Oikopleura methylation epigenetic]]
 
 Navratilova P, Danks GB, Long A, Butcher S, Manak JR, Thompson EM.
 
@@ -7,4 +7,4 @@ Epigenetics Chromatin. 2017 Jan 17;10:3. doi:10.1186/s13072-016-0110-4
 
 Sex-specific chromatin landscapes in an ultra-compact chordate genome.
 
-[[!pmid 28115992 desc="Chromatin domains usually smaller than 7 nucleosomes."]]
+[[!pmid 28115992 desc="Chromatin domains usually smaller than 7 nucleosomes.  5-methylcytosine detected by immunoprecipitation and microarray analysis (MeDIP-chip)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dfb3fe6..a27282b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -55,6 +55,7 @@ Genome
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
+ - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
  - The entire machinery required for performing NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
  - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,

Normalisation.
diff --git a/biblio/29291348.mdwn b/biblio/29291348.mdwn
index 3a713b6..7225a5c 100644
--- a/biblio/29291348.mdwn
+++ b/biblio/29291348.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias."]]
-[[!tag fingerprint transcriptomics]]
+[[!tag fingerprint transcriptome]]
 
 Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M.
 

Au bureau
diff --git a/biblio/29945865.mdwn b/biblio/29945865.mdwn
new file mode 100644
index 0000000..3ba0182
--- /dev/null
+++ b/biblio/29945865.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting."]]
+[[!tag transcriptome cell_type]]
+
+Development. 2018 Jul 11;145(13). pii: dev164640. doi:10.1242/dev.164640
+
+Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
+
+SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.
+
+[[!pmid 29945865 desc="SLAMseq in tissue (SLAM-ITseq).  Tissue-specific UPRT expression selectively incorporates 4-thiouracil in RNA.  Alkylation with iodoacetamide (IAA) leads to G → A mutations during reverse transcription, which are detected and quantified during data analysis."]]

Café encore.
diff --git a/biblio/29986741.mdwn b/biblio/29986741.mdwn
new file mode 100644
index 0000000..6c81d5b
--- /dev/null
+++ b/biblio/29986741.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Splicing heterogeneity: separating signal from noise."]]
+[[!tag splicing review single_cell]]
+
+Genome Biol. 2018 Jul 9;19(1):86. doi:10.1186/s13059-018-1467-4
+
+Wan Y, Larson DR.
+
+Splicing heterogeneity: separating signal from noise.
+
+[[!pmid 29986741 desc="Review covering splicing at the single-cell level"]]

Café
diff --git a/biblio/3138163.mdwn b/biblio/3138163.mdwn
new file mode 100644
index 0000000..b753818
--- /dev/null
+++ b/biblio/3138163.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Splice site selection, rate of splicing, and alternative splicing on nascent transcripts."]]
+[[!tag Drosophila splicing]]
+
+Genes Dev. 1988 Jun;2(6):754-65.
+
+Beyer AL, Osheim YN.
+
+Splice site selection, rate of splicing, and alternative splicing on nascent transcripts.
+
+[[!pmid 3138163 desc="Chromatin spread illustrating alternative splicing."]]

Precisions
diff --git a/biblio/27897270.mdwn b/biblio/27897270.mdwn
index a3048b3..431ea4e 100644
--- a/biblio/27897270.mdwn
+++ b/biblio/27897270.mdwn
@@ -7,4 +7,4 @@ Nat Commun. 2016 Nov 29;7:13296. doi:10.1038/ncomms13296
 
 TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol.
 
-[[!pmid 27897270 desc="Isothermal amplification for 3 h at 30 °C using a mixture of TthPrimPol for priming and and Φ29DNApol for extension."]]
+[[!pmid 27897270 desc="Isothermal amplification for 3 h at 30 °C using a mixture of TthPrimPol for priming and and Φ29DNApol for extension.  Target DNA was first denatured in an alkaline buffer."]]

Ketchup
diff --git a/biblio/27897270.mdwn b/biblio/27897270.mdwn
new file mode 100644
index 0000000..a3048b3
--- /dev/null
+++ b/biblio/27897270.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol."]]
+[[!tag method amplification enzyme primase]]
+
+Picher ÁJ, Budeus B, Wafzig O, Krüger C, García-Gómez S, Martínez-Jiménez MI, Díaz-Talavera A, Weber D, Blanco L, Schneider A.
+
+Nat Commun. 2016 Nov 29;7:13296. doi:10.1038/ncomms13296
+
+TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol.
+
+[[!pmid 27897270 desc="Isothermal amplification for 3 h at 30 °C using a mixture of TthPrimPol for priming and and Φ29DNApol for extension."]]

creating tag page tags/primase
diff --git a/tags/primase.mdwn b/tags/primase.mdwn
new file mode 100644
index 0000000..2b277c1
--- /dev/null
+++ b/tags/primase.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged primase"]]
+
+[[!inline pages="tagged(primase)" actions="no" archive="yes"
+feedshow=10]]

Prima
diff --git a/biblio/28911121.mdwn b/biblio/28911121.mdwn
index b30a1ab..e10b3df 100644
--- a/biblio/28911121.mdwn
+++ b/biblio/28911121.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase."]]
-[[!tag enzyme reverse_transcription]]
+[[!tag enzyme primase reverse_transcription]]
 
 Nucleic Acids Res. 2017 Sep 6;45(15):9046-9058. doi:10.1093/nar/gkx633
 

Café
diff --git a/biblio/30005597.mdwn b/biblio/30005597.mdwn
new file mode 100644
index 0000000..7969492
--- /dev/null
+++ b/biblio/30005597.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy."]]
+[[!tag nanopore review]]
+
+Genome Biol. 2018 Jul 13;19(1):90. doi:10.1186/s13059-018-1462-9
+
+Rang FJ, Kloosterman WP, de Ridder J.
+
+From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
+
+[[!pmid 30005597 desc="From R6 to R9.5."]]

Cleanup encore
diff --git a/tags/rna-seq.mdwn b/tags/rna-seq.mdwn
deleted file mode 100644
index bba2247..0000000
--- a/tags/rna-seq.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged rna-seq"]]
-
-[[!inline pages="tagged(rna-seq)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/rna.mdwn b/tags/rna.mdwn
deleted file mode 100644
index 36d49c2..0000000
--- a/tags/rna.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged rna"]]
-
-[[!inline pages="tagged(rna)" actions="no" archive="yes"
-feedshow=10]]

Cleanup.
diff --git a/biblio/17373481.mdwn b/biblio/17373481.mdwn
index ce7e81d..e4568cf 100644
--- a/biblio/17373481.mdwn
+++ b/biblio/17373481.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="5′-tailed sequencing primers improve sequencing quality of PCR products."]]
-[[!tag sanger sequencing]]
+[[!tag Sanger sequencing]]
 [[!pmid 17373481 desc="A long tail (40 bp, for instance) increases the size of the fragments to separate on gel, and therefore resolution in 5′"]]
diff --git a/tags/RNA-Seq.mdwn b/tags/RNA-Seq.mdwn
deleted file mode 100644
index bfbf634..0000000
--- a/tags/RNA-Seq.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RNA-Seq"]]
-
-[[!inline pages="tagged(RNA-Seq)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/heliscope.mdwn b/tags/heliscope.mdwn
deleted file mode 100644
index f1764df..0000000
--- a/tags/heliscope.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged heliscope"]]
-
-[[!inline pages="tagged(heliscope)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/parkinson.mdwn b/tags/parkinson.mdwn
deleted file mode 100644
index 0502e73..0000000
--- a/tags/parkinson.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged parkinson"]]
-
-[[!inline pages="tagged(parkinson)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/sanger.mdwn b/tags/sanger.mdwn
deleted file mode 100644
index c4e7100..0000000
--- a/tags/sanger.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged sanger"]]
-
-[[!inline pages="tagged(sanger)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/tfbs.mdwn b/tags/tfbs.mdwn
deleted file mode 100644
index 984b40b..0000000
--- a/tags/tfbs.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged tfbs"]]
-
-[[!inline pages="tagged(tfbs)" actions="no" archive="yes"
-feedshow=10]]

BUSCO
diff --git a/biblio/26059717.mdwn b/biblio/26059717.mdwn
new file mode 100644
index 0000000..7e725d2
--- /dev/null
+++ b/biblio/26059717.mdwn
@@ -0,0 +1,8 @@
+[[!meta title="BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs."]]
+[[!tag assembly]]
+
+Bioinformatics. 2015 Oct 1;31(19):3210-2. doi:10.1093/bioinformatics/btv351
+
+BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
+
+[[!pmid 26059717 desc="Benchmarking Universal Single-Copy Orthologs. Can be used to train predictors such as Augustus."]]
diff --git a/biblio/29220515.mdwn b/biblio/29220515.mdwn
new file mode 100644
index 0000000..342e62b
--- /dev/null
+++ b/biblio/29220515.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="BUSCO applications from quality assessments to gene prediction and phylogenomics."]]
+[[!tag assembly]]
+
+Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM.
+
+Mol Biol Evol. 2017 Dec 6. doi:10.1093/molbev/msx319
+
+BUSCO applications from quality assessments to gene prediction and phylogenomics.
+
+[[!pmid 29220515 desc="BUSCO v3 and examples of use."]]

Normalise.
diff --git a/biblio/30018084.mdwn b/biblio/30018084.mdwn
index 15291cb..dc0ce8c 100644
--- a/biblio/30018084.mdwn
+++ b/biblio/30018084.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing."]]
-[[!tag Drosophila Nanopore assembly]]
+[[!tag Drosophila nanopore assembly]]
 
 G3 (Bethesda). 2018 Jul 17. pii: g3.200162.2018. doi:10.1534/g3.118.200162
 
diff --git a/biblio/30087105.mdwn b/biblio/30087105.mdwn
index ed9f085..e0bb1a0 100644
--- a/biblio/30087105.mdwn
+++ b/biblio/30087105.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing."]]
-[[!tag Drosophila Nanopore assembly]]
+[[!tag Drosophila nanopore assembly]]
 
 G3 (Bethesda). 2018 Aug 7. pii: g3.200160.2018. doi:10.1534/g3.118.200160
 

ketchup
diff --git a/biblio/30087105.mdwn b/biblio/30087105.mdwn
new file mode 100644
index 0000000..ed9f085
--- /dev/null
+++ b/biblio/30087105.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing."]]
+[[!tag Drosophila Nanopore assembly]]
+
+G3 (Bethesda). 2018 Aug 7. pii: g3.200160.2018. doi:10.1534/g3.118.200160
+
+Miller DE, Staber C, Zeitlinger J, Hawley RS.
+
+Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing.
+
+[[!pmid 30087105 desc="29× coverage and N50 of 4.4. Mb in average.  A multiplexed NextSeq 500 run was used for polishing.  Optimisation of Nanopore throughput by reorganising pore groups periodically, extracting high molecular weight DNA with phenol/chloroform extration, and using more DNA in the library preparation.  Benchmark of various tools including minimap/miniasm and canu."]]

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Mot manquant
diff --git "a/Debian/debi\303\242neries/imprimanteBrother.en.po" "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
index d9f3c39..d515191 100644
--- "a/Debian/debi\303\242neries/imprimanteBrother.en.po"
+++ "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2018-08-22 12:55+0000\n"
-"PO-Revision-Date: 2018-08-22 21:59+0900\n"
+"PO-Revision-Date: 2018-08-22 22:01+0900\n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
@@ -47,9 +47,10 @@ msgid ""
 "tout semble se passer parfaitement sauf que rien ne sort de l'imprimante."
 msgstr ""
 "I ran into circles for more than one hour, before eventually understanding "
-"that one needs to install the `lib32stdc++6` in order to use the Brother "
-"drivers (HL-L2365DW printer) on an `amd64` system, since they are provided "
-"as `i386` packages. Only after, I realised that there was more than a hint "
-"in the [online instructions](http://support.brother.com/g/s/id/linux/en/"
-"before.html).  The hardest part was that without `lib32stdc++6`, everything "
-"seemed to work fine, except that nothing was coming out from the printer."
+"that one needs to install the `lib32stdc++6` package in order to use the "
+"Brother drivers (HL-L2365DW printer) on an `amd64` system, since they are "
+"provided as `i386` packages. Only after, I realised that there was more "
+"than a hint in the [online instructions](http://support.brother.com/g/s/id/"
+"linux/en/before.html).  The hardest part was that without `lib32stdc++6`, "
+"everything seemed to work fine, except that nothing was coming out from the "
+"printer."

updated PO files
diff --git "a/Debian/debi\303\242neries/imprimanteBrother.en.po" "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
index d9f3c39..2534769 100644
--- "a/Debian/debi\303\242neries/imprimanteBrother.en.po"
+++ "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2018-08-22 12:55+0000\n"
+"POT-Creation-Date: 2018-08-22 13:00+0000\n"
 "PO-Revision-Date: 2018-08-22 21:59+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 1.8.11\n"
 
 #. type: Plain text

Brother
diff --git "a/Debian/debi\303\242neries/imprimanteBrother.en.po" "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
index 9abb6d7..d9f3c39 100644
--- "a/Debian/debi\303\242neries/imprimanteBrother.en.po"
+++ "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
@@ -3,38 +3,38 @@
 # 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: 2018-08-22 12:55+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"
-"Language: \n"
+"PO-Revision-Date: 2018-08-22 21:59+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 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Imprimer avec Brother sur Debian\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Print with Brother from Debian\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -42,8 +42,14 @@ msgid ""
 "qu'il faut aussi installer le paquet `lib32stdc++6` quand on utilise les "
 "pilotes Brother (imprimante HL-L2365DW) sur un système `amd64`, puisqu'ils "
 "sont fournis sous la forme de paquets `i386`.  Pourtant il y a plus d'une "
-"piste dans les [instructions en "
-"ligne](http://support.brother.com/g/s/id/linux/en/before.html).  Le plus "
-"difficile était que sans `lib32stdc++6`, tout semble se passer parfaitement "
-"sauf que rien ne sort de l'imprimante."
+"piste dans les [instructions en ligne](http://support.brother.com/g/s/id/"
+"linux/en/before.html).  Le plus difficile était que sans `lib32stdc++6`, "
+"tout semble se passer parfaitement sauf que rien ne sort de l'imprimante."
 msgstr ""
+"I ran into circles for more than one hour, before eventually understanding "
+"that one needs to install the `lib32stdc++6` in order to use the Brother "
+"drivers (HL-L2365DW printer) on an `amd64` system, since they are provided "
+"as `i386` packages. Only after, I realised that there was more than a hint "
+"in the [online instructions](http://support.brother.com/g/s/id/linux/en/"
+"before.html).  The hardest part was that without `lib32stdc++6`, everything "
+"seemed to work fine, except that nothing was coming out from the printer."

updated PO files
diff --git "a/Debian/debi\303\242neries/imprimanteBrother.en.po" "b/Debian/debi\303\242neries/imprimanteBrother.en.po"
new file mode 100644
index 0000000..9abb6d7
--- /dev/null
+++ "b/Debian/debi\303\242neries/imprimanteBrother.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: 2018-08-22 12:55+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"
+"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=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Wed, 22 Aug 2018 21:41:32 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Imprimer avec Brother sur Debian\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"J'ai tourné en rond pendant plus d'une heure, avant de finir par comprendre "
+"qu'il faut aussi installer le paquet `lib32stdc++6` quand on utilise les "
+"pilotes Brother (imprimante HL-L2365DW) sur un système `amd64`, puisqu'ils "
+"sont fournis sous la forme de paquets `i386`.  Pourtant il y a plus d'une "
+"piste dans les [instructions en "
+"ligne](http://support.brother.com/g/s/id/linux/en/before.html).  Le plus "
+"difficile était que sans `lib32stdc++6`, tout semble se passer parfaitement "
+"sauf que rien ne sort de l'imprimante."
+msgstr ""

Grand frère II.
diff --git "a/Debian/debi\303\242neries/imprimanteBrother.mdwn" "b/Debian/debi\303\242neries/imprimanteBrother.mdwn"
new file mode 100644
index 0000000..c47656b
--- /dev/null
+++ "b/Debian/debi\303\242neries/imprimanteBrother.mdwn"
@@ -0,0 +1,13 @@
+[[!meta date="Wed, 22 Aug 2018 21:41:32 +0900"]]
+[[!meta updated="Wed, 22 Aug 2018 21:41:32 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Imprimer avec Brother sur Debian"]]
+
+J'ai tourné en rond pendant plus d'une heure, avant de finir par comprendre
+qu'il faut aussi installer le paquet `lib32stdc++6` quand on utilise les
+pilotes Brother (imprimante HL-L2365DW) sur un système `amd64`, puisqu'ils sont
+fournis sous la forme de paquets `i386`.  Pourtant il y a plus d'une piste dans
+les [instructions en ligne](http://support.brother.com/g/s/id/linux/en/before.html).
+Le plus difficile était que sans `lib32stdc++6`, tout semble se passer parfaitement
+sauf que rien ne sort de l'imprimante.

Droso
diff --git a/biblio/30018084.mdwn b/biblio/30018084.mdwn
index 51ea447..15291cb 100644
--- a/biblio/30018084.mdwn
+++ b/biblio/30018084.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing."]]
-[[!tag Nanopore assembly]]
+[[!tag Drosophila Nanopore assembly]]
 
 G3 (Bethesda). 2018 Jul 17. pii: g3.200162.2018. doi:10.1534/g3.118.200162
 

Normalisation.
diff --git a/biblio/20615941.mdwn b/biblio/20615941.mdwn
index 694c505..5a28f17 100644
--- a/biblio/20615941.mdwn
+++ b/biblio/20615941.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Global analysis of trans-splicing in Drosophila."]]
-[[!tag drosophila trans-splicing]]
+[[!tag Drosophila trans-splicing]]
 [[!pmid 20615941 desc="Hybrid experiment found cases of trans-splicing, but few."]]
diff --git a/biblio/20868489.mdwn b/biblio/20868489.mdwn
index 096fdae..bfc37a0 100644
--- a/biblio/20868489.mdwn
+++ b/biblio/20868489.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="An arthropod cis-regulatory element functioning in sensory organ precursor development dates back to the Cambrian."]]
-[[!tag enhancer sequence-conservation drosophila]]
+[[!tag enhancer sequence-conservation Drosophila]]
 [[!pmid 20868489 desc="The atonal sensory organ precursor enhancer (SOPE)"]]
diff --git a/biblio/23537633.mdwn b/biblio/23537633.mdwn
index 94ec47a..377c760 100644
--- a/biblio/23537633.mdwn
+++ b/biblio/23537633.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs."]]
-[[!tag histone nuclear_body promoter bidirectional drosophila ]]
+[[!tag histone nuclear_body promoter bidirectional Drosophila ]]
 
 Salzler HR, Tatomer DC, Malek PY, McDaniel SL, Orlando AN, Marzluff WF, Duronio RJ.
 
diff --git a/biblio/24631403.mdwn b/biblio/24631403.mdwn
index fdda40c..2a240b5 100644
--- a/biblio/24631403.mdwn
+++ b/biblio/24631403.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants."]]
-[[!tag drosophila cell_cycle]]
+[[!tag Drosophila cell_cycle]]
 
 Southall TD, Davidson CM, Miller C, Carr A, Brand AH.
 
diff --git a/biblio/26098021.mdwn b/biblio/26098021.mdwn
index 29639b7..92c76b6 100644
--- a/biblio/26098021.mdwn
+++ b/biblio/26098021.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Combining protein and mRNA quantification to decipher transcriptional regulation."]]
-[[!tag single_cell transcription_factor imaging drosophila]]
+[[!tag single_cell transcription_factor imaging Drosophila]]
 
 Xu H, Sepúlveda LA, Figard L, Sokac AM, Golding I.
 
diff --git a/biblio/26680200.mdwn b/biblio/26680200.mdwn
index 55c27dc..1233ffb 100644
--- a/biblio/26680200.mdwn
+++ b/biblio/26680200.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="An essential cell cycle regulation gene causes hybrid inviability in Drosophila."]]
-[[!tag drosophila cell_cycle]]
+[[!tag Drosophila cell_cycle]]
 
 Phadnis N, Baker EP, Cooper JC, Frizzell KA, Hsieh E, de la Cruz AF, Shendure 
 J, Kitzman JO, Malik HS.
diff --git a/tags/drosophila.mdwn b/tags/drosophila.mdwn
deleted file mode 100644
index 619c2eb..0000000
--- a/tags/drosophila.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged drosophila"]]
-
-[[!inline pages="tagged(drosophila)" actions="no" archive="yes"
-feedshow=10]]

Typo.
diff --git a/biblio/29934612.mdwn b/biblio/29934612.mdwn
index 26b5948..2df471a 100644
--- a/biblio/29934612.mdwn
+++ b/biblio/29934612.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Experimental evidence that thermal selection shapes mitochondrial genome evolution."]]
-[[!tag Drosophia mitochondrion evolution temperature]]
+[[!tag Drosophila mitochondrion evolution temperature]]
 
 Sci Rep. 2018 Jun 22;8(1):9500. doi:10.1038/s41598-018-27805-3
 
diff --git a/tags/Drosophia.mdwn b/tags/Drosophia.mdwn
deleted file mode 100644
index fb8b636..0000000
--- a/tags/Drosophia.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Drosophia"]]
-
-[[!inline pages="tagged(Drosophia)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/Drosophia
diff --git a/tags/Drosophia.mdwn b/tags/Drosophia.mdwn
new file mode 100644
index 0000000..fb8b636
--- /dev/null
+++ b/tags/Drosophia.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Drosophia"]]
+
+[[!inline pages="tagged(Drosophia)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/29934612.mdwn b/biblio/29934612.mdwn
new file mode 100644
index 0000000..26b5948
--- /dev/null
+++ b/biblio/29934612.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Experimental evidence that thermal selection shapes mitochondrial genome evolution."]]
+[[!tag Drosophia mitochondrion evolution temperature]]
+
+Sci Rep. 2018 Jun 22;8(1):9500. doi:10.1038/s41598-018-27805-3
+
+Lajbner Z, Pnini R, Camus MF, Miller J, Dowling DK.
+
+Experimental evidence that thermal selection shapes mitochondrial genome evolution.
+
+[[!pmid 29934612 desc="Experimental evidence for the “mitochondrial climatic hypothesis”.  Haplotypes only differ by non-coding or synonymous changes.  Wolbachia infection was a confounding factor and needed to be removed by antibiotic treatment."]]

creating tag page tags/coral
diff --git a/tags/coral.mdwn b/tags/coral.mdwn
new file mode 100644
index 0000000..3e793a9
--- /dev/null
+++ b/tags/coral.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged coral"]]
+
+[[!inline pages="tagged(coral)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/26656261.mdwn b/biblio/26656261.mdwn
new file mode 100644
index 0000000..36bc9c6
--- /dev/null
+++ b/biblio/26656261.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago."]]
+[[!tag coral population]]
+
+Sci Rep. 2015 Dec 10;5:18211. doi:10.1038/srep18211
+
+Shinzato C, Mungpakdee S, Arakaki N, Satoh N.
+
+Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago.
+
+[[!pmid 26656261 desc="Single population (K = 1 in ADMIXTURE analyisis).  PCA on 905,561 SNPs from 122 individuals shows four subpopulations corresponding roughly to island groups and suggests migration of only a few individuals."]]

creating tag page tags/chromosome
diff --git a/tags/chromosome.mdwn b/tags/chromosome.mdwn
new file mode 100644
index 0000000..c857eb3
--- /dev/null
+++ b/tags/chromosome.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged chromosome"]]
+
+[[!inline pages="tagged(chromosome)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/26848124.mdwn b/biblio/26848124.mdwn
new file mode 100644
index 0000000..6413ad5
--- /dev/null
+++ b/biblio/26848124.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-scale shotgun assembly using an in vitro method for long-range linkage."]]
+[[!tag sequencing method chromosome assembly]]
+
+Genome Res. 2016 Mar;26(3):342-50. doi:10.1101/gr.193474.115
+
+Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE.
+
+Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
+
+[[!pmid 26848124 desc="“Chicago”: in vitro assembly of artificial chromosomes, followed by Hi-C.  Sold as a kit by Dovetail genomics."]]

Syntax
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 39dde63..dfb3fe6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -54,7 +54,7 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
- - Chromatin domains are rarely longer than 7 nucleosomes ([Navratilova et al., 2017|biblio/28115992]).
+ - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
  - The entire machinery required for performing NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
  - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,

creating tag page tags/LAST
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
new file mode 100644
index 0000000..12a6a69
--- /dev/null
+++ b/tags/LAST.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged LAST"]]
+
+[[!inline pages="tagged(LAST)" actions="no" archive="yes"
+feedshow=10]]

Last-train
diff --git a/biblio/28039163.mdwn b/biblio/28039163.mdwn
new file mode 100644
index 0000000..b947998
--- /dev/null
+++ b/biblio/28039163.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Training alignment parameters for arbitrary sequencers with LAST-TRAIN."]]
+[[!tag LAST]]
+
+Bioinformatics. 2017 Mar 15;33(6):926-928. doi:10.1093/bioinformatics/btw742
+
+Hamada M, Ono Y, Asai K, Frith MC.
+
+Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
+
+[[!pmid 28039163 desc="Using trained parameters helps to reduce reference bias."]]

Correction.
diff --git a/biblio/20335363.mdwn b/biblio/20335363.mdwn
index 3834962..afde758 100644
--- a/biblio/20335363.mdwn
+++ b/biblio/20335363.mdwn
@@ -1,6 +1,10 @@
-[[!meta title=""]]
-[[!tag ]]
+[[!meta title="Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans."]]
+[[!tag Oikopleura]]
 
+Development. 2010 May;137(9):1483-92. doi:10.1242/dev.044503
 
+Sagane Y, Zech K, Bouquet JM, Schmid M, Bal U, Thompson EM.
 
-[[!pmid desc=""]]
+Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans.
+
+[[!pmid 20335363 desc="O. dioica has two cellulose synthase genes (Od-CesA1 and Od-CesA2)."]]

Cellulose.
diff --git a/biblio/20335363.mdwn b/biblio/20335363.mdwn
new file mode 100644
index 0000000..3834962
--- /dev/null
+++ b/biblio/20335363.mdwn
@@ -0,0 +1,6 @@
+[[!meta title=""]]
+[[!tag ]]
+
+
+
+[[!pmid desc=""]]
diff --git a/biblio/20972815.mdwn b/biblio/20972815.mdwn
new file mode 100644
index 0000000..9f2f695
--- /dev/null
+++ b/biblio/20972815.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The crystalline phase of cellulose changes under developmental control in a marine chordate."]]
+[[!tag Oikopleura]]
+
+Cell Mol Life Sci. 2011 May;68(9):1623-31. doi:10.1007/s00018-010-0556-7
+
+Nakashima K, Nishino A, Horikawa Y, Hirose E, Sugiyama J, Satoh N.
+
+The crystalline phase of cellulose changes under developmental control in a marine chordate.
+
+[[!pmid 20972815 desc="O. dioica has two cellulose synthase genes (Od-CesA1 and Od-CesA2) that are 68 % similar."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 246ca18..39dde63 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -95,7 +95,10 @@ Genes and pathways
 (See also other sections)
 
  - ~80 "house proteins" have been identified and more than half lack similarity
-   to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
+   to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
+ - 2 cellulose synthase genes were found by [[Sagane et al. (2010)|biblio/20335363]]
+   and [[Nakashima et al. (2011)|biblio/20972815]].  They are used to produce different
+   crystalline forms of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
  - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.

creating tag page tags/muscle
diff --git a/tags/muscle.mdwn b/tags/muscle.mdwn
new file mode 100644
index 0000000..4788562
--- /dev/null
+++ b/tags/muscle.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged muscle"]]
+
+[[!inline pages="tagged(muscle)" actions="no" archive="yes"
+feedshow=10]]

Muscle genes.
diff --git a/biblio/29319812.mdwn b/biblio/29319812.mdwn
new file mode 100644
index 0000000..be2c934
--- /dev/null
+++ b/biblio/29319812.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution."]]
+[[!tag Oikopleura muscle]]
+
+Inoue J, Satoh N.
+
+Mol Biol Evol. 2018 Apr 1;35(4):914-924. doi:10.1093/molbev/msy002
+
+Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution.
+
+[[!pmid 29319812 desc="Duplication of some muscle genes in the stem Oikopleura lineage, perhaps reflecting the importance of tail movement during larval and adult stages."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 92ac076..246ca18 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -103,6 +103,10 @@ Genes and pathways
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).
    They are expressed in the nervous system ([[Lynagh et al., 2018|biblio/30061402]]).
+ - Some muscle genes were duplicated in the _Oikopleura_ stem lineage
+   ([[Inoue & Satoh|biblio/29319812]]), prehaps reflecting the importance of
+   tail movements at larval and adult stages.
+
 
 Transcriptome
 -------------

NCBI Taxon ID.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0cc7071..92ac076 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -3,14 +3,15 @@
 Oikopleura
 ==========
 
-_Oikopleura dioica_ is a tunicate larvacean (synonym: urochordate
-appendicularian) plankton.  Thus, it belongs to the same "chordate" phylum as
-us.  As the name indicates, it is the only _dioecious_ species of _Oikopleura_
-(that is: male and female organisms are distinct).  Its reproduction is
-_semelparous_: the animals die afer releasing its gametes.  Each animal
-secretes a mucus "house" that is used for feeding (and perhaps defending).  The
-main house proteins are called _oikosins_ and half or them are unique to
-Oikopleura and related animals ("_Appendicularia_").
+_Oikopleura dioica_ ([NCBI:txid34765](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&amp;id=34765))
+is a tunicate larvacean (synonym: urochordate appendicularian) plankton.  Thus,
+it belongs to the same "chordate" phylum as us.  As the name indicates, it is
+the only _dioecious_ species of _Oikopleura_ (that is: male and female
+organisms are distinct).  Its reproduction is _semelparous_: the animals die
+afer releasing its gametes.  Each animal secretes a mucus "house" that is used
+for feeding (and perhaps defending).  The main house proteins are called
+_oikosins_ and half or them are unique to Oikopleura and related animals
+("_Appendicularia_").
 
 Some links:
 

Suppressive PCR.
diff --git a/biblio/7731798.mdwn b/biblio/7731798.mdwn
new file mode 100644
index 0000000..78722da
--- /dev/null
+++ b/biblio/7731798.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An improved PCR method for walking in uncloned genomic DNA."]]
+[[!tag method library]]
+
+Nucleic Acids Res. 1995 Mar 25;23(6):1087-8.
+
+Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA.
+
+An improved PCR method for walking in uncloned genomic DNA.
+
+[[!pmid 7731798 desc="First description of suppressive PCR in English ?"]]
diff --git a/biblio/rjbc1994_20_701-704.mdwn b/biblio/rjbc1994_20_701-704.mdwn
new file mode 100644
index 0000000..833e8ba
--- /dev/null
+++ b/biblio/rjbc1994_20_701-704.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Highly efficient subtractive hybridization of cDNA"]]
+[[!tag method library]]
+
+Russian Journal of Bioorganic Chemistry 1994, 20 (6):701-704
+
+S. A. Lukyanov, N. G. Gurskaya, K. A. Lukyanov, V. S. Tarabykin, E. D. Sverdlov
+
+Highly efficient subtractive hybridization of cDNA
+
+[First publication of the suppressive PCR ? (PDF, in Russian)](http://www.rjbc.ru/arc/20/6/0701-0704.pdf)

Latest in PubMed.
diff --git a/biblio/30061402.mdwn b/biblio/30061402.mdwn
new file mode 100644
index 0000000..5e609a3
--- /dev/null
+++ b/biblio/30061402.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Acid-sensing ion channels emerged over 600 Mya and are conserved throughout the deuterostomes."]]
+[[!tag Oikopleura]]
+
+Proc Natl Acad Sci U S A. 2018 Jul 30. pii: 201806614. doi:10.1073/pnas.1806614115
+
+Lynagh T, Mikhaleva Y, Colding JM, Glover JC, Pless SA.
+
+Acid-sensing ion channels emerged over 600 Mya and are conserved throughout the deuterostomes.
+
+[[!pmid 30061402 desc="O. dioica, like other deuterostomes, has acid-sensing ion channels (ASICs).  They are expressed in the nervous system."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ce67d9a..0cc7071 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -100,7 +100,8 @@ Genes and pathways
  - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
-
+ - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).
+   They are expressed in the nervous system ([[Lynagh et al., 2018|biblio/30061402]]).
 
 Transcriptome
 -------------

tag correction.
diff --git a/biblio/18007650.mdwn b/biblio/18007650.mdwn
index b9b753b..b83519c 100644
--- a/biblio/18007650.mdwn
+++ b/biblio/18007650.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Evolutionary developmental biology and genomics."]]
-[[!tag Oikopleura epigenetics]]
+[[!tag Oikopleura epigenetic]]
 
 Nat Rev Genet. 2007 Dec;8(12):932-42 doi:10.1038/nrg2226
 
diff --git a/tags/epigenetics.mdwn b/tags/epigenetics.mdwn
deleted file mode 100644
index 276b2d1..0000000
--- a/tags/epigenetics.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged epigenetics"]]
-
-[[!inline pages="tagged(epigenetics)" actions="no" archive="yes"
-feedshow=10]]

Methyl tranferases.
diff --git a/biblio/18007650.mdwn b/biblio/18007650.mdwn
new file mode 100644
index 0000000..b9b753b
--- /dev/null
+++ b/biblio/18007650.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary developmental biology and genomics."]]
+[[!tag Oikopleura epigenetics]]
+
+Nat Rev Genet. 2007 Dec;8(12):932-42 doi:10.1038/nrg2226
+
+Cañestro C, Yokoi H, Postlethwait JH.
+
+Evolutionary developmental biology and genomics.
+
+[[!pmid 18007650 desc="O. dioica only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 312a25b..ce67d9a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -56,9 +56,6 @@ Genome
  - Chromatin domains are rarely longer than 7 nucleosomes ([Navratilova et al., 2017|biblio/28115992]).
  - The entire machinery required for performing NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
- - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
- - ~80 "house proteins" have been identified and more than half lack similarity
-   to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
  - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,
    2010|biblio/21097902]], due to cloning and sequencing difficulties that may
    have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
@@ -89,8 +86,21 @@ Genome
    “Spots of sequence ultraconservation are almost systematically located
    in non coding regions, including introns that are larger than average
    in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
+
+
+Genes and pathways
+------------------
+
+(See also other sections)
+
+ - ~80 "house proteins" have been identified and more than half lack similarity
+   to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
+ - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.
+ - CYP1 family genes and their regulator AhR are not detectable
+   ([[Yadetie et al, 2012|biblio/22300585]]).
+
 
 Transcriptome
 -------------

Polish
diff --git a/tags/reverse_transcriptase.mdwn b/tags/reverse_transcriptase.mdwn
deleted file mode 100644
index 73bd59d..0000000
--- a/tags/reverse_transcriptase.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged reverse transcriptase"]]
-
-[[!inline pages="tagged(reverse_transcriptase)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index a8ba77b..9e31aa1 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -18,6 +18,7 @@ _(redaction in progress)_
    that is mistaken for a first-strand cDNA.  ActinomycinD inhibits DNA-dependent,
    but not RNA-dependent polymerase activity and is used to suppress these
    artefacts ([[Perocchi et al., 2007|biblio/17897965]], [[Kanamori-Katayama et al., 2011|biblio/21596820]]).
+ - Its error profile is different from other DNA polymerases ([[de Paz et al., 2018|biblio/29718339]]).
 
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 

Polish.
diff --git a/biblio/29718339.mdwn b/biblio/29718339.mdwn
index 3aed4e2..5791394 100644
--- a/biblio/29718339.mdwn
+++ b/biblio/29718339.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing"]]
-[[!tag method reverse_transcriptase]]
+[[!tag method reverse_transcription]]
 
 Nucleic Acids Res. 2018 Jul 27;46(13):e78. doi:10.1093/nar/gky296
 

creating tag page tags/reverse_transcriptase
diff --git a/tags/reverse_transcriptase.mdwn b/tags/reverse_transcriptase.mdwn
new file mode 100644
index 0000000..73bd59d
--- /dev/null
+++ b/tags/reverse_transcriptase.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged reverse transcriptase"]]
+
+[[!inline pages="tagged(reverse_transcriptase)" actions="no" archive="yes"
+feedshow=10]]

Dans le train.
diff --git a/biblio/29718339.mdwn b/biblio/29718339.mdwn
new file mode 100644
index 0000000..3aed4e2
--- /dev/null
+++ b/biblio/29718339.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing"]]
+[[!tag method reverse_transcriptase]]
+
+Nucleic Acids Res. 2018 Jul 27;46(13):e78. doi:10.1093/nar/gky296
+
+de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ
+
+High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
+
+[[!pmid 29718339 desc="Magnification via Nucleotide Imbalance Fidelity (MagNIFi).  Investigates Dpo4, Taq, AMV RT, Sequenase 2.0 and Phi29.  Confirms previous reports that when using a DNA template, the preferred misincorporation of the AMV reverse-transcriptase is A:dCTP (but other misincorporations are also frequent)."]]

minor.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c82d9ad..312a25b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -75,21 +75,22 @@ Genome
    ([[Denoeud et al., 2010|biblio/21097902]]).
  - Operons are enriched for houskeeping genes and depleted for developmental genes
    ([[Denoeud et al., 2010|biblio/21097902]]).
- - “LTR retrotransposons account for a significant part of the indel polymorphism in the Oikopleura genome.”
+ - “LTR retrotransposons account for a significant part of the indel polymorphism
+   in the _Oikopleura_ genome.”
    “Tor-3G elements are frequently inserted into exons and can be transcribed
-    together with their host gene, although transcripts initiated in the LTR
-    are also detected (Figure S11).”
+   together with their host gene, although transcripts initiated in the LTR
+   are also detected (Figure S11).”
    “The low allelic frequency of Tor-3G insertions is correlated with the
-    almost exclusive occurrence of heterozygous genotypes in the populations.
-    Moreover, experimental crosses between selected heterozygous parents for
-    the same insertion have thus far not resulted in homozygous offsprings.”
-    ([[Denoeud et al., 2010|biblio/21097902]]).
+   almost exclusive occurrence of heterozygous genotypes in the populations.
+   Moreover, experimental crosses between selected heterozygous parents for
+   the same insertion have thus far not resulted in homozygous offsprings.”
+   ([[Denoeud et al., 2010|biblio/21097902]]).
  - “Highly conserved elements (HCEs) lie around these developmental genes.”
    “Spots of sequence ultraconservation are almost systematically located
-    in non coding regions, including introns that are larger than average
-    in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
+   in non coding regions, including introns that are larger than average
+   in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
-   implicated in oogenesis [[Feng & Thompson, 2018|biblio/29969934]].
+   implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
 
 Transcriptome
 -------------

Dans le train.
diff --git a/biblio/29969934.mdwn b/biblio/29969934.mdwn
new file mode 100644
index 0000000..0a48e32
--- /dev/null
+++ b/biblio/29969934.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Specialization of CDK1 and Cyclin B paralog functions in a coenocystic mode of oogenic meiosis."]]
+[[!tag Oikopleura cell_cycle]]
+
+Cell Cycle. 2018 Jul 4. doi:10.1080/15384101.2018.1486167
+
+Feng H & Thompson EM
+
+Specialization of CDK1 and Cyclin B paralog functions in a coenocystic mode of oogenic meiosis. 
+
+[[!pmid 29969934 desc="_O. dioica_ has multiple CDK1 and Cyclin B paralogs."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e5c5bdf..c82d9ad 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -84,11 +84,12 @@ Genome
     Moreover, experimental crosses between selected heterozygous parents for
     the same insertion have thus far not resulted in homozygous offsprings.”
     ([[Denoeud et al., 2010|biblio/21097902]]).
- - ”Highly conserved elements (HCEs) lie around these developmental genes.”
+ - “Highly conserved elements (HCEs) lie around these developmental genes.”
    “Spots of sequence ultraconservation are almost systematically located
     in non coding regions, including introns that are larger than average
     in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
-
+ - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
+   implicated in oogenesis [[Feng & Thompson, 2018|biblio/29969934]].
 
 Transcriptome
 -------------

Café et tarte pécan.
diff --git a/biblio/30069045.mdwn b/biblio/30069045.mdwn
new file mode 100644
index 0000000..749021c
--- /dev/null
+++ b/biblio/30069045.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Creating a functional single-chromosome yeast."]]
+[[!tag yeast genome synthethic_biology]]
+
+Nature. 2018 Aug 1. doi:10.1038/s41586-018-0382-x
+
+Shao Y, Lu N, Wu Z, Cai C, Wang S, Zhang LL, Zhou F, Xiao S, Liu L, Zeng X, Zheng H, Yang C, Zhao Z, Zhao G, Zhou JQ, Xue X, Qin Z.
+
+Creating a functional single-chromosome yeast.
+
+[[!pmid 30069045 desc="Viable but outcompeted by wild type."]]

The genome paper
diff --git a/biblio/21097902.mdwn b/biblio/21097902.mdwn
new file mode 100644
index 0000000..1b40479
--- /dev/null
+++ b/biblio/21097902.mdwn
@@ -0,0 +1,18 @@
+[[!meta title="Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate."]]
+[[!tag Oikopleura]]
+
+Science. 2010 Dec 3;330(6009):1381-5. doi:10.1126/science.1194167
+
+Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H,
+Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J,
+Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S,
+Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H,
+Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M,
+Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, 
+Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR,
+Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN,
+Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D.
+
+Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.
+
+[[!pmid 21097902 desc="1,260 scaffolds (70.4 Mb), 395 Kb N50, 15,152 ESTs clusters in the reference assembly, excluding 4,196 the allelic scaffolds (45 Mb, 21.8 Kb N50)."]]

Typography.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0f30823..e5c5bdf 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -40,8 +40,8 @@ Genome
 
  - Germ cells contain 3 haploid chromosomes ([[Körner, 1952|biblio/43261846]]).
    There are also intriguing observations of somatic mitotic cells with 7
-   chromosomes (([[Körner, 1952|biblio/43261846]]) and meiotic cells with
-   8 haploid chromosomes [[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).
+   chromosomes ([[Körner, 1952|biblio/43261846]]) and meiotic cells with
+   8 haploid chromosomes ([[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
  - Genome size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later

Number of chromosomes.
diff --git a/biblio/10.1080_11250007309429248.mdwn b/biblio/10.1080_11250007309429248.mdwn
new file mode 100644
index 0000000..5c9a46e
--- /dev/null
+++ b/biblio/10.1080_11250007309429248.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome form and number in the larvacea"]]
+[[!tag Oikopleura]]
+
+Colombera D. & Fenaux R.
+
+Italian Journal of Zoology, 40:3-4, 347-353
+
+Chromosome form and number in the larvacea
+
+[[!doi 10.1080/11250007309429248 desc="Reports 16 chromosomes in meiotic cells (8 haploid chromosomes)."]]
diff --git a/biblio/43261846.mdwn b/biblio/43261846.mdwn
new file mode 100644
index 0000000..73a7f77
--- /dev/null
+++ b/biblio/43261846.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Untersuchungen über die Gehäusebildung bei Appendicularien (Oikopleura dioica Fol)"]]
+[[!tag Oikopleura]]
+
+Wilhelm Friedrich Körner
+
+Zeitschrift für Morphologie und Ökologie der Tiere Vol. 41, No. 1 (20.Mai 1952), pp. 1-53 
+
+Untersuchungen über die Gehäusebildung bei Appendicularien (Oikopleura dioica Fol)
+
+[Reports 3 haploid chromosomes in sperm and oocytes, one beign longer than the others.  Also reports an observation of 7 chromosomes in a somatic mitotic cell.](https://www.jstor.org/stable/43261846)
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cebb3e6..0f30823 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -38,8 +38,12 @@ Phylogeny
 Genome
 ------
 
+ - Germ cells contain 3 haploid chromosomes ([[Körner, 1952|biblio/43261846]]).
+   There are also intriguing observations of somatic mitotic cells with 7
+   chromosomes (([[Körner, 1952|biblio/43261846]]) and meiotic cells with
+   8 haploid chromosomes [[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
- - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
+ - Genome size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al,
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
    produced from the shotgun sequencing of sperm DNA from ~200 partially inbred
    males (11 successive sib-matings).  Two distinct haplotypes were found

One of the earliest paper in Japan ?
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7a33481..cebb3e6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -160,6 +160,6 @@ Ecology
  - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
-
+ - It was already reported to be frequent in Japanese waters [[in 1907 by T. Aida|biblio/AA0069577]].
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/AA0069577.mdwn b/biblio/AA0069577.mdwn
new file mode 100644
index 0000000..3d4802b
--- /dev/null
+++ b/biblio/AA0069577.mdwn
@@ -0,0 +1,8 @@
+[[!meta title="Appendicularia of Japanese Waters"]]
+[[!tag Oikopleura]]
+
+T. Aida
+
+The journal of the College of Science, Imperial University of Tokyo, Japan (東京帝國大學紀要. 理科) 23 pp. 1-25 , 1907-12-23
+
+NCID:AA0069577 [Reports that the most common appendicularian in Japan are O. longitudica, O. dioica and O. fusiformis.  They are “found almost in all seasons and in every part of the coast”.  Nevertheless, “even the most common species O. longitudica can not be taken at all times throughout the year”.](http://jairo.nii.ac.jp/0021/00019790/en)

Ketchup
diff --git a/biblio/30018084.mdwn b/biblio/30018084.mdwn
new file mode 100644
index 0000000..51ea447
--- /dev/null
+++ b/biblio/30018084.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing."]]
+[[!tag Nanopore assembly]]
+
+G3 (Bethesda). 2018 Jul 17. pii: g3.200162.2018. doi:10.1534/g3.118.200162
+
+Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS.
+
+Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing.
+
+[[!pmid 30018084 desc="Hybrid de novo assembly (Nanopore / Illumina / Optical) of the _Drosophila_ genome reaches a high (>98%) « BUSCO » score typical of high-quality mainstream reference assemblies. (BUSCO stands for « Benchmarking Universal Single-Copy Orthologs ».)"]]

Minor.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 31050f3..7a33481 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -139,7 +139,7 @@ Physiology
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_.  Some of the remaining ones show
    signs of neofunctionalisation or specialisation in their ancestral activity in
-   digestion or chemical defence. ([[Martí-Solans et al., 2016|biblio/27406791]]) 
+   digestion or chemical defence ([[Martí-Solans et al., 2016|biblio/27406791]]).
 
 
 Phenotypes
@@ -157,7 +157,7 @@ Ecology
 
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).
- - _O. Dioica_ has “a very large mutation rate, and/or a very large effective
+ - _O. dioica_ has “a very large mutation rate, and/or a very large effective
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
 

Syntax.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index affc1fb..31050f3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -139,7 +139,7 @@ Physiology
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_.  Some of the remaining ones show
    signs of neofunctionalisation or specialisation in their ancestral activity in
-   digestion or chemical defence. ([Martí-Solans et al., 2016|biblio/27406791]) 
+   digestion or chemical defence. ([[Martí-Solans et al., 2016|biblio/27406791]]) 
 
 
 Phenotypes

RA
diff --git a/biblio/27406791.mdwn b/biblio/27406791.mdwn
new file mode 100644
index 0000000..1ac5037
--- /dev/null
+++ b/biblio/27406791.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate."]]
+[[!tag Oikopleura]]
+
+Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C. 
+
+Mol Biol Evol. 2016 Sep;33(9):2401-16. doi:10.1093/molbev/msw118 
+
+Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate. 
+
+[[!pmid 27406791 desc="Some genes are lost (_Aldh1a_, _Cyp26_, _Rdh10_, _Rdh16_, and _Bco1_) and others show signs of neofunctionalisation (_RdhE2_, _Aldh8a1_). “_O. dioica_ did not contain atRA at concentrations that were likely to play any role in developmental or physiological processes.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b9deb05..affc1fb 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -136,6 +136,11 @@ Physiology
  - Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in _Oikopleura_
    (like in other non-vertebrates).  Conservation of critical residues and similarity
    in expression pattern suggest that its metabolic targets are the same as in other species.
+ - Most members of retinoic acid pathway gene network (biosynthesis, signalling
+   and degradation) are lost in _O. dioica_.  Some of the remaining ones show
+   signs of neofunctionalisation or specialisation in their ancestral activity in
+   digestion or chemical defence. ([Martí-Solans et al., 2016|biblio/27406791]) 
+
 
 Phenotypes
 ----------

creating tag page tags/Helicos
diff --git a/tags/Helicos.mdwn b/tags/Helicos.mdwn
new file mode 100644
index 0000000..1244247
--- /dev/null
+++ b/tags/Helicos.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Helicos"]]
+
+[[!inline pages="tagged(Helicos)" actions="no" archive="yes"
+feedshow=10]]

Tag.
diff --git a/biblio/18388294.mdwn b/biblio/18388294.mdwn
index 4c1f680..34e1bb6 100644
--- a/biblio/18388294.mdwn
+++ b/biblio/18388294.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Single-molecule DNA sequencing of a viral genome."]]
-[[!tag sequencing]]
+[[!tag sequencing Helicos]]
 [[!pmid 18388294 desc="Primary paper for Helicos sequencing."]]

HeliScopeCAGE.
diff --git a/biblio/21596820.mdwn b/biblio/21596820.mdwn
new file mode 100644
index 0000000..340bdb9
--- /dev/null
+++ b/biblio/21596820.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Unamplified cap analysis of gene expression on a single-molecule sequencer."]]
+[[!tag CAGE Helicos sequence_tag method]]
+
+Genome Res. 2011 Jul;21(7):1150-9. doi:10.1101/gr.115469.110
+
+Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y.
+
+Unamplified cap analysis of gene expression on a single-molecule sequencer.
+
+[[!pmid 21596820 desc="HeliScopeCAGE, a CAGE method for the Helicos sequencers.  Actinomycin D was added to the reverse-transcription to prevent antisense artefacts."]]

Ahmad 2018.
diff --git a/tags/EcoP15I.mdwn b/tags/EcoP15I.mdwn
index 7b3104f..a6f23cb 100644
--- a/tags/EcoP15I.mdwn
+++ b/tags/EcoP15I.mdwn
@@ -6,6 +6,7 @@ A few facts about EcoP15I
  - Cleavage is impaired by proteins bound between the sites [[Meisel et al., 1995|biblio/7796821]].
  - Positive bias for adenine stretches on the 5′ or 3′ side of CAGCAG [[Möncke-Buchner et al., 2009|biblio/19250940]].
  - Stimulated by AdoMet and sinefungin [[Raghavendra & Rao, 2005|biblio/16026759]].
+ - Single-site cleavage is possible with higher concentration of enzyme ([[Ahmad and co., 2018|biblio/29846668]]).
 
 Used in [[SuperSAGE|biblio/14676315]], [[HELP-tagging|biblio/20359321]], [[nanoCAGE|biblio/20543846]], [[CAGE|biblio/22362160]].  (non-exhaustive list)
 

Au bureau.
diff --git a/biblio/29846668.mdwn b/biblio/29846668.mdwn
new file mode 100644
index 0000000..5fbc74d
--- /dev/null
+++ b/biblio/29846668.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated."]]
+[[!tag EcoP15I]]
+
+Ahmad I, Kulkarni M, Gopinath A, Saikrishnan K.
+
+Nucleic Acids Res. 2018 Jul 6;46(12):6229-6237. doi:10.1093/nar/gky344
+
+Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.
+
+[[!pmid 29846668 desc="Single-site cleavage happens by cooperation between activated enzymes contacting each other by 3D diffusion, and therefore requires higher concentrations of enzyme than two-site cleavage, where contacts happen through 1D diffusion or looping."]]

In English.
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
index 8ef8f5d..c139ef1 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.en.po"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2018-07-09 21:07+0000\n"
-"PO-Revision-Date: 2018-07-10 05:51+0900\n"
+"PO-Revision-Date: 2018-07-10 06:08+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -32,11 +32,10 @@ msgid "[[!tag Debian]]\n"
 msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+#, no-wrap
 msgid "[[!meta title=\"Debconf cette année, c'est râpé.\"]]\n"
 msgstr ""
-"[[!meta title=\"Debconf cette année, c'est râpé.\n"
+"[[!meta title=\"Still not going to Debconf....\n"
 "\"]]\n"
 
 #. type: Plain text
@@ -48,6 +47,10 @@ msgid ""
 "décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le\n"
 "premier août.\n"
 msgstr ""
+"I was looking forward to this year's [Debconf in\n"
+"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective\n"
+"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
+"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
 
 #. type: Plain text
 msgid ""
@@ -55,6 +58,10 @@ msgid ""
 "de la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des "
 "vols très bon marché pour Tôkyô et Yokohama..."
 msgstr ""
+"Moving is a mixed feeling of happiness and excitation for what I am about\n"
+"to find, and melancholy about what and whom I am about to leave.  But "
+"flights\n"
+"to Tôkyô and Yokohama are very affordable."
 
 #. type: Plain text
 msgid ""
@@ -62,3 +69,6 @@ msgid ""
 "tokyodebian-team.pages.debian.net/), où ma première clé GPG a été signée par "
 "des développeurs Debian il y a fort longtemps."
 msgstr ""
+"Special thanks to the [Tôkyô Debian study\n"
+"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key\n"
+"signed by Debian developers a long time ago :)"

updated PO files
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
index ca61ee0..8ef8f5d 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.en.po"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -3,59 +3,62 @@
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-#, fuzzy
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-"Project-Id-Version: PACKAGE VERSION\n"
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-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"Project-Id-Version: \n"
+"POT-Creation-Date: 2018-07-09 21:07+0000\n"
+"PO-Revision-Date: 2018-07-10 05:51+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"Language: en\n"
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+"X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
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 msgid "[[!meta date=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+msgid "[[!meta title=\"Debconf cette année, c'est râpé.\"]]\n"
 msgstr ""
+"[[!meta title=\"Debconf cette année, c'est râpé.\n"
+"\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid ""
-"I was looking forward to this year's [Debconf in\n"
-"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the "
-"perspective\n"
-"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
-"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
+"Je me réjouissais de la tenue de la [18<sup>ème</sup> conférence Debian à\n"
+"Taiwan](https://debconf18.debconf.org/), pour la première fois en Asie, en\n"
+"espérant y participer pour la première fois aussi et profiter de l'absence de\n"
+"décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le\n"
+"premier août.\n"
 msgstr ""
 
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 msgid ""
-"Moving is a mixed feeling of happiness and excitation for what I am about to "
-"find, and melancholy about what and whom I am about to leave.  But flights "
-"to Tôkyô and Yokohama are very affordable."
+"Ce déménagement me donne de la joie pour ce que je vais rejoindre mais aussi "
+"de la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des "
+"vols très bon marché pour Tôkyô et Yokohama..."
 msgstr ""
 
 #. type: Plain text
 msgid ""
-"Special thanks to the [Tôkyô Debian study "
-"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key "
-"signed by Debian developers a long time ago :)"
+"Spéciale dédicace pour le [cercle d'étude Debian de Tôkyô](https://"
+"tokyodebian-team.pages.debian.net/), où ma première clé GPG a été signée par "
+"des développeurs Debian il y a fort longtemps."
 msgstr ""

En français, nom de Dieu !
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.mdwn" "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
index b8d9a60..f47a826 100644
--- "a/Debian/debi\303\242neries/no-debconf-2018.mdwn"
+++ "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
@@ -2,17 +2,19 @@
 [[!meta updated="Tue, 10 Jul 2018 05:35:20 +0900"]]
 [[!tag Debian]]
 
-[[!meta title="Not going to Debconf this year."]]
+[[!meta title="Debconf cette année, c'est râpé."]]
 
-I was looking forward to this year's [Debconf in
-Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective
-of attending it with no jet lag, but I happen to be moving to Okinawa and
-changing jobs on August 1<sup>st</sup>, right at the middle of it...
+Je me réjouissais de la tenue de la [18<sup>ème</sup> conférence Debian à
+Taiwan](https://debconf18.debconf.org/), pour la première fois en Asie, en
+espérant y participer pour la première fois aussi et profiter de l'absence de
+décalage horaire, mais voilà, je vais déménager au même moment, à Okinawa, le
+premier août.
 
-Moving is a mixed feeling of happiness and excitation for what I am about
-to find, and melancholy about what and whom I am about to leave.  But flights
-to Tôkyô and Yokohama are very affordable.
+Ce déménagement me donne de la joie pour ce que je vais rejoindre mais aussi de
+la mélancolie pour ce et ceux que nous allons quitter.  Mais il y a des vols
+très bon marché pour Tôkyô et Yokohama...
+
+Spéciale dédicace pour le [cercle d'étude Debian de
+Tôkyô](https://tokyodebian-team.pages.debian.net/), où ma première clé GPG a
+été signée par des développeurs Debian il y a fort longtemps.
 
-Special thanks to the [Tôkyô Debian study
-group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key
-signed by Debian developers a long time ago :)

updated PO files
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.en.po" "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
new file mode 100644
index 0000000..ca61ee0
--- /dev/null
+++ "b/Debian/debi\303\242neries/no-debconf-2018.en.po"
@@ -0,0 +1,61 @@
+# 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: 2018-07-09 20:46+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"
+"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=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Tue, 10 Jul 2018 05:35:20 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Not going to Debconf this year.\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid ""
+"I was looking forward to this year's [Debconf in\n"
+"Taiwan](https://debconf18.debconf.org/), the first in Asia, and the "
+"perspective\n"
+"of attending it with no jet lag, but I happen to be moving to Okinawa and\n"
+"changing jobs on August 1<sup>st</sup>, right at the middle of it...\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Moving is a mixed feeling of happiness and excitation for what I am about to "
+"find, and melancholy about what and whom I am about to leave.  But flights "
+"to Tôkyô and Yokohama are very affordable."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Special thanks to the [Tôkyô Debian study "
+"group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key "
+"signed by Debian developers a long time ago :)"
+msgstr ""

Je n'irai pas à Debconf.
diff --git "a/Debian/debi\303\242neries/no-debconf-2018.mdwn" "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
new file mode 100644
index 0000000..b8d9a60
--- /dev/null
+++ "b/Debian/debi\303\242neries/no-debconf-2018.mdwn"
@@ -0,0 +1,18 @@
+[[!meta date="Tue, 10 Jul 2018 05:35:20 +0900"]]
+[[!meta updated="Tue, 10 Jul 2018 05:35:20 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Not going to Debconf this year."]]
+
+I was looking forward to this year's [Debconf in
+Taiwan](https://debconf18.debconf.org/), the first in Asia, and the perspective
+of attending it with no jet lag, but I happen to be moving to Okinawa and
+changing jobs on August 1<sup>st</sup>, right at the middle of it...
+
+Moving is a mixed feeling of happiness and excitation for what I am about
+to find, and melancholy about what and whom I am about to leave.  But flights
+to Tôkyô and Yokohama are very affordable.
+
+Special thanks to the [Tôkyô Debian study
+group](https://tokyodebian-team.pages.debian.net/), where I got my GPG key
+signed by Debian developers a long time ago :)

Ein prosit.
diff --git a/biblio/20141418.mdwn b/biblio/20141418.mdwn
new file mode 100644
index 0000000..c2f2dba
--- /dev/null
+++ b/biblio/20141418.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates."]]
+[[!tag Oikopleura metabolism]]
+
+Zoolog Sci. 2010 Feb;27(2):128-33. doi:10.2108/zsj.27.128.
+
+Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates. 
+
+Cañestro C, Albalat R, Postlethwait JH.
+
+[[!pmid 20141418 desc="Adh3 is the only MDR-Adh in the _Oikopleura_ genome. It strictly conserves the eight residues that constitute the signature of all Adh3 and other residues as well, therefore probably metabolising the same types of substrates as in other species.  (Adh3 is the ancestral MDR-Adh genes in vertebrates; Adh1, 2 and 4 show signs of neofunctionalisation)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1466f8a..b9deb05 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -133,7 +133,9 @@ Physiology
 
  - Searching for an immune system, [[Denoeud et al., 2010|biblio/21097902]] excluded
    LRR proteins, as none of the 74 models found had a transmembrane domain.
-
+ - Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in _Oikopleura_
+   (like in other non-vertebrates).  Conservation of critical residues and similarity
+   in expression pattern suggest that its metabolic targets are the same as in other species.
 
 Phenotypes
 ----------

Train et café
diff --git a/biblio/28115992.mdwn b/biblio/28115992.mdwn
new file mode 100644
index 0000000..3a7c736
--- /dev/null
+++ b/biblio/28115992.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Sex-specific chromatin landscapes in an ultra-compact chordate genome."]]
+[[!tag Oikopleura epigenetic]]
+
+Navratilova P, Danks GB, Long A, Butcher S, Manak JR, Thompson EM.
+
+Epigenetics Chromatin. 2017 Jan 17;10:3. doi:10.1186/s13072-016-0110-4
+
+Sex-specific chromatin landscapes in an ultra-compact chordate genome.
+
+[[!pmid 28115992 desc="Chromatin domains usually smaller than 7 nucleosomes."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c2fd16c..1466f8a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -49,6 +49,7 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
+ - Chromatin domains are rarely longer than 7 nucleosomes ([Navratilova et al., 2017|biblio/28115992]).
  - The entire machinery required for performing NHEJ repair of DSB (which is
    conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).

creating tag page tags/vaccine
diff --git a/tags/vaccine.mdwn b/tags/vaccine.mdwn
new file mode 100644
index 0000000..097a68e
--- /dev/null
+++ b/tags/vaccine.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged vaccine"]]
+
+[[!inline pages="tagged(vaccine)" actions="no" archive="yes"
+feedshow=10]]

Ce matin.
diff --git a/biblio/29720524.mdwn b/biblio/29720524.mdwn
new file mode 100644
index 0000000..9dcb634
--- /dev/null
+++ b/biblio/29720524.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians."]]
+[[!tag HPV vaccine]]
+
+mSphere. 2018 May 2;3(3). pii: e00176-18 doi:10.1128/mSphere.00176-18
+
+Vargas-Robles D, Magris M, Morales N, de Koning MNC, Rodríguez I, Nieves T, Godoy-Vitorino F, Sánchez GI, Alcaraz LD, Forney LJ, Pérez ME, García-Briceño L, van Doorn LJ, Domínguez-Bello MG.
+
+High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians.
+
+[[!pmid 29720524 desc="HPV 39 is highly prevalent in Amerindians from the Amazonas state of Venezuela, but is not included in contemporary vaccines."]]
diff --git a/tags/FACS.mdwn b/tags/FACS.mdwn
deleted file mode 100644
index 1fa1cf2..0000000
--- a/tags/FACS.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged FACS"]]
-
-[[!inline pages="tagged(FACS)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/cytometry
diff --git a/tags/cytometry.mdwn b/tags/cytometry.mdwn
new file mode 100644
index 0000000..132707d
--- /dev/null
+++ b/tags/cytometry.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cytometry"]]
+
+[[!inline pages="tagged(cytometry)" actions="no" archive="yes"
+feedshow=10]]

Correct tags.
diff --git a/biblio/22668417.mdwn b/biblio/22668417.mdwn
index 1b4665a..aa2b50a 100644
--- a/biblio/22668417.mdwn
+++ b/biblio/22668417.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain."]]
-[[!tag trehalose FACS]]
+[[!tag trehalose cytometry]]
 
 Saxena A, Wagatsuma A, Noro Y, Kuji T, Asaka-Oba A, Watahiki A, Gurnot C, Fagiolini M, Hensch TK, Carninci P.
 
diff --git a/biblio/29903975.mdwn b/biblio/29903975.mdwn
index a7e5d2e..083ac1f 100644
--- a/biblio/29903975.mdwn
+++ b/biblio/29903975.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Ghost cytometry."]]
-[[!tag imaging method FACS]]
+[[!tag single_cell imaging cytometry]]
 
 Ota S, Horisaki R, Kawamura Y, Ugawa M, Sato I, Hashimoto K, Kamesawa R, Setoyama K, Yamaguchi S, Fujiu K, Waki K, Noji H.
 

Café
diff --git a/biblio/29903975.mdwn b/biblio/29903975.mdwn
new file mode 100644
index 0000000..a7e5d2e
--- /dev/null
+++ b/biblio/29903975.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ghost cytometry."]]
+[[!tag imaging method FACS]]
+
+Ota S, Horisaki R, Kawamura Y, Ugawa M, Sato I, Hashimoto K, Kamesawa R, Setoyama K, Yamaguchi S, Fujiu K, Waki K, Noji H.
+
+Science. 2018 Jun 15;360(6394):1246-1251. doi:10.1126/science.aan0096
+
+Ghost cytometry.
+
+[[!pmid 29903975 desc="Single-pixel imaging."]]

creating tag page tags/peroxydase
diff --git a/tags/peroxydase.mdwn b/tags/peroxydase.mdwn
new file mode 100644
index 0000000..77be76b
--- /dev/null
+++ b/tags/peroxydase.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged peroxydase"]]
+
+[[!inline pages="tagged(peroxydase)" actions="no" archive="yes"
+feedshow=10]]