Dernières modifications :

T4gp32.
diff --git a/biblio/15028277.mdwn b/biblio/15028277.mdwn
index 829aa67..92c0f44 100644
--- a/biblio/15028277.mdwn
+++ b/biblio/15028277.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="High-accuracy amplification of nanogram total RNA amounts for gene profiling."]]
-[[!tag enzyme ssbp]]
+[[!tag reverse_transcription ssbp]]
+
+Kenzelmann M, Klären R, Hergenhahn M, Bonrouhi M, Gröne HJ, Schmid W, Schütz G.
+
+Genomics. 2004 Apr;83(4):550-8 doi:10.1016/j.ygeno.2003.09.026
+
+High-accuracy amplification of nanogram total RNA amounts for gene profiling.
+
 [[!pmid 15028277 desc="Augment temperature, lower primer concentration, and add T4gp32 to enhance reverse transcription."]]
diff --git a/biblio/16461948.mdwn b/biblio/16461948.mdwn
index 91c86d6..6155b26 100644
--- a/biblio/16461948.mdwn
+++ b/biblio/16461948.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein."]]
-[[!tag reverse_transcription]]
+[[!tag reverse_transcription enzyme ssbp]]
 
 J Biomol Tech. 2005 Sep;16(3):239-47
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 62a3b8f..8f0d40b 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -5,7 +5,7 @@
 Additives that increase reaction performance:
 
  - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
- - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
+ - T4 bacteriophage gene 32 protein (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]], [[Piché _et al._, 2005|biblio/16461948]]).
 
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.

ActD.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 2f8af9a..62a3b8f 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -4,6 +4,7 @@
 
 Additives that increase reaction performance:
 
+ - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
  - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
 
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.

Cleanup.
diff --git a/tags/reverse-transcriptase.mdwn b/tags/reverse-transcriptase.mdwn
deleted file mode 100644
index 302204d..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
deleted file mode 100644
index a6d340d..0000000
--- a/tags/reverse-transcription.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged reverse-transcription"]]
-
-[[!inline pages="tagged(reverse-transcription)" actions="no" archive="yes"
-feedshow=10]]
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]]

Old
diff --git a/biblio/16461948.mdwn b/biblio/16461948.mdwn
new file mode 100644
index 0000000..91c86d6
--- /dev/null
+++ b/biblio/16461948.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein."]]
+[[!tag reverse_transcription]]
+
+J Biomol Tech. 2005 Sep;16(3):239-47
+
+Piché C, Schernthaner JP.
+
+Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein.
+
+[[!pmid 16461948 desc="T4gp32 increases the yield of the smallest cDNAs by 10 %."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 833287f..aaca0a6 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -661,9 +661,6 @@ Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus.
 16540077 [misc]
 The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task.
 
-16461948 [protocols]
-T4gp32 increases the yield of the smallest cDNAs by 10 %.
-
 2326177 [protocols]
 More inert than glycogen.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 0410921..2f8af9a 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -2,6 +2,10 @@
 
 (redaction in progress)
 
+Additives that increase reaction performance:
+
+ - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
+
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
  - It is also a source of antisense artefacts when the RT makes a second-strand cDNA

ActD.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 7d2e930..0410921 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -1,4 +1,12 @@
 [[!meta title="pages tagged reverse transcription"]]
 
-[[!inline pages="tagged(reverse_transcription)" actions="no" archive="yes"
-feedshow=10]]
+(redaction in progress)
+
+Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
+ - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
+ - It is also a source of antisense artefacts when the RT makes a second-strand cDNA
+   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]]).
+
+[[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Normalise.
diff --git a/biblio/10632587.mdwn b/biblio/10632587.mdwn
index 7338f2e..ac48bc0 100644
--- a/biblio/10632587.mdwn
+++ b/biblio/10632587.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Kv4.2 mRNA abundance and A-type K(+) current amplitude are linearly related in basal ganglia and basal forebrain neurons."]]
-[[!tag single_cell qPCR reverse-transcriptase]]
+[[!tag single_cell qPCR reverse_transcription]]
 
 J Neurosci. 2000 Jan 15;20(2):579-88.
 
diff --git a/biblio/16963776.mdwn b/biblio/16963776.mdwn
index 63fa0ec..9266027 100644
--- a/biblio/16963776.mdwn
+++ b/biblio/16963776.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Dynamic assembly of primers on nucleic acid templates."]]
-[[!tag enzyme reverse-transcriptase]]
+[[!tag enzyme reverse_transcription]]
 
 Nucleic Acids Res. 2006;34(17):4702-10. doi:10.1093/nar/gkl625
 
diff --git a/biblio/17897965.mdwn b/biblio/17897965.mdwn
index 60c5302..02fce7a 100644
--- a/biblio/17897965.mdwn
+++ b/biblio/17897965.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D."]]
-[[!tag reverse-transcription method]]
+[[!tag reverse_transcription method]]
 
 Nucleic Acids Res. 2007;35(19):e128 doi:10.1093/nar/gkm683
 

Old
diff --git a/biblio/17897965.mdwn b/biblio/17897965.mdwn
new file mode 100644
index 0000000..60c5302
--- /dev/null
+++ b/biblio/17897965.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D."]]
+[[!tag reverse-transcription method]]
+
+Nucleic Acids Res. 2007;35(19):e128 doi:10.1093/nar/gkm683
+
+Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM.
+
+Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.
+
+[[!pmid 17897965 desc="Adding actinomycin D suppresse self-priming."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5dc8477..833287f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -970,9 +970,6 @@ Digests single-stranded 5' phosphorylated DNA or RNA molecules
 12136033 [tags]
 The distribution of the SAGE tags follow a power law.
 
-17897965 [protocols]
-Adding actinomycin D suppresse self-priming.
-
 17936740 [enhancers]
 Another conserved enhancer in a developmental regulator that is not a transcription factor.
 

Spelling.
diff --git a/biblio/14990785.mdwn b/biblio/14990785.mdwn
index 482deef..f9ae203 100644
--- a/biblio/14990785.mdwn
+++ b/biblio/14990785.mdwn
@@ -7,4 +7,4 @@ Ghadessy FJ, Holliger P.
 
 A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system.
 
-[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween superfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]
+[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween surfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]

Old
diff --git a/biblio/9661199.mdwn b/biblio/9661199.mdwn
new file mode 100644
index 0000000..00516bb
--- /dev/null
+++ b/biblio/9661199.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Man-made cell-like compartments for molecular evolution."]]
+[[!tag emulsion]]
+
+Nat Biotechnol. 1998 Jul;16(7):652-6 doi:10.1038/nbt0798-652
+
+Tawfik DS, Griffiths AD.
+
+Man-made cell-like compartments for molecular evolution.
+
+[[!pmid 9661199 desc="Only the constructs encoding methylases escape degradation."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e4a5d1f..5dc8477 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -574,9 +574,6 @@ Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafis
 16280998 [patents]
 Perpetual-motion machines are not patentable.
 
-99661199 [emulsion]
-Only the constructs encoding methylases escape degradation.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 3de02b1..b72e5ee 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -7,16 +7,16 @@ How to add contents to droplets ?
 
 How to break the droplets ?
 
- - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
- - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
+ - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; surfactant: Triton X-100 0.1%).
+ - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; surfactant: Triton X-100 0.1% and Span 80 4.5%).
  - High salt:
-   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
-   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
- - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
+   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % Triton X-100 and Tris (oil: mineral, surfactant: ABIL WE09).
+   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; surfactant: Sun Soft No. 818SK).
+ - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, surfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % Triton X-100).
 
-Different kinds of superfactants:
+Different kinds of surfactants:
 
- - TritonX-100, Span 80, Tween 80 (many articles),
+ - Span 80 4.5 % and Tween 80 0.5 % (oil: mineral; primary paper: [[Tawfik _et al._, 1998|biblio/9661199]], followed by many others, sometimes adding Triton X-100 and changing the concentrations).
  - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
  - 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]]

Old
diff --git a/biblio/10471784.mdwn b/biblio/10471784.mdwn
new file mode 100644
index 0000000..235f8e2
--- /dev/null
+++ b/biblio/10471784.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="STABLE: protein-DNA fusion system for screening of combinatorial protein libraries in vitro."]]
+[[!tag emulsion selection]]
+
+FEBS Lett. 1999 Aug 27;457(2):227-30.
+
+Doi N, Yanagawa H.
+
+STABLE: protein-DNA fusion system for screening of combinatorial protein libraries in vitro.
+
+[[!pmid 10471784 desc="The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e76008f..e4a5d1f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -577,9 +577,6 @@ Perpetual-motion machines are not patentable.
 99661199 [emulsion]
 Only the constructs encoding methylases escape degradation.
 
-10471784 [emulsion]
-The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

No no, no no no no, no no no no limit !
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index d45975f..3de02b1 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -21,4 +21,4 @@ Different kinds of superfactants:
  - 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]]
 
-[[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]
+[[!inline pages="tagged(emulsion)" actions="no" limit=0]]

Old
diff --git a/biblio/11274352.mdwn b/biblio/11274352.mdwn
new file mode 100644
index 0000000..33a39fe
--- /dev/null
+++ b/biblio/11274352.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Directed evolution of polymerase function by compartmentalized self-replication."]]
+[[!tag selection polymerase emulsion]]
+
+Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4552-7 doi:10.1073/pnas.071052198
+
+Ghadessy FJ, Ong JL, Holliger P.
+
+Directed evolution of polymerase function by compartmentalized self-replication.
+
+[[!pmid 11274352 desc="No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 1bfc85c..e76008f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,12 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-12433997 [emulsion]
-Random primers were used to introduce mutations.
-
-11274352 [emulsion]
-No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/12482612.mdwn b/biblio/12482612.mdwn
new file mode 100644
index 0000000..e927a3e
--- /dev/null
+++ b/biblio/12482612.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry."]]
+[[!tag selection emulsion]]
+
+FEBS Lett. 2002 Dec 18;532(3):455-8
+
+Sepp A, Tawfik DS, Griffiths AD.
+
+Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry.
+
+[[!pmid 12482612 desc="As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5040d54..1bfc85c 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,9 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-12482612 [emulsion]
-As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent.
-
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 

Old
diff --git a/biblio/12697388.mdwn b/biblio/12697388.mdwn
new file mode 100644
index 0000000..df12ac4
--- /dev/null
+++ b/biblio/12697388.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-molecule PCR using water-in-oil emulsion."]]
+[[!tag emulsion PCR]]
+
+Nakano M, Komatsu J, Matsuura S, Takashima K, Katsura S, Mizuno A.
+
+J Biotechnol. 2003 Apr 24;102(2):117-24.
+
+Single-molecule PCR using water-in-oil emulsion.
+
+[[!pmid 12697388 desc="Uses the Triton X-100 contained in the PCR buffer as a surfactant."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e47098e..5040d54 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,12 +589,6 @@ Random primers were used to introduce mutations.
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-14990785 [emulsion]
-Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
-
-12697388 [emulsion]
-Uses the Triton X-100 contained in the PCR buffer as a surfactant.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/14500846.mdwn b/biblio/14500846.mdwn
new file mode 100644
index 0000000..d1eae5c
--- /dev/null
+++ b/biblio/14500846.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA display for in vitro selection of diverse peptide libraries."]]
+[[!tag emulsion selection]]
+
+Nucleic Acids Res. 2003 Oct 1;31(19):e118
+
+Yonezawa M, Doi N, Kawahashi Y, Higashinakagawa T, Yanagawa H.
+
+DNA display for in vitro selection of diverse peptide libraries.
+
+[[!pmid 14500846 desc="Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ae9947d..e47098e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -595,12 +595,6 @@ Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 12697388 [emulsion]
 Uses the Triton X-100 contained in the PCR buffer as a surfactant.
 
-14715296 [emulsion]
-Oil droplets containing water droplets can be FACS sorted.
-
-14500846 [emulsion]
-Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/14715296.mdwn b/biblio/14715296.mdwn
new file mode 100644
index 0000000..53056e1
--- /dev/null
+++ b/biblio/14715296.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting."]]
+[[!tag emulsion]]
+
+Bernath K, Hai M, Mastrobattista E, Griffiths AD, Magdassi S, Tawfik DS.
+
+Anal Biochem. 2004 Feb 1;325(1):151-7
+
+In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting.
+
+[[!pmid 14715296 desc="Oil droplets containing water droplets (w/o/w) can be FACS sorted."]]

Old
diff --git a/biblio/14985532.mdwn b/biblio/14985532.mdwn
new file mode 100644
index 0000000..1115e05
--- /dev/null
+++ b/biblio/14985532.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization."]]
+[[!tag emulsion selection enzyme]]
+
+Protein Eng Des Sel. 2004 Jan;17(1):3-11 doi:10.1093/protein/gzh001
+
+Cohen HM, Tawfik DS, Griffiths AD
+
+Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization.
+
+[[!pmid 14985532 desc="Uses 16% glycerol to promote star activity."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2ec868b..ae9947d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -592,9 +592,6 @@ No beads. A bacterial cel is used as a subcompartment maintaining gene and prote
 14990785 [emulsion]
 Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 
-14985532 [emulsion]
-Uses 16% glycerol to promote star activity.
-
 12697388 [emulsion]
 Uses the Triton X-100 contained in the PCR buffer as a surfactant.
 

Old
diff --git a/biblio/15156154.mdwn b/biblio/15156154.mdwn
new file mode 100644
index 0000000..a8c1d03
--- /dev/null
+++ b/biblio/15156154.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution."]]
+[[!tag selection polymerase]]
+
+Nat Biotechnol. 2004 Jun;22(6):755-9 doi:10.1038/nbt974
+
+Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P.
+
+Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution.
+
+[[!pmid 15156154 desc="Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5e926ce..2ec868b 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -604,9 +604,6 @@ Oil droplets containing water droplets can be FACS sorted.
 14500846 [emulsion]
 Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
 
-15156154 [emulsion]
-Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/15247328.mdwn b/biblio/15247328.mdwn
new file mode 100644
index 0000000..2ba3941
--- /dev/null
+++ b/biblio/15247328.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="In vitro selection of restriction endonucleases by in vitro compartmentalization."]]
+[[!tag emulsion selection enzyme]]
+
+Nucleic Acids Res. 2004 Jul 6;32(12):e95 doi:10.1093/nar/gnh096
+
+Doi N, Kumadaki S, Oishi Y, Matsumura N, Yanagawa H.
+
+In vitro selection of restriction endonucleases by in vitro compartmentalization.
+
+[[!pmid 15247328 desc="The cleaved DNA molecules are selected by filling of their ends with biotin-dUTP"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4d867e2..5e926ce 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -604,9 +604,6 @@ Oil droplets containing water droplets can be FACS sorted.
 14500846 [emulsion]
 Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
 
-15247328 [emulsion]
-The cleaved DNA molecules are selected by filling of their ends with biotin-dUTP
-
 15156154 [emulsion]
 Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs.
 

Syntax.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 41f66a5..d45975f 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -15,6 +15,7 @@ How to break the droplets ?
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
 Different kinds of superfactants:
+
  - TritonX-100, Span 80, Tween 80 (many articles),
  - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])

Expand.
diff --git a/biblio/14990785.mdwn b/biblio/14990785.mdwn
index 9b987ab..482deef 100644
--- a/biblio/14990785.mdwn
+++ b/biblio/14990785.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system."]]
-[[!tag emulsion product not_read]]
-[[!pmid 14990785 desc="Uses ABIL EM90"]]
+[[!tag emulsion DTT]]
+
+Protein Eng Des Sel. 2004 Mar;17(3):201-4 doi:10.1093/protein/gzh025
+
+Ghadessy FJ, Holliger P.
+
+A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system.
+
+[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween superfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index bb76020..41f66a5 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -14,6 +14,10 @@ How to break the droplets ?
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]), DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]].
+Different kinds of superfactants:
+ - TritonX-100, Span 80, Tween 80 (many articles),
+ - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
+ - 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]]
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/15522920.mdwn b/biblio/15522920.mdwn
new file mode 100644
index 0000000..8e2c16d
--- /dev/null
+++ b/biblio/15522920.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Covalent DNA display as a novel tool for directed evolution of proteins in vitro."]]
+[[!tag emulsion selection]]
+
+Protein Eng Des Sel. 2004 Sep;17(9):699-707. Epub 2004 Nov 2.
+
+Bertschinger J, Neri D.
+
+Covalent DNA display as a novel tool for directed evolution of proteins in vitro.
+
+[[!pmid 15522920 desc="A methyl transferase fusion protein which binds covalently 5-fluorodesoxycytosine, gets linked to the constructs in which it is encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f0aa4da..4d867e2 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,9 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-15522920 [emulsion]
-A methyl transferase fusion protein which binds covalently 5-fluorodesoxycytosine, gets linked to the constructs in which it is encoded.
-
 12482612 [emulsion]
 As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent.
 

Expand.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index c0b6ced..bb76020 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -3,6 +3,7 @@
 How to add contents to droplets ?
 
  - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Bernath _et al._, 2005|biblio/15644201]], nanodroplets were prepared with mineral oil, 7.5 % Span 80 and 2.5 % Tween 80, and incupated with the emulsion, with gentle mixing.
 
 How to break the droplets ?
 

Old
diff --git a/biblio/15644201.mdwn b/biblio/15644201.mdwn
new file mode 100644
index 0000000..644f9d4
--- /dev/null
+++ b/biblio/15644201.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery."]]
+[[!tag emulsion selection]]
+
+J Mol Biol. 2005 Feb 4;345(5):1015-26. doi:10.1016/j.jmb.2004.11.017
+
+Bernath K, Magdassi S, Tawfik DS.
+
+Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery.
+
+[[!pmid 15644201 desc="Selection pressure can be increased by reducing the volume of the spheres."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4984443..f0aa4da 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -592,9 +592,6 @@ Random primers were used to introduce mutations.
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-15644201 [emulsion]
-Selection pressure can be increased by reducing the volume of the spheres.
-
 14990785 [emulsion]
 Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 

454 superfactant.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 65071cf..c0b6ced 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -13,6 +13,6 @@ How to break the droplets ?
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]), DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]].
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Expand.
diff --git a/biblio/16056220.mdwn b/biblio/16056220.mdwn
index a54a5bc..4f26806 100644
--- a/biblio/16056220.mdwn
+++ b/biblio/16056220.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Genome sequencing in microfabricated high-density picolitre reactors."]]
-[[!tag emulsion sequencing]]
+[[!tag emulsion sequencing 454]]
+
+Nature. 2005 Sep 15;437(7057):376-80. doi:10.1038/nature03959
+
+Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM.
+
+Genome sequencing in microfabricated high-density picolitre reactors.
+
 [[!pmid 16056220 desc="Primary reference for “454” sequencing."]]

Old
diff --git a/biblio/16131588.mdwn b/biblio/16131588.mdwn
new file mode 100644
index 0000000..6f5f73f
--- /dev/null
+++ b/biblio/16131588.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization."]]
+[[!tag emulsion biotin selection ribozyme]]
+
+RNA. 2005 Oct;11(10):1555-62. doi:10.1261/rna.2121705
+
+Levy M, Griswold KE, Ellington AD.
+
+Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization.
+
+[[!pmid 16131588 desc="During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead if no blocking of biotin is added."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2bb9c61..4984443 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,9 +589,6 @@ As tyramide is converted to a free radical which reacts with neighbouring protei
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 
-16131588 [emulsion]
-During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead in no excess of biotin is added.
-
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index b263477..65071cf 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -11,6 +11,7 @@ How to break the droplets ?
  - High salt:
    - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+ - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
 Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
 

Typo.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 50b4ace..b263477 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -10,8 +10,8 @@ How to break the droplets ?
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
  - High salt:
    - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
-   - In [[Kojima _et al._, 2005|biblio|16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio|16214800]]).
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16214800.mdwn b/biblio/16214800.mdwn
index bc960cc..5bfec57 100644
--- a/biblio/16214800.mdwn
+++ b/biblio/16214800.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets."]]
-[[!tag emulsion]]
+[[!tag emulsion PCR]]
+
+Nucleic Acids Res. 2005 Oct 6;33(17):e150 doi:10.1093/nar/gni143
+
+Kojima T, Takei Y, Ohtsuka M, Kawarasaki Y, Yamane T, Nakano H.
+
+PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets.
+
 [[!pmid 16214800 desc="The composition of the mixture has been modified so that it stays stable in a PCR of 55 cycles of 10 minutes. Uses Sun Soft N° 818SK."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 4771a2c..50b4ace 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -8,6 +8,10 @@ How to break the droplets ?
 
  - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
- - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in presence of high salt (100 mM NaCl), SDS (1%), TritonX-100 (1%) (oil: mineral, superfactant: ABIL WE09).
+ - High salt:
+   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
+   - In [[Kojima _et al._, 2005|biblio|16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio|16214800]]).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16791213.mdwn b/biblio/16791213.mdwn
index 1fe192e..25fa521 100644
--- a/biblio/16791213.mdwn
+++ b/biblio/16791213.mdwn
@@ -1,3 +1,9 @@
 [[!meta title="Amplification of complex gene libraries by emulsion PCR."]]
-[[!tag emulsion]]
+[[!tag emulsion PCR]]
+
+Nat Methods. 2006 Jul;3(7):545-50 doi:10.1038/nmeth896
+
+Williams R, Peisajovich SG, Miller OJ, Magdassi S, Tawfik DS, Griffiths AD.
+
+Amplification of complex gene libraries by emulsion PCR.
 [[!pmid 16791213 desc="Protects the templates frome size bias by isolating them from each other."]]
diff --git a/biblio/16791214.mdwn b/biblio/16791214.mdwn
index 437bfcf..8099627 100644
--- a/biblio/16791214.mdwn
+++ b/biblio/16791214.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="BEAMing: single-molecule PCR on microparticles in water-in-oil emulsion."]]
 [[!tag emulsion biotin]]
+
+Nat Methods. 2006 Jul;3(7):551-9 doi:10.1038/nmeth898
+
+Diehl F, Li M, He Y, Kinzler KW, Vogelstein B, Dressman D
+
+BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions.
+
 [[!pmid 16791214 desc="Recommends (in Box 1) a double-biotin to avoid breaking the complexes at high temperatures."]]
diff --git a/biblio/16791215.mdwn b/biblio/16791215.mdwn
index 791dd70..7dfc274 100644
--- a/biblio/16791215.mdwn
+++ b/biblio/16791215.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Directed evolution by in vitro compartmentalization."]]
 [[!tag emulsion]]
+
+Nat Methods. 2006 Jul;3(7):561-70 doi:10.1038/nmeth897
+
+Miller OJ, Bernath K, Agresti JJ, Amitai G, Kelly BT, Mastrobattista E, Taly V, Magdassi S, Tawfik DS, Griffiths AD.
+
+Directed evolution by in vitro compartmentalization.
+
 [[!pmid 16791215 desc="Method for water in oil in water emulsion (w/o/w)."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 5e2895f..4771a2c 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -8,5 +8,6 @@ How to break the droplets ?
 
  - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
+ - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in presence of high salt (100 mM NaCl), SDS (1%), TritonX-100 (1%) (oil: mineral, superfactant: ABIL WE09).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Expand.
diff --git a/biblio/16233792.mdwn b/biblio/16233792.mdwn
index 454035d..e0edd5a 100644
--- a/biblio/16233792.mdwn
+++ b/biblio/16233792.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Single-molecule reverse transcription polymerase chain reaction using water-in-oil emulsion."]]
-[[!tag emulsion]]
+[[!tag emulsion reverse_transcription]]
+
+J Biosci Bioeng. 2005 Mar;99(3):293-5. doi:10.1263/jbb.99.293
+
+Nakano M, Nakai N, Kurita H, Komatsu J, Takashima K, Katsura S, Mizuno A.
+
+Single-molecule reverse transcription polymerase chain reaction using water-in-oil emulsion.
+
 [[!pmid 16233792 desc="The emulsion is destroyed by centrifugation after 13 cycles, and then the PCR is restarted for 30 cycles."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index df1139e..5e2895f 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -4,5 +4,9 @@ How to add contents to droplets ?
 
  - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
+How to break the droplets ?
+
+ - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
+ - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16432518.mdwn b/biblio/16432518.mdwn
new file mode 100644
index 0000000..640daae
--- /dev/null
+++ b/biblio/16432518.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="BEAMing up for detection and quantification of rare sequence variants."]]
+[[!tag emulsion]]
+
+Li M, Diehl F, Dressman D, Vogelstein B, Kinzler KW.
+
+Nat Methods. 2006 Feb;3(2):95-7. doi:10.1038/nmeth850
+
+BEAMing up for detection and quantification of rare sequence variants.
+
+[[!pmid 16432518 desc="RCA amplification of DNA coupled to beads, followed by single-base extension and flow sorting."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index aa4e6be..2bb9c61 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -1060,9 +1060,6 @@ After 10 weeks, elevated DNA strand break levels are detected in the sperm DNA o
 16902134 [networks]
 Behavioral graph coloring
 
-16432518 [emulsions]
-RCA amplification of DNA coupled to beads, followed by single-base extension and flow sorting.
-
 16449203 [enzymes]
 2'OMe RNAs can not be polyadenylated in vitro.
 

Try again.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 543069a..df1139e 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -2,7 +2,7 @@
 
 How to add contents to droplets ?
 
- - In [[Agresti et al., 2005|16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Syntax.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 711c7e3..543069a 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -2,7 +2,7 @@
 
 How to add contents to droplets ?
 
- - In [[16260754|Agresti et al., 2005]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Agresti et al., 2005|16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16260754.mdwn b/biblio/16260754.mdwn
new file mode 100644
index 0000000..a5de437
--- /dev/null
+++ b/biblio/16260754.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization."]]
+[[!tag emulsion selection ribozyme]]
+
+Agresti JJ, Kelly BT, Jäschke A, Griffiths AD.
+
+Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16170-5 doi:10.1073/pnas.0503733102
+
+Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization.
+
+[[!pmid 16260754 desc="Small molecules mixed with EtOH or DMSO were added by vortexing."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 339766f..aa4e6be 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -595,9 +595,6 @@ During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-16260754 [emulsion]
-Small molecules mixed with EtOH or DMSO were added by vortexing.
-
 15644201 [emulsion]
 Selection pressure can be increased by reducing the volume of the spheres.
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 7861ff2..711c7e3 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -1,3 +1,8 @@
 [[!meta title="pages tagged emulsion"]]
 
+How to add contents to droplets ?
+
+ - In [[16260754|Agresti et al., 2005]], small molecules mixed with EtOH or DMSO were added by vortexing.
+
+
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

creating tag page tags/selection
diff --git a/tags/selection.mdwn b/tags/selection.mdwn
new file mode 100644
index 0000000..1ee4e9d
--- /dev/null
+++ b/tags/selection.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged selection"]]
+
+[[!inline pages="tagged(selection)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/16242713.mdwn b/biblio/16242713.mdwn
new file mode 100644
index 0000000..6b0af64
--- /dev/null
+++ b/biblio/16242713.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization."]]
+[[!tag emulsion selection]]
+
+J Mol Biol. 2005 Nov 25;354(2):212-9. Epub 2005 Oct 3 doi:10.1016/j.jmb.2005.09.051
+
+Sepp A, Choo Y.
+
+Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization.
+
+[[!pmid 16242713 desc="With their Kd of 3pM, zinc finger protein fusions could be used instead of streptavitin or M.HaeIII to bind the DNA molecule in which they are encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 584dd85..339766f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,9 +589,6 @@ As tyramide is converted to a free radical which reacts with neighbouring protei
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 
-16242713 [emulsion]
-With their Kd of 3pM, zinc finger protein fusions could be used instead of streptavitin or M.HaeIII to bind the DNA molecule in which they are encoded.
-
 16131588 [emulsion]
 During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead in no excess of biotin is added.
 

Expansion.
diff --git a/biblio/15289471.mdwn b/biblio/15289471.mdwn
index 6097d7e..df2443d 100644
--- a/biblio/15289471.mdwn
+++ b/biblio/15289471.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Regional patterns of gene expression in human and chimpanzee brains."]]
-[[!tag chimpanzee brain visual_cortex variability]]
+[[!tag chimpanzee brain visual_cortex variability transcriptome]]
+
+Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K, Eichler EE, Pääbo S.
+
+Genome Res. 2004 Aug;14(8):1462-73 doi:10.1101/gr.2538704
+
+Regional patterns of gene expression in human and chimpanzee brains.
+
 [[!pmid 15289471 desc="Individual variations are stronger than regional variations in cortex. Developmental genes are implicated in inter-reigonal, but not inter-species variations. Differential interspecific variation correlates with recent chromosomal duplications."]]

Nettoyage.
diff --git a/biblio/To_Do b/biblio/To_Do
index ed0970e..584dd85 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -46,9 +46,6 @@ Noise due to RNA extraction is 40 times greater than noise due to replicate hybr
 12595569 [amplificaiton]
 Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subsequent cyanine labelling.
 
-11955710 [visual cortex]
-Cat visual cortex cDNAs hybridized to human macroarrays to study critical period mechanism
-
 11222780 [amplification]
 T7 pol generates aberrant template-unrelated products. This is fixed by reducing the concentration of oligo dT primers, and of enzymes. Under these conditions, 2 rounds of RNA linear amplification is not generatng too much bias. Small-volume protocol. T4gp32, a single stranded protein, increases RT processivity.
 
@@ -154,9 +151,6 @@ Apical localisation increases the robustness of development (more segmenatal def
 14732405 [promoters]
 Pax6 has at least two transcription start sites.
 
-15345244 [visual cortex]
-Differential display. Age-dependant variations account for 6.5% of the variations.
-
 15196954 [enhancers] [review]
 Gene networks.
 
@@ -169,9 +163,6 @@ Dual strategy using full length cDNAs and whole genome tiling arrays to annotate
 15001784 [networks] [tracked]
 Distribution of triads and tetrads in networks can cluster them in functional classes.
 
-15295028 [visual cortex] [tracked]
-Synaptic changes in dark-reared animals stimulated by 6 hours of light before sacrifice.
-
 15208707 [networks]
 
 4599081 [crick]
@@ -277,9 +268,6 @@ Alternative promoters which transcribe variants with different translational eff
 15342556 [genome]
 These blocks contain most validated and predicted transcription factor binding sites.
 
-15509747 [visual cortex]
-Another slightly different critical period, and another PV:GFP transgene.
-
 15849325 [genome]
 Proteomics to demonstrate that some short ORFs are translated.
 
@@ -394,9 +382,6 @@ Coordinated expression of e and y is necessary for spot formation. Ancestral pat
 15282333 [networks]
 CDS, 3'UTRs, but not 5'UTRs of highly connected genes of  the human and mouse coexpression networks evolve more slowly
 
-15009647 [visual cortex]
-Identifies immediate early genes that are upregulated in visual cortex after monocular enucleation.
-
 15860629 [networks]
 Model of network growth which takes into account the propension to link to newcommers or to good old friends.
 
@@ -436,9 +421,6 @@ The cells were pulled out from midly digested ganglia with glass microelectrodes
 15371555 [tags]
 Semi-random priming: the 5' oligo is N6-NlaIII.
 
-15901564 [visual cortex]
-OBCAM RNA and protein levels are higher juvenile and dark reared adults, compared to light reared adults.
-
 15911778 [networks]
 The muticommunauty structure of the air transortation network  explains why some cities with a high centrality are not hubs.
 
@@ -541,9 +523,6 @@ Usage of "Bayes Error Rate" instead of a cutoff on p-values. R packaged availabl
 16103215 [misc]
 Supports the idea that the only function of some RNA is to have been transcribed.
 
-16107646 [visual cortex]
-Substracted library spotted on microarrays.
-
 16094371 [networks]
 Functional validation.
 
@@ -565,9 +544,6 @@ Sequence surrounding UCRs might regulate negatively their activity.
 16141073 [genome]
 S/AS pairs usually show positive correlation of their expression.
 
-16195464 [visual cortex]
-Loss of function delays the closure of the critical period.
-
 16168087 [networks]
 Different collaboration network in different research consortiums.
 
@@ -670,15 +646,6 @@ Not read. Deletion of an enhancer conserved in mouse and chicken and its phenoty
 14701942 [enhancers]
 Not read. A pdx-1 enhancer conserved in human, mouse and chicken.
 
-10408598 [visual cortex]
-Not read. egr1 is down-regulated in dark-reared rats.
-
-11739581 [visual cortex]
-Not read. Phenotype of the egr1 KO for the activity-dependant plasticity in the visual cortex.
-
-8656291 [visual cortex]
-not read. Nuclear extracts from dark reared rats have a lesser binding activity to an egr1 probe.
-
 16314298 [protocols]
 Adding gold in PCR tubes enhances the yield when the cycling is quick.
 
@@ -742,9 +709,6 @@ Not read. Enhancers of Krox-20, conserved between chicken and mouse.
 16527264 [enhancers]
 Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus.
 
-16540572 [visual cortex]
-Not read. Monocular deprivation can lead to shifts in ocular dominance in adults if they are deprived of visual stumuli 10 days before the experiment...
-
 16540077 [misc]
 The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task.
 
@@ -781,12 +745,6 @@ By weakening the DNA-protein interaction, the authors acheived the suppression o
 16618967 [enzymes]
 The combined use of a complementary DNA oligo and DNA ligase suppresses the artifacts seen in RNA ligase adenylation.
 
-16709670 [visual cortex]
-Weakening the extracellular matrix influences the plasticity process.
-
-16723524 [visual cortex]
-Publicly available cell-type-specific expression patterns were used to analyse the results of whole-tissue microarray experiments.
-
 16344560 [alternative promoters]
 Detected an average of 3.1 promoters per gene.
 
@@ -1096,9 +1054,6 @@ Primary paper for CLICs (clusters in conservation).
 17284453 [misc]
 [not read] The 3' end of RefSeq protein-coding genes is enriched in putative binding sites (the 5' as well).
 
-17510325 [transcriptome]
-Small RNAs were directly labelled with pCpBiotin.
-
 18024554 [tags]
 A sort of Superverylong 3'SAGE.
 

creating tag page tags/HepG2
diff --git a/tags/HepG2.mdwn b/tags/HepG2.mdwn
new file mode 100644
index 0000000..a56fbc9
--- /dev/null
+++ b/tags/HepG2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged HepG2"]]
+
+[[!inline pages="tagged(HepG2)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/17510325.mdwn b/biblio/17510325.mdwn
new file mode 100644
index 0000000..4e77765
--- /dev/null
+++ b/biblio/17510325.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA maps reveal new RNA classes and a possible function for pervasive transcription."]]
+[[!tag ligation transcriptome small_RNA HepG2]]
+
+Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.
+
+Science. 2007 Jun 8;316(5830):1484-8 doi:10.1126/science.1138341
+
+RNA maps reveal new RNA classes and a possible function for pervasive transcription.
+
+[[!pmid 17510325 desc="Small RNAs were directly labelled with pCpBiotin.  Defines PASRs and PALRs as promoter-associated long or short RNAs."]]

Normalisation.
diff --git a/biblio/28911121.mdwn b/biblio/28911121.mdwn
index 143f947..b30a1ab 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 reverse_transcription]]
 
 Nucleic Acids Res. 2017 Sep 6;45(15):9046-9058. doi:10.1093/nar/gkx633
 

Pas lu.
diff --git a/biblio/26000487.mdwn b/biblio/26000487.mdwn
new file mode 100644
index 0000000..6f7ddda
--- /dev/null
+++ b/biblio/26000487.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells."]]
+[[!tag emulsion single_cell]]
+
+Cell. 2015 May 21;161(5):1187-1201. doi:10.1016/j.cell.2015.04.044
+
+Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L,
+Weitz DA, Kirschner MW.
+
+Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
+
+[[!pmid 26000487 desc="inDrop.  Uses photo-cleavable oligonucleotides."]]

Old
diff --git a/biblio/16141072.mdwn b/biblio/16141072.mdwn
new file mode 100644
index 0000000..054f834
--- /dev/null
+++ b/biblio/16141072.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The transcriptional landscape of the mammalian genome."]]
+[[!tag transcriptome mouse]]
+
+Science. 2005 Sep 2;309(5740):1559-63 doi:10.1126/science.1112014
+
+FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
+
+The transcriptional landscape of the mammalian genome.
+
+[[!pmid 16141072 desc="62.5 % of the mouse genome is transcribed."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2fe8d68..ed0970e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -307,15 +307,9 @@ Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for
 7732590 [misc] [review]
 Reminds that in some organisms, most transcripts share their 5' end.
 
-15590943 [genome]
-Distinguishes "stable" from "variable" deserts. Stable deserts contain more evolutionary conserved regions, compared to variable deserts.
-
 12538257 [misc]
 To create publication-quality figures, or on-the-fly graphics for a dynamic webpage.
 
-15647503 [genome]
-Alternative polyadenylation sites are more frequent in nuclear and RNA-binding protein coding genes than in membrane proteins.
-
 15620361 [genome]
 SACO is a serial analysis of chromatin occupancy, based on chromatin immunoprecipitation and sequencing of genomic sequence tags.
 
@@ -553,9 +547,6 @@ Substracted library spotted on microarrays.
 16094371 [networks]
 Functional validation.
 
-16141072 [genome]
-62.5 % of the mouse genome is transcribed.
-
 15608232 [networks]
 Comprehensive database featuring coexpression, co-occurence in the litterature, genomic neighbourhood in addition to high-throughput informations as protein-protein interaction.
 

Old
diff --git a/biblio/15539566.mdwn b/biblio/15539566.mdwn
new file mode 100644
index 0000000..3c056dc
--- /dev/null
+++ b/biblio/15539566.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Global identification of human transcribed sequences with genome tiling arrays."]]
+[[!tag transcriptome microarray]]
+
+Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M.
+
+Science. 2004 Dec 24;306(5705):2242-6 doi:10.1126/science.1103388
+
+Global identification of human transcribed sequences with genome tiling arrays.
+
+[[!pmid 15539566 desc="Oligonucleotide chips discover 10,595 novel transcribed sequences."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index b450357..2fe8d68 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -334,12 +334,6 @@ Correlation of SNP haplotypes with phenotypes.
 15647298 [alternative promoters]
 Example of alternative 5' exons which modify protein sequence (this is not the case with alternative TSS in the same 5' exon).
 
-15539566 [genome]
-Oligonucleotide chips discover 10,595 novel transcribed sequences.
-
-11181992 [genome]
-Defines RIDGEs : Regions of IncreaseD Gens Expression. SAGE-based study demonstrating low expression in chromosomes 4, 13, 18, 21.
-
 15572134 [misc]
 Uses the fact that some enhancers are transcribed to analyse chromatin looping by flurorescent in situ hybridisation.
 

Old
diff --git a/biblio/15256515.mdwn b/biblio/15256515.mdwn
new file mode 100644
index 0000000..edd8a23
--- /dev/null
+++ b/biblio/15256515.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Clustering of DNA sequences in human promoters."]]
+[[!tag promoter TATA-box]]
+
+Genome Res. 2004 Aug;14(8):1562-74 doi:10.1101/gr.1953904
+
+FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C.
+
+Clustering of DNA sequences in human promoters.
+
+[[!pmid 15256515 desc="Analysis of the distribution of all possible 8-mers in human proximal promoters. Identifiers 9 clusters of sequence. TATA found only in 2.6% of the promoters."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 50ee849..b450357 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -113,9 +113,6 @@ Engeneered T7 used to generate dye-terminated amplification products.
 15271495 [single cell]
 Review
 
-15256515 [genome] [tracked]
-Analysis of the distribution of all possible 8-mers in human proximal promoters. Identifiers 9 clusters of sequence. TATA found only in 2.6% of the promoters.
-
 9925643 [misc] [tracked]
 Using in vitro cell extracts, demonstrate a role for the ELAV family, ARE binding, HuR protein in mRNA stabilisation.
 

creating tag page tags/SAGE
diff --git a/tags/SAGE.mdwn b/tags/SAGE.mdwn
new file mode 100644
index 0000000..bebeb9d
--- /dev/null
+++ b/tags/SAGE.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged SAGE"]]
+
+[[!inline pages="tagged(SAGE)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/10581018.mdwn b/biblio/10581018.mdwn
new file mode 100644
index 0000000..3a0a464
--- /dev/null
+++ b/biblio/10581018.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Analysis of human transcriptomes."]]
+[[!tag SAGE sequence_tags]]
+
+Nat Genet. 1999 Dec;23(4):387-8.
+
+Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ,
+Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC,
+Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello
+JM, Polyak K, Zawel L, Kinzler KW, et al.
+
+Analysis of human transcriptomes.
+
+[[!pmid 10581018 desc="55 highly expressed transcripts make 18% of the RNA mass. 25 % of the RNA mass comprises 92% of the expressed transcriptome, at a copy number of 5 or less."]]
diff --git a/biblio/14707170.mdwn b/biblio/14707170.mdwn
new file mode 100644
index 0000000..ae324f8
--- /dev/null
+++ b/biblio/14707170.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An abundance of bidirectional promoters in the human genome."]]
+[[!tag promoter]]
+
+Genome Res. 2004 Jan;14(1):62-6 doi:10.1101/gr.1982804
+
+Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM.
+
+An abundance of bidirectional promoters in the human genome.
+
+[[!pmid 14707170 desc="Functional validation with luciferase assays."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 88c9c56..50ee849 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -107,9 +107,6 @@ Correlating subnetwork topology, correlation or inverse collrelation, and phase.
 10611672 [misc] [review]
 Describes the general attractions of the RNA world theme park to be built.
 
-14707170 [genome]
-Functionnal validaiton.
-
 9520387 [libraries]
 Engeneered T7 used to generate dye-terminated amplification products.
 
@@ -385,9 +382,6 @@ microRNAs target a large number of transcripts through a short 5' recognition se
 11597334 [mining]
 Template matching approach on expression vectors.
 
-10581018 [genome]
-55 highly expressed transcripts make 18% of the RNA mass. 25 % of the RNA mass comprises 92% of the expressed transcriptome, at a copy number of 5 or less.
-
 15785770 [misc]
 Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers.
 

Old
diff --git a/biblio/15272081.mdwn b/biblio/15272081.mdwn
new file mode 100644
index 0000000..95a7d69
--- /dev/null
+++ b/biblio/15272081.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation."]]
+[[!tag sequence_tags library]]
+
+Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11701-6. doi:10.1073/pnas.0403514101
+
+Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y.
+
+5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation.
+
+[[!pmid 15272081 desc="81% of the 5'/3' tag pairs could be used to amplify a cDNA by RT-PCR."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 524dacc..88c9c56 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -89,9 +89,6 @@ T4 DNA ligase used to ligate a double stranded cap-tag.
 3799962 [enzymes]
 Optimal : Donor/acceptor 5:1; hexammine cobalt chloride 5.0 mM, PEG8000 25%; ATP 100µM. Inhibitors: ATP > 100 µM, MN 2+ > 5mM, NaCl > 20 mM.
 
-15247329 [libraries] [tracked]
-Ligation of cDNA and methylated oligos, in presence of methy-sensitive restriction enzymes, eliminates the cDNA dimer product du to mass action.
-
 14513556 [libraries]
 Hybridises single-stranded tester plasmid and driver PCR product, then purified single strand molecules out of duplexes using hydroxyapatite.
 
@@ -101,9 +98,6 @@ A method to amplify two distinguishable substrates in the same PCR tube, so that
 12582258 [misc]
 Direct labeling of 10µg total RNA.
 
-15272081 [libraries]
-81% of the 5'/3' tag pairs could be used to amplify a cDNA by RT-PCR.
-
 8125298 [libraries]
 Oligo capping primary paper.
 

Old
diff --git a/biblio/15247329.mdwn b/biblio/15247329.mdwn
new file mode 100644
index 0000000..449750a
--- /dev/null
+++ b/biblio/15247329.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry."]]
+[[!tag method library ligation]]
+
+So AP, Turner RF, Haynes CA.
+
+Nucleic Acids Res. 2004 Jul 6;32(12):e96. doi:10.1093/nar/gnh082
+
+Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry.
+
+[[!pmid 15247329 desc="Ligation of cDNA and methylated oligos, in presence of methy-sensitive restriction enzymes, eliminates the cDNA dimer product du to mass action."]]

Pas lu complètement.
diff --git a/biblio/28851704.mdwn b/biblio/28851704.mdwn
new file mode 100644
index 0000000..8e03640
--- /dev/null
+++ b/biblio/28851704.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Psychrophilic proteases dramatically reduce single cell RNA-seq artifacts: A molecular atlas of kidney development."]]
+[[!tag enzyme single_cell]]
+
+Development. 2017 Aug 29. pii: dev.151142. doi:10.1242/dev.151142
+
+Adam M, Potter AS, Potter SS.
+
+Psychrophilic proteases dramatically reduce single cell RNA-seq artifacts: A molecular atlas of kidney development.
+
+[[!pmid 28851704 desc="“ a method for single-cell dissociation using a cold active protease from Bacillus licheniformis, which is a soil bacterium that can grow in a wide range of temperatures and has been isolated from Himalayan glaciers”"]]

Old
diff --git a/biblio/15070753.mdwn b/biblio/15070753.mdwn
new file mode 100644
index 0000000..2e16c75
--- /dev/null
+++ b/biblio/15070753.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries."]]
+[[!tag library epigenetic DNAse-hypersensitivity]]
+
+Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA.
+
+Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4537-42
+
+Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries.
+
+[[!pmid 15070753 desc="Library of DNAseI ends, to map hypersensitive sites. Substrraction with a HS-depleted tester."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index d16ba75..524dacc 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -104,9 +104,6 @@ Direct labeling of 10µg total RNA.
 15272081 [libraries]
 81% of the 5'/3' tag pairs could be used to amplify a cDNA by RT-PCR.
 
-14973331 [libraries]
-cDNAs substracted by their former templates. DNS cleaves DNA from DNA/RNA duplexes, leaving RNA molecules intact. This would suggest the strong reduction of abundant transcripts.
-
 8125298 [libraries]
 Oligo capping primary paper.
 
@@ -125,9 +122,6 @@ Engeneered T7 used to generate dye-terminated amplification products.
 15271495 [single cell]
 Review
 
-15070753 [libraries]
-Library of DNAseI ends, to map hypersensitive sites. Substrraction with a HS-depleted tester.
-
 15256515 [genome] [tracked]
 Analysis of the distribution of all possible 8-mers in human proximal promoters. Identifiers 9 clusters of sequence. TATA found only in 2.6% of the promoters.
 

Old
diff --git a/biblio/14973331.mdwn b/biblio/14973331.mdwn
new file mode 100644
index 0000000..54f4f7b
--- /dev/null
+++ b/biblio/14973331.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Simple cDNA normalization using kamchatka crab duplex-specific nuclease."]]
+[[!tag enzyme]]
+
+Nucleic Acids Res. 2004 Feb 18;32(3):e37. doi:10.1093/nar/gnh031
+
+Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA.
+
+Simple cDNA normalization using kamchatka crab duplex-specific nuclease.
+
+[[!pmid 14973331 desc="cDNAs substracted by their former templates. DNS cleaves DNA from DNA/RNA duplexes, leaving RNA molecules intact. This would suggest the strong reduction of abundant transcripts."]]

Sans limite.
diff --git a/tags/single_cell.mdwn b/tags/single_cell.mdwn
index 9e646a4..4d9f372 100644
--- a/tags/single_cell.mdwn
+++ b/tags/single_cell.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged single_cell"]]
 
-[[!inline pages="tagged(single_cell)" actions="no"
-feedshow=10]]
+[[!inline pages="tagged(single_cell)" actions="no" limit=0]]

Plus de détails.
diff --git a/tags/single_cell.mdwn b/tags/single_cell.mdwn
index 6cde757..9e646a4 100644
--- a/tags/single_cell.mdwn
+++ b/tags/single_cell.mdwn
@@ -1,4 +1,4 @@
 [[!meta title="pages tagged single_cell"]]
 
-[[!inline pages="tagged(single_cell)" actions="no" archive="yes"
+[[!inline pages="tagged(single_cell)" actions="no"
 feedshow=10]]

Normalisation.
diff --git a/biblio/26083756.mdwn b/biblio/26083756.mdwn
index f9a34f8..0dcfbde 100644
--- a/biblio/26083756.mdwn
+++ b/biblio/26083756.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Single-cell chromatin accessibility reveals principles of regulatory variation."]]
-[[!tag single-cell ATAC-seq tag]]
+[[!tag single_cell ATAC-seq tag]]
 
 Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590
 
diff --git a/biblio/26387834.mdwn b/biblio/26387834.mdwn
index 5714307..cbba73e 100644
--- a/biblio/26387834.mdwn
+++ b/biblio/26387834.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells."]]
-[[!tag single_cells cell_cycle mouse]]
+[[!tag single_cell cell_cycle mouse]]
 
 Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P.
 
diff --git a/biblio/27412862.mdwn b/biblio/27412862.mdwn
index c6da8f1..f3f24b2 100644
--- a/biblio/27412862.mdwn
+++ b/biblio/27412862.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates."]]
-[[!tag not_read single_cells genome microfluidic]]
+[[!tag not_read single_cell genome microfluidic]]
 
 Leung K, Klaus A, Lin BK, Laks E, Biele J, Lai D, Bashashati A, Huang YF,
 Aniba R, Moksa M, Steif A, Mes-Masson AM, Hirst M, Shah SP, Aparicio S, Hansen

Expand ; cleanup.
diff --git a/biblio/12019793.mdwn b/biblio/12019793.mdwn
index d75085c..d992b36 100644
--- a/biblio/12019793.mdwn
+++ b/biblio/12019793.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Extra-long first-strand cDNA synthesis."]]
-[[!tag thermo-enhancement library]]
+[[!tag thermo-enhancement library enzyme trehalose]]
+
+Biotechniques. 2002 May;32(5):984-5.
+
+Carninci P, Shiraki T, Mizuno Y, Muramatsu M, Hayashizaki Y.
+
+Extra-long first-strand cDNA synthesis.
+
 [[!pmid 12019793 desc="First publication of our laboratory using a mixture of trehalose and sorbitol. T4gp32 does not seem to improve trehalose-enhanced protocols at standard concentrations."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index de9f8d2..d16ba75 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -64,18 +64,12 @@ Single cell RT-PCR.
 12711698 [amplification] [tracked]
 Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones).
 
-12188181 [libraries]
-Nuclear integrity preserved during tissue grinding.
-
 12560512 [amplification] [tracked]
 «Semi-linear» Taq polymerase amplification used on the cDNA sample at the labelling step.
 
 14602935 [amplification] [tracked]
 Performs SMART, then exponential PCR, then random-primed klenow labelling.
 
-11414214 [libraries]
-Alternative to homopolymeric priming: the use of GN5 3' overhanging oligls as a template for second strand cDNA synthesis.
-
 12398200 [amplification]
 Advocates a systematic round of RNA amplificatin, becaus it reduces interarray variability.
 
@@ -86,22 +80,12 @@ direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligat
 9373199 [libraries]
 Oligo-capping to build 5' ou FL cDNA libraries.
 
-11337467 [libraries]
-Oligo-capping to study transcription initiation genomewide.
-
-11375929 [libraries]
-Oligo-capping to fine-map transcription start sites.
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
 14704353 [libraries] [tracked]
 T4 DNA ligase used to ligate a double stranded cap-tag.
 
-11730011 [libraries]
-Type IIS restriction digest followed py 3'primer ligation, to rempve the poly A from cDNA.
-
-
 3799962 [enzymes]
 Optimal : Donor/acceptor 5:1; hexammine cobalt chloride 5.0 mM, PEG8000 25%; ATP 100µM. Inhibitors: ATP > 100 µM, MN 2+ > 5mM, NaCl > 20 mM.
 
@@ -126,9 +110,6 @@ cDNAs substracted by their former templates. DNS cleaves DNA from DNA/RNA duplex
 8125298 [libraries]
 Oligo capping primary paper.
 
-11042159 [libraries]
-Biotin-labeled RNA to remove hybridizing cDNA.
-
 12902159 [networks]
 Correlating subnetwork topology, correlation or inverse collrelation, and phase.
 

Old
diff --git a/biblio/4342972.mdwn b/biblio/4342972.mdwn
new file mode 100644
index 0000000..14995a5
--- /dev/null
+++ b/biblio/4342972.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Purification and properties of bacteriophage T4-induced RNA ligase."]]
+[[!tag enzyme ligase]]
+
+Proc Natl Acad Sci U S A. 1972 Oct;69(10):3009-13.
+
+Silber R, Malathi VG, Hurwitz J.
+
+Purification and properties of bacteriophage T4-induced RNA ligase.
+
+[[!pmid 4342972 desc="0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f7e5668..de9f8d2 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -560,9 +560,6 @@ A lot of proximal promoters are histone-free. This includes genes which are inac
 15598744 [networks]
 Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 megamodules.
 
-4342972 [enzymes]
-0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay.
-
 16024824 [enhancers]
 The ultraconserved elements in the Irx clusters are transcription enhancers.
 

Old
diff --git a/biblio/3299268.mdwn b/biblio/3299268.mdwn
new file mode 100644
index 0000000..651bdd5
--- /dev/null
+++ b/biblio/3299268.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Synthesis and reactivity of intermediates formed in the T4 RNA ligase reaction."]]
+[[!tag enzyme ligase adenylylation]]
+
+Nucleic Acids Res. 1987 Jul 10;15(13):5289-303.
+
+Hoffmann PU, McLaughlin LW.
+
+Synthesis and reactivity of intermediates formed in the T4 RNA ligase reaction.
+
+[[!pmid 3299268 desc="Synthesis of adenylated RNA.  ssNpR(A) are good acceptors.  pCpN are good donors."]]
diff --git a/biblio/3978074.mdwn b/biblio/3978074.mdwn
new file mode 100644
index 0000000..b43d508
--- /dev/null
+++ b/biblio/3978074.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Donor activation in the T4 RNA ligase reaction. "]]
+[[!tag enzyme ligase adenylylation]]
+
+McLaughlin LW, Piel N, Graeser E.
+
+Biochemistry. 1985 Jan 15;24(2):267-73.
+
+Donor activation in the T4 RNA ligase reaction.
+
+[[!pmid 3978074 desc="Adenylated RNA is a better substrate for T4 RNA ligase."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9fd4445..f7e5668 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -83,12 +83,6 @@ Advocates a systematic round of RNA amplificatin, becaus it reduces interarray v
 T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation.
 direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos.
 
-3978074 [enzymes]
-Adenylated RNA is a better substrate for T4 RNA ligase.
-
-3299268 [enzymes]
-Synthesis of adenylated RNA
-
 9373199 [libraries]
 Oligo-capping to build 5' ou FL cDNA libraries.
 
@@ -830,9 +824,6 @@ HCC (1 mM) promotes intermolecular ligation. This effect is countered by monoval
 386284 [protocols]
 A low ATP concentration contributes to the attainment of high yields. ATP regenerating systems allow to work at sub-stoechiometric concentrations. Rnase A can be used as a SSBP. Spermine enhances yield.
 
-724498 [enzymes]
-Optimal temperature between 0 and 15 degrees. 15-20 % DMSO enhance the reaction. pCp is easily ligated to the 3' end of tRNAs, but the 5' end of tRNAs is difficult to ligate to pCp if it is engaged in a double helix.
-
 9380524 [protocols]
 Concentrations as high as 1 M or 2.5 M can strongly improve the yield.
 

Old
diff --git a/biblio/724498.mdwn b/biblio/724498.mdwn
new file mode 100644
index 0000000..b94f7c7
--- /dev/null
+++ b/biblio/724498.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reactions at the termini of tRNA with T4 RNA ligase."]]
+[[!tag enzyme ligase]]
+
+Nucleic Acids Res. 1978 Oct;5(10):3665-77.
+
+Bruce AG, Uhlenbeck OC.
+
+Reactions at the termini of tRNA with T4 RNA ligase.
+
+[[!pmid 724498 desc="Optimal temperature between 0 and 15 degrees. 15-20 % DMSO enhance the reaction. pCp is easily ligated to the 3' end of tRNAs, but the 5' end of tRNAs is difficult to ligate to pCp if it is engaged in a double helix."]]

Expand.
diff --git a/biblio/197518.mdwn b/biblio/197518.mdwn
index da139cd..55ec911 100644
--- a/biblio/197518.mdwn
+++ b/biblio/197518.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Importance of 5′-terminal blocking structure to stabilize mRNA in eukaryotic protein synthesis."]]
 [[!tag enzyme buffer pyrophosphatase]]
+
+Proc Natl Acad Sci U S A. 1977 Jul;74(7):2734-8.
+
+Shimotohno K, Kodama Y, Hashimoto J, Miura KI.
+
+Importance of 5'-terminal blocking structure to stabilize mRNA in eukaryotic protein synthesis.
+
 [[!pmid 197518 desc="In this study, TAP is used in 0.1 M NaAc (pH 5.5), 5 mM EDTA, during 90 min at 30℃."]]

Dans le train.
diff --git a/biblio/24857550.mdwn b/biblio/24857550.mdwn
new file mode 100644
index 0000000..11748f2
--- /dev/null
+++ b/biblio/24857550.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Unambiguous identification of miRNA:target site interactions by different types of ligation reactions."]]
+[[!tag method ligase]]
+
+Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E, Rajewsky N.
+
+Mol Cell. 2014 Jun 19;54(6):1042-1054. doi:10.1016/j.molcel.2014.03.049
+
+Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.
+
+[[!pmid 24857550 desc="Endogenous activity (speculated to be tRNA ligase) detected in the negative controls."]]

Expand.
diff --git a/biblio/16963776.mdwn b/biblio/16963776.mdwn
index 7ec0dcc..63fa0ec 100644
--- a/biblio/16963776.mdwn
+++ b/biblio/16963776.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Dynamic assembly of primers on nucleic acid templates."]]
-[[!tag enzyme]]
+[[!tag enzyme reverse-transcriptase]]
+
+Nucleic Acids Res. 2006;34(17):4702-10. doi:10.1093/nar/gkl625
+
+Leal NA, Sukeda M, Benner SA.
+
+Dynamic assembly of primers on nucleic acid templates.
+
 [[!pmid 16963776 desc="MMuLV reverse-transcriptase can not use 5′ NH₂ 8-mers for DNA-dependant DNA polymerisation."]]

Old
diff --git a/biblio/320212.mdwn b/biblio/320212.mdwn
new file mode 100644
index 0000000..e6104ba
--- /dev/null
+++ b/biblio/320212.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates."]]
+[[!tag enzyme ligase]]
+
+J Biol Chem. 1977 Mar 10;252(5):1732-8.
+
+Sugino A, Snoper TJ, Cozzarelli NR.
+
+Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates.
+
+[[!pmid 320212 desc="Activation of donors requires 3'OH acceptors. Acceptors can be exchanged."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index da937a1..9fd4445 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -569,9 +569,6 @@ Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 mega
 4342972 [enzymes]
 0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay.
 
-320212 [enzymes]
-Activation of donors requires 3'OH acceptors. Acceptors can be exchanged.
-
 16024824 [enhancers]
 The ultraconserved elements in the Irx clusters are transcription enhancers.
 

Expand.
diff --git a/biblio/202926.mdwn b/biblio/202926.mdwn
index 51605f8..16293ca 100644
--- a/biblio/202926.mdwn
+++ b/biblio/202926.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="End labeling of enzymatically decapped mRNA."]]
 [[!tag enzyme buffer pyrophosphatase phosphatase]]
+
+Efstratiadis A, Vournakis JN, Donis-Keller H, Chaconas G, Dougall DK, Kafatos FC.
+
+Nucleic Acids Res. 1977 Dec;4(12):4165-74.
+
+End labeling of enzymatically decapped mRNA.
+
 [[!pmid 202926 desc="TAP can be  assayed by degrading gamma 32P ATP. 250 mM phosphate inhibits TAP. 10 mM phosphate inhibits BAP."]]

Old
diff --git a/biblio/2657738.mdwn b/biblio/2657738.mdwn
new file mode 100644
index 0000000..c19aa29
--- /dev/null
+++ b/biblio/2657738.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I."]]
+[[!tag enzyme buffer manganese]]
+
+Tabor S, Richardson CC.
+
+Proc Natl Acad Sci U S A. 1989 Jun;86(11):4076-80
+
+Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I.
+
+[[!pmid 2657738 desc="Isocitrate used to buffer Mn2+ ions."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f64b163..da937a1 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -554,9 +554,6 @@ Defines origons as subnetworks originating from a single TF (in their model - a
 15861189 [mining]
 Uses "compare plots"
 
-2657738 [enzymes]
-Isocitrate used to buffer Mn2+ ions.
-
 15740627 [amplification]
 Introduces a T3 promoter during the second strand synthesis. Very nice introduction.
 

Expand.
diff --git a/biblio/7796821.mdwn b/biblio/7796821.mdwn
index 0647d7b..223a289 100644
--- a/biblio/7796821.mdwn
+++ b/biblio/7796821.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis."]]
 [[!tag EcoP15I enzyme]]
+
+Meisel A, Mackeldanz P, Bickle TA, Krüger DH, Schroeder C.
+
+EMBO J. 1995 Jun 15;14(12):2958-66
+
+Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.
+
 [[!pmid 7796821 desc="Protein bound to the DNA between the EcoP15I sites interfers negatively with cleavage."]]

Old
diff --git a/biblio/8663453.mdwn b/biblio/8663453.mdwn
new file mode 100644
index 0000000..c166b2c
--- /dev/null
+++ b/biblio/8663453.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Archaebacterial DNA polymerases tightly bind uracil-containing DNA."]]
+[[!tag enzyme ligase]]
+
+J Biol Chem. 1996 Jul 26;271(30):17692-6.
+
+Lasken RS, Schuster DM, Rashtchian A.
+
+Archaebacterial DNA polymerases tightly bind uracil-containing DNA.
+
+[[!pmid 8663453 desc="Uracil RNA does not have the same inhibiting effect on PCR."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 1ad05be..f64b163 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -662,9 +662,6 @@ Assessed wether some gene sets based on common function, cytogenetic location, p
 15737411 [misc]
 Single-tube nested PCR using two different annealing temperatures.
 
-8663453 [enzymes]
-Uracil RNA does not have the same inhibiting effect on PCR.
-
 11574151 [neurogenin]
 Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafish ngn1 is).
 

Old
diff --git a/biblio/10446205.mdwn b/biblio/10446205.mdwn
new file mode 100644
index 0000000..2c6f485
--- /dev/null
+++ b/biblio/10446205.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The mitochondrial RNA ligase from Leishmania tarentolae can join RNA molecules bridged by a complementary RNA."]]
+[[!tag enzyme ligase]]
+
+Blanc V, Alfonzo JD, Aphasizhev R, Simpson L.
+
+J Biol Chem. 1999 Aug 20;274(34):24289-96.
+
+The mitochondrial RNA ligase from Leishmania tarentolae can join RNA molecules bridged by a complementary RNA.
+
+[[!pmid 10446205 desc="L. tar mitochondrial RNA ligase performs 100x better on nicked dsRNA than T4RNL1."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e432687..1ad05be 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -572,9 +572,6 @@ Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 mega
 4342972 [enzymes]
 0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay.
 
-10446205 [enzymes]
-L. tar mitochondrial RNA ligase performs 100x better on nicked dsRNA than T4RNL1.
-
 320212 [enzymes]
 Activation of donors requires 3'OH acceptors. Acceptors can be exchanged.
 

Dans le train
diff --git a/biblio/28911121.mdwn b/biblio/28911121.mdwn
new file mode 100644
index 0000000..143f947
--- /dev/null
+++ b/biblio/28911121.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase."]]
+[[!tag enzyme reverse-transcription]]
+
+Nucleic Acids Res. 2017 Sep 6;45(15):9046-9058. doi:10.1093/nar/gkx633
+
+Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L.
+
+Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase.
+
+[[!pmid 28911121 desc="“PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.”"]]

Dans le train.
diff --git a/biblio/28821669.mdwn b/biblio/28821669.mdwn
new file mode 100644
index 0000000..30d3eea
--- /dev/null
+++ b/biblio/28821669.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcriptomic Analysis of Ribosome-Bound mRNA in Cortical Neurites In Vivo."]]
+[[!tag translatome mouse neuron]]
+
+J Neurosci. 2017 Sep 6;37(36):8688-8705. doi:10.1523/JNEUROSCI.3044-16.2017
+
+Ouwenga R, Lake AM, O'Brien D, Mogha A, Dani A, Dougherty JD.
+
+Transcriptomic Analysis of Ribosome-Bound mRNA in Cortical Neurites In Vivo.
+
+[[!pmid 28821669 desc="“These additional mRNAs may indicate the existence of signaling pathways that employ spatial control of translation to regulate nuclear functions.”"]]

Old
diff --git a/biblio/10672035.mdwn b/biblio/10672035.mdwn
new file mode 100644
index 0000000..f47cf4b
--- /dev/null
+++ b/biblio/10672035.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations."]]
+[[!tag enzyme phosphatase]]
+
+Rina M, Pozidis C, Mavromatis K, Tzanodaskalaki M, Kokkinidis M, Bouriotis V.
+
+Eur J Biochem. 2000 Feb;267(4):1230-8 doi:10.1046/j.1432-1327.2000.01127.x
+
+Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations.
+
+[[!pmid 10672035 desc="Primary paper for antarctic phosphatase. Says that it is strongly inhibited by Zn2+ and EDTA, but this apparently false for Zn2+"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5ee8935..e432687 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -560,9 +560,6 @@ Isocitrate used to buffer Mn2+ ions.
 15740627 [amplification]
 Introduces a T3 promoter during the second strand synthesis. Very nice introduction.
 
-10672035 [enzymes]
-Primary paper for antarctic phosphatase. Says that it is strongly inhibited by Zn2+ and EDTA, but this apparently false for Zn2+
-
 15741315 [enhancers] [not read]
 Transcribed enhancers in Drosophila.
 

Old
diff --git a/biblio/11589698.mdwn b/biblio/11589698.mdwn
new file mode 100644
index 0000000..83765e5
--- /dev/null
+++ b/biblio/11589698.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Engineering the properties of a cold active enzyme through rational redesign of the active site."]]
+[[!tag enzyme phosphatase]]
+
+Eur J Biochem. 2001 Oct;268(19):5074-80.
+
+Tsigos I, Mavromatis K, Tzanodaskalaki M, Pozidis C, Kokkinidis M, Bouriotis V.
+
+Engineering the properties of a cold active enzyme through rational redesign of the active site.
+
+[[!pmid 11589698 desc="Antarctic phosphatase. The buffer contains 1mM Zn2+"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2c4d475..5ee8935 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -563,9 +563,6 @@ Introduces a T3 promoter during the second strand synthesis. Very nice introduct
 10672035 [enzymes]
 Primary paper for antarctic phosphatase. Says that it is strongly inhibited by Zn2+ and EDTA, but this apparently false for Zn2+
 
-11589698 [enzymes]
-The buffer contains 1mM Zn2+
-
 15741315 [enhancers] [not read]
 Transcribed enhancers in Drosophila.
 

Old
diff --git a/biblio/11782527.mdwn b/biblio/11782527.mdwn
new file mode 100644
index 0000000..46eb34b
--- /dev/null
+++ b/biblio/11782527.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation."]]
+[[!tag enzyme PCR]]
+
+Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):596-601 doi:10.1073/pnas.012372799
+
+Hogrefe HH, Hansen CJ, Scott BR, Nielson KB.
+
+Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation.
+
+[[!pmid 11782527 desc="dTTP is deaminated to dUTP during PCR, which causes the synthesis of uracil-containing DNA, a potent inhibitor of archeal DNA polymerases."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 08f37e3..2c4d475 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -674,9 +674,6 @@ Single-tube nested PCR using two different annealing temperatures.
 8663453 [enzymes]
 Uracil RNA does not have the same inhibiting effect on PCR.
 
-11782527 [enzymes]
-dTTP is deaminated to dUTP during PCR, which causes the synthesis of uracil-containing DNA, a potent inhibitor of archeal DNA polymerases.
-
 11574151 [neurogenin]
 Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafish ngn1 is).
 

Correction.
diff --git a/biblio/12503310.mdw b/biblio/12503310.mdwn
similarity index 100%
rename from biblio/12503310.mdw
rename to biblio/12503310.mdwn

Longer comment.
diff --git a/biblio/11814287.mdwn b/biblio/11814287.mdwn
index 07e0280..4f51e41 100644
--- a/biblio/11814287.mdwn
+++ b/biblio/11814287.mdwn
@@ -7,4 +7,4 @@ Anal Biochem. 2002 Feb 15;301(2):168-74 doi:10.1006/abio.2001.5474
 
 A highly efficient method for long-chain cDNA synthesis using trehalose and betaine.
 
-[[!pmid 11814287 desc="Effects of trehalose and betaine on reverse-transcriptase are additive."]]
+[[!pmid 11814287 desc="Effects of trehalose and betaine on reverse-transcriptase are additive.  Betain improves reverse-transcription by decreasing melting temperature of structured molecules."]]

More metadata.
diff --git a/biblio/11814287.mdwn b/biblio/11814287.mdwn
index 82f1883..07e0280 100644
--- a/biblio/11814287.mdwn
+++ b/biblio/11814287.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="A highly efficient method for long-chain cDNA synthesis using trehalose and betaine."]]
 [[!tag thermo-enhancement method enzyme betaine]]
+
+Spiess AN, Ivell R.
+
+Anal Biochem. 2002 Feb 15;301(2):168-74 doi:10.1006/abio.2001.5474
+
+A highly efficient method for long-chain cDNA synthesis using trehalose and betaine.
+
 [[!pmid 11814287 desc="Effects of trehalose and betaine on reverse-transcriptase are additive."]]

Old
diff --git a/biblio/12228725.mdwn b/biblio/12228725.mdwn
new file mode 100644
index 0000000..3580f74
--- /dev/null
+++ b/biblio/12228725.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains."]]
+[[!tag enzyme ligase]]
+
+Ho CK, Shuman S.
+
+Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12709-14 doi:10.1073/pnas.192184699
+
+Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.
+
+[[!pmid 12228725 desc="Investigates ATP, Mg2+, Mn2+, and pH."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9f1d516..08f37e3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -302,9 +302,6 @@ CAGE & ESTs to express all microarray results in TPM (Transcripts per million).
 15372072 [miRNA]
 It is necessary to inactivate the drosha RNase to detect the capped precursors correctly.
 
-12228725 [enzymes]
-Investigates ATP, Mg2+, Mn2+, and pH.
-
 15339661 [genome]
 Open chromatin fibers contain both active and inactive genes.
 

Old
diff --git a/biblio/12503310.mdw b/biblio/12503310.mdw
new file mode 100644
index 0000000..c28814e
--- /dev/null
+++ b/biblio/12503310.mdw
@@ -0,0 +1,10 @@
+[[!meta title="Purification of histidine-tagged T4 RNA ligase from E. coli."]]
+[[!tag enzyme ligase]]
+
+Biotechniques. 2002 Dec;33(6):1256-60
+
+Wang QS, Unrau PJ.
+
+Purification of histidine-tagged T4 RNA ligase from E. coli.
+
+[[!pmid 12503310 desc="De-adenylation of T4 RNA ligase is required prior using adenylated substrates. Incubating with pyrophosphate during some purification steps does the job. Commercial T4 usually contains mostly de-adenylated enzyme. Mesuring reaction efficiency without ATP gives adenylation levels."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 672d15e..9f1d516 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -89,9 +89,6 @@ Adenylated RNA is a better substrate for T4 RNA ligase.
 3299268 [enzymes]
 Synthesis of adenylated RNA
 
-12503310 [enzymes]
-De-adenylation of T4 RNA ligase is required prior using adenylated substrates. Incubating with pyrophosphate during some purification steps does the job. Commercial T4 usually contains mostly de-adenylated enzyme. Mesuring reaction efficiency without ATP gives adenylation levels.
-
 9373199 [libraries]
 Oligo-capping to build 5' ou FL cDNA libraries.
 

Old
diff --git a/biblio/12611899.mdwn b/biblio/12611899.mdwn
new file mode 100644
index 0000000..27bc7f7
--- /dev/null
+++ b/biblio/12611899.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Structure-function analysis of T4 RNA ligase 2."]]
+[[!tag enzyme ligase]]
+
+J Biol Chem. 2003 May 16;278(20):17601-8 doi:10.1074/jbc.M300817200
+
+Yin S, Ho CK, Shuman S.
+
+Structure-function analysis of T4 RNA ligase 2.
+
+[[!pmid 12611899 desc="Investigates pH and ATP concentration"]]
diff --git a/biblio/12933796.mdwn b/biblio/12933796.mdwn
index 694a8e7..6dcddc9 100644
--- a/biblio/12933796.mdwn
+++ b/biblio/12933796.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Genetic and biochemical analysis of the functional domains of yeast tRNA ligase."]]
 [[!tag enzyme ligase tRNA not_read]]
+
+J Biol Chem. 2003 Nov 7;278(45):43928-38 doi:10.1074/jbc.M307839200
+
+Sawaya R, Schwer B, Shuman S.
+
+Genetic and biochemical analysis of the functional domains of yeast tRNA ligase.
+
 [[!pmid 12933796 desc="Trl1 can be separated in three funcionnal polypeptides : a cyclic phosphodiesterase, a A/GTP-dependant polynucleotide kinase, and an ATP-dependant 3′-hydroxyl,2′-phosphate – 5′-phosphate ligase."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ee485c9..672d15e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -308,9 +308,6 @@ It is necessary to inactivate the drosha RNase to detect the capped precursors c
 12228725 [enzymes]
 Investigates ATP, Mg2+, Mn2+, and pH.
 
-12611899 [enzymes]
-Investigates pH and ATP concentration.
-
 15339661 [genome]
 Open chromatin fibers contain both active and inactive genes.
 

Old
diff --git a/biblio/14654700.mdwn b/biblio/14654700.mdwn
new file mode 100644
index 0000000..8754087
--- /dev/null
+++ b/biblio/14654700.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1."]]
+[[!tag enzyme ligase]]
+
+Nucleic Acids Res. 2003 Dec 15;31(24):7247-54 doi:10.1093/nar/gkg914
+
+Blondal T, Hjorleifsdottir SH, Fridjonsson OF, Aevarsson A, Skirnisdottir S, Hermannsdottir AG, Hreggvidsson GO, Smith AV, Kristjansson JK.
+
+Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1.
+
+[[!pmid 14654700 desc="Optimal pH between 6 and 7. Enhanced by 25% PEG 6000 and 1 mM HCC."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f12412e..ee485c9 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -584,9 +584,6 @@ A lot of proximal promoters are histone-free. This includes genes which are inac
 15598744 [networks]
 Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 megamodules.
 
-14654700 [enzymes]
-Optimal pH between 6 and 7. Enhanced by 25% PEG 6000 and 1mM HCC.
-
 4342972 [enzymes]
 0.1 mM PPi inhibits RNL1. Polypurines concatenate better than polypyrimidines. Primary paper for the RNA ligase assay.
 

Old
diff --git a/biblio/14962393.mdwn b/biblio/14962393.mdwn
new file mode 100644
index 0000000..cb71fe4
--- /dev/null
+++ b/biblio/14962393.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Structure and mechanism of RNA ligase."]]
+[[!tag enzyme ligase adenylylation]]
+
+Structure. 2004 Feb;12(2):327-39 doi:10.1016/j.str.2004.01.011
+
+Ho CK, Wang LK, Lima CD, Shuman S.
+
+Structure and mechanism of RNA ligase.
+
+[[!pmid 14962393 desc="Primary paper for Rnl2(1-249) which ligates AppRNA in abscence of ATP, ten times faster than the full length enzyme."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 3ec6bc4..f12412e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -554,9 +554,6 @@ Very sharp expression patterns.
 15979195 [enhancers]
 A 5' GC-rich / AT-rich, and a conversely 3' AT-rich / GC-rich motifs were discovered. The change in nucleotide composition seems to delinate the boundaries of the enhancers.
 
-14962393 [enzymes]
-Primary paper for Rnl2(1-249) which ligates AppRNA in abscence of ATP, ten times faster than the full length enzyme.
-
 15778709 [networks]
 The resulting networks allow non-transcription factors to regulate a gene. The direct neighborhood of Myc is enriched in its direct targets.
 

Old
diff --git a/biblio/14967495.mdwn b/biblio/14967495.mdwn
new file mode 100644
index 0000000..bc7e2e5
--- /dev/null
+++ b/biblio/14967495.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization of bacteriophage KVP40 and T4 RNA ligase 2."]]
+[[!tag enzyme ligase]]
+
+Virology. 2004 Feb 5;319(1):141-51 doi:10.1016/j.virol.2003.10.037
+
+Yin S, Kiong Ho C, Miller ES, Shuman S.
+
+Characterization of bacteriophage KVP40 and T4 RNA ligase 2.
+
+[[!pmid 14967495 desc="One more tool in the box?"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 6202b2d..3ec6bc4 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -305,9 +305,6 @@ CAGE & ESTs to express all microarray results in TPM (Transcripts per million).
 15372072 [miRNA]
 It is necessary to inactivate the drosha RNase to detect the capped precursors correctly.
 
-14967495 [enzymes]
-One more tool in the box?
-
 12228725 [enzymes]
 Investigates ATP, Mg2+, Mn2+, and pH.
 

creating tag page tags/adenylylation
diff --git a/tags/adenylylation.mdwn b/tags/adenylylation.mdwn
new file mode 100644
index 0000000..0c0fe76
--- /dev/null
+++ b/tags/adenylylation.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged adenylylation"]]
+
+[[!inline pages="tagged(adenylylation)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/15037782.mdwn b/biblio/15037782.mdwn
new file mode 100644
index 0000000..c348204
--- /dev/null
+++ b/biblio/15037782.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Practical and general synthesis of 5'-adenylated RNA (5'-AppRNA)."]]
+[[!tag enzyme ligase adenylylation]]
+
+RNA. 2004 Apr;10(4):731-46. doi:10.1261/rna.5247704
+
+Silverman SK.
+
+Practical and general synthesis of 5'-adenylated RNA (5'-AppRNA).
+
+[[!pmid 15037782 desc="The adenylation of RNA by T4 RNL1 is enhanced when they are annealed to a DNA oligos, leaving 3-4 protruding 5'ribonucleotides."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index d678dcf..6202b2d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -605,9 +605,6 @@ Activation of donors requires 3'OH acceptors. Acceptors can be exchanged.
 16024824 [enhancers]
 The ultraconserved elements in the Irx clusters are transcription enhancers.
 
-15037782 [enzymes]
-The adenylation of RNA by T4 RNL1 is enhanced when they are annealed to a DNA oligos, leaving 3-4 protruding 5'ribonucleotides.
-
 15899965 [enhancers]
 Out of 126 ultraconserved elements in a melanogaster / A. Gambiae comparison, only 1 is intergenic, the other being mostly ncRNA and exons.
 

Old.
diff --git a/biblio/15084599.mdwn b/biblio/15084599.mdwn
new file mode 100644
index 0000000..c539406
--- /dev/null
+++ b/biblio/15084599.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2."]]
+[[!tag enzyme ligase]]
+
+J Biol Chem. 2004 Jul 23;279(30):31337-47. doi:10.1074/jbc.M402394200
+
+Nandakumar J, Ho CK, Lima CD, Shuman S.
+
+RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2.
+
+[[!pmid 15084599 desc="Can ligate RNA at a 3'-OH/5'-P nick in a RNA/RNA or RNA/DNA duplex."]]
diff --git a/biblio/15851476.mdwn b/biblio/15851476.mdwn
new file mode 100644
index 0000000..882afcf
--- /dev/null
+++ b/biblio/15851476.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2."]]
+[[!tag enzyme ligase]]
+
+Nandakumar J, Shuman S.
+
+J Biol Chem. 2005 Jun 24;280(25):23484-9. doi:10.1074/jbc.M500831200
+
+Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2.
+
+[[!pmid 15851476 desc="Complete Appylation by RNL2 is possible in absence of Mg2+, but is slower."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index bf358a9..d678dcf 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -332,9 +332,6 @@ Alternative promoters which transcribe variants with different translational eff
 15342556 [genome]
 These blocks contain most validated and predicted transcription factor binding sites.
 
-15084599 [enzymes]
-Further characterisation of the enzyme.
-
 15509747 [visual cortex]
 Another slightly different critical period, and another PV:GFP transgene.
 
@@ -977,9 +974,6 @@ Breadth-first search: organises a network in a layered hierarchy. Highest nodes
 16893951 [amplification]
 Combined use of T7 polymerase and helicase, strong strand displacement, and branched rolling circle isothermal amplification.
 
-15084599 [enzymes]
-Complete Appylation by RNL2 is possible in absence of Mg2+, but is slower.
-
 16964210 [amplification]
 Apparently, DNA - RNA hybridisation is very tolerant to mismatches.
 

Brush up.
diff --git a/biblio/15611301.mdwn b/biblio/15611301.mdwn
index 4750b6e..b32a116 100644
--- a/biblio/15611301.mdwn
+++ b/biblio/15611301.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1."]]
-[[!tag enzyme]]
+[[!tag ligase enzyme]]
+
+Sawaya R, Schwer B, Shuman S.
+
+RNA. 2005 Jan;11(1):107-13. doi:10.1261/rna.7193705
+
+Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1.
+
 [[!pmid 15611301 desc="Could it be used to 2' kinate RNA oligos?"]]

Old
diff --git a/biblio/15642699.mdwn b/biblio/15642699.mdwn
new file mode 100644
index 0000000..73542b0
--- /dev/null
+++ b/biblio/15642699.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties."]]
+[[!tag enzyme ligase]]
+
+Nucleic Acids Res. 2005 Jan 7;33(1):135-42. doi:10.1093/nar/gki149
+
+Blondal T, Thorisdottir A, Unnsteinsdottir U, Hjorleifsdottir S, Aevarsson A, Ernstsson S, Fridjonsson OH, Skirnisdottir S, Wheat JO, Hermannsdottir AG, Sigurdsson ST, Hreggvidsson GO, Smith AV, Kristjansson JK.
+
+Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties.
+
+[[!pmid 15642699 desc="Preference for circularisation. Optimum : 65-70 °C, 25 µM ATP, pH 7.5-8, 10× more efficient than commercial ones."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4a0fddb..bf358a9 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -365,9 +365,6 @@ Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for
 7732590 [misc] [review]
 Reminds that in some organisms, most transcripts share their 5' end.
 
-15642699 [enzymes]
-Preference for circularisation. Optimum : 65-70ºC, 25µM ATP, pH 7.5-8, 10x more efficient than commercial ones.
-
 15590943 [genome]
 Distinguishes "stable" from "variable" deserts. Stable deserts contain more evolutionary conserved regions, compared to variable deserts.
 

old
diff --git a/biblio/15653639.mdwn b/biblio/15653639.mdwn
new file mode 100644
index 0000000..f36add3
--- /dev/null
+++ b/biblio/15653639.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins."]]
+[[!tag enzyme ligase]]
+
+Nucleic Acids Res. 2005 Jan 14;33(1):388-99 doi:10.1093/nar/gki174
+
+Englert M, Beier H.
+
+Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins.
+
+[[!pmid 15653639 desc="Ligates 2'-3'P molecules to 5'OH. Has a broad substrate range."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index de90bf1..4a0fddb 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -377,9 +377,6 @@ To create publication-quality figures, or on-the-fly graphics for a dynamic webp
 15647503 [genome]
 Alternative polyadenylation sites are more frequent in nuclear and RNA-binding protein coding genes than in membrane proteins.
 
-15653639 [enzymes]
-Ligates 2'-3'P molecules to 5'OH. Has a broad substrate range.
-
 15620361 [genome]
 SACO is a serial analysis of chromatin occupancy, based on chromatin immunoprecipitation and sequencing of genomic sequence tags.
 

Old.
diff --git a/biblio/15520289.mdwn b/biblio/15520289.mdwn
index 4544374..42fcc47 100644
--- a/biblio/15520289.mdwn
+++ b/biblio/15520289.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity."]]
 [[!tag cap enzyme]]
+
+Lavie L, Maldener E, Brouha B, Meese EU, Mayer J.
+
+Genome Res. 2004 Nov;14(11):2253-60 doi:10.1101/gr.2745804
+
+The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity.
+
 [[!pmid 15520289 desc="The presence of an extra G in pseudogenes suggests that many reverse-transcriptases can reverse transcribe the cap."]]
diff --git a/biblio/15897197.mdwn b/biblio/15897197.mdwn
new file mode 100644
index 0000000..dd5b00c
--- /dev/null
+++ b/biblio/15897197.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel 3'-ribonuclease and 3'-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D."]]
+[[!tag ligase enzyme]]
+
+Zhu H, Shuman S.
+
+J Biol Chem. 2005 Jul 15;280(28):25973-81 doi:10.1074/jbc.M504002200
+
+Novel 3′-ribonuclease and 3′-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D.
+
+[[!pmid 15897197 desc="These activities depend on Mn2+, and could be used to generate a 3'rNOH or 3'rNp oligo."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index fa184b4..de90bf1 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -563,9 +563,6 @@ Conserved in human, mouse and oppossum. What about fish ?
 15919954 [miRNA]
 Very sharp expression patterns.
 
-15897197 [enzymes]
-These activities depend on Mn2+, and could be used to generate a 3'rNOH or 3'rNp oligo.
-
 15979195 [enhancers]
 A 5' GC-rich / AT-rich, and a conversely 3' AT-rich / GC-rich motifs were discovered. The change in nucleotide composition seems to delinate the boundaries of the enhancers.
 

creating tag page tags/Taq
diff --git a/tags/Taq.mdwn b/tags/Taq.mdwn
new file mode 100644
index 0000000..b47d659
--- /dev/null
+++ b/tags/Taq.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Taq"]]
+
+[[!inline pages="tagged(Taq)" actions="no" archive="yes"
+feedshow=10]]

Old.
diff --git a/biblio/16299470.mdwn b/biblio/16299470.mdwn
new file mode 100644
index 0000000..ef2e4cf
--- /dev/null
+++ b/biblio/16299470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The wild-type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides."]]
+[[!tag enzyme Taq ligase]]
+
+EMBO Rep. 2006 Jan;7(1):59-65. doi:10.1038/sj.embor.7400576
+
+Vengrova S, Dalgaard JZ.
+
+The wild-type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides.
+
+[[!pmid 16299470 desc="The T4 DNA ligase can join 5′p to 2′OH 3′p or 2′p 3′OH nucleotides. The Taq polymerase can elongate across up to three ribonucleotides."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 95819cf..fa184b4 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -776,9 +776,6 @@ Detailed protocol for Terminal Continuation (TC).
 16344560 [promoters] [oligo-capping]
 Estimates as 88% the frequency of full length cDNA produced by the oligo-capping method
 
-16299470 [enzymes]
-The T4 DNA ligase can join 5'p to 2'OH 3'p or 2'p 3'OH nucleotides. The Taq polymerase can elongate across up to three ribonucleotides.
-
 16251272 [misc]
 Transcriptional repressor involved in splicing.
 

Old.
diff --git a/biblio/17024178.mdwn b/biblio/17024178.mdwn
new file mode 100644
index 0000000..394dd85
--- /dev/null
+++ b/biblio/17024178.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus."]]
+[[!tag enzyme amplification]]
+
+EMBO J. 2006 Oct 18;25(20):4933-42. doi:10.1038/sj.emboj.7601368
+
+Imbert I, Guillemot JC, Bourhis JM, Bussetta C, Coutard B, Egloff MP, Ferron F, Gorbalenya AE, Canard B.
+
+A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus.
+
+[[!pmid 17024178 desc="This enzyme is dependant on Mn2+ and does not require a primer."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ec8007e..95819cf 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -995,9 +995,6 @@ Complete Appylation by RNL2 is possible in absence of Mg2+, but is slower.
 16964210 [amplification]
 Apparently, DNA - RNA hybridisation is very tolerant to mismatches.
 
-17024178 [enzymes]
-This enzyme is dependant on Mn2+ and does not require a primer.
-
 16971463 [enzymes]
 Degrades single-strand DNA, not RNA nor double strand DNA.
 

Old.
diff --git a/biblio/17290226.mdwn b/biblio/17290226.mdwn
new file mode 100644
index 0000000..2167a30
--- /dev/null
+++ b/biblio/17290226.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps."]]
+[[!tag enzyme ligase]]
+
+Gu J, Lu H, Tippin B, Shimazaki N, Goodman MF, Lieber MR.
+
+EMBO J. 2007 Feb 21;26(4):1010-23. doi:10.1038/sj.emboj.7601559
+
+XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps.
+
+[[!pmid 17290226 desc="Requires the Ku heterodimer."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2b3e18b..ec8007e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -1100,9 +1100,6 @@ Whole-genome analysis of sequences flanking restriction sites, some of which bei
 15884678 [misc]
 Intronic LNA 14-mer to inhibit the gene-specific amplification of genomic DNA during RT-PCR.
 
-17290226 [enzymes]
-Requres the Ku heterodimer.
-
 17267814 [tags]
 The novel transcripts have an average of 0.84 copies per cell.