Dernières modifications :

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.
 

Fatigué ?
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 3c3d10a..3a3f8f1 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2017-09-10 12:19+0000\n"
-"PO-Revision-Date: 2017-09-11 10:24+0900\n"
+"PO-Revision-Date: 2017-09-11 10:25+0900\n"
 "Last-Translator: Charles Plessy <plessy@riken.jp>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -49,7 +49,7 @@ msgid ""
 msgstr ""
 "Last month, there has been <a href=\"https://lists.debian.org/debian-"
 "project/2017/08/msg00011.html\">an interesting discussion about off-line "
-"GnuPG keys and their storage systems]</a> on the debian-project@l.d.o "
-"mailing list.  I tried to summarise it in the Debian wiki, in particular by "
-"creating two [new](https://wiki.debian.org/OfflineMasterKey) [pages](https://"
-"wiki.debian.org/GnuPG/StubKeys)."
+"GnuPG keys and their storage systems</a> on the debian-project@l.d.o mailing "
+"list.  I tried to summarise it in the Debian wiki, in particular by creating "
+"two [new](https://wiki.debian.org/OfflineMasterKey) [pages](https://wiki."
+"debian.org/GnuPG/StubKeys)."

Try again.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 1590121..3c3d10a 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -7,8 +7,8 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2017-09-10 12:19+0000\n"
-"PO-Revision-Date: 2017-09-10 21:19+0900\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
+"PO-Revision-Date: 2017-09-11 10:24+0900\n"
+"Last-Translator: Charles Plessy <plessy@riken.jp>\n"
 "Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
@@ -47,9 +47,9 @@ msgid ""
 "créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"
 "(https://wiki.debian.org/GnuPG/StubKeys)."
 msgstr ""
-"Last month, there has been [an interesting discussion about off-line GnuPG "
-"keys and their storage systems]((https://lists.debian.org/debian-"
-"project/2017/08/msg00011.html) on the debian-project@l.d.o mailing list.  I "
-"tried to summarise it in the Debian wiki, in particular by creating two [new]"
-"(https://wiki.debian.org/OfflineMasterKey) [pages](https://wiki.debian.org/"
-"GnuPG/StubKeys)."
+"Last month, there has been <a href=\"https://lists.debian.org/debian-"
+"project/2017/08/msg00011.html\">an interesting discussion about off-line "
+"GnuPG keys and their storage systems]</a> on the debian-project@l.d.o "
+"mailing list.  I tried to summarise it in the Debian wiki, in particular by "
+"creating two [new](https://wiki.debian.org/OfflineMasterKey) [pages](https://"
+"wiki.debian.org/GnuPG/StubKeys)."

Revert "Avoid line breaks in Markdown link."
This reverts commit c5f26b80529a2e19acfa7e1db43743800ff4df96.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 3c0deb2..1590121 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -40,9 +40,9 @@ msgstr "[[!meta title=\"Summary of the discussion on off-line keys.\"]]\n"
 
 #. type: Plain text
 msgid ""
-"Le mois dernier il y a eu "
-"[une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html)"
-", sur la liste debian-project@l.d.o.  "
+"Le mois dernier il y a eu [une discussion intéressante au sujet des clés "
+"GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/"
+"debian-project/2017/08/msg00011.html), sur la liste debian-project@l.d.o.  "
 "J'ai tenté de résumer la discussion dans le wiki Debian, un particulier en "
 "créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"
 "(https://wiki.debian.org/GnuPG/StubKeys)."

Revert "Try HTML."
This reverts commit 127f34bdbccb337ab6da0128f1aabd1988b9cd26.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index ea95944..3c0deb2 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -41,7 +41,7 @@ msgstr "[[!meta title=\"Summary of the discussion on off-line keys.\"]]\n"
 #. type: Plain text
 msgid ""
 "Le mois dernier il y a eu "
-"<a href='https://lists.debian.org/debian-project/2017/08/msg00011.html'>une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage</a>"
+"[une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html)"
 ", sur la liste debian-project@l.d.o.  "
 "J'ai tenté de résumer la discussion dans le wiki Debian, un particulier en "
 "créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"

Try HTML.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 3c0deb2..ea95944 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -41,7 +41,7 @@ msgstr "[[!meta title=\"Summary of the discussion on off-line keys.\"]]\n"
 #. type: Plain text
 msgid ""
 "Le mois dernier il y a eu "
-"[une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html)"
+"<a href='https://lists.debian.org/debian-project/2017/08/msg00011.html'>une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage</a>"
 ", sur la liste debian-project@l.d.o.  "
 "J'ai tenté de résumer la discussion dans le wiki Debian, un particulier en "
 "créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"

Avoid line breaks in Markdown link.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 1590121..3c0deb2 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -40,9 +40,9 @@ msgstr "[[!meta title=\"Summary of the discussion on off-line keys.\"]]\n"
 
 #. type: Plain text
 msgid ""
-"Le mois dernier il y a eu [une discussion intéressante au sujet des clés "
-"GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/"
-"debian-project/2017/08/msg00011.html), sur la liste debian-project@l.d.o.  "
+"Le mois dernier il y a eu "
+"[une discussion intéressante au sujet des clés GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html)"
+", sur la liste debian-project@l.d.o.  "
 "J'ai tenté de résumer la discussion dans le wiki Debian, un particulier en "
 "créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"
 "(https://wiki.debian.org/GnuPG/StubKeys)."

updated PO files
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index 4ffc817..1590121 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2017-09-10 12:12+0000\n"
+"POT-Creation-Date: 2017-09-10 12:19+0000\n"
 "PO-Revision-Date: 2017-09-10 21:19+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text

Traduction.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
index c43a154..4ffc817 100644
--- "a/Debian/debi\303\242neries/clefHorsLigne.en.po"
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -3,46 +3,53 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2017-09-10 12:12+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2017-09-10 21:19+0900\n"
+"Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
+"X-Generator: Poedit 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
 msgstr ""
+"[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
+"[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"Résumé de la discussion sur les clés hors ligne.\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"Summary of the discussion on off-line keys.\"]]\n"
 
 #. type: Plain text
 msgid ""
 "Le mois dernier il y a eu [une discussion intéressante au sujet des clés "
-"GnuPG hors ligne et de leurs supports de "
-"stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html), "
-"sur la liste debian-project@l.d.o.  J'ai tenté de résumer la discussion dans "
-"le wiki Debian, un particulier en créant deux "
-"[nouvelles](https://wiki.debian.org/OfflineMasterKey)  "
-"[pages](https://wiki.debian.org/GnuPG/StubKeys)."
+"GnuPG hors ligne et de leurs supports de stockage](https://lists.debian.org/"
+"debian-project/2017/08/msg00011.html), sur la liste debian-project@l.d.o.  "
+"J'ai tenté de résumer la discussion dans le wiki Debian, un particulier en "
+"créant deux [nouvelles](https://wiki.debian.org/OfflineMasterKey)  [pages]"
+"(https://wiki.debian.org/GnuPG/StubKeys)."
 msgstr ""
+"Last month, there has been [an interesting discussion about off-line GnuPG "
+"keys and their storage systems]((https://lists.debian.org/debian-"
+"project/2017/08/msg00011.html) on the debian-project@l.d.o mailing list.  I "
+"tried to summarise it in the Debian wiki, in particular by creating two [new]"
+"(https://wiki.debian.org/OfflineMasterKey) [pages](https://wiki.debian.org/"
+"GnuPG/StubKeys)."

updated PO files
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.en.po" "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
new file mode 100644
index 0000000..c43a154
--- /dev/null
+++ "b/Debian/debi\303\242neries/clefHorsLigne.en.po"
@@ -0,0 +1,48 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2017-09-10 12:12+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Résumé de la discussion sur les clés hors ligne.\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Le mois dernier il y a eu [une discussion intéressante au sujet des clés "
+"GnuPG hors ligne et de leurs supports de "
+"stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html), "
+"sur la liste debian-project@l.d.o.  J'ai tenté de résumer la discussion dans "
+"le wiki Debian, un particulier en créant deux "
+"[nouvelles](https://wiki.debian.org/OfflineMasterKey)  "
+"[pages](https://wiki.debian.org/GnuPG/StubKeys)."
+msgstr ""

Clés hors-ligne.
diff --git "a/Debian/debi\303\242neries/clefHorsLigne.mdwn" "b/Debian/debi\303\242neries/clefHorsLigne.mdwn"
new file mode 100644
index 0000000..e93a66a
--- /dev/null
+++ "b/Debian/debi\303\242neries/clefHorsLigne.mdwn"
@@ -0,0 +1,13 @@
+[[!meta date="Sun, 10 Sep 2017 21:06:29 +0900"]]
+[[!meta updated="Sun, 10 Sep 2017 21:06:29 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="Résumé de la discussion sur les clés hors ligne."]]
+
+Le mois dernier il y a eu [une discussion intéressante au sujet des clés GnuPG
+hors ligne et de leurs supports de
+stockage](https://lists.debian.org/debian-project/2017/08/msg00011.html), sur
+la liste debian-project@l.d.o.  J'ai tenté de résumer la discussion dans le
+wiki Debian, un particulier en créant deux
+[nouvelles](https://wiki.debian.org/OfflineMasterKey)
+[pages](https://wiki.debian.org/GnuPG/StubKeys).

Dans le train.
diff --git a/biblio/28666355.mdwn b/biblio/28666355.mdwn
new file mode 100644
index 0000000..0345576
--- /dev/null
+++ b/biblio/28666355.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation."]]
+[[!tag cap]]
+
+Rydzik AM, Warminski M, Sikorski PJ, Baranowski MR, Walczak S, Kowalska J, Zuberek J, Lukaszewicz M, Nowak E, W Claridge TD, Darzynkiewicz E, Nowotny M, Jemielity J.
+
+Nucleic Acids Res. 2017 Jun 28. doi:10.1093/nar/gkx569
+
+mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.
+
+[[!pmid 28666355 desc="Different conformation in eIF4E. Resists to hydrolysis by DcpS and Dcp2."]]

Old.
diff --git a/biblio/2020554.mdwn b/biblio/2020554.mdwn
new file mode 100644
index 0000000..f11b3ad
--- /dev/null
+++ b/biblio/2020554.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors."]]
+[[!tag libraries]]
+
+Nucleic Acids Res. 1991 Mar 11;19(5):1156 doi:10.1093/nar/19.5.1156
+
+Holton TA1, Graham MW.
+
+A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors.
+
+[[!pmid 2020554 desc="Tails open plasmid with ddT using terminal transferase."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ac58d91..2b3e18b 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -686,9 +686,6 @@ Different collaboration network in different research consortiums.
 16120967 [enzymes]
 Apparently, only one of the two head-to-head sites is cut...
 
-2020554 [libraries]
-Uses terminal transferase.
-
 16046619 [mining]
 When a group of TFs have more than one Transfac entry, only the most over-represented is taken into account to build the network.
 

Add missing PMID.
diff --git a/biblio/7760832.mdwn b/biblio/7760832.mdwn
index 5001116..dc10fb3 100644
--- a/biblio/7760832.mdwn
+++ b/biblio/7760832.mdwn
@@ -7,4 +7,4 @@ Edery I, Chu LL, Sonenberg N, Pelletier J.
 
 An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture).
 
-[[!pmid desc="An eIF-4E fusion protein is used to bind the caps of RNA/DNA duplexes. RNase A cuts single stranded RNAs, thus separating the complexes from the cDNA if they are not full length."]]
+[[!pmid 7760832 desc="An eIF-4E fusion protein is used to bind the caps of RNA/DNA duplexes. RNase A cuts single stranded RNAs, thus separating the complexes from the cDNA if they are not full length."]]

Old.
diff --git a/biblio/To_Do b/biblio/To_Do
index 9d4e9ba..ac58d91 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -1100,9 +1100,6 @@ Normalisation genes in qPCR should be validated in the particular systems studie
 17189378 [genetics] [not read] [patent]
 Whole-genome analysis of sequences flanking restriction sites, some of which being polymorphic.
 
-17299583 [libraries]
-There is a bias that might be caused by some sequence-specificity of the DNA ligase.
-
 15884678 [misc]
 Intronic LNA 14-mer to inhibit the gene-specific amplification of genomic DNA during RT-PCR.
 

Old.
diff --git a/biblio/17299583.mdwn b/biblio/17299583.mdwn
new file mode 100644
index 0000000..8e0af8d
--- /dev/null
+++ b/biblio/17299583.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing."]]
+[[!tag sequence_tags library]]
+
+PLoS One. 2007 Feb 14;2(2):e197.
+
+Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E.
+
+The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
+
+[[!pmid 17299583 desc="There is a bias that might be caused by some sequence-specificity of the DNA ligase."]]

More
diff --git a/biblio/28792927.mdwn b/biblio/28792927.mdwn
index 1586e84..321637c 100644
--- a/biblio/28792927.mdwn
+++ b/biblio/28792927.mdwn
@@ -9,4 +9,4 @@ Lander ES, Zhang F.
 
 Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.
 
-[[!pmid 28792927 desc="EMICERI and MOB3B cross-activate each other."]]
+[[!pmid 28792927 desc="A Cas9 SAM overexpression screen of 10,504 lncRNAs identifies 11 targets.  EMICERI and MOB3B cross-activate each other."]]

Biblio
diff --git a/biblio/28792927.mdwn b/biblio/28792927.mdwn
new file mode 100644
index 0000000..1586e84
--- /dev/null
+++ b/biblio/28792927.mdwn
@@ -0,0 +1,12 @@
+[[!meta title=" Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood."]]
+[[!tag non_coding ]]
+
+Nature. 2017 Aug 17;548(7667):343-346. doi:10.1038/nature23451
+
+Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F,
+Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS,
+Lander ES, Zhang F.
+
+Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.
+
+[[!pmid 28792927 desc="EMICERI and MOB3B cross-activate each other."]]

creating tag page tags/somatic_mutation
diff --git a/tags/somatic_mutation.mdwn b/tags/somatic_mutation.mdwn
new file mode 100644
index 0000000..72dbd52
--- /dev/null
+++ b/tags/somatic_mutation.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged somatic mutation"]]
+
+[[!inline pages="tagged(somatic_mutation)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/chimeric_transcript
diff --git a/tags/chimeric_transcript.mdwn b/tags/chimeric_transcript.mdwn
new file mode 100644
index 0000000..69da71b
--- /dev/null
+++ b/tags/chimeric_transcript.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged chimeric transcript"]]
+
+[[!inline pages="tagged(chimeric_transcript)" actions="no" archive="yes"
+feedshow=10]]

vieux.
diff --git a/biblio/15786810.mdwn b/biblio/15786810.mdwn
new file mode 100644
index 0000000..15b4888
--- /dev/null
+++ b/biblio/15786810.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="cDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases."]]
+[[!tag ]]
+
+Biotechniques. 2005 Mar;38(3):451-8.
+
+Ohara R, Kikuno RF, Kitamura H, Ohara O.
+
+cDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases.
+
+[[!pmid 15786810 desc="High size is preserved by ligating a 5'adapter before each amplification."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 1654f0b..9d4e9ba 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -449,9 +449,6 @@ Template matching approach on expression vectors.
 15785770 [misc]
 Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers.
 
-15786810 [libraries]
-High size is preserved by ligating a 5'adapter before each amplification.
-
 15778292 [genome]
 2n species covered 1x would be more efficient than n covered 2x for the discovery of conserved elements, but the resulting genome assemblies would be of a much poorer qualities.
 

Ce matin.
diff --git a/biblio/28847005.mdwn b/biblio/28847005.mdwn
new file mode 100644
index 0000000..cfbd5de
--- /dev/null
+++ b/biblio/28847005.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Public antibodies to malaria antigens generated by two LAIR1 insertion modalities."]]
+[[!tag antibody somatic_mutation chimeric_transcript]]
+
+Nature. 2017 Aug 23. doi:10.1038/nature23670.
+
+Pieper K, Tan J, Piccoli L, Foglierini M, Barbieri S, Chen Y, Silacci-Fregni
+C, Wolf T, Jarrossay D, Anderle M, Abdi A, Ndungu FM, Doumbo OK, Traore B, Tran
+TM, Jongo S, Zenklusen I, Crompton PD, Daubenberger C, Bull PC, Sallusto F,
+Lanzavecchia A.
+
+Public antibodies to malaria antigens generated by two LAIR1 insertion modalities.
+
+[[!pmid 28847005 desc="Exons “Switch region inserts derived from transcribed genes.“"]]

old
diff --git a/biblio/15489326.mdwn b/biblio/15489326.mdwn
new file mode 100644
index 0000000..1ac4256
--- /dev/null
+++ b/biblio/15489326.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="1274 full-open reading frames of transcripts expressed in the developing mouse nervous system."]]
+[[!tag library]]
+
+Genome Res. 2004 Oct;14(10B):2053-63. doi:10.1101/gr.2601304
+
+1274 full-open reading frames of transcripts expressed in the developing mouse nervous system.
+
+Bonaldo MF, Bair TB, Scheetz TE, Snir E, Akabogu I, Bair JL, Berger B, Crouch K, Davis A, Eyestone ME, Keppel C, Kucaba TA, Lebeck M, Lin JL, de Melo AI, Rehmann J, Reiter RS, Schaefer K, Smith C, Tack D, Trout K, Sheffield VC, Lin JJ, Casavant TL, Soares MB.
+
+[[!pmid 15489326 desc="Enrichement for large size flcDNA by size fractionation."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c9e0500..1654f0b 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).
 15297624 [miRNA]
 5' siRNAs induce transcriptinal silencing when targeted to the nucleus.
 
-15489326 [library] [tracked]
-Enrichement for large size flcDNA by size fractionation.
-
 15372072 [miRNA]
 It is necessary to inactivate the drosha RNase to detect the capped precursors correctly.
 

Vieux.
diff --git a/biblio/11768647.mdwn b/biblio/11768647.mdwn
new file mode 100644
index 0000000..c012fde
--- /dev/null
+++ b/biblio/11768647.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Serial analysis of gene expression in a single cell."]]
+[[!tag sequence_tags single_cell]]
+
+Schober MS, Min YN, Chen YQ.
+
+Biotechniques. 2001 Dec;31(6):1240-2.
+
+Serial analysis of gene expression in a single cell.
+
+[[!pmid 11768647 desc="Lysis in Dynabeads buffer, followed by first strand synthesis from poly-A."]]
diff --git a/biblio/9742245.mdwn b/biblio/9742245.mdwn
new file mode 100644
index 0000000..c302e66
--- /dev/null
+++ b/biblio/9742245.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Expression profiling of single cells using 3 prime end amplification (TPEA) PCR."]]
+[[!tag single_cell]]
+
+Dixon AK, Richardson PJ, Lee K, Carter NP, Freeman TC.
+
+Nucleic Acids Res. 1998 Oct 1;26(19):4426-31.
+
+Expression profiling of single cells using 3 prime end amplification (TPEA) PCR.
+
+[[!pmid 9742245 desc="Nucleus removed by spinning. 1st PCR with poly-T and random primer. 2nd PCR nested and gene specific."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 6698258..c9e0500 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -153,9 +153,6 @@ Engeneered T7 used to generate dye-terminated amplification products.
 15271495 [single cell]
 Review
 
-9742245 [single cell] [tracked]
-Nucleus removed by spinning. 1st PCR with poly-T and random primer. 2nd PCR nested and gene specific.
-
 15070753 [libraries]
 Library of DNAseI ends, to map hypersensitive sites. Substrraction with a HS-depleted tester.
 
@@ -335,9 +332,6 @@ Alternative promoters which transcribe variants with different translational eff
 14663149 [libraries] [tracked]
 5' 20mers to map transcription start sites, and mesaure their usage.
 
-11768647 [single cell]
-Lysis in Dynabeads buffer, followed by first strand synthesis from poly-A.
-
 15342556 [genome]
 These blocks contain most validated and predicted transcription factor binding sites.
 

creating tag page tags/lineage
diff --git a/tags/lineage.mdwn b/tags/lineage.mdwn
new file mode 100644
index 0000000..e30796c
--- /dev/null
+++ b/tags/lineage.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged lineage"]]
+
+[[!inline pages="tagged(lineage)" actions="no" archive="yes"
+feedshow=10]]

Ce matin.
diff --git a/biblio/28813413.mdwn b/biblio/28813413.mdwn
new file mode 100644
index 0000000..694526b
--- /dev/null
+++ b/biblio/28813413.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Polylox barcoding reveals haematopoietic stem cell fates realized in vivo."]]
+[[!tag single_cell lineage not_read]]
+
+Nature. 2017 Aug 16. doi:10.1038/nature23653
+
+Pei W, Feyerabend TB, Rössler J, Wang X, Postrach D, Busch K, Rode I, Klapproth K, Dietlein N, Quedenau C, Chen W, Sauer S, Wolf S, Höfer T, Rodewald HR.
+
+Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.
+
+[[!pmid 28813413 desc="Cre-loxP inversions and deletions generate hundred of thousands of combinations."]]

vieux
diff --git a/biblio/10632587.mdwn b/biblio/10632587.mdwn
new file mode 100644
index 0000000..7338f2e
--- /dev/null
+++ b/biblio/10632587.mdwn
@@ -0,0 +1,10 @@
+[[!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]]
+
+J Neurosci. 2000 Jan 15;20(2):579-88.
+
+Tkatch T, Baranauskas G, Surmeier DJ.
+
+Kv4.2 mRNA abundance and A-type K(+) current amplitude are linearly related in basal ganglia and basal forebrain neurons.
+
+[[!pmid 10632587 desc="Accute dissociation of slices before cell isolation. Variablility between RT lots? Evaluation of mRNA abundance through a serial dillution and callibration approach."]]
diff --git a/biblio/12399444.mdwn b/biblio/12399444.mdwn
new file mode 100644
index 0000000..bbc8e94
--- /dev/null
+++ b/biblio/12399444.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Identification of cell-specific messenger ribonucleic acids in oxytocinergic and vasopressinergic magnocellular neurons in rat supraoptic nucleus by single-cell differential hybridization."]]
+[[!tag single_cell library]]
+
+Yamashita M, Glasgow E, Zhang BJ, Kusano K, Gainer H.
+
+Endocrinology. 2002 Nov;143(11):4464-76. doi:10.1210/en.2002-220516
+
+Identification of cell-specific messenger ribonucleic acids in oxytocinergic and vasopressinergic magnocellular neurons in rat supraoptic nucleus by single-cell differential hybridization.
+
+[[!pmid 12399444 desc="Single cell cDNA library construction. 5' poly A added by terminal transferase."]]
diff --git a/biblio/12636919.mdwn b/biblio/12636919.mdwn
index 59fdd72..22c6d0c 100644
--- a/biblio/12636919.mdwn
+++ b/biblio/12636919.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Single-cell transcript analysis of pancreas development."]]
 [[!tag single_cell PCR]]
-[[!pmid desc="Single cell PCR with 2× poly T."]]
+
+Chiang MK, Melton DA.
+
+Dev Cell. 2003 Mar;4(3):383-93.
+
+Single-cell transcript analysis of pancreas development.
+
+[[!pmid 12636919 desc="Single cell PCR with 2× poly T."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ab2aa66..6698258 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -37,9 +37,6 @@ ggcacgcga/cc => C-box for dro hairy.
 10537171
 Full in situ random priming cDNA synthesis
 
-12399449 [single cell]
-Single cell cDNA library construction. 5' poly A added by terminal transferase. 
-
 9883850 [amplification]
 3 rounds of T7 RNA amplification (aRNA).
 
@@ -177,9 +174,6 @@ Differential distribution of TEs in the promoters. In 4.5% of the studied genes,
 15215383 [networks]
 1) Defines coregulated groups. TFs from these groups are proposed regulators of the group. 2) Analyses the predicted promoters with transfac or jaspar. 3) Builds a network from the results of 1) and 2).
 
-10632582 [single cell] [tracked]
-Accute dissociatin of slices before cell isolation. Variablility between RT lots? Evaluation of mRNA abundance through a serial dillution and callibration approach.
-
 12934013 [networks] [tracked]
 Defines metagenes as a set of genes from different organisms, that are each other's reciprocal best blast hit. Focuces on the highly clustered components of a metagene coexpression network.
 

Tag.
diff --git a/biblio/24079827.mdwn b/biblio/24079827.mdwn
index 1687532..3349ba7 100644
--- a/biblio/24079827.mdwn
+++ b/biblio/24079827.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation."]]
-[[!tag template_switching CAGE OSC]]
+[[!tag template_switching CAGE OSC LNA]]
 
 Harbers M, Kato S, de Hoon M, Hayashizaki Y, Carninici P, Plessy C.
 

From the past.
diff --git a/biblio/12703294.mdwn b/biblio/12703294.mdwn
new file mode 100644
index 0000000..7601771
--- /dev/null
+++ b/biblio/12703294.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Modified 3'-end amplification PCR for gene expression analysis in single cells."]]
+[[!tag single_cell qPCR]]
+
+Heams T, Kupiec JJ.
+
+Biotechniques. 2003 Apr;34(4):712-4, 716.
+
+Modified 3'-end amplification PCR for gene expression analysis in single cells.
+
+[[!pmid 12703294 desc="12703294 Improvement of TPEA method. Gets rid of the nucleus by centrifugation."]]
diff --git a/biblio/12736331.mdwn b/biblio/12736331.mdwn
new file mode 100644
index 0000000..3bfd101
--- /dev/null
+++ b/biblio/12736331.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity."]]
+[[!tag single_cell microarray heterogeneity]]
+
+Kamme F, Salunga R, Yu J, Tran DT, Zhu J, Luo L, Bittner A, Guo HQ, Miller N, Wan J, Erlander M.
+
+J Neurosci. 2003 May 1;23(9):3607-15.
+
+Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity.
+
+[[!pmid 12736331 desc="Proof of concept and method, from Johnson & Johnson, Acturus, and OmniViz."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 3280279..ab2aa66 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -107,15 +107,9 @@ Oligo-capping to fine-map transcription start sites.
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
-12736331 [single cell]
-Proof of concept and method, from Johnson & Johnson, Acturus, and OmniViz.
-
 14704353 [libraries] [tracked]
 T4 DNA ligase used to ligate a double stranded cap-tag.
 
-12703294 [single cells]
-Improvement of TPEA method. Gets rid of the nucleus by centrifugation.
-
 11730011 [libraries]
 Type IIS restriction digest followed py 3'primer ligation, to rempve the poly A from cDNA.
 

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

Hop
diff --git a/biblio/28746310.mdwn b/biblio/28746310.mdwn
new file mode 100644
index 0000000..469bf32
--- /dev/null
+++ b/biblio/28746310.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hypothalamic stem cells control ageing speed partly through exosomal miRNAs."]]
+[[!tag not_read exosome ageing mouse]]
+
+Nature. 2017 Jul 26. doi:10.1038/nature23282
+
+Zhang Y, Kim MS, Jia B, Yan J, Zuniga-Hertz JP, Han C, Cai D.
+
+Hypothalamic stem cells control ageing speed partly through exosomal miRNAs.
+
+[[!pmid 28746310 desc="Treatement with exosomes partially compensates the loss of exosome-secreting cells, which causes accelerated ageing."]]

Ref
diff --git a/biblio/25417166.mdwn b/biblio/25417166.mdwn
new file mode 100644
index 0000000..3fba336
--- /dev/null
+++ b/biblio/25417166.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Toehold switches: de-novo-designed regulators of gene expression."]]
+[[!tag not_read synthethic_biology]]
+
+Cell. 2014 Nov 6;159(4):925-39. doi:10.1016/j.cell.2014.10.002
+
+Green AA, Silver PA, Collins JJ, Yin P.
+
+Toehold switches: de-novo-designed regulators of gene expression.
+
+[[!pmid 25417166 desc="Toehold switches are similar to conventional riboregulators, except that they have less sequence constraints, allowing for larger-scale multiplexing."]]

k-fé
diff --git a/biblio/28483779.mdwn b/biblio/28483779.mdwn
new file mode 100644
index 0000000..f87a3d8
--- /dev/null
+++ b/biblio/28483779.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Heritable L1 retrotransposition in the mouse primordial germline and early embryo."]]
+[[!tag mouse repeat]]
+
+Genome Res. 2017 May 8. doi:10.1101/gr.219022.116
+
+Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH Jr, Ewing AD, Faulkner GJ.
+
+Heritable L1 retrotransposition in the mouse primordial germline and early embryo.
+
+[[!pmid 28483779 desc="One de novo insertion per eight mice. L1 or SINE retrotransposition may also happen in the primordial germ cells."]]

Cleanup.
diff --git a/biblio/15047890.mdwn b/biblio/15047890.mdwn
new file mode 100644
index 0000000..9a59fb3
--- /dev/null
+++ b/biblio/15047890.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene discovery in genetically labeled single dopaminergic neurons of the retina."]]
+[[!tag single_cell library]]
+
+Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):5069-74. doi:10.1073/pnas.0400913101
+
+Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola E.
+
+Gene discovery in genetically labeled single dopaminergic neurons of the retina.
+
+[[!pmid 15047890 desc="Uses SMART7, PCR and multiple aRNA rounds."]]
diff --git a/biblio/7760832.mdwn b/biblio/7760832.mdwn
new file mode 100644
index 0000000..5001116
--- /dev/null
+++ b/biblio/7760832.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture)."]]
+[[!tag cap libraries]]
+
+Mol Cell Biol. 1995 Jun;15(6):3363-71.
+
+Edery I, Chu LL, Sonenberg N, Pelletier J.
+
+An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture).
+
+[[!pmid desc="An eIF-4E fusion protein is used to bind the caps of RNA/DNA duplexes. RNase A cuts single stranded RNAs, thus separating the complexes from the cDNA if they are not full length."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 45debae..3280279 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -64,9 +64,6 @@ Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT R
 10499525 [single cell]
 Single cell RT-PCR.
 
-15047890 [single cell]
-Uses SMART7, PCR, and multiple aRNA rounds.
-
 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).
 
@@ -797,9 +794,6 @@ 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.
 
-7760832 [libraries]
-An eIF-4E fusion protein is used to bind the caps of RNA/DNA duplexes. RNase A cuts single stranded RNAs, thus separating the complexes from the cDNA if they are not full length.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Cleanup.
diff --git a/biblio/16204192.mdwn b/biblio/16204192.mdwn
new file mode 100644
index 0000000..349971e
--- /dev/null
+++ b/biblio/16204192.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels."]]
+[[!tag single_cell]]
+
+Genome Res. 2005 Oct;15(10):1388-92.
+
+Bengtsson M, Ståhlberg A, Rorsman P, Kubista M.
+
+Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels.
+
+[[!pmid 16204192 desc="Geometric mean can be more relevant than arithmetic mean when the expression follows a lognormal distribution."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4bd092a..45debae 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -722,9 +722,6 @@ When a group of TFs have more than one Transfac entry, only the most over-repres
 11842121 [mining]
 Normalisation between print tips.
 
-16204192 [single cells]
-Geometric mean can be more relevant than arithmetic mean when the expression follows a lognormal distribution.
-
 16141248 [networks]
 Primary paper for the GeneNT R library. Clustering using direct and shortest-path distances.
 

Featured article in NAR.
diff --git a/biblio/28645155.mdwn b/biblio/28645155.mdwn
new file mode 100644
index 0000000..c123374
--- /dev/null
+++ b/biblio/28645155.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome."]]
+[[!tag prokaryote chromatin not_read]]
+
+Nucleic Acids Res. 2017 Jun 22. doi:10.1093/nar/gkx541
+
+Hacker WC, Li S, Elcock AH.
+
+Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.
+
+[[!pmid 28645155 desc="“The chromosomal models have features similar to those of a fractal globule.”"]]

Normalise tags.
diff --git a/biblio/24053768.mdwn b/biblio/24053768.mdwn
index 0d15310..afcf8d9 100644
--- a/biblio/24053768.mdwn
+++ b/biblio/24053768.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="3' terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing."]]
-[[!tag Deep-RACE sRNA]]
+[[!tag RACE sRNA]]
 
 Goldfarb KC, Cech TR
 

Add tag.
diff --git a/biblio/16629394.mdwn b/biblio/16629394.mdwn
index 1c097d5..407c97e 100644
--- a/biblio/16629394.mdwn
+++ b/biblio/16629394.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Amplification and analysis of cDNA generated from a single cell by 5'-RACE: application to isolation of antibody heavy and light chain variable gene sequences from single B cells."]]
-[[!tag RACE]]
+[[!tag single_cell RACE]]
 
 Biotechniques. 2006 Apr;40(4):469-70, 472, 474
 

Café
diff --git a/biblio/21483721.mdwn b/biblio/21483721.mdwn
new file mode 100644
index 0000000..40571a4
--- /dev/null
+++ b/biblio/21483721.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms."]]
+[[!tag method microscopy]]
+
+PLoS Biol. 2011 Apr;9(4):e1001041. doi:10.1371/journal.pbio.1001041.
+
+Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY.
+
+A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.
+
+[[!pmid 21483721 desc="miniSOG is a fluorescent protein that liberates singlet oxygen to polymerise diaminobenzidine (DAB), a contrast agent for electron microscopy."]]

Café.
diff --git a/biblio/28751582.mdwn b/biblio/28751582.mdwn
new file mode 100644
index 0000000..58a2e12
--- /dev/null
+++ b/biblio/28751582.mdwn
@@ -0,0 +1,16 @@
+[[!meta title="ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells."]]
+[[!tag method chromatin microscopy]]
+
+Science. 2017 Jul 28;357(6349). pii: eaag0025. doi:10.1126/science.aag0025.
+
+Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC.
+
+ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.
+
+[[!pmid 28751582 desc="The membrane-permeable anthraquinone dye DRAQ5 (646/697
+nm) was identified by a screen for its capacity to produce singlet oxygen,
+which polymerises diaminobenzidine (DAB), which binds the electron-dense osmium
+tetroxide (OsO4).  Use of this stain suggests that there are 30 nm fibers may
+be rare in vivo or an artefact of chromatin purification.  The authors suggest
+that the absence of higher-order fibers helps compaction, because disordered
+chromatin chains have shorter persistence length."]]

Add missing PMID.
diff --git a/biblio/28673998.mdwn b/biblio/28673998.mdwn
index f2ca67d..23c4daf 100644
--- a/biblio/28673998.mdwn
+++ b/biblio/28673998.mdwn
@@ -7,4 +7,4 @@ Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW.
 
 Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.
 
-[[!pmid desc="« The formation of two Watson–Crick base pairs leads to a much higher affinity of GpppG than GMP for a CC template (Kd of ∼0.2 mM vs. ∼20 mM, respectively). » « The tight binding of GpppG to a CC template suggests that GpppG might be an ideal primer for the initiation of template copying by primer extension. The resulting RNAs would begin with a 5ʹ cap-like GpppG moiety, suggesting a potential evolutionary origin for the eukaryotic mRNA 5ʹ-cap structure. »"]]
+[[!pmid 28673998 desc="« The formation of two Watson–Crick base pairs leads to a much higher affinity of GpppG than GMP for a CC template (Kd of ∼0.2 mM vs. ∼20 mM, respectively). » « The tight binding of GpppG to a CC template suggests that GpppG might be an ideal primer for the initiation of template copying by primer extension. The resulting RNAs would begin with a 5ʹ cap-like GpppG moiety, suggesting a potential evolutionary origin for the eukaryotic mRNA 5ʹ-cap structure. »"]]

Normalise tags.
diff --git a/biblio/22761851.mdwn b/biblio/22761851.mdwn
index 80ad52a..93fad2e 100644
--- a/biblio/22761851.mdwn
+++ b/biblio/22761851.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Non-random integration of the HPV genome in cervical cancer."]]
-[[!tag HPV RACE-PCR]]
+[[!tag HPV RACE]]
 
 PLoS One. 2012;7(6):e39632. doi:10.1371/journal.pone.0039632
 

Long time ago.
diff --git a/biblio/16629394.mdwn b/biblio/16629394.mdwn
new file mode 100644
index 0000000..1c097d5
--- /dev/null
+++ b/biblio/16629394.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Amplification and analysis of cDNA generated from a single cell by 5'-RACE: application to isolation of antibody heavy and light chain variable gene sequences from single B cells."]]
+[[!tag RACE]]
+
+Biotechniques. 2006 Apr;40(4):469-70, 472, 474
+
+Ozawa T, Kishi H, Muraguchi A.
+
+Amplification and analysis of cDNA generated from a single cell by 5'-RACE: application to isolation of antibody heavy and light chain variable gene sequences from single B cells.
+
+[[!pmid 16629394 desc="50 % success on B cells to amplify the Ig variable region with polyG tailing and nested PCR."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 0219090..4bd092a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -932,9 +932,6 @@ Concentrations as high as 1 M or 2.5 M can strongly improve the yield.
 16533910 [enhancers]
 The directionality of the CNEs is often conserved beween paralogous loci.
 
-16629394 [single cells]
-50 % success on B cells to amplify the Ig variable region with polyG tailing and nested PCR.
-
 16682450 [misc]
 The structure of the genetic code favours secondary structures in coding RNA.
 

Biblio.
diff --git a/biblio/28673998.mdwn b/biblio/28673998.mdwn
new file mode 100644
index 0000000..f2ca67d
--- /dev/null
+++ b/biblio/28673998.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex."]]
+[[!tag cap]]
+
+Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7659-7664. doi:10.1073/pnas.1704006114
+
+Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW. 
+
+Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.
+
+[[!pmid desc="« The formation of two Watson–Crick base pairs leads to a much higher affinity of GpppG than GMP for a CC template (Kd of ∼0.2 mM vs. ∼20 mM, respectively). » « The tight binding of GpppG to a CC template suggests that GpppG might be an ideal primer for the initiation of template copying by primer extension. The resulting RNAs would begin with a 5ʹ cap-like GpppG moiety, suggesting a potential evolutionary origin for the eukaryotic mRNA 5ʹ-cap structure. »"]]

creating tag page tags/information
diff --git a/tags/information.mdwn b/tags/information.mdwn
new file mode 100644
index 0000000..ac0ae29
--- /dev/null
+++ b/tags/information.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged information"]]
+
+[[!inline pages="tagged(information)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/CRISPR
diff --git a/tags/CRISPR.mdwn b/tags/CRISPR.mdwn
new file mode 100644
index 0000000..322aa4a
--- /dev/null
+++ b/tags/CRISPR.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged CRISPR"]]
+
+[[!inline pages="tagged(CRISPR)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/storage
diff --git a/tags/storage.mdwn b/tags/storage.mdwn
new file mode 100644
index 0000000..fe9311a
--- /dev/null
+++ b/tags/storage.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged storage"]]
+
+[[!inline pages="tagged(storage)" actions="no" archive="yes"
+feedshow=10]]

Café.
diff --git a/biblio/28700573.mdwn b/biblio/28700573.mdwn
new file mode 100644
index 0000000..69a86d0
--- /dev/null
+++ b/biblio/28700573.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria."]]
+[[!tag method information storage biotechnology CRISPR]]
+
+Nature. 2017 Jul 20;547(7663):345-349. doi:10.1038/nature23017
+
+Shipman SL, Nivala J, Macklis JD, Church GM.
+
+CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.
+
+[[!pmid 28700573 desc="Frame order encoded by sequential transfections."]]

creating tag page tags/__40__TL__41__DNA
diff --git a/tags/__40__TL__41__DNA.mdwn b/tags/__40__TL__41__DNA.mdwn
new file mode 100644
index 0000000..819a0a6
--- /dev/null
+++ b/tags/__40__TL__41__DNA.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged (TL)DNA"]]
+
+[[!inline pages="tagged(__40__TL__41__DNA)" actions="no" archive="yes"
+feedshow=10]]

jet lag
diff --git a/biblio/18656947.mdwn b/biblio/18656947.mdwn
new file mode 100644
index 0000000..a6aa4cc
--- /dev/null
+++ b/biblio/18656947.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Triazole-linked analogue of deoxyribonucleic acid ((TL)DNA): design, synthesis, and double-strand formation with natural DNA."]]
+[[!tag (TL)DNA not_read]]
+
+Org Lett. 2008 Sep 4;10(17):3729-32. doi: 10.1021/ol801230k. Epub 2008 Jul 26.
+
+Isobe H, Fujino T, Yamazaki N, Guillot-Nieckowski M, Nakamura E.
+
+Triazole-linked analogue of deoxyribonucleic acid ((TL)DNA): design, synthesis, and double-strand formation with natural DNA.
+
+[[!pmid 18656947 desc="Synthesized using click chemistry.  (TL)DNA-DNA duplexes are more stable than DNA-DNA ones."]]

Café.
diff --git a/biblio/28655330.mdwn b/biblio/28655330.mdwn
new file mode 100644
index 0000000..701c3f1
--- /dev/null
+++ b/biblio/28655330.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="NicE-seq: high resolution open chromatin profiling."]]
+[[!tag method chromatin epigenetic]]
+
+Genome Biol. 2017 Jun 28;18(1):122. doi:10.1186/s13059-017-1247-6
+
+V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf and Sriharsa Pradhan
+
+NicE-seq: high resolution open chromatin profiling.
+
+[[!pmid 28655330 desc="Uses Nt-CviPII nickase.  Extra peaks observed in fixed cells."]]

creating tag page tags/2Ome
diff --git a/tags/2Ome.mdwn b/tags/2Ome.mdwn
new file mode 100644
index 0000000..8fb6348
--- /dev/null
+++ b/tags/2Ome.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged 2Ome"]]
+
+[[!inline pages="tagged(2Ome)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/modified_base
diff --git a/tags/modified_base.mdwn b/tags/modified_base.mdwn
new file mode 100644
index 0000000..8b39112
--- /dev/null
+++ b/tags/modified_base.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged modified base"]]
+
+[[!inline pages="tagged(modified_base)" actions="no" archive="yes"
+feedshow=10]]

Café.
diff --git a/biblio/28504680.mdwn b/biblio/28504680.mdwn
new file mode 100644
index 0000000..e08327d
--- /dev/null
+++ b/biblio/28504680.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nm-seq maps 2'-O-methylation sites in human mRNA with base precision."]]
+[[!tag method modified_base 2Ome]]
+
+Nat Methods. 2017 Jul;14(7):695-698. doi:10.1038/nmeth.4294
+
+Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, Dominissini D, He C.
+
+Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.
+
+[[!pmid 28504680 desc=""]]

creating tag page tags/outreach
diff --git a/tags/outreach.mdwn b/tags/outreach.mdwn
new file mode 100644
index 0000000..890e2c7
--- /dev/null
+++ b/tags/outreach.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged outreach"]]
+
+[[!inline pages="tagged(outreach)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/education
diff --git a/tags/education.mdwn b/tags/education.mdwn
new file mode 100644
index 0000000..6c901cd
--- /dev/null
+++ b/tags/education.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged education"]]
+
+[[!inline pages="tagged(education)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/28591116.mdwn b/biblio/28591116.mdwn
new file mode 100644
index 0000000..63014f4
--- /dev/null
+++ b/biblio/28591116.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A synthetic biology approach to integrative high school STEM training."]]
+[[!tag open_science education outreach]]
+
+Nat Biotechnol. 2017 Jun 7;35(6):591-595. doi:10.1038/nbt.3896
+
+Dubé S, Orr D, Dempsey B, Wieden HJ.
+
+A synthetic biology approach to integrative high school STEM training.
+
+[[!pmid 28591116 desc="The iGEM competition for high schools."]]

creating tag page tags/AI
diff --git a/tags/AI.mdwn b/tags/AI.mdwn
new file mode 100644
index 0000000..04b3aff
--- /dev/null
+++ b/tags/AI.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged AI"]]
+
+[[!inline pages="tagged(AI)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/open_science
diff --git a/tags/open_science.mdwn b/tags/open_science.mdwn
new file mode 100644
index 0000000..34a2ce6
--- /dev/null
+++ b/tags/open_science.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged open science"]]
+
+[[!inline pages="tagged(open_science)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/automation
diff --git a/tags/automation.mdwn b/tags/automation.mdwn
new file mode 100644
index 0000000..1cda6a7
--- /dev/null
+++ b/tags/automation.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged automation"]]
+
+[[!inline pages="tagged(automation)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/AI_37_2642.mdwn b/biblio/AI_37_2642.mdwn
new file mode 100644
index 0000000..3df228f
--- /dev/null
+++ b/biblio/AI_37_2642.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery."]]
+[[!tag AI open_science automation]]
+
+AI Magazine, Spring 2016, Vol 37, No 1, pp 39–49
+
+Hiroaki Kitano
+
+Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery
+
+[[“Deep phenotyping”, “combinatorial hypothesis generation”, “advanced intelligence”.|https://www.aaai.org/ojs/index.php/aimagazine/article/view/2642]]

Markdown.
diff --git a/biblio/28495877.mdwn b/biblio/28495877.mdwn
index cd31bc8..8c1b62b 100644
--- a/biblio/28495877.mdwn
+++ b/biblio/28495877.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="A maternal-effect selfish genetic element in <i>Caenorhabditis elegans</i>."]]
+[[!meta title="A maternal-effect selfish genetic element in Caenorhabditis elegans."]]
 [[!tag genetics development]]
 
 Science. 2017 Jun 9;356(6342):1051-1055. doi:10.1126/science.aan0621

Markup.
diff --git a/biblio/28495877.mdwn b/biblio/28495877.mdwn
index 560c9d0..cd31bc8 100644
--- a/biblio/28495877.mdwn
+++ b/biblio/28495877.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="A maternal-effect selfish genetic element in _Caenorhabditis elegans_."]]
+[[!meta title="A maternal-effect selfish genetic element in <i>Caenorhabditis elegans</i>."]]
 [[!tag genetics development]]
 
 Science. 2017 Jun 9;356(6342):1051-1055. doi:10.1126/science.aan0621

Dans le train.
diff --git a/biblio/28495877.mdwn b/biblio/28495877.mdwn
new file mode 100644
index 0000000..560c9d0
--- /dev/null
+++ b/biblio/28495877.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A maternal-effect selfish genetic element in _Caenorhabditis elegans_."]]
+[[!tag genetics development]]
+
+Science. 2017 Jun 9;356(6342):1051-1055. doi:10.1126/science.aan0621
+
+Ben-David E, Burga A, Kruglyak L.
+
+A maternal-effect selfish genetic element in _Caenorhabditis elegans_.
+
+[[!pmid 28495877 desc="The sup-35 gene is a paralog of rmd-2 that hijacks developmental regulators to terminate embryogenesis.  It is inhibited by pha-1, which was thought to be an essential developmental regulator by itself, but is dispensable in the absence of sup-35."]]

Consolidate.
diff --git a/biblio/28495919.mdwn b/biblio/28495919.mdwn
index 56f8552..1df5507 100644
--- a/biblio/28495919.mdwn
+++ b/biblio/28495919.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Alternative TSSs are co-regulated in single cells in the mouse brain."]]
-[[!tag single_cell STRT alternative_promoter]]
+[[!tag single_cell STRT promoter]]
 
 Mol Syst Biol. 2017 May 11;13(5):930. doi:10.15252/msb.20167374.
 

creating tag page tags/STRT
diff --git a/tags/STRT.mdwn b/tags/STRT.mdwn
new file mode 100644
index 0000000..40f47b3
--- /dev/null
+++ b/tags/STRT.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged STRT"]]
+
+[[!inline pages="tagged(STRT)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/alternative_promoter
diff --git a/tags/alternative_promoter.mdwn b/tags/alternative_promoter.mdwn
new file mode 100644
index 0000000..9e8434a
--- /dev/null
+++ b/tags/alternative_promoter.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged alternative promoter"]]
+
+[[!inline pages="tagged(alternative_promoter)" actions="no" archive="yes"
+feedshow=10]]

Lu
diff --git a/biblio/28495919.mdwn b/biblio/28495919.mdwn
new file mode 100644
index 0000000..56f8552
--- /dev/null
+++ b/biblio/28495919.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Alternative TSSs are co-regulated in single cells in the mouse brain."]]
+[[!tag single_cell STRT alternative_promoter]]
+
+Mol Syst Biol. 2017 May 11;13(5):930. doi:10.15252/msb.20167374.
+
+Karlsson K, Lönnerberg P, Linnarsson S.
+
+Alternative TSSs are co-regulated in single cells in the mouse brain.
+
+[[!pmid 28495919 desc="“out of the average of 26,500 detected molecules per cell, only 3,800 (14%), could be allocated to an annotated FANTOM TSS” “some genes showed extensive 3ʹ UTR expression”"]]

Markup.
diff --git a/biblio/14971053.mdwn b/biblio/14971053.mdwn
index 6c1b2f0..5947aba 100644
--- a/biblio/14971053.mdwn
+++ b/biblio/14971053.mdwn
@@ -7,4 +7,4 @@ Oliveri M, Daga A, Lunardi C, Navone R, Millo R, Puccetti A.
 
 DNase I behaves as a transcription factor which modulates Fas expression in human cells.
 
-[[!pmid 14971053 desc="“DNase I is internalized by human cells upon binding mannose 6-phosphate receptor” (CI-MPR)']]
+[[!pmid 14971053 desc="“DNase I is internalized by human cells upon binding mannose 6-phosphate receptor” (CI-MPR)"]]

Markup.
diff --git a/biblio/14971053.mdwn b/biblio/14971053.mdwn
index a180e51..6c1b2f0 100644
--- a/biblio/14971053.mdwn
+++ b/biblio/14971053.mdwn
@@ -7,4 +7,4 @@ Oliveri M, Daga A, Lunardi C, Navone R, Millo R, Puccetti A.
 
 DNase I behaves as a transcription factor which modulates Fas expression in human cells.
 
-[[!pmid 14971053 desc='"DNase I is internalized by human cells upon binding mannose 6-phosphate receptor" (CI-MPR)']]
+[[!pmid 14971053 desc="“DNase I is internalized by human cells upon binding mannose 6-phosphate receptor” (CI-MPR)']]
diff --git a/biblio/19734907.mdwn b/biblio/19734907.mdwn
index 0f7e2ce..d13f374 100644
--- a/biblio/19734907.mdwn
+++ b/biblio/19734907.mdwn
@@ -7,4 +7,4 @@ Nat Methods. 2009 Oct;6(10):745-51. doi:10.1038/nmeth.1370
 
 Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.
 
-[[!pmid 19734907 desc="'embryos were fixed by resuspending them in −20 °C methanol (80%). The tube was then placed on an overhead rotator at 4 °C for at least 1 h.'"]]
+[[!pmid 19734907 desc="“embryos were fixed by resuspending them in −20 °C methanol (80%). The tube was then placed on an overhead rotator at 4 °C for at least 1 h”"]]
diff --git a/biblio/28526029.mdwn b/biblio/28526029.mdwn
index 99abfae..ac2005f 100644
--- a/biblio/28526029.mdwn
+++ b/biblio/28526029.mdwn
@@ -7,4 +7,4 @@ BMC Biol. 2017 May 19;15(1):44. doi:10.1186/s12915-017-0383-5
 
 Cell fixation and preservation for droplet-based single-cell transcriptomics.
 
-[[!pmid 28526029 desc='"For rehydration, cells were either kept on ice after fixation (Fixed) or moved from –80 °C to 4 °C (Fixed 1 or 3 weeks) and kept in the cold throughout the procedure. Cells were pelleted at 1000 to 3000 × g, resuspended in PBS + 0.01% BSA, centrifuged again, resuspended in PBS + 0.01% BSA, passed through a 40- or 35-μm cell strainer, counted and diluted for Drop-seq in PBS + 0.01% BSA as described above. "']]
+[[!pmid 28526029 desc="“For rehydration, cells were either kept on ice after fixation (Fixed) or moved from –80 °C to 4 °C (Fixed 1 or 3 weeks) and kept in the cold throughout the procedure. Cells were pelleted at 1000 to 3000 × g, resuspended in PBS + 0.01% BSA, centrifuged again, resuspended in PBS + 0.01% BSA, passed through a 40- or 35-μm cell strainer, counted and diluted for Drop-seq in PBS + 0.01% BSA as described above.”"]]

Markup.
diff --git a/biblio/17332513.mdwn b/biblio/17332513.mdwn
index 9f7db37..5448198 100644
--- a/biblio/17332513.mdwn
+++ b/biblio/17332513.mdwn
@@ -7,4 +7,4 @@ Panchision DM, Chen HL, Pistollato F, Papini D, Ni HT, Hawley TS.
 
 Optimized flow cytometric analysis of central nervous system tissue reveals novel functional relationships among cells expressing CD133, CD15, and CD24.
 
-[[!pmid 17332513 desc='"On two occasions with papain and three occasions with TrypLE, we saw free-DNA aggregation even in the presence of DNase I, indicating substantial cell lysis.  We could not definitively determine the cause of this variability. Two additional papain and one TrypLE sample could not be properly assayed by hemocytometer because of DNA aggregation and so were discarded. Accutase and Liberase-1 never generated free DNA aggregates."']]
+[[!pmid 17332513 desc="“On two occasions with papain and three occasions with TrypLE, we saw free-DNA aggregation even in the presence of DNase I, indicating substantial cell lysis.  We could not definitively determine the cause of this variability. Two additional papain and one TrypLE sample could not be properly assayed by hemocytometer because of DNA aggregation and so were discarded. Accutase and Liberase-1 never generated free DNA aggregates.”"]]

Au bureau.
diff --git a/biblio/17332513.mdwn b/biblio/17332513.mdwn
new file mode 100644
index 0000000..9f7db37
--- /dev/null
+++ b/biblio/17332513.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Optimized flow cytometric analysis of central nervous system tissue reveals novel functional relationships among cells expressing CD133, CD15, and CD24."]]
+[[!tag DNAse_I method]]
+
+Stem Cells. 2007 Jun;25(6):1560-70. Epub 2007 Mar 1.
+
+Panchision DM, Chen HL, Pistollato F, Papini D, Ni HT, Hawley TS.
+
+Optimized flow cytometric analysis of central nervous system tissue reveals novel functional relationships among cells expressing CD133, CD15, and CD24.
+
+[[!pmid 17332513 desc='"On two occasions with papain and three occasions with TrypLE, we saw free-DNA aggregation even in the presence of DNase I, indicating substantial cell lysis.  We could not definitively determine the cause of this variability. Two additional papain and one TrypLE sample could not be properly assayed by hemocytometer because of DNA aggregation and so were discarded. Accutase and Liberase-1 never generated free DNA aggregates."']]
diff --git a/biblio/28526029.mdwn b/biblio/28526029.mdwn
index 08b22ae..99abfae 100644
--- a/biblio/28526029.mdwn
+++ b/biblio/28526029.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Cell fixation and preservation for droplet-based single-cell transcriptomics."]]
-[[!tag methanol fixation method single_cell]]
+[[!tag methanol fixation method single_cell DNAse_I]]
 
 Alles J, Karaiskos N, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N.
 

creating tag page tags/DNAse_I
diff --git a/tags/DNAse_I.mdwn b/tags/DNAse_I.mdwn
new file mode 100644
index 0000000..27dcce6
--- /dev/null
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+[[!meta title="pages tagged DNAse I"]]
+
+[[!inline pages="tagged(DNAse_I)" actions="no" archive="yes"
+feedshow=10]]

Au bureau.
diff --git a/biblio/14971053.mdwn b/biblio/14971053.mdwn
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+[[!meta title="DNase I behaves as a transcription factor which modulates Fas expression in human cells."]]
+[[!tag DNAse_I method]]
+
+Eur J Immunol. 2004 Jan;34(1):273-9.
+
+Oliveri M, Daga A, Lunardi C, Navone R, Millo R, Puccetti A.
+
+DNase I behaves as a transcription factor which modulates Fas expression in human cells.
+
+[[!pmid 14971053 desc='"DNase I is internalized by human cells upon binding mannose 6-phosphate receptor" (CI-MPR)']]