Dernières modifications :

Old
diff --git a/biblio/16079853.mdwn b/biblio/16079853.mdwn
new file mode 100644
index 0000000..5ed09c7
--- /dev/null
+++ b/biblio/16079853.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin."]]
+[[!tag RNA_polymerase]]
+
+Kravchenko JE, Rogozin IB, Koonin EV, Chumakov PM.
+
+Nature. 2005 Aug 4;436(7051):735-9.
+
+Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin.
+
+[[!pmid 16079853 desc="Alternative isoform of POLRMT (spRNAP-IV) lacking the mitochondria-targetting peptide."]]

Old
diff --git a/biblio/16540077.mdwn b/biblio/16540077.mdwn
new file mode 100644
index 0000000..f88efdc
--- /dev/null
+++ b/biblio/16540077.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR."]]
+[[!tag amplification PCR]]
+
+Salk JJ, Sanchez JA, Pierce KE, Rice JE, Soares KC, Wangh LJ.
+
+Anal Biochem. 2006 Jun 1;353(1):124-32 doi:10.1016/j.ab.2006.02.012
+
+Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR.
+
+[[!pmid 16540077 desc="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."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index af4f14a..7f3abe5 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -467,9 +467,6 @@ 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.
 
-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.
-
 9380524 [protocols]
 Concentrations as high as 1 M or 2.5 M can strongly improve the yield.
 

Old
diff --git a/biblio/16707659.mdwn b/biblio/16707659.mdwn
new file mode 100644
index 0000000..96e5eae
--- /dev/null
+++ b/biblio/16707659.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein."]]
+[[!tag amplification method ssbp]]
+
+Inoue J, Shigemori Y, Mikawa T.
+
+Nucleic Acids Res. 2006 May 17;34(9):e69 doi:10.1093/nar/gkl350
+
+Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein.
+
+[[!pmid 16707659 desc="By weakening the DNA-protein interaction, the authors acheived the suppression of the non-temlated products in rolling circle amplification."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index dba387f..af4f14a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -479,9 +479,6 @@ The directionality of the CNEs is often conserved beween paralogous loci.
 16682450 [misc]
 The structure of the genetic code favours secondary structures in coding RNA.
 
-16707659 [enzymes]
-By weakening the DNA-protein interaction, the authors acheived the suppression of the non-temlated products in rolling circle amplification.
-
 16618967 [enzymes]
 The combined use of a complementary DNA oligo and DNA ligase suppresses the artifacts seen in RNA ligase adenylation.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 87e02af..f6230ba 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -24,4 +24,7 @@ Reverse-transcription primers:
  - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
  - ... and many more (pseudo-random, ...)
 
+[[Single-strand binding proteins|ssbp]] are sometimes added to improve reverse
+transcriptions.
+
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]
diff --git a/tags/ssbp.mdwn b/tags/ssbp.mdwn
index d841fb0..c00ebba 100644
--- a/tags/ssbp.mdwn
+++ b/tags/ssbp.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged ssbp"]]
 
-[[!inline pages="tagged(ssbp)" actions="no" archive="yes"
-feedshow=10]]
+Single-strand binding proteins
+==============================
+
+(Often used as additives in molecular biology reactions.)
+
+[[!inline pages="tagged(ssbp)" actions="no" limit=0]]

Old
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 24fa500..87e02af 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -15,7 +15,7 @@ Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
    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]]).
 
-Reverse-transcriptases tolerate terminal mismatches: [[Mizuno et al.,1999 |biblio/9973624]].
+Reverse-transcriptases tolerate terminal mismatches: [[Mizuno et al., 1999|biblio/9973624]].
 
 Reverse-transcription primers:
 

Old
diff --git a/biblio/20716356.mdwn b/biblio/20716356.mdwn
new file mode 100644
index 0000000..f14389d
--- /dev/null
+++ b/biblio/20716356.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multi-targeted priming for genome-wide gene expression assays."]]
+[[!tag random_priming method]]
+
+BMC Genomics. 2010 Aug 17;11:477. doi:10.1186/1471-2164-11-477
+
+Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP.
+
+Multi-targeted priming for genome-wide gene expression assays.
+
+[[!pmid 20716356 desc="NDKTBBBBDWGS occurs one or more times in 76% of 6608 mRNAs present in budding yeast, but is absent in rRNA or tRNA."]]
diff --git a/biblio/9973624.mdwn b/biblio/9973624.mdwn
index af76a84..a2f3f88 100644
--- a/biblio/9973624.mdwn
+++ b/biblio/9973624.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display."]]
-[[!tag thermo-enhancement enzyme random_priming]]
+[[!tag thermo-enhancement enzyme random_priming reverse_transcription]]
 
 Mizuno Y, Carninci P, Okazaki Y, Tateno M, Kawai J, Amanuma H, Muramatsu M, Hayashizaki Y.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 9d9ac9d..24fa500 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -15,9 +15,13 @@ Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
    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]]).
 
+Reverse-transcriptases tolerate terminal mismatches: [[Mizuno et al.,1999 |biblio/9973624]].
+
 Reverse-transcription primers:
 
  - "N15" random pentadecamers: [[Stangegaard et al., 2006|biblio/16708763]].
- - ... and many more (not-so-random; pseudo-random, ...)
+ - Multi-targeted primers (MTP): [[Adomas et al., 2010|biblio/20716356]].
+ - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
+ - ... and many more (pseudo-random, ...)
 
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Old
diff --git a/biblio/12448877.mdwn b/biblio/12448877.mdwn
index d18baa8..868eb9b 100644
--- a/biblio/12448877.mdwn
+++ b/biblio/12448877.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Global amplification of cDNA from limiting amounts of tissue. An improved method for gene cloning and analysis"]]
-[[!tag RACE ligase amplification protocol]]
+[[!tag RACE ligase amplification library]]
 
 Mol Biotechnol. 2002 Nov;22(3):223-30 doi:10.1385/MB:22:3:223
 
diff --git a/biblio/16708763.mdwn b/biblio/16708763.mdwn
index ab4171f..4206c78 100644
--- a/biblio/16708763.mdwn
+++ b/biblio/16708763.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA."]]
-[[!tag protocols cDNA oligonucleotides hybridisation random_priming reverse_transcription]]
+[[!tag library cDNA oligonucleotides hybridisation random_priming reverse_transcription]]
 
 Biotechniques. 2006 May;40(5):649-57.
 
diff --git a/biblio/17124291.mdwn b/biblio/17124291.mdwn
new file mode 100644
index 0000000..d51c322
--- /dev/null
+++ b/biblio/17124291.mdwn
@@ -0,0 +1,7 @@
+[[!meta title="Distinct populations of primary and secondary effectors during RNAi in C. elegans."]]
+[[!tag sRNA library method]]
+
+
+Distinct populations of primary and secondary effectors during RNAi in C. elegans.
+
+[[!pmid 17124291 desc="5′ppp RNAs cloned by first ligating an adenylylated linker to the 3′ of the RNAs, and then after reverse-transcription ligating another adenylylated linker to the 3′ end of the first-strand cDNA."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 03a946d..dba387f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -623,9 +623,6 @@ Function of an enhancer lost in teleosts transferred to another one.
 15020752 [tags]
 Rescures circularised concatemers by partial digestion.
 
-17124291 [miRNA]
-5'ppp RNAs cloned using a "ligation independant" protocol.
-
 17158288 [miRNA]
 Small RNA cloned by 3' polyadenylation and 5' RACE.
 
diff --git a/tags/protocol.mdwn b/tags/protocol.mdwn
deleted file mode 100644
index e1f0929..0000000
--- a/tags/protocol.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged protocol"]]
-
-[[!inline pages="tagged(protocol)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/protocols.mdwn b/tags/protocols.mdwn
deleted file mode 100644
index e3020ac..0000000
--- a/tags/protocols.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged protocols"]]
-
-[[!inline pages="tagged(protocols)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 8f0d40b..9d9ac9d 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -8,10 +8,16 @@ Additives that increase reaction performance:
  - 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.
  - 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]]).
 
+Reverse-transcription primers:
+
+ - "N15" random pentadecamers: [[Stangegaard et al., 2006|biblio/16708763]].
+ - ... and many more (not-so-random; pseudo-random, ...)
+
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Old
diff --git a/biblio/To_Do b/biblio/To_Do
index 838ec06..03a946d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -386,9 +386,6 @@ Normalisation between print tips.
 16227618 [mirna]
 The intergenic transcripts do not seem to be polymerised by pol IV
 
-16199517 [mining]
-Assessed wether some gene sets based on common function, cytogenetic location, predicted regulators, ... are enriched in differentially expressed genes.
-
 15737411 [misc]
 Single-tube nested PCR using two different annealing temperatures.
 

Il y a quelques jours.
diff --git a/biblio/29335281.mdwn b/biblio/29335281.mdwn
new file mode 100644
index 0000000..1eea23b
--- /dev/null
+++ b/biblio/29335281.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High-throughput identification of RNA nuclear enrichment sequences."]]
+[[!tag non-coding localisation screen]]
+
+Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL.
+
+EMBO J. 2018 Jan 15. pii: e98452. doi:10.15252/embj.201798452
+
+High-throughput identification of RNA nuclear enrichment sequences.
+
+[[!pmid 29335281 desc="Identifies a Xist-specific modif and a C-rich motif."]]

creating tag page tags/transcriptomics
diff --git a/tags/transcriptomics.mdwn b/tags/transcriptomics.mdwn
new file mode 100644
index 0000000..e8ebe77
--- /dev/null
+++ b/tags/transcriptomics.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged transcriptomics"]]
+
+[[!inline pages="tagged(transcriptomics)" actions="no" archive="yes"
+feedshow=10]]

Ce matin.
diff --git a/biblio/29291348.mdwn b/biblio/29291348.mdwn
new file mode 100644
index 0000000..3a713b6
--- /dev/null
+++ b/biblio/29291348.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias."]]
+[[!tag fingerprint transcriptomics]]
+
+Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M.
+
+Nat Biotechnol. 2018 Feb;36(2):190-195. doi:10.1038/nbt.4045
+
+Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.
+
+[[!pmid 29291348 desc="Sequences are flanked with UMIs.  The library is split in two parts.  The first is tagmented and sequenced as usual.  The second is circularised, tagemented and sequenced.  Thus, UMI pairing information is recovered and both ends can be assembled even if they are in separate tagments."]]

Old
diff --git a/biblio/18369765.mdwn b/biblio/18369765.mdwn
new file mode 100644
index 0000000..340bb3b
--- /dev/null
+++ b/biblio/18369765.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Microfluidic devices for high-throughput gene expression profiling of single hESC-derived neural stem cells."]]
+[[!tag single_cell beads microfluidic reverse_transcription]]
+
+Chen Y, Zhong JF.
+
+Methods Mol Biol. 2008;438:293-303. doi:10.1007/978-1-59745-133-8_22
+
+Microfluidic devices for high-throughput gene expression profiling of single hESC-derived neural stem cells.
+
+[[!pmid 18369765 desc="Another implementation of reverse-transcription on beads"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 01f580a..838ec06 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -566,9 +566,6 @@ Degrades single-strand DNA, not RNA nor double strand DNA.
 16964207 [misc]
 Reommends to use only dbSNP entries which have a phred score higher than 40.
 
-15693942 [mining]
-Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations.
-
 16698958 [enhancers]
 Defines the concept of "maximal N-mers".
 
@@ -791,12 +788,6 @@ Did not find FANTOM3 CAGE tags.
 17412960 [qtl]
 First analysis within a breed, then second analysis comparing small and giant breeds.
 
-16105897 [mining]
-Two genes of opposite expression profiles define a "top scoring pair", and are used to sort the other genes.
-
-18369765 [microfluidics]
-Another implementation of the revese-transcription on beads.
-
 18417536 [enhancers]
 First report of a conserved enhancer in a coding sequence ?
 

Old
diff --git a/biblio/11328886.mdwn b/biblio/11328886.mdwn
new file mode 100644
index 0000000..417e453
--- /dev/null
+++ b/biblio/11328886.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new mathematical model for relative quantification in real-time RT-PCR."]]
+[[!tag PCR normalisation]]
+
+Nucleic Acids Res. 2001 May 1;29(9):e45.
+
+Pfaffl MW
+
+A new mathematical model for relative quantification in real-time RT-PCR.
+
+[[!pmid 11328886 desc="Method of normalisation taking PCR efficiency into account."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 700fcf5..01f580a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -695,9 +695,6 @@ Isolation, lysis and isothermal amplification in a PDMS chip.
 17632057 [promoters]
 Transcription of 5' fragments was detected on promoters of genes which produce less than one full-length transcript per cell.
 
-11328886 [pcr]
-Method of normalisation taking PCR efficiency into account.
-
 17550599 [enhancers]
 35 % of conserved Drosophila enhancers are transcribed (as detected by tiling arrays).
 
diff --git a/tags/PCR.mdwn b/tags/PCR.mdwn
index a35601a..263fe8b 100644
--- a/tags/PCR.mdwn
+++ b/tags/PCR.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged PCR"]]
 
-[[!inline pages="tagged(PCR)" actions="no" archive="yes"
-feedshow=10]]
+[[!inline pages="tagged(PCR)" limit=0]]

Old
diff --git a/tags/RACE-PCR.mdwn b/tags/RACE-PCR.mdwn
deleted file mode 100644
index 1281885..0000000
--- a/tags/RACE-PCR.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RACE-PCR"]]
-
-[[!inline pages="tagged(RACE-PCR)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/protocol
diff --git a/tags/protocol.mdwn b/tags/protocol.mdwn
new file mode 100644
index 0000000..e1f0929
--- /dev/null
+++ b/tags/protocol.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged protocol"]]
+
+[[!inline pages="tagged(protocol)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/12448877.mdwn b/biblio/12448877.mdwn
new file mode 100644
index 0000000..d18baa8
--- /dev/null
+++ b/biblio/12448877.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Global amplification of cDNA from limiting amounts of tissue. An improved method for gene cloning and analysis"]]
+[[!tag RACE ligase amplification protocol]]
+
+Mol Biotechnol. 2002 Nov;22(3):223-30 doi:10.1385/MB:22:3:223
+
+Reddy MK, Nair S, Sopory SK.
+
+Global amplification of cDNA from limiting amounts of tissue. An improved method for gene cloning and analysis.
+
+[[!pmid 12448877 desc="Ligating a DNA adaptor 3′ to the FScDNA using T4 RNA ligase."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c387d33..700fcf5 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -473,9 +473,6 @@ 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.
 
-12448877 [protocols]
-Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase.
-
 9380524 [protocols]
 Concentrations as high as 1 M or 2.5 M can strongly improve the yield.
 
diff --git a/tags/RACE.mdwn b/tags/RACE.mdwn
index ca36e4a..702e78e 100644
--- a/tags/RACE.mdwn
+++ b/tags/RACE.mdwn
@@ -1,4 +1,3 @@
 [[!meta title="pages tagged RACE"]]
 
-[[!inline pages="tagged(RACE)" actions="no" archive="yes"
-feedshow=10]]
+[[!inline pages="tagged(RACE)" limit=0]]

Old
diff --git a/biblio/19624849.mdwn b/biblio/19624849.mdwn
new file mode 100644
index 0000000..ad1cce3
--- /dev/null
+++ b/biblio/19624849.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data."]]
+[[!tag tags CAGE power_law normalisation]]
+
+Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.
+
+Genome Biol. 2009;10(7):R79. doi:10.1186/gb-2009-10-7-r79
+
+Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
+
+[[!pmid 19624849 desc="Power-law normalisation for CAGE."]]

Old
diff --git a/biblio/12136033.mdwn b/biblio/12136033.mdwn
new file mode 100644
index 0000000..0c2efb5
--- /dev/null
+++ b/biblio/12136033.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="General statistics of stochastic process of gene expression in eukaryotic cells."]]
+[[!tag SAGE power_law]]
+
+Kuznetsov VA, Knott GD, Bonner RF.
+
+Genetics. 2002 Jul;161(3):1321-32.
+
+General statistics of stochastic process of gene expression in eukaryotic cells.
+
+[[!pmid 12136033 desc="The distribution of the SAGE tags follow a power law."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index d73e64a..c387d33 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -734,9 +734,6 @@ Digests single-stranded 5' phosphorylated DNA or RNA molecules
 14999098 [mining]
 [not read] Power law in microarray data.
 
-12136033 [tags]
-The distribution of the SAGE tags follow a power law.
-
 17936740 [enhancers]
 Another conserved enhancer in a developmental regulator that is not a transcription factor.
 
diff --git a/tags/power_law.mdwn b/tags/power_law.mdwn
index 27e846e..5d38526 100644
--- a/tags/power_law.mdwn
+++ b/tags/power_law.mdwn
@@ -1,4 +1,16 @@
 [[!meta title="pages tagged power law"]]
 
-[[!inline pages="tagged(power_law)" actions="no" archive="yes"
-feedshow=10]]
+Power law in high-throughput biology
+====================================
+
+(very parcellar; work in progress).
+
+Reverse-cumulative distribution of SAGE tags was shown by [[Kuznetstov, Knott &
+Bonner (2002)|biblio/12136033]] to follow a power law.  [[Balwierz et al.,
+2009|biblio/19624849]] showed the same for CAGE tags and and implemented a
+normalisation method fitting the data to the power law.
+
+Power laws are also seen in other areas, for instance in parameters describing
+network topologies ([[Barabási & Albert, 1999|biblio/10521342]]).
+
+[[!inline pages="tagged(power_law)" limit=0]]

Old
diff --git a/biblio/7082652.mdwn b/biblio/7082652.mdwn
new file mode 100644
index 0000000..f9e911d
--- /dev/null
+++ b/biblio/7082652.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reversal of T4 RNA ligase."]]
+[[!tag ligase]]
+
+Krug M, Uhlenbeck OC.
+
+Biochemistry. 1982 Apr 13;21(8):1858-64.
+
+Reversal of T4 RNA ligase.
+
+[[!pmid 7082652 desc="T4RNL1 & AMP can remove or exchange 3′ phosphate from RNA molecles.  Thus, 3′-P is not a good blocking group. "]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ed99b9d..d73e64a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -38,9 +38,6 @@ Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
-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.
-
 14513556 [libraries]
 Hybridises single-stranded tester plasmid and driver PCR product, then purified single strand molecules out of duplexes using hydroxyapatite.
 
@@ -350,9 +347,6 @@ The ultraconserved elements in the Irx clusters are transcription enhancers.
 15899965 [enhancers]
 Out of 126 ultraconserved elements in a melanogaster / A. Gambiae comparison, only 1 is intergenic, the other being mostly ncRNA and exons.
 
-7082652 [enzymes]
-T4RNL1 & AMP can  remove or exchange 3' pNp from RNA molecles.
-
 12429865 [tags]
 Provides an easy access to various statistical tests.
 
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index afc1dd1..015ca74 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -13,7 +13,7 @@ On T4 RNL1:
    Adenylation efficiency after 6h: C >> U ~ A > G ([[McLaughlin et al., 1985|biblio/3978074]]).
  - Also used for single-strand DNA ligation ([[Tessier, Brousserau & Vernet, 1986|biblio/3799962]])
    with PEG and hexamine cobalt chloride (HCC) as additives.
-
+ - Can dephoshporylate RNA 3′ ends ([[Krug & Uhlenbeck, 1982|biblio/7082652]]).  
 
 On T4 RNL2:
 

Old
diff --git a/biblio/3799962.mdwn b/biblio/3799962.mdwn
new file mode 100644
index 0000000..2bed881
--- /dev/null
+++ b/biblio/3799962.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase."]]
+[[!tag ligase]]
+
+Anal Biochem. 1986 Oct;158(1):171-8.
+
+Tessier DC, Brousseau R, Vernet T.
+
+Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase.
+
+[[!pmid 3799962 desc="ssDNA ligation. 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."]]
diff --git a/biblio/3978074.mdwn b/biblio/3978074.mdwn
index b43d508..718b858 100644
--- a/biblio/3978074.mdwn
+++ b/biblio/3978074.mdwn
@@ -7,4 +7,4 @@ 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."]]
+[[!pmid 3978074 desc="Adenylated RNA is a better substrate for T4 RNA ligase.  Adenylation efficiency after 6h: C >> U ~ A > G."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 6fc507c..afc1dd1 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -2,10 +2,18 @@
 
 Work in progress.
 
+Ligases are inhibited by high concentrations of ATP ([[Tessier, Brousserau &
+Vernet, 1986|biblio/3799962]] and many others).
+
 On T4 RNL1:
 
  - Using poly-A as substrate for circularisation, minimal length is 8, optimal
    is 10, and then efficiency decreases slowly ([[Kaufmann, Klein & Littauer, 1974|biblio/4609429]]).
+ - Adenylated RNA is a better substrate for T4 RNA ligase.
+   Adenylation efficiency after 6h: C >> U ~ A > G ([[McLaughlin et al., 1985|biblio/3978074]]).
+ - Also used for single-strand DNA ligation ([[Tessier, Brousserau & Vernet, 1986|biblio/3799962]])
+   with PEG and hexamine cobalt chloride (HCC) as additives.
+
 
 On T4 RNL2:
 

Cleanup.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 51c0ac0..6fc507c 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -5,7 +5,7 @@ Work in progress.
 On T4 RNL1:
 
  - Using poly-A as substrate for circularisation, minimal length is 8, optimal
-   is 10, and then efficiency decreases slowly [[Kaufmann, Klein & Littauer, 1974|biblio/4609429]].
+   is 10, and then efficiency decreases slowly ([[Kaufmann, Klein & Littauer, 1974|biblio/4609429]]).
 
 On T4 RNL2:
 
diff --git a/tags/ligation.mdwn b/tags/ligation.mdwn
deleted file mode 100644
index fbc09b0..0000000
--- a/tags/ligation.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged ligation"]]
-
-[[!inline pages="tagged(ligation)" actions="no" archive="yes"
-feedshow=10]]

Old
diff --git a/biblio/4609429.mdwn b/biblio/4609429.mdwn
new file mode 100644
index 0000000..33ec324
--- /dev/null
+++ b/biblio/4609429.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="T4 RNA ligase: substrate chain length requirements."]]
+[[!tag ligase]]
+
+FEBS Lett. 1974 Sep 15;46(1):271-5.
+
+Kaufmann G, Klein T, Littauer UZ.
+
+T4 RNA ligase: substrate chain length requirements.
+
+[[!pmid 4609429 desc="For circularisation, (pA)8 is the shortest substrate, and the reaction is most efficient with (pA)10. The ligation efficicency then decreases with substrate length."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 68e22c2..ed99b9d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -353,9 +353,6 @@ Out of 126 ultraconserved elements in a melanogaster / A. Gambiae comparison, on
 7082652 [enzymes]
 T4RNL1 & AMP can  remove or exchange 3' pNp from RNA molecles.
 
-4609429 [enzymes]
-(pA)8 is the smallet substrate, and the reaction is most efficient with (pA)10. The ligation efficicency then decreas with substrate length.
-
 12429865 [tags]
 Provides an easy access to various statistical tests.
 
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index d80e08e..51c0ac0 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -2,6 +2,11 @@
 
 Work in progress.
 
+On T4 RNL1:
+
+ - Using poly-A as substrate for circularisation, minimal length is 8, optimal
+   is 10, and then efficiency decreases slowly [[Kaufmann, Klein & Littauer, 1974|biblio/4609429]].
+
 On T4 RNL2:
 
  - Primary paper: [[Ho et al., 2002|biblio/12228725]].

Pro-cap
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 7442037..082ef11 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,6 +4,8 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
+ - See the Wikipedia for [[CAGE methods|https://en.wikipedia.org/wiki/Cap_analysis_gene_expression]] (Cap Analysis Gene Expression).
+
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
  - Oligo-capping ([[Maruyama et al., 1994|biblio/8125298]]): dephosphorylate,
@@ -21,8 +23,12 @@ Methods for enriching capped RNAs.
    reads through the cap structure and chemical bond, and integrates the reverse
    complement of the oligonucleotide to the first-strand cDNA.
 
- - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
+ - [[Clepet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
    DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
    RNA ligase and a single-stranded linker.
 
+ - [[Kwak et al., 2013|biblio/23430654]] modified oligo-capping to create Pro-cap, a method for nuclear
+   run-on analysis at single-nucleotide resulution.
+
+
 [[!inline pages="tagged(cap)" limit=0]]

Old
diff --git a/biblio/20543846.mdwn b/biblio/20543846.mdwn
index dbc95cf..c3e763d 100644
--- a/biblio/20543846.mdwn
+++ b/biblio/20543846.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan."]]
-[[!tag sequence_tags cap EcoP15I]]
+[[!tag sequence_tags cap EcoP15I nanoCAGE]]
 [[!pmid 20543846 desc="nanoCAGE and CAGEscan with read length of 36 bases."]]
diff --git a/biblio/22362160.mdwn b/biblio/22362160.mdwn
new file mode 100644
index 0000000..9a8ad8c
--- /dev/null
+++ b/biblio/22362160.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing."]]
+[[!tag sequence_tags CAGE EcoP15I]]
+
+Nat Protoc. 2012 Feb 23;7(3):542-61. doi:10.1038/nprot.2012.005
+
+Takahashi H, Lassmann T, Murata M, Carninci P.
+
+5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
+
+[[!pmid 22362160 desc="CAGE version with EcoP15I cleavage."]]
diff --git a/tags/EcoP15I.mdwn b/tags/EcoP15I.mdwn
index cd37927..7b3104f 100644
--- a/tags/EcoP15I.mdwn
+++ b/tags/EcoP15I.mdwn
@@ -7,4 +7,6 @@ A few facts about EcoP15I
  - Positive bias for adenine stretches on the 5′ or 3′ side of CAGCAG [[Möncke-Buchner et al., 2009|biblio/19250940]].
  - Stimulated by AdoMet and sinefungin [[Raghavendra & Rao, 2005|biblio/16026759]].
 
+Used in [[SuperSAGE|biblio/14676315]], [[HELP-tagging|biblio/20359321]], [[nanoCAGE|biblio/20543846]], [[CAGE|biblio/22362160]].  (non-exhaustive list)
+
 [[!inline pages="tagged(EcoP15I)" actions="no" limit=0]]

Old
diff --git a/biblio/20543846.mdwn b/biblio/20543846.mdwn
index e7bbeb1..dbc95cf 100644
--- a/biblio/20543846.mdwn
+++ b/biblio/20543846.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan."]]
-[[!tag sequence_tags cap]]
+[[!tag sequence_tags cap EcoP15I]]
 [[!pmid 20543846 desc="nanoCAGE and CAGEscan with read length of 36 bases."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 84b9deb..68e22c2 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -356,9 +356,6 @@ T4RNL1 & AMP can  remove or exchange 3' pNp from RNA molecles.
 4609429 [enzymes]
 (pA)8 is the smallet substrate, and the reaction is most efficient with (pA)10. The ligation efficicency then decreas with substrate length.
 
-173425 [enzymes]
-The distance between the EcoP15I sites can be as much as a few kilobasepairs.
-
 12429865 [tags]
 Provides an easy access to various statistical tests.
 

Old
diff --git a/biblio/1734285.mdwn b/biblio/1734285.mdwn
index 5294a79..2b9921b 100644
--- a/biblio/1734285.mdwn
+++ b/biblio/1734285.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage."]]
-[[!tag enzyme]]
+[[!tag EcoP15I enzyme]]
 
 Nature. 1992 Jan 30;355(6359):467-9 doi:10.1038/355467a0
 
diff --git a/tags/EcoP15I.mdwn b/tags/EcoP15I.mdwn
index 22ee4d2..cd37927 100644
--- a/tags/EcoP15I.mdwn
+++ b/tags/EcoP15I.mdwn
@@ -1,4 +1,10 @@
 [[!meta title="pages tagged EcoP15I"]]
 
-[[!inline pages="tagged(EcoP15I)" actions="no" archive="yes"
-feedshow=10]]
+A few facts about EcoP15I
+
+ - Cleaves inversely oriented sites that can be as far a a few kilobases apart [[Meisel et al., 1992|biblio/1734285]].
+ - Cleavage is impaired by proteins bound between the sites [[Meisel et al., 1995|biblio/7796821]].
+ - Positive bias for adenine stretches on the 5′ or 3′ side of CAGCAG [[Möncke-Buchner et al., 2009|biblio/19250940]].
+ - Stimulated by AdoMet and sinefungin [[Raghavendra & Rao, 2005|biblio/16026759]].
+
+[[!inline pages="tagged(EcoP15I)" actions="no" limit=0]]

Old
diff --git a/biblio/1734285.mdwn b/biblio/1734285.mdwn
new file mode 100644
index 0000000..5294a79
--- /dev/null
+++ b/biblio/1734285.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage."]]
+[[!tag enzyme]]
+
+Nature. 1992 Jan 30;355(6359):467-9 doi:10.1038/355467a0
+
+Meisel A, Bickle TA, Krüger DH, Schroeder C.
+
+Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage.
+
+[[!pmid 1734285 desc="The distance between the sites can be as far as a few kb."]]

Old
diff --git a/biblio/To_Do b/biblio/To_Do
index 587bb3e..84b9deb 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -4,18 +4,6 @@ Nature 430, 85 - 88 (01 July 2004); doi:10.1038/nature02698
 Evolutionary changes in cis and trans gene regulation 
 PATRICIA J. WITTKOPP, BELINDA K. HAERUM & ANDREW G. CLARK 
 
-
-Nature 411, 41 - 42 (03 May 2001); doi:10.1038/35075138  
-Lethality and centrality in protein networks 
-The most highly connected proteins in the cell are the most important for its survival. 
-
-
-Nature \ 430, 88 - 93 (01 July 2004); doi:10.1038/nature02555
-Nature AOP, published online 9 June 2004
-Evidence for dynamically organized modularity in the yeast proteinprotein interaction network 
-JING-DONG J. HAN1, NICOLAS BERTIN1, TONG HAO1, DEBRA S. GOLDBERG2, GABRIEL F. BERRIZ2, LAN V. ZHANG2, DENIS DUPUY1, ALBERTHA J. M. WALHOUT1,*, MICHAEL E. CUSICK1, FREDERICK P. ROTH2 & MARC VIDAL1 
-
-
 1557406
 Adds a second round of amplification
 
@@ -103,9 +91,6 @@ Apical localisation increases the robustness of development (more segmenatal def
 14732405 [promoters]
 Pax6 has at least two transcription start sites.
 
-15196954 [enhancers] [review]
-Gene networks.
-
 15379890 [alternative promoters]
 RLM-RACE to identify variants. CHIP to confirm TBP on TATA-less promoters. Luciferase assays to confirm new promoters.
 
@@ -386,9 +371,6 @@ 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.
 
-16094371 [networks]
-Functional validation.
-
 16077029 [misc]
 Suppressive PCR allows the use of one gene-specific primer, and one random primer. Asymetric cloning is the second safeguard against background.
 
@@ -404,9 +386,6 @@ Sequence surrounding UCRs might regulate negatively their activity.
 16141073 [genome]
 S/AS pairs usually show positive correlation of their expression.
 
-16168087 [networks]
-Different collaboration network in different research consortiums.
-
 16120967 [enzymes]
 Apparently, only one of the two head-to-head sites is cut...
 
@@ -416,9 +395,6 @@ When a group of TFs have more than one Transfac entry, only the most over-repres
 11842121 [mining]
 Normalisation between print tips.
 
-16141248 [networks]
-Primary paper for the GeneNT R library. Clustering using direct and shortest-path distances.
-
 16227618 [mirna]
 The intergenic transcripts do not seem to be polymerised by pol IV
 
@@ -713,9 +689,6 @@ ChIp, then extraction of tags.
 15582152 [misc]
 No correlation between in situ expression pattern and gene ontology in the brain.
 
-17470793 [networks]
-[not read] Reshaping of networks to a tree-like structure using renormalisation.
-
 17405768 [microfluidics]
 Cycling 100 times (94°C for 30 s, 55°C for 30 s, and 72°C for 60 s) in 0.1% DDM, x1 Pfu Buffer before use improves product yield.
 
@@ -740,9 +713,6 @@ Transcription of 5' fragments was detected on promoters of genes which produce l
 11328886 [pcr]
 Method of normalisation taking PCR efficiency into account.
 
-17609372 [networks]
-Disease network.
-
 17550599 [enhancers]
 35 % of conserved Drosophila enhancers are transcribed (as detected by tiling arrays).
 
@@ -815,9 +785,6 @@ Identifies specific genes of neurons, astrocytes and oligodendrocytes.
 18195365 [misc]
 After 10 weeks, elevated DNA strand break levels are detected in the sperm DNA of mice raised near a highway or a steel factory, but not in controls breezing the same but filtered air.
 
-16902134 [networks]
-Behavioral graph coloring
-
 16449203 [enzymes]
 2'OMe RNAs can not be polyadenylated in vitro.
 
@@ -851,9 +818,6 @@ Two genes of opposite expression profiles define a "top scoring pair", and are u
 18369765 [microfluidics]
 Another implementation of the revese-transcription on beads.
 
-18362361 [networks]
-[not read] Algorithm to transform a time serie into a graph.
-
 18417536 [enhancers]
 First report of a conserved enhancer in a coding sequence ?
 

creating tag page tags/power_law
diff --git a/tags/power_law.mdwn b/tags/power_law.mdwn
new file mode 100644
index 0000000..27e846e
--- /dev/null
+++ b/tags/power_law.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged power law"]]
+
+[[!inline pages="tagged(power_law)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/10521342.mdwn b/biblio/10521342.mdwn
new file mode 100644
index 0000000..baa61ed
--- /dev/null
+++ b/biblio/10521342.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Emergence of scaling in random networks"]]
+[[!tag power_law network]]
+
+Barabási AL, Albert R
+
+Science. 1999 Oct 15;286(5439):509-12
+
+Emergence of scaling in random networks
+
+[[!pmid 10521342 desc="Power law connectivity of actor collaborations in www and power grids"]]

Old
diff --git a/biblio/11988575.mdwn b/biblio/11988575.mdwn
new file mode 100644
index 0000000..30e1924
--- /dev/null
+++ b/biblio/11988575.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Specificity and stability in topology of protein networks."]]
+[[!tag network]]
+
+Science. 2002 May 3;296(5569):910-3 doi:10.1126/science.1065103
+
+Maslov S, Sneppen K.
+
+Specificity and stability in topology of protein networks.
+
+[[!pmid 11988575 desc="'The hub node and its immediate surroundings tend to separate from other hubs' : highly connected nodes have low-connected partners in the protein and transcriptional  networks."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8a703a5..587bb3e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -278,9 +278,6 @@ Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers
 15788456 [not read]
 Implicates a atpxyz gene in a neurodevelopmental function.
 
-11988575 [networks]
-"The hub node and its immediate surroundings tend to separate from other hubs" : highly connected nodes have low-connected partners in the protein and transcriptional  networks.
-
 15690032 [enhancers]
 Coordinated expression of e and y is necessary for spot formation. Ancestral patterning mechanisms provide possible pigmentation patterns through transcription factors recruitement.
 

Old
diff --git a/biblio/11333967.mdwn b/biblio/11333967.mdwn
new file mode 100644
index 0000000..f265083
--- /dev/null
+++ b/biblio/11333967.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Lethality and centrality in protein networks."]]
+[[!tag network yeast]]
+
+Nature. 2001 May 3;411(6833):41-2 doi:10.1038/35075138
+
+Jeong H, Mason SP, Barabási AL, Oltvai ZN.
+
+Lethality and centrality in protein networks.
+
+[[!pmid 11333967 desc="Hubs of the yeast protein network are more frequently encoded by essential genes than other nodes."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 82e130d..8a703a5 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -127,9 +127,6 @@ He was a Genius.
 13309339 [crick]
 Cristallographical arguments supporting the existence of two main classes of plant viruses: helicoidal ans icosaedral.
 
-11333967 [networks]
-Hubs of the yeast protein network are more frequently encoded by essential genes than other nodes.
-
 6866101 [crick]
 Reverse learning hypothesis.
 

Old
diff --git a/biblio/12060727.mdwn b/biblio/12060727.mdwn
new file mode 100644
index 0000000..c2782c8
--- /dev/null
+++ b/biblio/12060727.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Community structure in social and biological networks."]]
+[[!tag network]]
+
+Girvan M, Newman ME.
+
+Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7821-6. doi:10.1073/pnas.122653799
+
+Community structure in social and biological networks.
+
+[[!pmid 12060727 desc="Delineates "communauties" by removing one by one the edges having the higest "betweenness". (computer intensive)"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 0f69fa0..82e130d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -296,9 +296,6 @@ Tags are also frequently found in the CDS, but rarely in the 3'UTR. Tag number i
 15893974 [enhancers] [not read]
 vent2 and id3 regulator elements identified by xenopus-human comparisons.
 
-12060727 [networks]
-Delineates "communauties" by removing one by one the edges having the higest "betweenness". (computer intensive)
-
 15923379 [enzymes]
 50 residues were mutated and tested for complementation in a Trl1 null yeast strain.
 

Old
diff --git a/biblio/12538875.mdwn b/biblio/12538875.mdwn
new file mode 100644
index 0000000..835b4c6
--- /dev/null
+++ b/biblio/12538875.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Modular organization of cellular networks."]]
+[[!tag network]]
+
+Rives AW, Galitski T.
+
+Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1128-33 doi:10.1073/pnas.0237338100
+
+Modular organization of cellular networks.
+
+[[!pmid 12538875 desc="Distances between nodes are computed and used to cluster the nodes. Modules are inferred from this cluster."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 40b6ec8..0f69fa0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -257,9 +257,6 @@ KO of a mouse-medaka conserved enhancer with expected phenotype.
 15528436 [misc]
 The poly-U tract could be implicated in decapping and 5' degradation of the 5' product of the cleavage of mRNA by miRNA.
 
-12538875 [networks]
-Distances between nodes are computed and used to cluster the nodes. Modules are inferred from this cluster.
-
 15735639 [genome]
 3' conserved 8-mers led to identificationo of putative miRNAs.
 

Old
diff --git a/biblio/12902159.mdwn b/biblio/12902159.mdwn
new file mode 100644
index 0000000..3d95a51
--- /dev/null
+++ b/biblio/12902159.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic analysis of gene expression relationships in transcriptional regulatory networks."]]
+[[!tag network]]
+
+Trends Genet. 2003 Aug;19(8):422-7 doi:10.1016/S0168-9525(03)00175-6
+
+Yu H, Luscombe NM, Qian J, Gerstein M.
+
+Genomic analysis of gene expression relationships in transcriptional regulatory networks.
+
+[[!pmid 12902159 desc="Correlating subnetwork topology, correlation or inverse collrelation, and phase."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 993b7ba..40b6ec8 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -62,9 +62,6 @@ A method to amplify two distinguishable substrates in the same PCR tube, so that
 12582258 [misc]
 Direct labeling of 10µg total RNA.
 
-12902159 [networks]
-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.
 
@@ -83,15 +80,9 @@ Discusses the intests of comparing close species to detect positive selection, a
 12547512 [enhancers]
 Differential distribution of TEs in the promoters. In 4.5% of the studied genes, TE sequences contain expermientally validated TransFac binding sites.
 
-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.
-
 9409673 [neurogenin]
 Primary paper for zebrafish.
 
-15079056 [networks] [tracked]
-Combines protein-protein, and transcriptional interactions. Identifies "motifs", subnetworks with 2, 3, or 4 nodes, that are over-represented. Most 4-node motifs are the combination of 3-node motifs.
-
 11418835 [Crick]
 Discussees unconscious"online systems" ("zombies"), and wonder whether they use the same networks as consciousness, and whether what differenciates them is the level of firing synchrony.
 
@@ -121,9 +112,6 @@ RLM-RACE to identify variants. CHIP to confirm TBP on TATA-less promoters. Lucif
 14593172 [genome]
 Dual strategy using full length cDNAs and whole genome tiling arrays to annotate the Arabidopsis genome.
 
-15001784 [networks] [tracked]
-Distribution of triads and tetrads in networks can cluster them in functional classes.
-
 4599081 [crick]
 Comments on his discovery, 20 years later.
 
@@ -221,9 +209,6 @@ Proteomics to demonstrate that some short ORFs are translated.
 15197164 [genome]
 RT-PCR on putative 5'-3' EST pairs.
 
-14530453 [networks] [tracked]
-Matrix representation of networks to detect regulatory circuits.
-
 11099257 [mining] [review]
 Summarises a lot of clustering algorithms.
 

creating tag page tags/single_chain
diff --git a/tags/single_chain.mdwn b/tags/single_chain.mdwn
new file mode 100644
index 0000000..317ce7a
--- /dev/null
+++ b/tags/single_chain.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged single chain"]]
+
+[[!inline pages="tagged(single_chain)" actions="no" archive="yes"
+feedshow=10]]

Dans le train
diff --git a/biblio/29295920.mdwn b/biblio/29295920.mdwn
new file mode 100644
index 0000000..128592f
--- /dev/null
+++ b/biblio/29295920.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Migration-based selections of antibodies that convert bone marrow into trafficking microglia-like cells that reduce brain amyloid β."]]
+[[!tag single_chain antibody reprogramming]]
+
+Han KH, Arlian BM, Macauley MS, Paulson JC, Lerner RA.
+
+Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):E372-E381. doi:10.1073/pnas.1719259115
+
+Migration-based selections of antibodies that convert bone marrow into trafficking microglia-like cells that reduce brain amyloid β.
+
+[[!pmid 29295920 desc="A library of single-chain antibodies was transfected in bone-marrow cells, which were translated in mice. The cells that migrated in the brain were enriched for a synthetic gene expressing an #antibody that binds Vimentin and causes it to be phosphorylated."]]

Old
diff --git a/biblio/15190252.mdwn b/biblio/15190252.mdwn
new file mode 100644
index 0000000..01ec2b1
--- /dev/null
+++ b/biblio/15190252.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evidence for dynamically organized modularity in the yeast protein-protein interaction network."]]
+[[!tag network]]
+
+Nature. 2004 Jul 1;430(6995):88-93 doi:10.1038/nature02555
+
+Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M.
+
+Evidence for dynamically organized modularity in the yeast protein-protein interaction network.
+
+[[!pmid 15190252 desc="Date hubs and party hubs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9bedb8a..993b7ba 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -83,9 +83,6 @@ Discusses the intests of comparing close species to detect positive selection, a
 12547512 [enhancers]
 Differential distribution of TEs in the promoters. In 4.5% of the studied genes, TE sequences contain expermientally validated TransFac binding sites.
 
-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).
-
 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.
 
@@ -127,8 +124,6 @@ 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.
 
-15208707 [networks]
-
 4599081 [crick]
 Comments on his discovery, 20 years later.
 
@@ -144,9 +139,6 @@ He was a Genius.
 13309339 [crick]
 Cristallographical arguments supporting the existence of two main classes of plant viruses: helicoidal ans icosaedral.
 
-15190252 [networks]
-Date hubs vs. Party hubs.
-
 11333967 [networks]
 Hubs of the yeast protein network are more frequently encoded by essential genes than other nodes.
 

Old
diff --git a/biblio/15282333.mdwn b/biblio/15282333.mdwn
new file mode 100644
index 0000000..459029a
--- /dev/null
+++ b/biblio/15282333.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservation and coevolution in the scale-free human gene coexpression network."]]
+[[!tag network]]
+
+Jordan IK, Mariño-Ramírez L, Wolf YI, Koonin EV.
+
+Mol Biol Evol. 2004 Nov;21(11):2058-70 doi:10.1093/molbev/msh222
+
+Conservation and coevolution in the scale-free human gene coexpression network.
+
+[[!pmid 15282333 desc="CDS, 3′ UTRs, but not 5′ UTRs of highly connected genes of the human and mouse coexpression networks evolve more slowly"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e68f2e5..9bedb8a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -186,9 +186,6 @@ Evidence for a whole genome duplication in teleosts.
 12555104 [crick]
 Competinc cellular assemblies could provide a neural correlate of conciousness.
 
-15289483 [networks]
-Monitoring 20-min intervals over 8-h and 16-h.
-
 15229602 [genome]
 Uses a hybrid melanogaster / simulans approach, to demonstrate that interspecific variations in gene expression mostly originate from modification of cis-regulation.
 
@@ -286,9 +283,6 @@ The poly-U tract could be implicated in decapping and 5' degradation of the 5' p
 12538875 [networks]
 Distances between nodes are computed and used to cluster the nodes. Modules are inferred from this cluster.
 
-15297301 [networks]
-graph, Rgraphviz, and RBGL packages.
-
 15735639 [genome]
 3' conserved 8-mers led to identificationo of putative miRNAs.
 
@@ -319,9 +313,6 @@ Implicates a atpxyz gene in a neurodevelopmental function.
 15690032 [enhancers]
 Coordinated expression of e and y is necessary for spot formation. Ancestral patterning mechanisms provide possible pigmentation patterns through transcription factors recruitement.
 
-15282333 [networks]
-CDS, 3'UTRs, but not 5'UTRs of highly connected genes of  the human and mouse coexpression networks evolve more slowly
-
 15894530 [misc]
 M. leprae has a lot of pseudogenes, but its clonality suggest that they appeared before its spread.
 

creating tag page tags/drug_delivery
diff --git a/tags/drug_delivery.mdwn b/tags/drug_delivery.mdwn
new file mode 100644
index 0000000..bb15b98
--- /dev/null
+++ b/tags/drug_delivery.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged drug delivery"]]
+
+[[!inline pages="tagged(drug_delivery)" actions="no" archive="yes"
+feedshow=10]]

Today.
diff --git a/biblio/29295927.mdwn b/biblio/29295927.mdwn
new file mode 100644
index 0000000..1c5ecbb
--- /dev/null
+++ b/biblio/29295927.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel concept of the smart NIR-light-controlled drug release of black phosphorus nanostructure for cancer therapy."]]
+[[!tag drug_delivery]]
+
+Qiu M, Wang D, Liang W, Liu L, Zhang Y, Chen X, Sang DK, Xing C, Li Z, Dong B, Xing F, Fan D, Bao S, Zhang H, Cao Y.
+
+Proc Natl Acad Sci U S A. 2018 Jan 2. pii: 201714421. doi:10.1073/pnas.1714421115
+
+Novel concept of the smart NIR-light-controlled drug release of black phosphorus nanostructure for cancer therapy.
+
+[[!pmid 29295927 desc="black phosphorus sheets embedded in hydrogels."]]

Consolidation.
diff --git a/biblio/15705831.mdwn b/biblio/15705831.mdwn
index 7ce9030..0b47995 100644
--- a/biblio/15705831.mdwn
+++ b/biblio/15705831.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Accelerating networks in biology, engineering and society."]]
-[[!tag networks]]
+[[!tag network]]
 
 Science. 2005 Feb 11;307(5711):856-8 doi:10.1126/science.1103737
 
diff --git a/biblio/15908506.mdwn b/biblio/15908506.mdwn
index 36e0e14..0a4bac4 100644
--- a/biblio/15908506.mdwn
+++ b/biblio/15908506.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli."]]
-[[!tag networks]]
+[[!tag network]]
 
 Proc Natl Acad Sci U S A. 2005 May 31;102(22):7841-6. doi:10.1073/pnas.0500365102
 
diff --git a/biblio/15911778.mdwn b/biblio/15911778.mdwn
index 4a20eb6..c73698a 100644
--- a/biblio/15911778.mdwn
+++ b/biblio/15911778.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles."]]
-[[!tag networks]]
+[[!tag network]]
 
 Proc Natl Acad Sci U S A. 2005 May 31;102(22):7794-9. doi:10.1073/pnas.0407994102
 

Correction.
diff --git a/biblio/15372033.mdwn b/biblio/15372033.mdwn
index 5f639d5..9eeaa6c 100644
--- a/biblio/15372033.mdwn
+++ b/biblio/15372033.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Nature. 2004 Sep 16;431(7006):308-12."]]
+[[!meta title="Genomic analysis of regulatory network dynamics reveals large topological changes."]]
 [[!tag network]]
 
 Nature. 2004 Sep 16;431(7006):308-12 doi:10.1038/nature02782

Old
diff --git a/biblio/15372033.mdwn b/biblio/15372033.mdwn
new file mode 100644
index 0000000..5f639d5
--- /dev/null
+++ b/biblio/15372033.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Nature. 2004 Sep 16;431(7006):308-12."]]
+[[!tag network]]
+
+Nature. 2004 Sep 16;431(7006):308-12 doi:10.1038/nature02782
+
+Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.
+
+Genomic analysis of regulatory network dynamics reveals large topological changes.
+
+[[!pmid 15372033 desc="Primary paper for SANDY. Distinguishes "endogenous" from "exogenous" networks, and introduces transient hubs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 86859b0..e68f2e5 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -189,9 +189,6 @@ Competinc cellular assemblies could provide a neural correlate of conciousness.
 15289483 [networks]
 Monitoring 20-min intervals over 8-h and 16-h.
 
-15372033 [networks]
-Primary paper for SANDY. Distinguishes "endogenous" from "exogenous" networks, and introduces transient hubs.
-
 15229602 [genome]
 Uses a hybrid melanogaster / simulans approach, to demonstrate that interspecific variations in gene expression mostly originate from modification of cis-regulation.
 
@@ -220,9 +217,6 @@ Open chromatin fibers contain both active and inactive genes.
 15314228 [genome]
 Codon usage has been preserved during human-mouse evolution.
 
-15343339 [networks]
-Defines "condition invariant", "condition enabled", "condition expanded", and "condition altered" transcription factor binding behaviour.
-
 15328367 [alternative promoters]
 Alternative promoters which transcribe variants with different translational efficiencies.
 
@@ -247,9 +241,6 @@ Summarises a lot of clustering algorithms.
 15239836 [mining]
 To take into account the discrete distributin of SAGE tags.
 
-15598746 [networking]
-Two types of subgraphs are distinguished. Type I are abundant and form giant componants. Type II are rare and form clusters. The belonging to class I and II depend on global network propertiesm and vice-versa.
-
 15588312 [mining]
 Trains learning machines with a GO categor, and interrogates a 40 000 genes x 55 tissues matrix of microarray results.
 
@@ -382,9 +373,6 @@ Two mouse/fugu conserved regions (-66kb, -62kb), only one has an enhancer activi
 15990270 [enhancers] [not read]
 Conserved in mammals but not in chicken.
 
-15603590 [networks]
-Based on a transcriptional regulatory network which contains only 20% of the E. coli genes. Shows that there is no feedback loop at a purely transcriptional level. As a consequence, eht network can be represented by five hierarchical layers.
-
 15967424 [enhancers] [not read]
 This one is conserved between human and mouse. Not tested in ZF.
 
@@ -415,9 +403,6 @@ Transcribed enhancers in Drosophila.
 15961632 [genome]
 A lot of proximal promoters are histone-free. This includes genes which are inactive, but are ready to react.
 
-15598744 [networks]
-Uses Self-Organising Maps to aggregate the transcriptome of B cells into 12 megamodules.
-
 16024824 [enhancers]
 The ultraconserved elements in the Irx clusters are transcription enhancers.
 
@@ -448,9 +433,6 @@ Supports the idea that the only function of some RNA is to have been transcribed
 16094371 [networks]
 Functional validation.
 
-15608232 [networks]
-Comprehensive database featuring coexpression, co-occurence in the litterature, genomic neighbourhood in addition to high-throughput informations as protein-protein interaction.
-
 16077029 [misc]
 Suppressive PCR allows the use of one gene-specific primer, and one random primer. Asymetric cloning is the second safeguard against background.
 

Old
diff --git a/biblio/15674285.mdwn b/biblio/15674285.mdwn
new file mode 100644
index 0000000..7f2f341
--- /dev/null
+++ b/biblio/15674285.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Self-similarity of complex networks."]]
+[[!tag network method]]
+
+Song C, Havlin S, Makse HA.
+
+Nature. 2005 Jan 27;433(7024):392-5 doi:10.1038/nature03248
+
+Self-similarity of complex networks.
+
+[[!pmid 15674285 desc="Introduces a box-based renormalisation procedure, to demonstrate the link between scale-invariance and self-similarity."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 07fe203..86859b0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -295,9 +295,6 @@ The poly-U tract could be implicated in decapping and 5' degradation of the 5' p
 12538875 [networks]
 Distances between nodes are computed and used to cluster the nodes. Modules are inferred from this cluster.
 
-15674285 [networks]
-Introduces a box-based renormalisation procedure, to demonstrate the link between scale-invariance and self-similarity.
-
 15297301 [networks]
 graph, Rgraphviz, and RBGL packages.
 

Old
diff --git a/biblio/15705831.mdwn b/biblio/15705831.mdwn
new file mode 100644
index 0000000..7ce9030
--- /dev/null
+++ b/biblio/15705831.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Accelerating networks in biology, engineering and society."]]
+[[!tag networks]]
+
+Science. 2005 Feb 11;307(5711):856-8 doi:10.1126/science.1103737
+
+Mattick JS, Gagen MJ.
+
+Accelerating networks in biology, engineering and society.
+
+[[!pmid 15705831 desc="The proportion of regulators increases with the size of the network."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c953016..07fe203 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -322,9 +322,6 @@ Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers
 15564293 [misc]
 [not read] Normalisations based on uni/multivariate models, rather than substraction of the mean followed by divisoin by sd, are much more effective at detecting covariations.
 
-15705831 [networks]
-The proportion of regulators increases with the size of the network.
-
 15788456 [not read]
 Implicates a atpxyz gene in a neurodevelopmental function.
 

Old
diff --git a/biblio/15729348.mdwn b/biblio/15729348.mdwn
new file mode 100644
index 0000000..c6c86ac
--- /dev/null
+++ b/biblio/15729348.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Functional cartography of complex metabolic networks."]]
+[[!tag network]]
+
+Nature. 2005 Feb 24;433(7028):895-900 doi:10.1038/nature03288
+
+Guimerà R, Nunes Amaral LA.
+
+Functional cartography of complex metabolic networks.
+
+[[!pmid 15729348 desc="New method to partition networks in modules. Defines provincial hubs and non-hub connectors, the latter being more conserved in evolution."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 718dc30..c953016 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -298,9 +298,6 @@ Distances between nodes are computed and used to cluster the nodes. Modules are
 15674285 [networks]
 Introduces a box-based renormalisation procedure, to demonstrate the link between scale-invariance and self-similarity.
 
-15729348 [networks]
-New method to partition networks in modules. Defines provincial hubs and non-hub connectors, the latter being more conserved in evolution.
-
 15297301 [networks]
 graph, Rgraphviz, and RBGL packages.
 
@@ -412,9 +409,6 @@ 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.
 
-15778709 [networks]
-The resulting networks allow non-transcription factors to regulate a gene. The direct neighborhood of Myc is enriched in its direct targets.
-
 15861189 [mining]
 Uses "compare plots"
 

Old
diff --git a/biblio/15833122.mdwn b/biblio/15833122.mdwn
new file mode 100644
index 0000000..166630a
--- /dev/null
+++ b/biblio/15833122.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An evolutionary and functional assessment of regulatory network motifs."]]
+[[!tag network]]
+
+Mazurie A, Bottani S, Vergassola M.
+
+Genome Biol. 2005;6(4):R35. doi:10.1186/gb-2005-6-4-r35
+
+An evolutionary and functional assessment of regulatory network motifs.
+
+[[!pmid 15833122 desc="Five well-documented examples to question the relevance of network motifs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f823c9d..718dc30 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -340,9 +340,6 @@ 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
 
-15833122 [networks]
-Five well-documented example to question the relevance of network motifs.
-
 15894530 [misc]
 M. leprae has a lot of pseudogenes, but its clonality suggest that they appeared before its spread.
 

Aujourd'hui
diff --git a/biblio/29211708.mdwn b/biblio/29211708.mdwn
new file mode 100644
index 0000000..75b46d3
--- /dev/null
+++ b/biblio/29211708.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators."]]
+[[!tag repeat]]
+
+Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik M, Wysocka J.
+
+Nature. 2017 Dec 6. doi:10.1038/nature25179
+
+Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators.
+
+[[!pmid 29211708 desc="A CRISPR-Cas9 screen identifies several chromatin regulators (such as the human silencing hub (HUSH) complex subunits MPP8 and TASOR, or MORC2) that repress the expression of L1 elements and their host genes."]]

Old
diff --git a/biblio/15860629.mdwn b/biblio/15860629.mdwn
new file mode 100644
index 0000000..82cc546
--- /dev/null
+++ b/biblio/15860629.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Team assembly mechanisms determine collaboration network structure and team performance."]]
+[[!tag network]]
+
+Science. 2005 Apr 29;308(5722):697-702. doi:10.1126/science.1106340
+
+Guimerà R, Uzzi B, Spiro J, Amaral LA.
+
+Team assembly mechanisms determine collaboration network structure and team performance.
+
+[[!pmid 15860629 desc="Model of network growth which takes into account the propension to link to newcommers or to good old friends."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 119068d..f823c9d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -340,9 +340,6 @@ 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
 
-15860629 [networks]
-Model of network growth which takes into account the propension to link to newcommers or to good old friends.
-
 15833122 [networks]
 Five well-documented example to question the relevance of network motifs.
 

Old
diff --git a/biblio/15897470.mdwn b/biblio/15897470.mdwn
new file mode 100644
index 0000000..e4fae52
--- /dev/null
+++ b/biblio/15897470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A network analysis of committees in the U.S. House of Representatives."]]
+[[!tag network]]
+
+Porter MA, Mucha PJ, Newman ME, Warmbrand CM.
+
+Proc Natl Acad Sci U S A. 2005 May 17;102(20):7057-62. doi:10.1073/pnas.0500191102
+
+A network analysis of committees in the U.S. House of Representatives.
+
+[[!pmid 15897470 desc="A representative-committee network is projected into a committee network, which is subsequently clustered using single-linkage approach."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4138e53..119068d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -349,9 +349,6 @@ Five well-documented example to question the relevance of network motifs.
 15894530 [misc]
 M. leprae has a lot of pseudogenes, but its clonality suggest that they appeared before its spread.
 
-15897470 [networks]
-A representative-committee network is projected into a committee network, which is subsequently clustered using single-linkage approach.
-
 15905473 [tags]
 Tags are also frequently found in the CDS, but rarely in the 3'UTR. Tag number is correlated with transcript length.
 

Old
diff --git a/biblio/15908506.mdwn b/biblio/15908506.mdwn
new file mode 100644
index 0000000..36e0e14
--- /dev/null
+++ b/biblio/15908506.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli."]]
+[[!tag networks]]
+
+Proc Natl Acad Sci U S A. 2005 May 31;102(22):7841-6. doi:10.1073/pnas.0500365102
+
+Balázsi G, Barabási AL, Oltvai ZN.
+
+Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.
+
+[[!pmid 15908506 desc="Defines origons as subnetworks originating from a single TF (in their model - a directed regulatory network - there is no strong component)."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 0b3d5ae..4138e53 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -424,9 +424,6 @@ A 5' GC-rich / AT-rich, and a conversely 3' AT-rich / GC-rich motifs were discov
 15778709 [networks]
 The resulting networks allow non-transcription factors to regulate a gene. The direct neighborhood of Myc is enriched in its direct targets.
 
-15908506 [networks]
-Defines origons as subnetworks originating from a single TF (in their model - a directed regulatory network - there is no strong component).
-
 15861189 [mining]
 Uses "compare plots"
 

Old
diff --git a/biblio/15911778.mdwn b/biblio/15911778.mdwn
new file mode 100644
index 0000000..4a20eb6
--- /dev/null
+++ b/biblio/15911778.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles."]]
+[[!tag networks]]
+
+Proc Natl Acad Sci U S A. 2005 May 31;102(22):7794-9. doi:10.1073/pnas.0407994102
+
+Guimerà R, Mossa S, Turtschi A, Amaral LA.
+
+The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles.
+
+[[!pmid 15911778 desc="The muticommunauty structure of the air transortation network explains why some cities with a high centrality are not hubs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index d845434..0b3d5ae 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -376,9 +376,6 @@ Repeat Associated siRNA (rasiRNA) were detected in zebrafish.
 15939778 [single cells]
 The cells were pulled out from midly digested ganglia with glass microelectrodes.
 
-15911778 [networks]
-The muticommunauty structure of the air transortation network  explains why some cities with a high centrality are not hubs.
-
 15944709 [miRNA]
 A polII transcription factor implicated in the regulation of a human miRNA cluster.
 
@@ -541,9 +538,6 @@ Not read. A pdx-1 enhancer conserved in human, mouse and chicken.
 16314298 [protocols]
 Adding gold in PCR tubes enhances the yield when the cycling is quick.
 
-16400149 [networks]
-In this changing network, most parameters except the clustering coefficient depend on the width of the smoothing window.
-
 15899964 [promoters]
 ChIP on chip focused on the preinitiation complexes of the ENCODE regions.
 

Nettoyage.
diff --git a/biblio/16400149.mdwn b/biblio/16400149.mdwn
new file mode 100644
index 0000000..34019ac
--- /dev/null
+++ b/biblio/16400149.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Empirical analysis of an evolving social network."]]
+[[!tag network]]
+
+Science. 2006 Jan 6;311(5757):88-90 doi:10.1126/science.1116869
+
+Kossinets G, Watts DJ.
+
+Empirical analysis of an evolving social network.
+
+[[!pmid 16400149 desc="In this changing network, most parameters except the clustering coefficient depend on the width of the smoothing window."]]

creating tag page tags/exonuclease
diff --git a/tags/exonuclease.mdwn b/tags/exonuclease.mdwn
new file mode 100644
index 0000000..3aa0263
--- /dev/null
+++ b/tags/exonuclease.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged exonuclease"]]
+
+[[!inline pages="tagged(exonuclease)" actions="no" archive="yes"
+feedshow=10]]

Bonané
diff --git a/biblio/28911316.mdwn b/biblio/28911316.mdwn
new file mode 100644
index 0000000..99d1124
--- /dev/null
+++ b/biblio/28911316.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Optimizing T4 DNA polymerase conditions enhances the efficiency of one-step sequence- and ligation-independent cloning."]]
+[[!tag library exonuclease method]]
+
+Biotechniques. 2017 Sep 1;63(3):125-130. doi:10.2144/000114588
+
+Islam MN, Lee KW, Yim HS, Lee SH, Jung HC, Lee JH, Jeong JY.
+
+Optimizing T4 DNA polymerase conditions enhances the efficiency of one-step sequence- and ligation-independent cloning.
+
+[[!pmid 28911316 desc="Use of T4 DNA polymerase at 50 °C as an exonuclease for generating sinngle-strand overhangs."]]

creating tag page tags/3__8242___end
diff --git a/tags/3__8242___end.mdwn b/tags/3__8242___end.mdwn
new file mode 100644
index 0000000..b612549
--- /dev/null
+++ b/tags/3__8242___end.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged 3′ end"]]
+
+[[!inline pages="tagged(3__8242___end)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/click
diff --git a/tags/click.mdwn b/tags/click.mdwn
new file mode 100644
index 0000000..0fda3f4
--- /dev/null
+++ b/tags/click.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged click"]]
+
+[[!inline pages="tagged(click)" actions="no" archive="yes"
+feedshow=10]]

Click.
diff --git a/biblio/28449108.mdwn b/biblio/28449108.mdwn
new file mode 100644
index 0000000..3670044
--- /dev/null
+++ b/biblio/28449108.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation."]]
+[[!tag 3′_end click method sequence_tags]]
+
+Routh A, Ji P, Jaworski E, Xia Z, Li W, Wagner EJ.
+
+Nucleic Acids Res. 2017 Jul 7;45(12):e112. doi:10.1093/nar/gkx286
+
+Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.
+
+[[!pmid 28449108 desc="Azido termination followed by click ligation of a 5′ linker."]]

creating tag page tags/polyamides
diff --git a/tags/polyamides.mdwn b/tags/polyamides.mdwn
new file mode 100644
index 0000000..0c75a04
--- /dev/null
+++ b/tags/polyamides.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged polyamides"]]
+
+[[!inline pages="tagged(polyamides)" actions="no" archive="yes"
+feedshow=10]]

Onigiri
diff --git a/biblio/29192133.mdwn b/biblio/29192133.mdwn
new file mode 100644
index 0000000..4bf72d6
--- /dev/null
+++ b/biblio/29192133.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Synthetic transcription elongation factors license transcription across repressive chromatin."]]
+[[!tag drug elongation polyamides]]
+
+Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A,
+Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu
+M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ.
+
+Science. 2017 Nov 30. pii: eaan6414. doi:10.1126/science.aan6414
+
+Synthetic transcription elongation factors license transcription across repressive chromatin.
+
+[[!pmid 29192133 desc="Syn-TEFs.  A BET inhibitor drug (JQ1) linked to a pyrrole- and imidazole-based polyamide targetting the motif AAGAAGAAG rescues Frataxin (FXN) in patient cells by promoting transcript elongation to paused polymerases."]]

Correct tag.
diff --git a/biblio/8125298.mdwn b/biblio/8125298.mdwn
index da9cfad..455d62d 100644
--- a/biblio/8125298.mdwn
+++ b/biblio/8125298.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides."]]
-[[!tag cap method libraries]]
+[[!tag cap method library]]
 
 Gene. 1994 Jan 28;138(1-2):171-4.
 

Enhance.
diff --git a/biblio/23430654.mdwn b/biblio/23430654.mdwn
index 6bf463d..d38342a 100644
--- a/biblio/23430654.mdwn
+++ b/biblio/23430654.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Precise maps of RNA polymerase reveal how promoters direct initiation and pausing."]]
-[[!tag method sequence_tags transcriptome polymerase]]
+[[!tag method sequence_tags transcriptome polymerase oligo-capping]]
 
 Kwak H, Fuda NJ, Core LJ, Lis JT.
 
@@ -7,4 +7,4 @@ Science. 2013 Feb 22;339(6122):950-3. doi: 10.1126/science.1229386.
 
 Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
 
-[[!pmid 23430654 desc="PRO-seq and PRO-cap."]]
+[[!pmid 23430654 desc="PRO-seq and PRO-cap (based on oligo-capping). Incorporation of biotin-NTPs cause the polymerase to stop, thus brings single-nucleotide resolution."]]

Pas lu.
diff --git a/biblio/28835501.mdwn b/biblio/28835501.mdwn
new file mode 100644
index 0000000..ae65218
--- /dev/null
+++ b/biblio/28835501.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres."]]
+[[!tag virus genome not_read]]
+
+J Virol. 2017 Oct 27;91(22). pii: e01137-17. doi:10.1128/JVI.01137-17
+
+Zhang E, Bell AJ, Wilkie GS, Suárez NM, Batini C, Veal CD, Armendáriz-Castillo I, Neumann R, Cotton VE, Huang Y, Porteous DJ, Jarrett RF, Davison AJ, Royle NJ.
+
+Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres.
+
+[[!pmid 28835501 desc="Stable insertion in the telomeres of a single ancestor of Europeans 2.4 ± 1 ky ago."]]

Add primary paper.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 89da0e5..d80e08e 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -4,6 +4,7 @@ Work in progress.
 
 On T4 RNL2:
 
+ - Primary paper: [[Ho et al., 2002|biblio/12228725]].
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
  - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]]).

Typographie.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index d455a16..89da0e5 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -6,13 +6,13 @@ On T4 RNL2:
 
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
- - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]].
+ - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]]).
  - The RNA acceptor strand participates to its ligation by promoting
    adenylylation of the donor, and by promoting the formation of the
    phosphodiester bond.  With DNA, this step is 35 times slower
    ([[Nandakumar et al., 2005|biblio/15851476]]).
  - The K227Q mutation prevents transfer of the andenylyl residue from the
-   linker to RNA ends, thus prevents unwanted ligation products. 
-   [[Viollet et al., 2011|biblio/21722378]]
+   linker to RNA ends, thus prevents unwanted ligation products
+   ([[Viollet et al., 2011|biblio/21722378]]).
 
 [[!inline pages="tagged(ligase)" limit=0]]

Ligation to DNA.
diff --git a/biblio/14967495.mdwn b/biblio/14967495.mdwn
index bc7e2e5..2cea274 100644
--- a/biblio/14967495.mdwn
+++ b/biblio/14967495.mdwn
@@ -7,4 +7,5 @@ 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?"]]
+[[!pmid 14967495 desc="One more tool in the box? Ligation of RNA to an acceptor
+where the last base is DNA is stronlgy suppressed."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 2490e33..d455a16 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -6,6 +6,11 @@ On T4 RNL2:
 
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
+ - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]].
+ - The RNA acceptor strand participates to its ligation by promoting
+   adenylylation of the donor, and by promoting the formation of the
+   phosphodiester bond.  With DNA, this step is 35 times slower
+   ([[Nandakumar et al., 2005|biblio/15851476]]).
  - The K227Q mutation prevents transfer of the andenylyl residue from the
    linker to RNA ends, thus prevents unwanted ligation products. 
    [[Viollet et al., 2011|biblio/21722378]]

RNL2 etc.
diff --git a/biblio/15205470.mdwn b/biblio/15205470.mdwn
index eae98df..e53f0f3 100644
--- a/biblio/15205470.mdwn
+++ b/biblio/15205470.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes."]]
-[[!tag ligation]]
+[[!tag ligase]]
 
 Nucleic Acids Res. 2004 Jun 17;32(11):e86 doi:10.1093/nar/gnh085
 
diff --git a/biblio/15247329.mdwn b/biblio/15247329.mdwn
index 449750a..5170fe6 100644
--- a/biblio/15247329.mdwn
+++ b/biblio/15247329.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry."]]
-[[!tag method library ligation]]
+[[!tag method library ligase]]
 
 So AP, Turner RF, Haynes CA.
 
diff --git a/biblio/17018278.mdwn b/biblio/17018278.mdwn
new file mode 100644
index 0000000..717d7bc
--- /dev/null
+++ b/biblio/17018278.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward."]]
+[[!tag ligase]]
+
+Nandakumar J, Shuman S, Lima CD.
+
+Cell. 2006 Oct 6;127(1):71-84
+
+RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.
+
+[[!pmid 17018278 desc="Structure-function analysis of sealing of nicked duplexes."]]
diff --git a/biblio/17510325.mdwn b/biblio/17510325.mdwn
index 4e77765..1e45767 100644
--- a/biblio/17510325.mdwn
+++ b/biblio/17510325.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="RNA maps reveal new RNA classes and a possible function for pervasive transcription."]]
-[[!tag ligation transcriptome small_RNA HepG2]]
+[[!tag ligase 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.
 
diff --git a/biblio/21722378.mdwn b/biblio/21722378.mdwn
new file mode 100644
index 0000000..f23d364
--- /dev/null
+++ b/biblio/21722378.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis"]]
+[[!tag ligase method enzyme]]
+
+Viollet S, Fuchs RT, Munafo DB, Zhuang F, Robb GB.
+
+BMC Biotechnol. 2011 Jul 1;11:72. doi: 10.1186/1472-6750-11-72.
+
+T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis
+
+[[!pmid 21722378 desc="The K227Q mutation prevents transfer of the adenylyl residue from the adapter to unwanted targets."]]
diff --git a/biblio/4000951.mdwn b/biblio/4000951.mdwn
index 7ea3887..5214692 100644
--- a/biblio/4000951.mdwn
+++ b/biblio/4000951.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase."]]
-[[!tag ligation method]]
+[[!tag ligase method]]
 
 Nucleic Acids Res. 1985 Mar 25;13(6):1997-2008.
 
diff --git a/biblio/To_Do b/biblio/To_Do
index 20363d9..d845434 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -700,9 +700,6 @@ Reommends to use only dbSNP entries which have a phred score higher than 40.
 15693942 [mining]
 Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations.
 
-17018278 [enzymes]
-Not Read
-
 16698958 [enhancers]
 Defines the concept of "maximal N-mers".
 
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 90de02b..2490e33 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -1,4 +1,13 @@
 [[!meta title="pages tagged ligase"]]
 
-[[!inline pages="tagged(ligase)" actions="no" archive="yes"
-feedshow=10]]
+Work in progress.
+
+On T4 RNL2:
+
+ - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
+ - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
+ - The K227Q mutation prevents transfer of the andenylyl residue from the
+   linker to RNA ends, thus prevents unwanted ligation products. 
+   [[Viollet et al., 2011|biblio/21722378]]
+
+[[!inline pages="tagged(ligase)" limit=0]]

Old
diff --git a/biblio/16723398.mdwn b/biblio/16723398.mdwn
new file mode 100644
index 0000000..6d86193
--- /dev/null
+++ b/biblio/16723398.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Modularity and community structure in networks."]]
+[[!tag network]]
+
+Newman ME
+
+Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8577-82 doi:10.1073/pnas.0601602103
+
+Modularity and community structure in networks.
+
+[[!pmid 16723398 desc="Iterative division method with rules for stopping. Uses a "modularity matrix"."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index a1dddfe..20363d9 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -637,9 +637,6 @@ Few of them overlap FANTOM3 transcripts, but 32/36 can be detected by RT-PCR.
 16751773 [small RNAs]
 The mutation was found by quantitative trait locus (QTL) and single nucleotide polymorphism (SNP) analysis.
 
-16723398 [networks]
-Iterative division method with rules for stopping. Uses a "modularity matrix".
-
 16751776 [small RNAs]
 Loci encoding piRNAs are conserved, but not the piRNA themselves.
 

Old
diff --git a/biblio/17003135.mdwn b/biblio/17003135.mdwn
new file mode 100644
index 0000000..b6885b0
--- /dev/null
+++ b/biblio/17003135.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic analysis of the hierarchical structure of regulatory networks."]]
+[[!tag network]]
+
+Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14724-31 doi:10.1073/pnas.0508637103
+
+Yu H, Gerstein M.
+
+Genomic analysis of the hierarchical structure of regulatory networks.
+
+[[!pmid 17003135 desc="Breadth-first search: organises a network in a layered hierarchy. Highest nodes tend to be influencial, middle to have a high betweenness, and lowest to be essential."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 0457f8c..a1dddfe 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -688,9 +688,6 @@ Not read. 85 % of the fly genome is transcribed, and 30 % contributes to mature
 16930954 [enhancers]
 Not read. Human-mouse conserved enhancer in fgf15.
 
-17003135 [networks]
-Breadth-first search: organises a network in a layered hierarchy. Highest nodes tend to be influencial, middle to have a high betweenness, and lowest to be essential.
-
 16893951 [amplification]
 Combined use of T7 polymerase and helicase, strong strand displacement, and branched rolling circle isothermal amplification.
 

Old
diff --git a/biblio/17185604.mdwn b/biblio/17185604.mdwn
new file mode 100644
index 0000000..2ed2c80
--- /dev/null
+++ b/biblio/17185604.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Relating three-dimensional structures to protein networks provides evolutionary insights."]]
+[[!tag network]]
+
+Science. 2006 Dec 22;314(5807):1938-41 doi:10.1126/science.1136174
+
+Kim PM, Lu LJ, Xia Y, Gerstein MB.
+
+Relating three-dimensional structures to protein networks provides evolutionary insights.
+
+[[!pmid 17185604 desc="Mutually exclusive interactions defined by distinguishing interfaces on the nodes."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9fa531f..0457f8c 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -763,9 +763,6 @@ This sequence does not confer the cell cycle properties of mir-29b to siRNAs.
 16175253 [nanotechnologies]
 Continuous washing is necessary for efficient DDM coating.
 
-17185604 [networks]
-Mutually exclusive interactions defined by distinguishing interfaces on the nodes.
-
 17159156 [enhancers]
 Function of an enhancer lost in teleosts transferred to another one.
 

Old
diff --git a/biblio/17656717.mdwn b/biblio/17656717.mdwn
new file mode 100644
index 0000000..bb81e45
--- /dev/null
+++ b/biblio/17656717.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The product space conditions the development of nations."]]
+[[!tag network]]
+
+Science. 2007 Jul 27;317(5837):482-7 doi:10.1126/science.1144581
+
+Hidalgo CA, Klinger B, Barabási AL, Hausmann R.
+
+The product space conditions the development of nations.
+
+[[!pmid 17656717 desc="Derives a product network from per-country export data, and analyses how the countries evolve in time within this network."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 772cacd..9fa531f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -862,9 +862,6 @@ eQTL approach using bayesian statistics and Markoc chains.
 12671682 [normalisation]
 Global normalisation does not allow to survey broad increases or decreases of the total transcriptional activity. This method is more suited when this happens.
 
-17656717 [networks]
-Derives a product network from per-country export data, and analyses how the countries evolve in time within this network.
-
 17703193 [promoters]
 Some genes are up-regulated by the loss of TBP.
 

Old
diff --git a/biblio/15944704.mdwn b/biblio/15944704.mdwn
new file mode 100644
index 0000000..48cf541
--- /dev/null
+++ b/biblio/15944704.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Uncovering the overlapping community structure of complex networks in nature and society."]]
+[[!tag network]]
+
+Nature. 2005 Jun 9;435(7043):814-8.
+
+Palla G, Derényi I, Farkas I, Vicsek T.
+
+Uncovering the overlapping community structure of complex networks in nature and society.
+
+[[!pmid 15944704 desc="Adjascent k-clique communities can share nodes while staying distinct. This allows to create networks of communities."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index de718c3..772cacd 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -937,9 +937,6 @@ The buffer is dried on the lid of the tube, and one cell is deposited in a small
 17412706 [enzymes]
 An interesting protein that condensates DNA.
 
-15944704 [networks]
-Adjascent k-clique communities can share nodes while staying distinct. This allows to create networks of communitiest.
-
 15289330 [pcr]
 A method for selecting normalisation genes.
 

Old
diff --git a/biblio/15205470.mdwn b/biblio/15205470.mdwn
new file mode 100644
index 0000000..eae98df
--- /dev/null
+++ b/biblio/15205470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes."]]
+[[!tag ligation]]
+
+Nucleic Acids Res. 2004 Jun 17;32(11):e86 doi:10.1093/nar/gnh085
+
+Cole K, Truong V, Barone D, McGall G.
+
+Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes.
+
+[[!pmid 15205470 desc="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."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9f82fcf..de718c3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -47,10 +47,6 @@ 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).
 
-15205470 [libraries] [tracked]
-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.
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 

Old
diff --git a/biblio/12613261.mdwn b/biblio/12613261.mdwn
new file mode 100644
index 0000000..16d8677
--- /dev/null
+++ b/biblio/12613261.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Probe generation directly from small numbers of cells for DNA microarray studies."]]
+[[!tag random_priming amplification]]
+
+Biotechniques. 2003 Feb;34(2):386-8, 390, 392-3
+
+Xiang CC, Chen M, Kozhich OA, Phan QN, Inman JM, Chen Y, Brownstein MJ.
+
+Probe generation directly from small numbers of cells for DNA microarray studies.
+
+[[!pmid 12613261 desc="Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT RT."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e246214..9f82fcf 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -41,9 +41,6 @@ Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subseq
 12161654 [misc]
 Fluorescent bar-coded oligos to monitor transcription in vivo.
 
-12613261 [amplification]
-Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT RT.
-
 10499525 [single cell]
 Single cell RT-PCR.
 

Old
diff --git a/biblio/11222780.mdwn b/biblio/11222780.mdwn
new file mode 100644
index 0000000..62d9aa8
--- /dev/null
+++ b/biblio/11222780.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Quantitative analysis of mRNA amplification by in vitro transcription."]]
+[[!tag ssbp reverse_transcription amplification]]
+
+Nucleic Acids Res. 2001 Mar 1;29(5):E29
+
+Baugh LR, Hill AA, Brown EL, Hunter CP.
+
+Quantitative analysis of mRNA amplification by in vitro transcription.
+
+[[!pmid 11222780 desc="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."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 153377a..e246214 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -38,9 +38,6 @@ 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.
 
-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.
-
 12161654 [misc]
 Fluorescent bar-coded oligos to monitor transcription in vivo.
 

Old
diff --git a/biblio/10748532.mdwn b/biblio/10748532.mdwn
index 6ab3a03..fe246d5 100644
--- a/biblio/10748532.mdwn
+++ b/biblio/10748532.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="High-fidelity mRNA amplification for gene profiling."]]
-[[!tag amplification]]
+[[!tag template_switching amplification]]
+
+Nat Biotechnol. 2000 Apr;18(4):457-9 doi:10.1038/74546
+
+Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM.
+
+High-fidelity mRNA amplification for gene profiling.
+
 [[!pmid 10748532 desc="Combines template switch with aRNA amplification"]]

Old
diff --git a/biblio/15560142.mdwn b/biblio/15560142.mdwn
new file mode 100644
index 0000000..3141d76
--- /dev/null
+++ b/biblio/15560142.mdwn
@@ -0,0 +1,9 @@
+[[!meta title="Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis."]]
+[[!tag amplification isothermal method]]
+
+Biotechniques. 2004 Nov;37(5):854-7
+
+Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, Wang S, Kurn N.
+
+Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis.
+[[!pmid 15560142 desc="Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for linear amplification."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 99763d3..153377a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -263,9 +263,6 @@ Two types of subgraphs are distinguished. Type I are abundant and form giant com
 15588312 [mining]
 Trains learning machines with a GO categor, and interrogates a 40 000 genes x 55 tissues matrix of microarray results.
 
-15560142 [amplification]
-Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for linear amplification.
-
 7732590 [misc] [review]
 Reminds that in some organisms, most transcripts share their 5' end.
 

Expand.
diff --git a/biblio/17071717.mdwn b/biblio/17071717.mdwn
index 06041cf..7aa49cb 100644
--- a/biblio/17071717.mdwn
+++ b/biblio/17071717.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Gene expression profiling of single cells on large-scale oligonucleotide arrays."]]
-[[!tag single_cell amplification oligonucleotides]]
+[[!tag single_cell amplification oligonucleotides reverse_transcription]]
+
+Nucleic Acids Res. 2006;34(21):e143 doi:10.1093/nar/gkl740
+
+Hartmann CH, Klein CA.
+
+Gene expression profiling of single cells on large-scale oligonucleotide arrays.
+
 [[!pmid 17071717 desc="High concentration of a dT and random primers mix in reverse transcription."]]

Old
diff --git a/biblio/16542485.mdwn b/biblio/16542485.mdwn
new file mode 100644
index 0000000..4d53a75
--- /dev/null
+++ b/biblio/16542485.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level."]]
+[[!tag amplification template_switching]]
+
+Genome Biol. 2006;7(3):R18 doi:10.1186/gb-2006-7-3-r18
+
+Subkhankulova T, Livesey FJ.
+
+Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level.
+
+[[!pmid 16542485 desc="SMART has a much lower false discovery rate (FDR), but compresses the expression ratios."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 7fee431..99763d3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -647,9 +647,6 @@ They are not found in other cell types.
 16751343 [non-coding RNA]
 Few of them overlap FANTOM3 transcripts, but 32/36 can be detected by RT-PCR.
 
-16542485 [amplification]
-SMART has a much lower false discovery rate (FDR), but compresses the expression ratios.
-
 16751773 [small RNAs]
 The mutation was found by quantitative trait locus (QTL) and single nucleotide polymorphism (SNP) analysis.
 

Old
diff --git a/biblio/16308152.mdwn b/biblio/16308152.mdwn
new file mode 100644
index 0000000..a64c86b
--- /dev/null
+++ b/biblio/16308152.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA amplification strategies for small sample populations."]]
+[[!tag method amplification template_switching]]
+
+Methods. 2005 Nov;37(3):229-37 doi:10.1016/j.ymeth.2005.09.003
+
+Ginsberg SD
+
+RNA amplification strategies for small sample populations.
+
+[[!pmid 16308152 desc="Detailed protocol for Terminal Continuation (TC)."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 51e4673..7fee431 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -32,9 +32,6 @@ ggcacgcga/cc => C-box for dro hairy.
 10537171
 Full in situ random priming cDNA synthesis
 
-9883850 [amplification]
-3 rounds of T7 RNA amplification (aRNA).
-
 12593794 [general]
 Noise due to RNA extraction is 40 times greater than noise due to replicate hybridisation
 
@@ -539,9 +536,6 @@ Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafis
 16280998 [patents]
 Perpetual-motion machines are not patentable.
 
-16308152 [amplification]
-Detailed protocol for Terminal Continuation (TC).
-
 16224006 [IP]
 20 % of the human coding genome is patented.
 
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 79fa05a..370aa19 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,7 +2,10 @@
 
 (work in progress)
 
- - In the "_terminal continuation_" method, [[Che et al., 2004|biblio/14647400]]
-   essentially do template switching with DNA oligonucleotides ending in `CCC`.
+ - The "_terminal continuation_" method ([[Ginsberg et al.,
+   2002|biblio/12462399]], [[Che et al., 2004|biblio/14647400]]) is essentially
+   a template switching with DNA oligonucleotides ending in `CCC` or `GGG`.  `AAA`
+   and `TTT` were also tested.  An extensive protocol was published in
+   [[Ginsberg, 2005|biblio/16308152]].
 
 [[!inline pages="tagged(template_switching)" limit=0]]

Expand.
diff --git a/biblio/15107803.mdwn b/biblio/15107803.mdwn
new file mode 100644
index 0000000..7f66640
--- /dev/null
+++ b/biblio/15107803.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Combined histochemical staining, RNA amplification, regional, and single cell cDNA analysis within the hippocampus."]]
+[[!tag template_switching single_cell not_read]]
+
+Lab Invest. 2004 Aug;84(8):952-62 doi:10.1038/labinvest.3700110
+
+Ginsberg SD, Che S.
+
+Combined histochemical staining, RNA amplification, regional, and single cell cDNA analysis within the hippocampus.
+
+[[!pmid 15107803 desc="Template switching in single cells, in 2004."]]

Expand.
diff --git a/biblio/12462399.mdwn b/biblio/12462399.mdwn
index 1b2ad8a..a1cf3a3 100644
--- a/biblio/12462399.mdwn
+++ b/biblio/12462399.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="RNA Amplification in Brain Tissues."]]
-[[!tag template_switching]]
-[[!pmid 12462399  desc="Comparison of template swithching oligos ending in -AAA, -CCC, -GGG or -TTT. No qualitative difference for the CCC and GGG variants were reported."]]
+[[!tag amplification template_switching]]
+
+Neurochem Res. 2002 Oct;27(10):981-92
+
+Ginsberg SD, Che S.
+
+RNA amplification in brain tissues.
+
+[[!pmid 12462399 desc="Comparison of template swithching oligos ending in -AAA, -CCC, -GGG or -TTT. No qualitative difference for the CCC and GGG variants were reported."]]

Expand.
diff --git a/biblio/14647400.mdwn b/biblio/14647400.mdwn
index 0e0259e..319fe50 100644
--- a/biblio/14647400.mdwn
+++ b/biblio/14647400.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Amplification of RNA transcripts using terminal continuation."]]
-[[!tag template_switching]]
-[[!pmid desc="Templates switching with an oligonucleotide ending in a mixture of Gs and Cs."]]
+[[!tag amplification template_switching]]
+
+Che S, Ginsberg SD.
+
+Lab Invest. 2004 Jan;84(1):131-7.
+
+Amplification of RNA transcripts using terminal continuation.
+
+[[!pmid 14647400 desc="Templates switching with a DNA oligonucleotide ending in a mixture of Gs and Cs."]]
diff --git a/tags/template-switching.mdwn b/tags/template-switching.mdwn
deleted file mode 100644
index abc760c..0000000
--- a/tags/template-switching.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged template-switching"]]
-
-[[!inline pages="tagged(template-switching)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 800093f..79fa05a 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged template_switching"]]
 
-[[!inline pages="tagged(template_switching)" actions="no" archive="yes"
-feedshow=10]]
+(work in progress)
+
+ - In the "_terminal continuation_" method, [[Che et al., 2004|biblio/14647400]]
+   essentially do template switching with DNA oligonucleotides ending in `CCC`.
+
+[[!inline pages="tagged(template_switching)" limit=0]]

Correct link.
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 206f832..7442037 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -17,8 +17,8 @@ Methods for enriching capped RNAs.
    single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
  - Cap-jumping ([[Efimov et al., 2001|biblio/11713326]]): oxidize diols,
-   covalently bind a 3′-amine oligonucleotide.  The [[reverse_transcriptase]]
-   ireads through the cap structure and chemical bond, and integrates the reverse
+   covalently bind a 3′-amine oligonucleotide.  The [[reverse transcriptase|reverse_transcription]]
+   reads through the cap structure and chemical bond, and integrates the reverse
    complement of the oligonucleotide to the first-strand cDNA.
 
  - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4

Expand.
diff --git a/biblio/11713326.mdwn b/biblio/11713326.mdwn
index 1a698d9..7a677af 100644
--- a/biblio/11713326.mdwn
+++ b/biblio/11713326.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach."]]
 [[!tag cap method]]
+
+Efimov VA, Chakhmakhcheva OG, Archdeacon J, Fernandez JM, Fedorkin ON, Dorokhov YL, Atabekov JG.Efimov VA1, Chakhmakhcheva OG, Archdeacon J, Fernandez JM, Fedorkin ON, Dorokhov YL, Atabekov JG.
+
+Nucleic Acids Res. 2001 Nov 15;29(22):4751-9.
+
+Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach.
+
 [[!pmid 11713326 desc="Binds an oligonucleotide to the cap using its free diol group, and integrates its sequence to the full-length cDNA using template-switching."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 9a0c954..206f832 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -16,6 +16,11 @@ Methods for enriching capped RNAs.
    the first-strand cDNA, ligate a double-stranded adapter ending with a
    single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
+ - Cap-jumping ([[Efimov et al., 2001|biblio/11713326]]): oxidize diols,
+   covalently bind a 3′-amine oligonucleotide.  The [[reverse_transcriptase]]
+   ireads through the cap structure and chemical bond, and integrates the reverse
+   complement of the oligonucleotide to the first-strand cDNA.
+
  - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
    DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
    RNA ligase and a single-stranded linker.

Old
diff --git a/biblio/10471753.mdwn b/biblio/10471753.mdwn
new file mode 100644
index 0000000..495da5a
--- /dev/null
+++ b/biblio/10471753.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Regulation of average length of complex PCR product."]]
+[[!tag PCR amplification]]
+
+Nucleic Acids Res. 1999 Sep 15;27(18):e23.
+
+Shagin DA, Lukyanov KA, Vagner LL, Matz MV.
+
+Regulation of average length of complex PCR product.
+
+[[!pmid 10471753 desc="Amplify preferentially long PCR product with a single
+primer. Shorter molecules have a higher probability of undergoing
+inhibitory intramolecular interactions. (suppressive PCR)"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c6266c0..51e4673 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -26,11 +26,6 @@ Review citing the 2 upper articles
 * Says that exponential (65+25 cycles) is more faithful than linear.
 * Limits [dNTP] to produce only 3' cDNA that are a few hundrer base pairs long.
 
-10471753
-Amplify preferentially long PCR product with a single
-primer. Shorter molecules have a higher probability of undergoing
-inhibitory intramolecular interactions.
-
 http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020178
 ggcacgcga/cc => C-box for dro hairy.
 
@@ -61,15 +56,6 @@ 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).
 
-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.
-
-12398200 [amplification]
-Advocates a systematic round of RNA amplificatin, becaus it reduces interarray variability.
-
 15205470 [libraries] [tracked]
 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.
@@ -580,9 +566,6 @@ In this changing network, most parameters except the clustering coefficient depe
 15899964 [promoters]
 ChIP on chip focused on the preinitiation complexes of the ENCODE regions.
 
-10471753 [amplification]
-Single-primer PCR with a moderate suppressive effect can be used to regulate the product size.
-
 16407397 [enhancers]
 Idenification of conserved enhancers of shh hundreds of kp far of the coding sequence.
 

Old
diff --git a/biblio/8125298.mdwn b/biblio/8125298.mdwn
new file mode 100644
index 0000000..da9cfad
--- /dev/null
+++ b/biblio/8125298.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides."]]
+[[!tag cap method libraries]]
+
+Gene. 1994 Jan 28;138(1-2):171-4.
+
+Maruyama K, Sugano S.
+
+Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.
+
+[[!pmid 8125298 desc="Oligo capping primary paper."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8028f58..c6266c0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -89,9 +89,6 @@ A method to amplify two distinguishable substrates in the same PCR tube, so that
 12582258 [misc]
 Direct labeling of 10µg total RNA.
 
-8125298 [libraries]
-Oligo capping primary paper.
-
 12902159 [networks]
 Correlating subnetwork topology, correlation or inverse collrelation, and phase.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 78ca0f3..9a0c954 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,11 +6,11 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
- - Oligo-capping ([[Suzuki et al., 1999|biblio/9373149]]): dephosphorylate,
+ - Oligo-capping ([[Maruyama et al., 1994|biblio/8125298]]): dephosphorylate,
    uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
    with T4 RNA ligase.
 
-(wip: Fromont-racine et al., Maruyama et al.)
+(wip: Fromont-racine et al.)
 
  - CapSelect ([[Schmidt et al., 1999|biblio/10518626]]): Add a poly-A tail to
    the first-strand cDNA, ligate a double-stranded adapter ending with a

Minor edits.
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 27bfd58..78ca0f3 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,16 +6,18 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
- - Oligo-capping [[Suzuki et al., 1999|biblio/9373149]]: dephosphorylate, uncover functional
-   phosphate with decapping enzyme, and ligate RNA adaptor with T4 RNA ligase.
+ - Oligo-capping ([[Suzuki et al., 1999|biblio/9373149]]): dephosphorylate,
+   uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
+   with T4 RNA ligase.
 
 (wip: Fromont-racine et al., Maruyama et al.)
 
- - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
-   cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
-   overhang, and prime second-strand synthesis.
+ - CapSelect ([[Schmidt et al., 1999|biblio/10518626]]): Add a poly-A tail to
+   the first-strand cDNA, ligate a double-stranded adapter ending with a
+   single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
- - [[Cleptet et al., 2004|biblio/14704363]] used oligo-capping, but used T4 DNA ligase and a double-stranded
-   adapter with NNNNNN overhang instead of T4 RNA ligase and a single-stranded linker.
+ - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
+   DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
+   RNA ligase and a single-stranded linker.
 
 [[!inline pages="tagged(cap)" limit=0]]

Old
diff --git a/biblio/163011.mdwn b/biblio/163011.mdwn
new file mode 100644
index 0000000..c0853f9
--- /dev/null
+++ b/biblio/163011.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A blocked structure at the 5' terminus of mRNA from cytoplasmic polyhedrosis virus."]]
+[[!tag cap not_read]]
+
+Nature. 1975 Jan 31;253(5490):374-5
+
+Furuichi Y, Miura K.
+
+A blocked structure at the 5' terminus of mRNA from cytoplasmic polyhedrosis virus.
+
+[[!pmid 163011 desc="Discovery of the cap."]]
diff --git a/biblio/9373149.mdwn b/biblio/9373149.mdwn
new file mode 100644
index 0000000..eff393a
--- /dev/null
+++ b/biblio/9373149.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library."]]
+[[!tag cap library method]]
+
+Gene. 1997 Oct 24;200(1-2):149-56.
+
+Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S.
+
+Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.
+
+[[!pmid 9373149 desc="Oligo-capping to build 5′ or FL cDNA libraries."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8db5444..8028f58 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -74,9 +74,6 @@ 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.
 
-9373199 [libraries]
-Oligo-capping to build 5' ou FL cDNA libraries.
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 1ca3e1f..27bfd58 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,6 +6,11 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
+ - Oligo-capping [[Suzuki et al., 1999|biblio/9373149]]: dephosphorylate, uncover functional
+   phosphate with decapping enzyme, and ligate RNA adaptor with T4 RNA ligase.
+
+(wip: Fromont-racine et al., Maruyama et al.)
+
  - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.

Consolidation.
diff --git a/biblio/2020554.mdwn b/biblio/2020554.mdwn
index f11b3ad..a155d56 100644
--- a/biblio/2020554.mdwn
+++ b/biblio/2020554.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors."]]
-[[!tag libraries]]
+[[!tag library]]
 
 Nucleic Acids Res. 1991 Mar 11;19(5):1156 doi:10.1093/nar/19.5.1156
 
diff --git a/biblio/7760832.mdwn b/biblio/7760832.mdwn
index dc10fb3..ad0cce4 100644
--- a/biblio/7760832.mdwn
+++ b/biblio/7760832.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture)."]]
-[[!tag cap libraries]]
+[[!tag cap library]]
 
 Mol Cell Biol. 1995 Jun;15(6):3363-71.
 
diff --git a/tags/libraries.mdwn b/tags/libraries.mdwn
deleted file mode 100644
index f649073..0000000
--- a/tags/libraries.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged libraries"]]
-
-[[!inline pages="tagged(libraries)" actions="no" archive="yes"
-feedshow=10]]

Old
diff --git a/biblio/1923806.mdwn b/biblio/1923806.mdwn
new file mode 100644
index 0000000..84ef60b
--- /dev/null
+++ b/biblio/1923806.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oligodeoxyribonucleotide ligation to single-stranded cDNAs: a new tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification."]]
+[[!tag library]]
+
+Nucleic Acids Res. 1991 Oct 11;19(19):5227-32
+
+Edwards JB, Delort J, Mallet J.
+
+Oligodeoxyribonucleotide ligation to single-stranded cDNAs: a new tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification.
+
+[[!pmid 1923806 desc="T4 RNA ligase to graft DNA linkers at the end of cDNAs."]]

Expand.
diff --git a/biblio/16708763.mdwn b/biblio/16708763.mdwn
index d9d1551..ab4171f 100644
--- a/biblio/16708763.mdwn
+++ b/biblio/16708763.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA."]]
-[[!tag protocols cDNA oligonucleotides hybridisation random_priming]]
+[[!tag protocols cDNA oligonucleotides hybridisation random_priming reverse_transcription]]
+
+Biotechniques. 2006 May;40(5):649-57.
+
+Stangegaard M, Dufva IH, Dufva M.
+
+Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA.
+
 [[!pmid 16708763 desc="Almost 100% of the RNA molecules are primed (using massive amounts of oligonucleotides)."]]

Expand/correct.
diff --git a/biblio/10037822.mdwn b/biblio/10037822.mdwn
index 1b4f93b..9c0a63a 100644
--- a/biblio/10037822.mdwn
+++ b/biblio/10037822.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Amplification of cDNA ends based on template-switching effect and step-out PCR."]]
 [[!tag template_switching PCR method ]]
+
+Nucleic Acids Res. 1999 Mar 15;27(6):1558-60.
+
+Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A.
+
+Amplification of cDNA ends based on template-switching effect and step-out PCR.
+
 [[!pmid 10037822 desc="To counter template-switching happening from inside the oligonucleotide instead of its tail."]]
diff --git a/biblio/12089562.mdwn b/biblio/12089562.mdwn
index 2e378cf..0bf567c 100644
--- a/biblio/12089562.mdwn
+++ b/biblio/12089562.mdwn
@@ -7,4 +7,4 @@ Nat Biotechnol. 2002 Jul;20(7):738-42.
 
 Amine-modified random primers to label probes for DNA microarrays.
 
-[[!pmid desc="Incorporates aminoallyl-dUTP instead of cy3/5dUTP. Uses priming hexamers with a amino C6dT in 5′. This allows to reduce by 10 folds the quantity of RNA as a starting material. Presence of amplification products of t/rRNAs is not a problem when « optimal » quantities of total RNA are used."]]
+[[!pmid 12089562 desc="Incorporates aminoallyl-dUTP instead of cy3/5dUTP. Uses priming hexamers with a amino C6dT in 5′. This allows to reduce by 10 folds the quantity of RNA as a starting material. Presence of amplification products of t/rRNAs is not a problem when « optimal » quantities of total RNA are used."]]

Text not available.
diff --git a/biblio/8247743.mdwn b/biblio/8247743.mdwn
new file mode 100644
index 0000000..b1d9844
--- /dev/null
+++ b/biblio/8247743.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Synthesis of full-length cDNA using DNA-capped mRNA."]]
+[[!tag cap method not_read]]
+
+Nucleic Acids Symp Ser. 1993;(29):143-4.
+
+Sekine S, Kato S.
+
+Synthesis of full-length cDNA using DNA-capped mRNA.
+
+[[!pmid 8247743 desc="Similar to oligo-capping."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index cc9b731..1ca3e1f 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,6 +4,8 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
+ - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
+
  - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.

Old
diff --git a/biblio/14704363.mdwn b/biblio/14704363.mdwn
new file mode 100644
index 0000000..6816e33
--- /dev/null
+++ b/biblio/14704363.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improved full-length cDNA production based on RNA tagging by T4 DNA ligase."]]
+[[!tag cap method]]
+
+Nucleic Acids Res. 2004 Jan 2;32(1):e6 doi:10.1093/nar/gng158
+
+Clepet C, Le Clainche I, Caboche M.
+
+Improved full-length cDNA production based on RNA tagging by T4 DNA ligase.
+
+[[!pmid 14704363 desc="T4 DNA ligase used to ligate a double stranded cap-tag."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index fbc7431..8db5444 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -80,9 +80,6 @@ Oligo-capping to build 5' ou FL cDNA libraries.
 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.
-
 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.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index b21b128..cc9b731 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,8 +4,11 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
- - [[CapSelect|biblio/10518626]]: Add a poly-A tail to the first-strand
+ - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.
 
+ - [[Cleptet et al., 2004|biblio/14704363]] used oligo-capping, but used T4 DNA ligase and a double-stranded
+   adapter with NNNNNN overhang instead of T4 RNA ligase and a single-stranded linker.
+
 [[!inline pages="tagged(cap)" limit=0]]

Syntax
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index b41aee6..b21b128 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,7 +4,7 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
- - [[CapSelect|biblio/10518626.mdwn]]: Add a poly-A tail to the first-strand
+ - [[CapSelect|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.
 

Cleanup.
diff --git a/tags/capi.mdwn b/tags/capi.mdwn
deleted file mode 100644
index c8d832d..0000000
--- a/tags/capi.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged capi"]]
-
-[[!inline pages="tagged(capi)" actions="no" archive="yes"
-feedshow=10]]

Expand.
diff --git a/biblio/10518626.mdwn b/biblio/10518626.mdwn
index f2e1e16..f69b0d8 100644
--- a/biblio/10518626.mdwn
+++ b/biblio/10518626.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs."]]
 [[!tag cap method enzyme manganese]]
+
+Nucleic Acids Res. 1999 Nov 1;27(21):e31.
+
+Schmidt WM, Mueller MW.
+
+CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs.
+
 [[!pmid 10518626 desc="In presence of the 5' cap and Mn2+, the SuperScriptII enzyme adds 3-4 extra dC residues to the first strand cDNA."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 8c0c7c0..b41aee6 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -1,4 +1,11 @@
 [[!meta title="pages tagged cap"]]
 
-[[!inline pages="tagged(cap)" actions="no" archive="yes"
-feedshow=10]]
+Methods for enriching capped RNAs.
+
+(work in progress)
+
+ - [[CapSelect|biblio/10518626.mdwn]]: Add a poly-A tail to the first-strand
+   cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
+   overhang, and prime second-strand synthesis.
+
+[[!inline pages="tagged(cap)" limit=0]]