List of papers for students' presentation

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Papers for student presentation
Paper title Publication details Tutor Local dataset
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data. Orenstein & Shamir, Nucleic Acids Res, 42, e63, 2014.
PMID: 24500199
Giovanna jolma2013 (738 DNA motifs)
uniprobe_mouse (386 DNA motifs)
Canonical nucleosome organization at promoters forms during genome activation. Zhang et al., Genome Research 24, 260-266, 2014.
PMID: 24285721
Romain danRer7/zhang14
Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Park et al., Nucleic Acids Res 42, 3736-3749, 2014.
PMID: 24413663
Rene sacCer3/park14
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Kundaje et al., Genome Research 22, 1735-1747, 2012.
PMID: 22955985
Romain hg19/encode/GSE35586
Human promoters are intrinsically directional. Duttke et al., Mol Cell 57, 674-684, 2015.
PMID: 25639469
Rene hg19/duttke15
Two independent transcription initiation codes overlap on vertebrate core promoters. Haberle et al., Nature. 2014 Mar 20;507(7492):381-5
PMID: 24531765
Rene danRer7/nepal13
Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Locke et al.,Clin Epigenetics. 2015 May 1;7:52
PMID: 25960784
Giovanna hg19/locke15
An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression Yu et al., Cancer Cell. 2010
PMID: 20478527
Philipp hg18/yu10
A global change in RNA polymerase II pausing during the Drosophila midblastula transition. Chen et al., Elife 2013
PMID: 23951546
Rene dm6/chen13
Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. Rey et al., PLoS Biology 2011
PMID: 21364973
Philipp mm9/rey11
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Creyghton et al., PNAS 2010
PMID: 21106759
Giovanna mm9/creyghton10
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters Koch et al., Nat Struct Mol Biol. 2011
PMID: 21765417
Rene mm9/koch11
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection Yardimci et al., NAR 2014
PMID: 25294828
Philipp hg19/yardimci14
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. Fu et al. PLoS Genet. 4, e1000138, 2008.
PMID: 18654629
Giovanna hg18/schones08
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. O'Malley et al., Cell. Sep 8;166(6), 2016.
PMID: 27610578
Rene Arabidopsis DAPv1 O'Malley2016
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiaite Reprogramming. Soufi et al., Cell 161(3), 555-568, 2015.
PMID: 25892221
Romain hg19/soufi12
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Thomas-Chollier et al., Nucleic Acids Res. v.40(4), 2012.
PMID: 22156162
Giovanna External resource: RSAT
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. Halbritter et al., NAR 2014
PMID: 24174536
Philipp External resource: GeneProf