For each paper we offer a tutor that can help with any question you
might have.
These are the e-mail addresses for each tutor:
Paper status:
| Available | |
| Not Available |
| 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) hg19/encode/Uniform-TFBS |
|
| 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 hg19/encode/Duke-DNaseI-HS |
|
| 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
hg18/barski07 hg18/boyle08 |
|
| 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 hg19/kelly12 | |
| 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 | |