Papers for presentation by students

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:
Philipp Bucher: philipp.bucher@epfl.ch
Giovanna Ambrosini: giovanna.ambrosini@epfl.ch
Sunil Kumar: kumar.sunil@epfl.ch
Rene Dreos: rene.dreos@epfl.ch
Romain Groux: romain.groux@epfl.ch

Paper status:
Available
Not Available

Papers for student presentation
Paper title Publication details Tutor 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
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 hg18/johnson07
Two independent transcription initiation codes overlap on vertebrate core promoters. Haberle et al., Nature 507, 381-385, 2014.
PMID: 24531765
Rene
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Zhang et al, Nat Struct Mol Biol 16, 847-852, 2009.
PMID: 19620965
Rene sacCer3/zhang09
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Albert et al, Nature 446, 572-576, 2007.
PMID: 17392789
Philipp
Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Zhao and Stormo, Nature Biotech 29, 480-483, 2011.
PMID: 21654662
Giovanna
MACE: model based analysis of ChIP-exo. Wang et al., Nucleic Acids Res 42, e156, 2014.
PMID: 25249628
Philipp hg19/encode
An atlas of active enhancers across human cell types and tissues Andersson et al., Nature 507, 455-461, 2014.
PMID: 24670763
Philipp hg19/fantom5 hg19/roadmap hg19/anderrson14
DNA-Binding Specificities of Human Transcription Factors. Jolma et al., Cell 152, 327-339, 2013.
PMID: 23332764
Giovanna
Transcription factor binding dynamics during human ES cell differentiation. Tsankov et al., Nature 518, 344-349, 2015.
PMID: 25693565
Rene hg19/roadmap/tsankov15
Dissecting neural differentiation regulatory networks through epigenetic footprinting. Ziller et al., Nature 518, 355-359, 2015.
PMID: 25533951
Philipp hg19/ziller15 (partial)
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Waszak et al., Cell 162, 1039-1050, 2015.
PMID: 26300124
Sunil hg19/waszak15
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
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Sherwood et al., Nature Biotech 32, 171-178, 2014.
PMID: 24441470
Romain
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Cheng et al., Genome Research 22, 1658-1667, 2012.
PMID: 22955978
Sunil hg19/ENCODE
Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Weber et al., Mol Cell 53, 819-830, 2014.
PMID: 24606920
Romain dm3/weber14
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
Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Locke et al., Clin Epigenetics 7, 52, 2015.
PMID: 25960784
Giovanna hg19/locke15
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Ross-Innes et al., Nature 481, 389-393, 2012.
PMID: 22217937
Sunil hg18/ross12
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Koch et al., Nat Struct Mol Biol 18, 956-963, 2011.
PMID: 21765417
Philipp mm9/koch11 (partial data)
Human promoters are intrinsically directional. Duttke et al., Mol Cell 57, 674-684, 2015.
PMID: 25639469
Rene
Epigenetic and transcriptional determinants of the human breast. Gascard et al., Nat Commun 6, 6351, 2015.
PMID: 25690954
Romain
CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Haberle et al., Nucleic Acids Res 43, e51, 2015.
PMID: 25653163
Rene