Papers for presentation by students

Choose one of the following papers for oral presentation, then mark your selection using the following doodle:

http://doodle.com/avk4c2sb5wdbnguu

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

Paper status:
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Papers for student presentation
Paper title Publication details Tutor
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
Charting a dynamic DNA methylation landscape of the human genome. Ziller et al., Nature 500, 477-481, 2013.
PMID: 23925113
Sunil
An atlas of active enhancers across human cell types and tissues Andersson et al., Nature 507, 455-461, 2014.
PMID: 24670763
Sunil
Two independent transcription initiation codes overlap on vertebrate core promoters. Haberle et al., Nature 507, 381-385, 2014.
PMID: 24531765
Rene
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Koch et al. Nat Struct Mol Biol. 18, 956-63, 2011.
PMID: 21765417
Philipp
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Hesselberth et al. Nat Methods. 6, 283-289, 2009.
PMID: 19305407
Philipp
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Core et al, Nature Genetics 46, 1311-1320, 2014.
PMID: 25383968
Rene
Human promoters are intrinsically directional. Duttke et al, Mol Cell 57, 674-684, 2015.
PMID: 25639469
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
The DNA-encoded nucleosome organization of a eukaryotic genome. Kaplan et al, Nature 458, 362-366, 2009.
PMID: 19092803
Rene
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Vavouri et al, Genome Biology 13, R110, 2012.
PMID: 23186133
Rene
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Albert et al, Nature 446, 572-576, 2007.
PMID: 17392789
Philipp
An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example. Chen et al., BMC Genomics, 2014.
PMID: 24564277
Giovanna
DNA-Binding Specificities of Human Transcription Factors. Jolma et al., Cell 152, 327-339, 2013.
PMID: 23332764
Giovanna
Universality of core promoter elements?
    The above is a brief comunication that lead to the retraction of the following paper:
Genomic organization of human transcription initiation complexes.
    Read both papers and present the case
Siebert and Soding, Nature. 2014 Jul 24;511(7510).
PMID: 25056067

Venters and Pugh, Nature 502, 53-58, 2013.
PMID: 24048476

Retraction: 25079311

Sunil
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
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Hoffman et al., Nature Methods 9, 473-476, 2012.
PMID: 22426492
Philipp
Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data. Zhang et al., PLoS One 7, e32095, 2012.
PMID: 22393380
Sunil