List of papers for students' presentations

For each paper we offer a tutor that can help with any question you might have.
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Papers for student presentations
Paper title Publication details Tutor Local dataset
Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk Tehranchi et al., Cell 2016
PMID: 27087447
Philipp SRP058204
(not needed)
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Zuo and Stormo, Genetics 2014
PMID: 25209146
Philipp
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages Schmidt et al., Cell 2012
PMID: 22244452
Philipp E-MTAB-437
(hg19, mm9)
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Perez-Rico et al., Genome Res. 2017
PMID: 27965291
Philipp GSE75734
Optional: GSE74231
Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE Li et al., RNA Biol. 2015
PMID: 25747261
Philipp spo2/li15
spo2/epd
spo2/pombase
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Morton et al., Plant Cell 2014
PMID: 25035402
Rene araTha1/morton14
Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast Kubik et al., Mol Cell 2015
PMID: 26545077
Rene sacCer3/kubik15
Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution Sadeh et al., Mol Cell 2016
PMID: 27496019
Rene sacCer3/sadeh16
Genome-wide identification of regulatory elements in Sertoli cells. Maatouk et al., Develop. 2017
PMID: 28087634
Rene mm9/maatouk17
ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors Starick S.R., et al. Genome Res. 2015
PMID: 25720775
Giovanna hg19/starick15
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity Weirauch M.T., et al., Cell. 2014
PMID: 25215497
Giovanna CIS-BP Database: Catalog of Inferred Sequence Binding Preferences
Transposition of native chromatin for fast and sensitive epigenetic profiling of open chromatin, DNA-binding proteins and nucleosome position Buenrostro J.D., et al., Nature Methods 2013
PMID: 24097267
Romain hg19/buenrostro13.html
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
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
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