Reading Papers List, 2019


As selected at RECOMB/ISCB Regulatory systems Genomics 2020
(Papers are listed alphabetically by title)

  • Accurate prediction of cell type-specific transcription factor binding (Genome Biol 2019) Keilwagen J, Posch S, Grau J.
  • An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences (Nature Genetics 2019) Gulko B, Siepel A.
  • Characterizing protein-DNA binding event subtypes in ChIP-exo data (Bioinformatics 2019) Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S.
  • Chromatin features constrain structural variation across evolutionary timescales (PNAS 2019) Fudenberg G, Pollard KS.
  • cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data (Nature Methods 2019) Bravo Gonzalez-Blas C, Minnoye L, Papasokrati D, Aibar S, Hulselmans G, Christiaens V, Davie K, Wouters J, Aerts S.
  • Detection of RNA-DNA binding sites in long noncoding RNAs (Nucl Acids Res 2019) Kuo CC, Hanzelmann S, Senturk Cetin N, Frank S, Zajzon B, Derks JP, Akhade VS, Ahuja G, Kanduri C, Grummt I, Kurian L, Costa IG.
  • Exploring single-cell data with deep multitasking neural networks (Nature Methods 2019) Amodio M, van Dijk D, Srinivasan K, Chen WS, Mohsen H, Moon KR, Campbell A, Zhao Y, Wang X, Venkataswamy M, Desai A, Ravi V, Kumar P, Montgomery R, Wolf G, Krishnaswamy S.
  • GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs (Bioinformatics 2019) Shrikumar A, Prakash E, Kundaje A.
  • Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts (Bioinformatics 2019) Nair S, Kim DS, Perricone J, Kundaje A.
  • Transcriptional cofactors display specificity for distinct types of core promoters (Nature 2019) Haberle V, Arnold CD, Pagani M, Rath M, Schernhuber K, Stark A.


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