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RSG with DREAM 2019 | November 4-6, 2019 | New York, USA |Reading Papers List, 2017-2018

Reading Papers List, 2017-2018


As selected at RECOMB/ISCB Regulatory systems Genomics 2019
(Papers are listed alphabetically by title)

  • A web server for comparative analysis of single-cell RNA-seq data (Nat Commun. 2018) Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z
  • Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data (Cell Systems 2018) Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. O'Neill, David M. Gilbert, Jian Ma
  • Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding (Cell Systems 2018) Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R
  • DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. (PLoS Comput Biol. 2018) Mitra S, Biswas A, Narlikar L
  • Enhancer RNA profiling predicts transcription factor activity (Genome Res. 2018) Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD
  • GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs (Bioinformatics 2018) Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A
  • Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data (Nat Biotechnol. 2018) Zhu Q, Shah S, Dries R, Cai L, Yuan GC
  • Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. (Epigenetics Chromatin 2018) Behjati Ardakani F, Kattler K, Nordström K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH
  • Quantifying the similarity of topological domains across normal and cancer human cell types (Bioinformatics 2018) Sauerwald N, Kingsford C
  • Reconstructing differentiation networks and their regulation from time series single-cell expression data (Genome Res. 2018) Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z
  • SCENIC: single-cell regulatory network inference and clustering. (Nat Methods 2017) Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S
  • SigMat: a classification scheme for gene signature matching (Bioinformatics 2018) Xiao J, Blatti C, Sinha S
  • The impact of rare variation on gene expression across tissues (Nature 2017) Xin Li, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna, Michael C. Bassik, Jason D. Merker, GTEx Consortium, Ira M. Hall, Alexis Battle, Stephen B. Montgomery
  • Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. (Nat Commun. 2017) Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B


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