Reading Papers List

Reading Papers List, 2019

Like last year, we are planning to announce a "Recommended Reading List of Papers in Regulatory and Systems Genomics" at the RECOMB/ISCB Conference on Regulatory and Systems Genomics on November 16-19, 2020. Our goal is to identify seminal papers that introduced not only new biological insights, but also key computational methodologies for interpreting biological datasets that have had and will continue to have a lasting impact in the field of Computational Regulatory and Systems Genomics.

This year we employed a comprehensive nominations process where all eligible papers (i.e. published in 2019 and presented at either RegSys at ISMB or RECOMB/ISCB RegSys in 2017, 2018, or 2019) were automatically nominated. The full list of 39 papers is available here:

https://tinyurl.com/y5bdphlc

We now ask you, as a previous participant of this conference, and as a member of the RegSys community, to cast your votes for 5 of these publications using the link above.

We encourage all authors of the nominated publications to participate in the voting process, but please do not vote for your own papers, or papers from your lab ;).

The deadline for casting your votes is 11:59pm (EST) on Wednesday, Nov 18th. The results will be announced on Thursday, Nov 19th.

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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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