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RSG with DREAM & Cytoscape Workshop | November 6 - 9, 2016 | Phoenix, AZ | Top Reading Papers 2016


 As selected at RECOMB/ISCB Regulatory and Systems Genomics 2016

(Papers are listed alphabetically by title)

A widespread role of the motif environment in transcription factor binding across diverse protein families, Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. Genome Research 2015 Sep;25(9):1268-80

Affinity regression predicts the recognition code of nucleic acid-binding proteins, Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Nature Biotechnology 2015 Dec;33(12):1242-1249

Analysis of computational footprinting methods for DNase sequencing experiments, Gusmao E, Allhoff M, Zenke M, Costa I. Nature Methods 2016 Apr;13(4):303-9

Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks, Kelley DR, Snoek J, Rinn J. Genome Research 2016 Jul;26(7):990-9

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes, Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Proc Natl Acad Sci U S A 2015 Nov 24;112(47):E6456-65

Evaluating the impact of single nucleotide variants on transcription factor binding, Shi W, Fornes O, Mathelier A, Wasserman WW. Nucleic Acids Research 2016 Aug 4. pii: gkw691

Inferring causal molecular networks: empirical assessment through a community-based effort, Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Nature Methods 2016 Apr;13(4):310-8

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens, Chasman D, Walters KB, Lopes TJ, Eisfeld AJ, Kawaoka Y, Roy S. PLoS Computational Biology 2016 Jul 12;12(7):e1005013

Models of human core transcriptional regulatory circuitries, Saint-Andre V, Federation AJ, Lin CY, Abraham BJ, Reddy J, Lee TI, Bradner JE, Young RA. Genome Research 2016 Mar;26(3):385-96

Pathways on demand: automated reconstruction of human signaling networks, Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Npj Systems Biology And Applications, vol. 2 p. 16002.