Remo Rohs

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Ana Carolina Dantas MachadoUniversity of California, San DiegoVerifisert e-postadresse på alumni.usc.edu
Tianyin ZhouGoogleVerifisert e-postadresse på usc.edu
Richard S. MannProfessor of Biochemistry, Neuroscience and Systems Biology, Zuckerman Mind Brain Behavior InstituteVerifisert e-postadresse på columbia.edu
Lin YangGoogleVerifisert e-postadresse på usc.edu
Barry HonigColumbia UniversityVerifisert e-postadresse på columbia.edu
Tsu-Pei ChiuAssistant Professor (Teaching), University of Southern CaliforniaVerifisert e-postadresse på usc.edu
Iris DrorUniversity of California, Los Angeles (UCLA)Verifisert e-postadresse på mednet.ucla.edu
Harmen J. BussemakerColumbia UniversityVerifisert e-postadresse på columbia.edu
Peng LiuScientist, Department of Biostatistics and Medical Informatics & Carbone Cancer Center, UW-MadisonVerifisert e-postadresse på wisc.edu
Raluca GordanAssociate Professor, Duke UniversityVerifisert e-postadresse på duke.edu
Beibei XinPhD, University of Southern CaliforniaVerifisert e-postadresse på usc.edu
Rosa Di FeliceUniversity of Southern California, Los Angeles USA and CNR-NANO-S3 Italy (on leave)Verifisert e-postadresse på usc.edu
Matthew SlatteryUniversity of Minnesota Medical SchoolVerifisert e-postadresse på umn.edu
Rohit JoshiCDFD-HyderabadVerifisert e-postadresse på cdfd.org.in
Satyanarayan RaoAssistant Professor, IIT RoorkeeVerifisert e-postadresse på bt.iitr.ac.in
Lin ChenProfessor of Biological Sciences and Chemistry, University of Southern CaliforniaVerifisert e-postadresse på usc.edu
Jinsen LiUniversity of Southern CaliforniaVerifisert e-postadresse på usc.edu
Todd R. RileyAssistant Professor, UMass BostonVerifisert e-postadresse på umb.edu
Peter Z. QinProfessor of Chemistry, University of Southern CaliforniaVerifisert e-postadresse på usc.edu
Ning ShenZhejiang UniversityVerifisert e-postadresse på zju.edu.cn

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Remo Rohs

Professor and Chair of Quantitative and Computational Biology, University of Southern California

Verifisert e-postadresse på usc.edu - Startside

Computational Biology Structural Biology Bioinformatics Machine Learning Drug Design


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The role of DNA shape in protein–DNA recognition R Rohs, SM West, A Sosinsky, P Liu, RS Mann, B Honig Nature 461 (7268), 1248-1253, 2009	1208	2009
Origins of specificity in protein-DNA recognition R Rohs, X Jin, SM West, R Joshi, B Honig, RS Mann Annual Review of Biochemistry 79, 233-269, 2010	1076	2010
Absence of a simple code: how transcription factors read the genome M Slattery, T Zhou, L Yang, AC Dantas Machado, R Gordân, R Rohs Trends in Biochemical Sciences 39 (9), 381-399, 2014	604	2014
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins M Slattery, T Riley, P Liu, N Abe, P Gomez-Alcala, I Dror, T Zhou, R Rohs, ... Cell 147 (6), 1270-1282, 2011	562	2011
Functional specificity of a Hox protein mediated by the recognition of minor groove structure R Joshi, JM Passner, R Rohs, R Jain, A Sosinsky, MA Crickmore, V Jacob, ... Cell 131 (3), 530-543, 2007	393	2007
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape R Gordân, N Shen, I Dror, T Zhou, J Horton, R Rohs, ML Bulyk Cell Reports 3 (4), 1093-1104, 2013	378	2013
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale T Zhou, L Yang, Y Lu, I Dror, AC Dantas Machado, T Ghane, R Di Felice, ... Nucleic Acids Research 41 (W1), W56-W62, 2013	341	2013
Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations R Rohs, I Bloch, H Sklenar, Z Shakked Nucleic Acids Research 33 (22), 7048-7057, 2005	311	2005
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs M Kitayner, H Rozenberg, R Rohs, O Suad, D Rabinovich, B Honig, ... Nature Structural & Molecular Biology 17 (4), 423-429, 2010	278	2010
Quantitative modeling of transcription factor binding specificities using DNA shape T Zhou, N Shen, L Yang, N Abe, J Horton, RS Mann, HJ Bussemaker, ... Proceedings of the National Academy of Sciences USA 112 (15), 4654-4659, 2015	264	2015
Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers I Barozzi, M Simonatto, S Bonifacio, L Yang, R Rohs, S Ghisletti, G Natoli Molecular Cell 54 (5), 844-857, 2014	249	2014
Methylene blue binding to DNA with alternating GC base sequence: a modeling study R Rohs, H Sklenar, R Lavery, B Röder Journal of the American Chemical Society 122 (12), 2860-2866, 2000	215	2000
Probing DNA shape and methylation state on a genomic scale with DNase I A Lazarovici, T Zhou, A Shafer, AC Dantas Machado, TR Riley, ... Proceedings of the National Academy of Sciences USA 110 (16), 6376-6381, 2013	210	2013
Deconvolving the recognition of DNA shape from sequence N Abe, I Dror, L Yang, M Slattery, T Zhou, HJ Bussemaker, R Rohs, ... Cell 161 (2), 307-318, 2015	206	2015
Quantum annealing versus classical machine learning applied to a simplified computational biology problem RY Li, R Di Felice, R Rohs, DA Lidar npj Quantum Information 4 (1), 14, 2018	189	2018
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo GE Zentner, S Kasinathan, B Xin, R Rohs, S Henikoff Nature Communications 6, 8733, 2015	182	2015
A widespread role of the motif environment in transcription factor binding across diverse protein families I Dror, T Golan, C Levy, R Rohs, Y Mandel-Gutfreund Genome Research 25 (9), 1268-1280, 2015	171	2015
Unraveling determinants of transcription factor binding outside the core binding site M Levo, E Zalckvar, E Sharon, AC Dantas Machado, Y Kalma, ... Genome Research 25 (7), 1018-1029, 2015	169	2015
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding TP Chiu, F Comoglio, T Zhou, L Yang, R Paro, R Rohs Bioinformatics 32 (8), 1211-1213, 2016	166	2016
DNA shape features improve transcription factor binding site predictions in vivo A Mathelier, B Xin, TP Chiu, L Yang, R Rohs, WW Wasserman Cell Systems 3 (3), 278-286, 2016	165	2016

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