Theo dõi
Remo Rohs
Remo Rohs
Professor and Chair of Quantitative and Computational Biology, University of Southern California
Email được xác minh tại usc.edu - Trang chủ
Tiêu đề
Trích dẫn bởi
Trích dẫn bởi
Năm
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
12372009
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
10992010
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
6092014
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
5702011
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
4012007
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
3852013
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
3462013
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
3162005
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
2892010
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
2682015
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
2552014
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
2162000
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
2122015
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
2082013
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
2042018
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
1862015
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
1752015
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
1722015
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
1702016
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
1682016
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