Publications

52.

N.S. Tangprasertchai, R. Di Felice, X. Zhang, I.M. Slaymaker, C. Vazquez Reyes, W. Jiang, R. Rohs, and P.Z. Qin:
CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling.
ACS Chem. Biol. In press (2017)
Supplementary Information

51.

J.M. Sagendorf, H.M. Berman*, and R. Rohs*:
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Nucleic Acids Res. In press (2017)
Supplementary Information
*Corresponding authors.

50.

L. Yang, Y. Orenstein, A. Jolma, Y. Yin, J. Taipale, R. Shamir*, and R. Rohs*:
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
Mol. Syst. Biol. 13, 910 (2017)
Supplementary Information
*Corresponding authors.

49.

S. Schwörer, F. Becker, C. Feller, A.H. Baig, U. Köber, H. Henze, J.M. Kraus, B. Xin, A. Lechel, D.B. Lipka, C.S. Varghese, M. Schmidt, R. Rohs, R. Aebersold, K.L. Medina, H. A. Kestler, F. Neri, J. von Maltzahn, S. Tümpel, and K.L. Rudolph KL:
Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.
Nature 540, 428-432 (2016)
Supplementary Information
See Press Coverage for Nature News and Views and Leibniz Institute on Aging press release.

48.

S. Schöne, M. Jurk, M.B. Helabad, I. Dror, I. Lebars, B. Kieffer, P. Imhof, R. Rohs, M. Vingron, M. Thomas-Chollier, and S.H. Meijsing:
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
Nat. Commun. 7, 12621 (2016)
Supplementary Information
See Press Coverage for Max Planck Society press release.

47.

A. Mathelier, B. Xin, T.P. Chiu, L. Yang, R. Rohs*, and W.W. Wasserman*:
DNA shape features improve transcription factor binding site predictions in vivo.
Cell Syst. 3, 278-286 (2016)
Supplementary Information
*Corresponding authors.
See Press Coverage for Cell Syst. Preview.

46.

G. Kuzu, E.G. Kaye, J. Chery, T. Siggers, L. Yang, J.R. Dobson, S. Boor, J. Bliss, W. Liu, G. Jogl, R. Rohs, N.D. Singh, M.L. Bulyk, M.Y. Tolstorukov, and E. Larschan:
Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation.
PLOS Genet. 12, e1006120 (2016)
Supplementary Information

45.

I. Dror, R. Rohs, and Y. Mandel-Gutfreund:
How motif environment affects transcription factor search dynamics: Finding a needle in a haystack.
BioEssays 38, 605-612 (2016)
See Press Coverage for BioEssays highlight.

44.

T.P. Chiu, F. Comoglio, T. Zhou, L. Yang, R. Paro, and R. Rohs*:
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
Bioinformatics 32, 1211-1213 (2016)
Supplementary Information
*Corresponding author.

43.

G.E. Zentner, S. Kasinathan, B. Xin, R. Rohs, and S. Henikoff:
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
Nat. Commun. 6, 8733 (2015)
Supplementary Information

42.

N.S. Tangprasertchai, X. Zhang, Y. Ding, K. Tham, R. Rohs, I.S. Haworth, and P. Z. Qin:
An integrated spin-labeling/computational-modeling approach for mapping global structures of nucleic acids.
Methods Enzymol. 564, 427-453 (2015)

41.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2015/16
I. Dror, T. Golan, C. Levy, R. Rohs*, and Y. Mandel-Gutfreund*:
A widespread role of the motif environment on transcription factor binding across diverse protein families.
Genome Res. 25, 1268-1280 (2015)
Supplementary Information
*Corresponding authors.

40.

Z. Deng, Q. Wang, Z. Liu, M. Zhang, A.C. Dantas Machado, T.P. Chiu, C. Feng, Q. Zhang, L. Yu, L. Qi, J. Zheng, X. Wang, X.M. Huo, X. Qi, X. Li, W. Wu, R. Rohs*, Y. Li*, and Z. Chen*:
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
Nat. Commun. 6, 7642 (2015)
Supplementary Information
*Corresponding authors.

39.

R. Rohs*, A.C. Dantas Machado, and L. Yang:
Exposing the secrets of sex determination.
Nat. Struct. Mol. Biol. 22, 437-438 (2015)
*Corresponding author.

38.

F. Comoglio, T. Schlumpf, V. Schmid, R. Rohs, C. Beisel, and R. Paro:
High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins.
Cell Rep. 11, 821-834 (2015)
Supplementary Information

37.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2014/15
N. Abe, I. Dror, L. Yang, M. Slattery, T. Zhou, H.J. Bussemaker, R. Rohs*, and R.S. Mann*:
Deconvolving the recognition of DNA sequence from shape.
Cell 161, 307-318 (2015)
Supplementary Information
*Corresponding authors.
See Press Coverage for Nat. Rev. Genet. and other commentaries.

36.

M. Levo, E. Zalckvar, E. Sharon, A.C. Dantas Machado, Y. Kalma, M. Lotan-Pompan, A. Weinberger, Z. Yakhini, R. Rohs, and E. Segal:
Unraveling determinants of transcription factor binding outside the core-binding site.
Genome Res. 25, 1018-1029 (2015)
Supplementary Information
See Press Coverage for Nat. Genet. and other commentaries.

35.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2015/16
T. Zhou,&, N. Shen,&, L. Yang, N. Abe, J. Horton, R.S. Mann, H.J. Bussemaker, R. Gordân*, and R. Rohs*:
Quantitative modeling of transcription factor binding specificities using DNA shape.
Proc. Natl. Acad. Sci. USA 112, 4654-4659 (2015)
Supplementary Information
&Equal contributions. *Corresponding authors.
See Press Coverage for PNAS and other commentaries.

34.

T. Hadžić, D. Park, K.C. Abruzzi, L. Yang, J.S. Trigg, R. Rohs, M. Rosbash, and P.H. Taghert:
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.
Nucleic Acids Res. 43, 2199-2215 (2015)
Supplementary Information

33.

T.P. Chiu,&, L. Yang,&, T. Zhou, B.J. Main, S.C. Parker, S.V. Nuzhdin, T.D. Tullius, and R. Rohs*:
GBshape: a genome browser database for DNA shape annotations.
Nucleic Acids Res. 43, D103-109 (2015)
Supplementary Information
&Equal contributions. *Corresponding author.

32.

A.C. Dantas Machado, T. Zhou, S. Rao, P. Goel, C. Rastogi, A. Lazarovici, H.J. Bussemaker*, and R. Rohs*:
Evolving insights on how cytosine methylation affects protein-DNA binding.
Brief. Funct. Genomics 14(1), 61-73 (2014)
*Corresponding authors.

31.

Feature Review
M. Slattery*, T. Zhou, L. Yang, A.C. Dantas Machado, R. Gordân*, and R. Rohs*:
Absence of a simple code: how transcription factors read the genome.
Trends Biochem. Sci. 39(9), 381-399 (2014)
*Corresponding authors.

30.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2013/14
I. Barozzi, M. Simonatto, S. Bonifacio, L. Yang, R. Rohs, S. Ghisletti, and G. Natoli:
Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.
Mol. Cell 54, 844-857 (2014)
Supplementary Information

29.

X. Zhang, A.C. Dantas Machado, Y. Ding, Y. Chen, Y. Lu, Y. Duan, K.W. Tham, L. Chen, R. Rohs*, and P.Z. Qin*:
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
Nucleic Acids Res. 42, 2789-2797 (2014)
Supplementary Information
*Corresponding authors.

28.

NAR Breakthrough Article
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2013/14
L. Yang, T. Zhou, I. Dror, A. Mathelier, W.W. Wasserman, R. Gordân, and R. Rohs*:
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res. 42, D148-155 (2014)
Supplementary Information
*Corresponding author.

27.

I. Dror, T. Zhou, Y. Mandel-Gutfreund*, and R. Rohs*:
Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
Nucleic Acids Res. 42, 430-441 (2014)
Supplementary Information
*Corresponding authors.

26.

A. Eldar, H. Rozenberg, Y. Diskin-Posner, R. Rohs, and Z. Shakked:
Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Nucleic Acids Res. 41, 8748-8759 (2013)
Supplementary Information

25.

Y. Chen, X. Zhang, A.C. Dantas Machado, Y. Ding, Z. Chen, P.Z. Qin, R. Rohs, and L. Chen:
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.
Nucleic Acids Res. 41, 8368-8376 (2013)
Supplementary Information

24.

T. Zhou, L. Yang, Y. Lu, I. Dror, A.C. Dantas Machado, T. Ghane, R. Di Felice, and R. Rohs*:
DNAshape: a method for the high-throughput prediction of DNA structural features on a genome-wide scale.
Nucleic Acids Res. 41, W56-62 (2013)
Supplementary Information
*Corresponding author.

23.

S.P. Hancock, T. Ghane, D. Cascio, R. Rohs, R. Di Felice, and R.C. Johnson:
Control of minor groove width and Fis protein binding by the purine 2-amino group.
Nucleic Acids Res. 41, 6750-6760 (2013)
Supplementary Information

22.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
R. Gordân, N. Shen&, I. Dror,&, T. Zhou,&, J. Horton, R. Rohs*, and M.L. Bulyk*:
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Cell Rep. 3, 1093-1104 (2013)
Supplementary Information
&Equal contributions. *Corresponding authors.

21.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
A. Lazarovici, T. Zhou,&, A. Shafer&, A.C. Dantas Machado,&, T. Riley, R. Sandstrom, P.J. Sabo, Y. Lu, R. Rohs*, J.A. Stamatoyannopoulos*, and H.J. Bussemaker*:
Probing DNA shape and methylation state on a genomic scale with DNase I.
Proc. Natl. Acad. Sci. USA 110, 6376-6381 (2013)
Supplementary Information

&Equal contributions. *Corresponding authors.

20.

Y.P. Chang, M. Xu, A.C. Dantas Machado, X.J. Yu, R. Rohs*, and X.S. Chen*:
Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen.
Cell Rep. 3, 1117-1127 (2013)
Supplementary Information
*Corresponding authors.

19.

A.C. Dantas Machado, S.B. Saleebyan, B.T. Holmes, M. Karelina, J. Tam, S.Y. Kim, K.H. Kim, I. Dror, E. Hodis, E. Martz, P.A. Compeau, and R. Rohs*:
Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.
Biochem. Mol. Biol. Educ. 40, 400-401 (2012)
*Corresponding author.

18.

Y. Chen, D.L. Bates, R. Dey, P. Chen, A.C. Dantas Machado, I.A. Laird-Offringa, R. Rohs, and L. Chen:
DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation
Cell Rep. 2, 1197-1206 (2012)
Supplementary Information

17.

R. Harris&, T. Mackoy&, A.C. Dantas Machado&,#, D. Xu, R. Rohs*, and M.O. Fenley*:
Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes
Chapter 3 in T. Schlick, Editor. Innovations in Biomolecular Modeling and Simulation. Volume 2, 53-80 (2012). Biomolecular Sciences Series, Royal Society of Chemistry, RCS Publishing, London, UK.
&Equal contribution. *Corresponding authors.

16.

RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2011
M. Slattery, T. Riley, P. Liu, N. Abe, P.Gomez-Alcala, I. Dror, T. Zhou, R. Rohs*, B. Honig*, H.J. Bussemaker*, and R.S. Mann*:
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Cell 147, 1270-1282 (2011)
Supplementary Information
*Corresponding authors.
See Press Coverage for Cell Preview and other commentaries.

15.

E.P. Bishop*, R. Rohs*, S.C.J. Parker*, S.M. West, R.S. Mann, B. Honig, and T.D. Tullius:
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA
ACS Chem. Biol. 6(12), 1314-1320 (2011)
Supplementary Information
*Equal contribution.

14.

B. Honig* and R. Rohs*:
Biophysics: Flipping Watson and Crick
Nature 470, 472-473 (2011)
*Corresponding authors.

13.

R. Rohs*, X. Jin*, S.M. West, R. Joshi, B. Honig, and R.S. Mann:
Origins of specificity in protein-DNA recognition
Annu. Rev. Biochem. 79, 233-269 (2010)
*Equal contribution.

12.

S.M. West, R. Rohs, R.S. Mann, and B. Honig:
Electrostatic interactions between arginines and the minor groove in the nucleosome
J. Biomol. Struct. Dyn. 27, 861–866 (2010)

11.

M. Kitayner*, H. Rozenberg*, R. Rohs*, O. Suad, D. Rabinovich, B. Honig, and Zippora Shakked:
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs
Nat. Struct. Mol. Biol. 17, 423–429 (2010)
Supplementary Information
*Equal contribution.
See Press Coverage for Nat. Struct. Mol. Biol. News and Views.

10.

R. Rohs*, S.M. West*, A. Sosinky, P. Liu, R.S. Mann, and B. Honig:
The role of DNA shape in protein-DNA recognition
Nature 461, 1248-1253 (2009)
Supplementary Information
*Equal contribution.
See Press Coverage for Nature News and Views and other commentaries.

9.

R. Rohs, S.M. West, P. Liu, and B. Honig:
Nuance in the double-helix and its role in protein-DNA recognition
Curr. Op. Struct. Biol. 19, 171-177 (2009)

8.

R. Joshi, J.M. Passner*, R. Rohs*, R. Jain*, A. Sosinsky*, M.A. Crickmore, V. Jacob, A.K. Aggarwal, B. Honig, and R.S. Mann:
Functional specificity of a Hox protein mediated by the recognition of minor groove structure
Cell 131, 530-543 (2007)
Supplemental Data
*Equal contribution.
See Press Coverage for Nat. Struct. Mol. Biol. News and Views.

7.

H. Sklenar, D. Wüstner, and R. Rohs:
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians
J. Comput. Chem. 27, 309-315 (2006)

6.

R. Rohs*, I. Bloch, H. Sklenar, and Z. Shakked:
Molecular flexibility in ab-initio drug docking to DNA: Binding-site and binding-mode transitions in all-atom Monte Carlo simulations
Nucleic Acids Res. 33, 7048-7057 (2005)
*Corresponding author.

5.

R. Rohs*, H. Sklenar, and Z. Shakked:
Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites
Structure 13, 1499-1509 (2005)
Download Figures 1-7 in high resolution (737 kB)
*Corresponding author.
See Press Coverage for Structure Preview.

4.

R. Rohs* and H. Sklenar:
Methylene blue binding to DNA with alternating AT base sequence: Minor groove binding is favored over intercalation
J. Biomol. Struct. Dyn. 21, 699-711 (2004)
*Corresponding author.

3.

R. Rohs and H. Sklenar:
Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects
Indian J. Biochem. Biophys. 38, 1-6 (2001)
Invited paper.

2.

R. Rohs, H. Sklenar, R. Lavery, and B. Röder:
Methylene blue binding to DNA with alternating GC base sequence: A modeling study
J. Am. Chem. Soc. 122, 2860-2866 (2000)

1.

R. Rohs, C. Etchebest, and R. Lavery:
Unraveling proteins: A molecular mechanics study
Biophys. J. 76, 2760-2768 (1999)

April 26, 2017
Remo accepted reappointment as Vice Chair of USC's Department of Biological Sciences through August 2019. Fight on!

April 20, 2017
We published our interactive tool for structural analysis of protein-DNA complexes in NAR. Congrats, Jared!

March 20, 2017
Tsu-Pei was awarded the prestigious Manning Endowed Fellowship. Congrats, Tsu-Pei!

March 20, 2017
Beibei was awarded a competitive Research Enhancement Fellowship. Congrats, Beibei!

February 6, 2017
Our new Mol. Syst. Biol. paper provides systematic analysis of DNA shape readout for many protein families. Congrats, Lin!

November 30, 2016
Our new Nature paper with the Leibniz Institute on Aging reveals role of Hoxa9 in muscle stem cell aging.

November 8, 2016
Our recent Dror et al. Genome Res. paper received a RECOMB/ISCB Top-10 Paper Award in regulatory and systems genomics in 2015/16.

August 31, 2016
Carolina defended her Ph.D. thesis with flying colors. Congratulations, Carolina!

August 18, 2016
Our new paper proves the impact of DNA shape on in vivo TF binding based on 400 human ChIP-seq datasets.

August 16, 2016
Remo was promoted to Full Professor of Biological Sciences at USC. Fight on!

July 14, 2016
Remo was elected Head of Computational Biology and Bioinformatics at USC. Fight on!

June 6, 2016
Lin defended his Ph.D. thesis with flying colors. Congratulations, Lin!

May 4, 2016
Tsu-Pei received a competitive Enhancement Fellowship from the USC Graduate School. Congratulations, Tsu-Pei!

May 3, 2016
Lin received the highest honor for a USC graduate student, the PhD Achievement Award. Congratulations, Lin!

May 3, 2016
Remo was introduced as the incoming Vice Chair of the Department of Biological Sciences and Director of Biological Sciences Studies.

April 20, 2016
Remo presented our recent Zhou et al. PNAS paper as one of the few selected Highlights at the recent RECOMB conference.

April 19, 2016
Carolina received the Harrison M. Kurtz Award and Tsu-Pei the William E. Trusten Award. Congrats, Carolina and Tsu-Pei!.

April 6, 2016
Remo received the USC Mentoring award in the category mentoring of graduate students. Best award ever!

March 16, 2016
Remo received the ACS OpenEye Outstanding Junior Faculty Award in Computational Chemistry at the American Chemical Society National Meeting.

January 28. 2016
Remo received Tenure at USC and was promoted to Associate Professor. Fight on!

November 18, 2015
Our recent Abe et al. Cell and Zhou et al. PNAS papers were voted as RECOMB/ISCB Top Papers in regulatory and systems genomics in 2014/15.

Recent news

August 21-25, 2016
Symposium on Modeling Water and Solvation in Biochemistry: Developments and Applications, American Chemical Society National Meeting, Philadelphia, PA

July 5-8, 2016
Meeting on Measuring and Modeling Quantitative Sequence-Function Relationships, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, NY

April 17-21, 2016
RECOMB 2016 Conference, Santa Monica, CA

March 23, 2016
Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany

March 15-19, 2016
CSHL Meeting on Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, NY

March 7-10, 2016
Workshop on Regulatory Genomics and Epigenomics, Simons Institute for the Theory of Computing, UC Berkeley, Berkeley, CA

February 5-7, 2016
Bridge@USC and Michelson Center for Convergent Biosciences Retreat, Catalina Island, CA

January 31- February 5, 2016
Epigenomics 2016 Meeting, Rio Mar, Puerto Rico

January 19, 2016
Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA

Recent presentations

BISC 321 syllabus
Multidisciplinary Seminar: Science, Technology, and Society

BISC 577a syllabus
Computational Molecular Biology Laboratory