Publications

57.

J. Li, J.M. Sagendorf, T.P. Chiu, M. Pasi, A. Perez, and R. Rohs*:
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
Nucleic Acids Res. 45, 12877-12887 (2017)
Supplementary Information
*Corresponding author.

56.

T.P. Chiu, S. Rao, R.S. Mann, B. Honig, and R. Rohs*:
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.
Nucleic Acids Res. 45, 12565-12576 (2017)
Supplementary Information
*Corresponding author.

55.

J. Li, A.C. Dantas Machado, M. Guo, J.M. Sagendorf, Z. Zhou, L. Jiang, X. Chen, D. Wu, L. Qu, Z. Chen, L. Chen*, R. Rohs*, and Y. Chen*:
Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site.
Biochemistry 56, 3745-3753 (2017)
Supplementary Information
*Corresponding authors.

54.

W. Ma, L. Yang, R. Rohs*, and W.S. Noble*:
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.
Bioinformatics 33, 3003-3010 (2017)
Supplementary Information
*Corresponding authors.

53.

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.12, 1489-1493 (2017)
Supplementary Information

52.

J.M. Sagendorf, H.M. Berman*, and R. Rohs*:
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Nucleic Acids Res. 45, W89-W97 (2017)
Supplementary Information
*Corresponding authors.

51.

S. Kasinathan, G.E. Zentner, B. Xin, R. Rohs, and S. Henikoff:
Correspondence: Reply to 'DNA shape is insufficient to explain binding'.
Nat. Commun. 8, 15644 (2017)

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:
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-D109 (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, 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, 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-D155 (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-W62 (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, 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
*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)

November 20, 2017
We expanded our high-throughput prediction method to 13 DNA shape features with a new publication in NAR. Congrats, Jinsen!

November 20, 2017
Our recent Yang et al. Mol. Syst. Biol. paper received a RECOMB/ISCB Top-10 Paper Award in regulatory and systems genomics in 2016/17.

October 11, 2017
We published a new method to derive minor-groove electrostatic potential on a genomic scale in NAR. Congrats, Tsu-Pei!

August 16, 2017
Remo started the Quantitative Biology (QBIO) major at the interface of biology and computer science.

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!

Recent news

September 28, 2017
Faculty of Biological Sciences Seminar, Pontificia Universidad Católica de Chile, Santiago, Chile

September 23-26, 2017
Molecular Biosystems Conference on Eukaryotic Gene Regulation & Functional Genomics, Puerto Varas, Chile

August 20-24, 2017
Symposium on Molecular Recognition, 254th American Chemical Society Meeting, Washington, DC

May 24, 2017
Workshop “Mathematical Oncology: Modeling Clinical Data for Maximum Patient Benefit”, University of Southern California, Los Angeles, CA

April 28, 2017
Department of Bioinformatics and Genomics, University of North Carolina, NC

April 13, 2017
Department of Chemistry, University of Utah, Salt Lake City, UT

March 22, 2017
Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN

March 9, 2017
Program in Quantitative and Computational Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ

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