Remo Rohs

Affiliations

Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089.
Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089.
Department of Computer Science, University of Southern California, Los Angeles, CA 90089.

Publications (29)

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Xiaolin Wu , Bo Cao , Patricia Aquino , Tsu-Pei Chiu , Chao Chen , Susu Jiang , Zixin Deng , Shi Chen , Lianrong Wang , James E Galagan , Peter C Dedon

Author Correction: Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.

Nature

Avec: Simon Schwörer , Friedrich Becker , Christian Feller , Ali H Baig , Ute Köber , Henriette Henze , Johann M Kraus , Beibei Xin , André Lechel , Daniel B Lipka , Christy S Varghese , Manuel Schmidt , Ruedi Aebersold , Kay L Medina , Hans A Kestler , Francesco Neri , Julia von Maltzahn , Stefan Tümpel , K Lenhard Rudolph

Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors.

Journal of molecular biology

Avec: Judith F Kribelbauer , Xiang-Jun Lu , Richard S Mann , Harmen J Bussemaker

Genome information processing by the INO80 chromatin remodeler positions nucleosomes.

Nature communications

Avec: Elisa Oberbeckmann , Nils Krietenstein , Vanessa Niebauer , Yingfei Wang , Kevin Schall , Manuela Moldt , Tobias Straub , Karl-Peter Hopfner , Philipp Korber , Sebastian Eustermann

Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method.

bioRxiv : the preprint server for biology

Avec: Jinsen Li , Tsu-Pei Chiu ,

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

Journal of molecular biology

Avec: Xiao Lei , Jun Zhao , Jared M Sagendorf , Niroop Rajashekar , Jiang Xu , Ana Carolina Dantas Machado , Chandani Sen , Pinghui Feng , Lin Chen

Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.

Nucleic acids research

Avec: Jinsen Li ,

Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism.

bioRxiv : the preprint server for biology

Avec: Yuanzhong Pan , Tsu-Pei Chiu , Lili Zhou , Priscilla Chan , Tia Tyrsett Kuo , Francesca Battaglin , Shivani Soni , Priya Jayachandra , Jingyi Jessica Li , Heinz-Josef Lenz , Shannon M Mumenthaler , Evanthia Roussos Torres , Steve A Kay

Predicting DNA structure using a deep learning method.

Nature communications

Avec: Jinsen Li , Tsu-Pei Chiu ,

RNAscape: geometric mapping and customizable visualization of RNA structure.

Nucleic acids research

Avec: Raktim Mitra , Ari S Cohen ,

Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.

Nucleic acids research

Avec: Ana Carolina Dantas Machado , Brendon H Cooper , Xiao Lei , Rosa Di Felice , Lin Chen ,

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.

Nucleic acids research

Avec: Jared M Sagendorf , Nicholas Markarian , Helen M Berman ,

DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity.

bioRxiv : the preprint server for biology

Avec: Raktim Mitra , Jinsen Li , Jared M Sagendorf , Yibei Jiang , Tsu-Pei Chiu ,

DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.

Nucleic acids research

Avec: Brendon H Cooper , Ana Carolina Dantas Machado , Yan Gan , Oscar M Aparicio ,

Humanizing the yeast origin recognition complex.

Nature communications

Avec: Clare S K Lee , Ming Fung Cheung , Jinsen Li , Yongqian Zhao , Wai Hei Lam , Vincy Ho , Yuanliang Zhai , Danny Leung , Bik-Kwoon Tye

Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.

Bioinformatics (Oxford, England)

Avec: Brendon H Cooper , Tsu-Pei Chiu ,

CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid.

Biochemistry

Avec: Yue Li , Brendon H Cooper , Yukang Liu , Difei Wu , Xiaojun Zhang , Peter Z Qin

DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model.

bioRxiv : the preprint server for biology

Avec: Jesse A Weller ,

Physicochemical models of protein-DNA binding with standard and modified base pairs.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Tsu-Pei Chiu , Satyanarayan Rao ,

Structure-Based Drug Design with a Deep Hierarchical Generative Model.

Journal of chemical information and modeling

Avec: Jesse A Weller ,

Geometric deep learning of protein-DNA binding specificity.

Nature methods

Avec: Raktim Mitra , Jinsen Li , Jared M Sagendorf , Yibei Jiang , Ari S Cohen , Tsu-Pei Chiu , Cameron J Glasscock ,

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.

Nucleic acids research

Avec: Tsu-Pei Chiu , Beibei Xin , Nicholas Markarian , Yingfei Wang ,

Regulatory encoding of quantitative variation in spatial activity of a

Science advances

Avec: Yann Le Poul , Yaqun Xin , Liucong Ling , Bettina Mühling , Rita Jaenichen , David Hörl , David Bunk , Hartmann Harz , Heinrich Leonhardt , Yingfei Wang , Elena Osipova , Mariam Museridze , Deepak Dharmadhikari , Eamonn Murphy , Stephan Preibisch , Benjamin Prud'homme , Nicolas Gompel

The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.

Biochemistry

Avec: Samuel Lara-Gonzalez , Ana Carolina Dantas Machado , Satyanarayan Rao , Andrew A Napoli , Jens Birktoft , Rosa Di Felice , Catherine L Lawson

Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.

Biophysical journal

Avec: Yibei Jiang , Tsu-Pei Chiu , Raktim Mitra ,

PNAbind: Structure-based prediction of protein-nucleic acid binding using graph neural networks.

bioRxiv : the preprint server for biology

Avec: Jared M Sagendorf , Raktim Mitra , Jiawei Huang , Xiaojiang S Chen ,

Hand2 represses non-cardiac cell fates through chromatin remodeling at

bioRxiv : the preprint server for biology

Avec: Valerie Komatsu , Brendon Cooper , Paul Yim , Kira Chan , Wesley Gong , Lucy Wheatley , Scott E Fraser , Le A Trinh

DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.

Nucleic acids research

Avec: Victoria A Bonnell , Yuning Zhang , Alan S Brown , John Horton , Gabrielle A Josling , Tsu-Pei Chiu , Shaun Mahony , Raluca Gordân , Manuel Llinás

Structure-based prediction of protein-nucleic acid binding using graph neural networks.

Biophysical reviews

Avec: Jared M Sagendorf , Raktim Mitra , Jiawei Huang , Xiaojiang S Chen ,

Réseau de co-auteurs

Tsu-Pei Chiu 11 collaborations

Jinsen Li 6 collaborations

Jared M Sagendorf 6 collaborations

Raktim Mitra 6 collaborations

Ana Carolina Dantas Machado 4 collaborations

Brendon H Cooper 4 collaborations

Yingfei Wang 3 collaborations

Yibei Jiang 3 collaborations

Beibei Xin 2 collaborations

Xiao Lei 2 collaborations

Lin Chen 2 collaborations

Ari S Cohen 2 collaborations

Rosa Di Felice 2 collaborations

Nicholas Markarian 2 collaborations

Jesse A Weller 2 collaborations

Satyanarayan Rao 2 collaborations

Jiawei Huang 2 collaborations

Xiaojiang S Chen 2 collaborations

Xiaolin Wu 1 collaboration

Bo Cao 1 collaboration

Patricia Aquino 1 collaboration

Chao Chen 1 collaboration

Susu Jiang 1 collaboration

Zixin Deng 1 collaboration

Shi Chen 1 collaboration

Lianrong Wang 1 collaboration

James E Galagan 1 collaboration

Peter C Dedon 1 collaboration

Simon Schwörer 1 collaboration

Friedrich Becker 1 collaboration

Christian Feller 1 collaboration

Ali H Baig 1 collaboration

Ute Köber 1 collaboration

Henriette Henze 1 collaboration

Johann M Kraus 1 collaboration

André Lechel 1 collaboration

Daniel B Lipka 1 collaboration

Christy S Varghese 1 collaboration

Manuel Schmidt 1 collaboration

Ruedi Aebersold 1 collaboration

Kay L Medina 1 collaboration

Hans A Kestler 1 collaboration

Francesco Neri 1 collaboration

Julia von Maltzahn 1 collaboration

Stefan Tümpel 1 collaboration

K Lenhard Rudolph 1 collaboration

Judith F Kribelbauer 1 collaboration

Xiang-Jun Lu 1 collaboration

Richard S Mann 1 collaboration

Harmen J Bussemaker 1 collaboration

Elisa Oberbeckmann 1 collaboration

Nils Krietenstein 1 collaboration

Vanessa Niebauer 1 collaboration

Kevin Schall 1 collaboration

Manuela Moldt 1 collaboration

Tobias Straub 1 collaboration

Karl-Peter Hopfner 1 collaboration

Philipp Korber 1 collaboration

Sebastian Eustermann 1 collaboration

Jun Zhao 1 collaboration

Niroop Rajashekar 1 collaboration

Jiang Xu 1 collaboration

Chandani Sen 1 collaboration

Pinghui Feng 1 collaboration

Yuanzhong Pan 1 collaboration

Lili Zhou 1 collaboration

Priscilla Chan 1 collaboration

Tia Tyrsett Kuo 1 collaboration

Francesca Battaglin 1 collaboration

Shivani Soni 1 collaboration

Priya Jayachandra 1 collaboration

Jingyi Jessica Li 1 collaboration

Heinz-Josef Lenz 1 collaboration

Shannon M Mumenthaler 1 collaboration

Evanthia Roussos Torres 1 collaboration

Steve A Kay 1 collaboration

Helen M Berman 1 collaboration

Yan Gan 1 collaboration

Oscar M Aparicio 1 collaboration

Clare S K Lee 1 collaboration

Ming Fung Cheung 1 collaboration

Yongqian Zhao 1 collaboration

Wai Hei Lam 1 collaboration

Vincy Ho 1 collaboration

Yuanliang Zhai 1 collaboration

Danny Leung 1 collaboration

Bik-Kwoon Tye 1 collaboration

Yue Li 1 collaboration

Yukang Liu 1 collaboration

Difei Wu 1 collaboration

Xiaojun Zhang 1 collaboration

Peter Z Qin 1 collaboration

Cameron J Glasscock 1 collaboration

Yann Le Poul 1 collaboration

Yaqun Xin 1 collaboration

Liucong Ling 1 collaboration

Bettina Mühling 1 collaboration

Rita Jaenichen 1 collaboration

David Hörl 1 collaboration

David Bunk 1 collaboration

Hartmann Harz 1 collaboration

Heinrich Leonhardt 1 collaboration

Elena Osipova 1 collaboration

Mariam Museridze 1 collaboration

Deepak Dharmadhikari 1 collaboration

Eamonn Murphy 1 collaboration

Stephan Preibisch 1 collaboration

Benjamin Prud'homme 1 collaboration

Nicolas Gompel 1 collaboration

Samuel Lara-Gonzalez 1 collaboration

Andrew A Napoli 1 collaboration

Jens Birktoft 1 collaboration

Catherine L Lawson 1 collaboration

Valerie Komatsu 1 collaboration

Brendon Cooper 1 collaboration

Paul Yim 1 collaboration

Kira Chan 1 collaboration

Wesley Gong 1 collaboration

Lucy Wheatley 1 collaboration

Scott E Fraser 1 collaboration

Le A Trinh 1 collaboration

Victoria A Bonnell 1 collaboration

Yuning Zhang 1 collaboration

Alan S Brown 1 collaboration

John Horton 1 collaboration

Gabrielle A Josling 1 collaboration

Shaun Mahony 1 collaboration

Raluca Gordân 1 collaboration

Manuel Llinás 1 collaboration