Remo Rohs

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 50

Top Topics

Circulating Tumor

Top Venues

Nucleic acids research

Nature communications

bioRxiv : the preprint server for biology

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

This page only lists publications with an associated author ORCID identifier.

Publications

Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Jesse A Weller, Remo Rohs
Structure-Based Drug Design with a Deep Hierarchical Generative Model. Journal of chemical information and modeling 64 (16) (2024)
Raktim Mitra, Ari S Cohen, Remo Rohs
RNAscape: geometric mapping and customizable visualization of RNA structure. Nucleic acids research (2024)
Jesse A Weller, Remo Rohs
Structure-Based Drug Design with a Deep Hierarchical Generative Model. Journal of chemical information and modeling 64 (16) (2024)
Jinsen Li, Remo Rohs
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers. Nucleic acids research 52 (W1) (2024)
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, Remo Rohs, Evanthia Roussos Torres, Steve A Kay
Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism. bioRxiv : the preprint server for biology (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Jesse A Weller, Remo Rohs
Structure-Based Drug Design with a Deep Hierarchical Generative Model. Journal of chemical information and modeling (2024)
Raktim Mitra, Ari S Cohen, Remo Rohs
RNAscape: geometric mapping and customizable visualization of RNA structure. Nucleic acids research 52 (W1) (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Jinsen Li, Remo Rohs
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers. Nucleic acids research (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Jared M Sagendorf, Raktim Mitra, Jiawei Huang, Xiaojiang S Chen, Remo Rohs
PNAbind: Structure-based prediction of protein-nucleic acid binding using graph neural networks. bioRxiv : the preprint server for biology (2024)
Jesse A Weller, Remo Rohs
Structure-Based Drug Design with a Deep Hierarchical Generative Model. Journal of chemical information and modeling (2024)
Jesse A Weller, Remo Rohs
Structure-Based Drug Design with a Deep Hierarchical Generative Model. Journal of chemical information and modeling 64 (16) (2024)
Jesse A Weller, Remo Rohs
DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model. bioRxiv : the preprint server for biology (2024)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Predicting DNA structure using a deep learning method. Nature communications 15 (1) (2024)
Raktim Mitra, Ari S Cohen, Remo Rohs
RNAscape: geometric mapping and customizable visualization of RNA structure. Nucleic acids research 52 (W1) (2024)
Jinsen Li, Remo Rohs
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers. Nucleic acids research 52 (W1) (2024)
Yuanzhong Pan, Tsu-Pei Chiu, Lili Zhou, Priscilla Chan, Tia Tyrsett Kuo, Francesca Battaglin, Shivani Soni, Priya Jayachandran, Jingyi Jessica Li, Heinz-Josef Lenz, Shannon M Mumenthaler, Remo Rohs, Evanthia Roussos Torres, Steve A Kay
Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism. bioRxiv : the preprint server for biology (2024)
Raktim Mitra, Jinsen Li, Jared M Sagendorf, Yibei Jiang, Ari S Cohen, Tsu-Pei Chiu, Cameron J Glasscock, Remo Rohs
Geometric deep learning of protein-DNA binding specificity. Nature methods (2024)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Jesse A Weller, Remo Rohs
DrugHIVE: A Deep Hierarchical Variational Autoencoder for the Structure-Based Design of Drug-Like Molecules. bioRxiv : the preprint server for biology (2023)
Yue Li, Brendon H Cooper, Yukang Liu, Difei Wu, Xiaojun Zhang, Remo Rohs, Peter Z Qin
CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry (2023)
Brendon H Cooper, Ana Carolina Dantas Machado, Yan Gan, Oscar M Aparicio, Remo Rohs
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors. Nucleic acids research (2023)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method. bioRxiv : the preprint server for biology (2023)
Tsu-Pei Chiu, Satyanarayan Rao, Remo Rohs
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 120 (4) (2023)
Raktim Mitra, Jinsen Li, Jared M Sagendorf, Yibei Jiang, Tsu-Pei Chiu, Remo Rohs
DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity. bioRxiv : the preprint server for biology (2023)
Valerie Komatsu, Brendon Cooper, Paul Yim, Kira Chan, Wesley Gong, Lucy Wheatley, Remo Rohs, Scott E Fraser, Le A Trinh
Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements. bioRxiv : the preprint server for biology (2023)
Brendon H Cooper, Ana Carolina Dantas Machado, Yan Gan, Oscar M Aparicio, Remo Rohs
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors. Nucleic acids research (2023)
Brendon H Cooper, Tsu-Pei Chiu, Remo Rohs
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics. Bioinformatics (Oxford, England) 38 (22) (2022)
Clare S K Lee, Ming Fung Cheung, Jinsen Li, Yongqian Zhao, Wai Hei Lam, Vincy Ho, Remo Rohs, Yuanliang Zhai, Danny Chi Yeu Leung, Bik-Kwoon Tye
Humanizing the yeast origin recognition complex. Nature communications 12 (1) (2021)
Elisa Oberbeckmann, Nils Krietenstein, Vanessa Niebauer, Yingfei Wang, Kevin Schall, Manuela Moldt, Tobias Straub, Remo Rohs, Karl-Peter Hopfner, Philipp Korber, Sebastian Eustermann
Genome information processing by the INO80 chromatin remodeler positions nucleosomes. Nature communications 12 (1) (2021)
Samuel Lara-Gonzalez, Ana Carolina Dantas Machado, Satyanarayan Rao, Andrew A Napoli, Jens Birktoft, Rosa Di Felice, Remo Rohs, Catherine L Lawson
The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry 59 (48) (2020)
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, Remo Rohs, Stephan Preibisch, Benjamin Prud'homme, Nicolas Gompel
Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Science advances 6 (49) (2020)
Xiaolin Wu, Bo Cao, Patricia Aquino, Tsu-Pei Chiu, Chao Chen, Susu Jiang, Zixin Deng, Shi Chen, Remo Rohs, Lian-Rong Wang, James E Galagan, Peter C Dedon
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 117 (25) (2020)
Beibei Xin, Remo Rohs
Relationship between histone modifications and transcription factor binding is protein family specific. Genome research (2018)
Satyanarayan Rao, Tsu-Pei Chiu, Judith F Kribelbauer, Richard S Mann, Harmen J Bussemaker, Remo Rohs
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. Epigenetics & chromatin 11 (1) (2018)
Narin S Tangprasertchai, Rosa Di Felice, Xiaojun Zhang, Ian M Slaymaker, Carolina Vazquez Reyes, Wei Jiang, Remo Rohs, Peter Z Qin
CRISPR-Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling. ACS chemical biology 12 (6) (2017)
Lin Yang, Yaron Orenstein, Arttu Jolma, Yimeng Yin, Jussi Taipale, Ron Shamir, Remo Rohs
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models. Molecular systems biology 13 (2) (2017)
Jun Li, Ana Carolina Dantas Machado, Ming Guo, Jared M Sagendorf, Zhan Zhou, Longying Jiang, Xiaojuan Chen, Daichao Wu, Lingzhi Qu, Zhuchu Chen, Lin Chen, Remo Rohs, Yongheng Chen
Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site. Biochemistry 56 (29) (2017)