José N. Onuchic

Center for Theoretical Biological Physics

Biochemistry, Genetics and Molecular BiologyMaterials SciencePhysics and Astronomy

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 3%percentile

1.1Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Nucleic Acids Research(2020)10.1093/nar/gkaa818

Top 24%

0.851DataRank

Top 24%35 citations

Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman-Aiden +4 more

Papers

Driven by 42 papers — median percentile 56. Top paper: “Probing the folding free energy landscape of the src-SH3 protein domain”.

Probing the folding free energy landscape of the src-SH3 protein domain

Proceedings of the National Academy of Sciences(2002)10.1073/pnas.242293099

N/A

6.3DataRank · unranked

141 citations

José N. Onuchic, Charles L. Brooks, Joan-Emma Shea

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Nucleic Acids Research(2020)10.1093/nar/gkaa818

Top 24%

0.851DataRank

Top 24%35 citations

Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman-Aiden +4 more

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.30.547175

Top 65%

0.208DataRank

Top 65%3 citations

Olga Dudchenko, Juan Antonio Rodríguez, Cynthia Pérez Estrada, Marianne Dehasque, Claudia Fontsere +27 more

A data-driven chromatin model reveals spatial and dynamic features of genome organization

Proceedings of the National Academy of Sciences(2026)10.1073/pnas.2530583123

N/A

0.104DataRank · unranked

1 citations

Matheus F. Mello, Ronaldo J. Oliveira, Esteban Dodero-Rojas, Sumitabha Brahmachari, Vinícius G. Contessoto +4 more

Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits

Bioinformatics(2020)10.1093/bioinformatics/btaa785

N/A

0DataRank · unranked

5 citations

Danya Gordin, Ataur Katebi, Herbert Levine, José N. Onuchic, Mingyang Lu +1 more

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Science(2021)10.1126/science.abe2218

N/A

0DataRank · unranked

302 citations

Olga Dudchenko, Ahmed M.O. Elbatsh, Sumitabha Brahmachari, Jonne A. Raaijmakers, Tom van Schaik +59 more

Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer

British Journal of Cancer(2021)10.1038/s41416-021-01385-y

N/A

0DataRank · unranked

109 citations

Jun Hyoung Park, Harsimran Kaur, Kwang Hwa Jung, Sukjin Yang, Shubham Tripathi +7 more

Mechanistic basis of propofol-induced disruption of kinesin processivity

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2023659118

N/A

0DataRank · unranked

10 citations

Susan P. Gilbert, José N. Onuchic, Biman Jana, Mandira Dutta

Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.15.435496

N/A

0DataRank · unranked

5 citations

Fenny H. F. Tang, Christopher Markosian, Virginia J. Yao, Fernanda I. Staquicini, Esteban Dodero-Rojas +16 more

Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.30.458222

N/A

0DataRank · unranked

4 citations

Daniela I. Staquicini, Prashant Dogra, Esteban Dodero-Rojas, Fenny H. F. Tang, Tracey L. Smith +10 more

Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma

Biophysics Reviews(2022)10.1063/5.0080512

N/A

0DataRank · unranked

44 citations

Vitor B. P. Leite, Susmita Roy, Supriyo Bhattacharyya, Atish Mohanty, Srisairam Achuthan +11 more

Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167788

N/A

0DataRank · unranked

8 citations

José N. Onuchic, Karissa Y. Sanbonmatsu, Jigneshkumar Dahyabhai Prajapati

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Molecular Biology and Evolution(2022)10.1093/molbev/msac091

N/A

0DataRank · unranked

13 citations

Daniela I. Staquicini, Prashant Dogra, Esteban Dodero-Rojas, Joseph H. Lubin, Fenny H. F. Tang +12 more

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.01.478655

N/A

0DataRank · unranked

4 citations

Olga Dudchenko, Erez Lieberman Aiden, Peter G. Wolynes, José N. Onuchic, Michele Di Pierro +1 more

Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.03.506488

N/A

0DataRank · unranked

2 citations

Sumitabha Brahmachari, Vinícius G. Contessoto, Ryan R. Cheng, Antonio B. Oliveira Junior, Michele Di Pierro +2 more

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.07.519534

N/A

0DataRank · unranked

2 citations

Federico Bocci, Qing Nie, José N. Onuchic, Andre Levchenko, Tae-Yun Kang

An Associative Memory Hamiltonian Model for DNA and Nucleosomes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.15.512163

N/A

0DataRank · unranked

1 citations

José N. Onuchic, Michele Di Pierro, Weiqi Lu

BAP1 is a novel regulator of HIF-1α

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2217840120

N/A

0DataRank · unranked

30 citations

Qian Wang, Alicia A. Zolondick, Fang Bai, Mika Steele-Tanji, Joelle Sacks Suarez +23 more

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues

Nature Communications(2023)10.1038/s41467-023-35909-2

N/A

0DataRank · unranked

29 citations

Olga Dudchenko, Erez Lieberman Aiden, Peter G. Wolynes, José N. Onuchic, Michele Di Pierro +1 more

Structural reorganization and relaxation dynamics of axially stressed chromosomes

Biophysical Journal(2023)10.1016/j.bpj.2023.03.029

N/A

0DataRank · unranked

13 citations

Sumitabha Brahmachari, Vinícius G. Contessoto, Ryan R. Cheng, Antonio B. Oliveira Junior, Michele Di Pierro +2 more

Theoretical and computational tools to model multistable gene regulatory networks

Reports on Progress in Physics(2023)10.1088/1361-6633/acec88

N/A

0DataRank · unranked

12 citations

Dongya Jia, Qing Nie, Mohit Kumar Jolly, José N. Onuchic, Federico Bocci

Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

eLife(2023)10.7554/elife.89262

N/A

0DataRank · unranked

8 citations

Federico Bocci, Qing Nie, José N. Onuchic, Andre Levchenko, Tae-Yun Kang

An associative memory Hamiltonian model for DNA and nucleosomes

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011013

N/A

0DataRank · unranked

4 citations

José N. Onuchic, Michele Di Pierro, Weiqi Lu

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

(2023)10.7554/elife.89262.1

N/A

0DataRank · unranked

2 citations

Federico Bocci, Qing Nie, José N. Onuchic, Andre Levchenko, Tae-Yun Kang

Theoretical and computational tools to model multistable gene regulatory networks

arXiv (Cornell University)(2023)10.48550/arxiv.2302.07401

N/A

0DataRank · unranked

0 citations

Dongya Jia, Qing Nie, Mohit Kumar Jolly, José N. Onuchic, Federico Bocci

Structure and inhibition of SARS-CoV-2 spike refolding in membranes

Science(2024)10.1126/science.adn5658

N/A

0DataRank · unranked

52 citations

Zhuan Qin, Esteban Dodero-Rojas, Shilei Ding, Jérémie Prévost, Yaozong Chen +10 more

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Cell(2024)10.1016/j.cell.2024.06.002

N/A

0DataRank · unranked

45 citations

Olga Dudchenko, Juan Antonio Rodríguez, Cynthia Pérez Estrada, Marianne Dehasque, Claudia Fontsere +51 more

Machine learning in biological physics: From biomolecular prediction to design

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2311807121

N/A

0DataRank · unranked

13 citations

M. Mateos, José N. Onuchic, Ivan Coluzza, Faruck Morcos, Jonathan Martin

Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2405231121

N/A

0DataRank · unranked

12 citations

Yoshie Yoshikawa, Veronica Angela Maria Vitto, Lorenzo Modesti, Michael Minaai, Sandra Pastorino +31 more

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

RNA(2024)10.1261/rna.079767.123

N/A

0DataRank · unranked

11 citations

Susmit Narayan Chaudhury, Jigneshkumar Dahyabhai Prajapati, José N. Onuchic, Karissa Y. Sanbonmatsu, Erdong Ding

Designing proteins: Mimicking natural protein sequence heterogeneity

The Journal of Chemical Physics(2024)10.1063/5.0232831

N/A

0DataRank · unranked

1 citations

Jonathan Martin, José N. Onuchic, Faruck Morcos, Ivan Coluzza, M. Mateos

High-throughput prediction of peptide structural conformations with AlphaFold2

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.03.626727

N/A

0DataRank · unranked

3 citations

Christopher Markosian, S.K. Burley, Paul C. Whitford, José N. Onuchic, Renata Pasqualini +2 more

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

eLife(2024)10.7554/elife.89262.2

N/A

0DataRank · unranked

0 citations

Federico Bocci, Qing Nie, José N. Onuchic, Andre Levchenko, Tae-Yun Kang

Evolving concepts of the protein universe

iScience(2025)10.1016/j.isci.2025.112012

N/A

0DataRank · unranked

13 citations

Lauren Porter, Tsui‐Fen Chou, Shasha Chong, Fabrizio Chiti, Joseph W. Schafer +10 more

Biguanides antithetically regulate tumor properties by the dose-dependent mitochondrial reprogramming-driven c-Src pathway

Cell Reports Medicine(2025)10.1016/j.xcrm.2025.101941

N/A

0DataRank · unranked

11 citations

K.H. Jung, Dongya Jia, Sukjin Yang, Kuldeep S. Attri, Songyeon Ahn +21 more

Simulating biomolecules for physiological timescales

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.103039

N/A

0DataRank · unranked

10 citations

José N. Onuchic, Paul C. Whitford

Computational modeling of cancer cell metabolism along the catabolic-anabolic axes

npj Systems Biology and Applications(2025)10.1038/s41540-025-00525-x

N/A

0DataRank · unranked

7 citations

Herbert Levine, Benny Abraham Kaipparettu, José N. Onuchic, Jason T. George, Dongya Jia +1 more

Critical Role of Mg2+ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.5c02586

N/A

0DataRank · unranked

7 citations

Anushree Sinha, Avijit Mainan, Karissa Y. Sanbonmatsu, José N. Onuchic, Susmita Roy +2 more

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

RNA(2025)10.1261/rna.080274.124

N/A

0DataRank · unranked

2 citations

Erdong Ding, Nathan Jespersen, José N. Onuchic, Karissa Y. Sanbonmatsu, Susmit Narayan Chaudhury

Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry

Nature Communications(2020)10.1038/s41467-020-17997-6

N/A

0DataRank · unranked

207 citations

Xiaoli Qi, Xin Yu, Yang Liu, Chan-I Chung, Fang Bai +14 more

Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation

Journal of The Royal Society Interface(2020)10.1098/rsif.2020.0500

N/A

0DataRank · unranked

39 citations

Mingyang Lu, Madeline Galbraith, Herbert Levine, José N. Onuchic, Dongya Jia +1 more

Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype

Frontiers in Oncology(2020)10.3389/fonc.2020.01426

N/A

0DataRank · unranked

33 citations

B. Bishal Paudel, Corey E. Hayford, Keisha N. Hardeman, Herbert Levine, José N. Onuchic +2 more

José N. Onuchic

Indexed papers

Top data-sharing exemplar

Papers