James J. Collins

Also affiliated with Harvard University, Massachusetts Institute of Technology

Biochemistry, Genetics and Molecular Biology

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 48 papers. Top paper: “ImmGen at 15”.

ImmGen at 15

Nature Immunology(2020)10.1038/s41590-020-0687-4

N/A

2.8DataRank · unranked

81 citations

Stephanie Vargas Aguilar, Oscar A. Aguilar, Rhys S. Allan, El Ad David Amir, Véronique Angeli +94 more

Deep generative design of RNA aptamers using structural predictions

Nature Computational Science(2024)10.1038/s43588-024-00720-6

N/A

1.8DataRank · unranked

73 citations

Dongchen He, Aarti Krishnan, Liang Hong, Alexander Wang, Jiuming Wang +14 more

Nucleic acid detection with CRISPR-Cas13a/C2c2

Science(2017)10.1126/science.aam9321

N/A

1.2DataRank · unranked

3722 citations

Omar O. Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J. Dy, Julia Joung +15 more

A Deep Learning Approach to Antibiotic Discovery

Cell(2020)10.1016/j.cell.2020.01.021

N/A

1.1DataRank · unranked

2079 citations

Kevin Yang, Kyle Swanson, Wengong Jin, Andrés Cubillos-Ruiz, Nina M. Donghia +15 more

Wisdom of crowds for robust gene network inference

Nature Methods(2012)10.1038/nmeth.2016

N/A

1.1DataRank · unranked

1765 citations

Daniel Marbach, James C. Costello, Robert Küffner, Nicole M Vega, Robert J. Prill +5 more

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Nature(2014)10.1038/nature13920

N/A

0.893DataRank · unranked

384 citations

Patrick Cahan, Alex K. Shalek, Rahul Satija, A. Jay DaleyKeyser, Hu Li +11 more

CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development

Nature Cell Biology(2022)10.1038/s41556-022-00884-1

N/A

0.824DataRank · unranked

29 citations

Caroline Kubaczka, Wade W. Sugden, Mohamad Najia, Ran Jing, Arianna Markel +7 more

Transcriptome Analysis Identifies Regulators of Hematopoietic Stem and Progenitor Cells

Stem Cell Reports(2013)10.1016/j.stemcr.2013.07.004

N/A

0.675DataRank · unranked

89 citations

Brian S. Garrison, Tata Nageswara Rao, Tal Shay, Jeff Ericson, Francis Kim +7 more

Catalase activity deficiency sensitizes multidrug-resistant Mycobacterium tuberculosis to the ATP synthase inhibitor bedaquiline

Nature Communications(2024)10.1038/s41467-024-53933-8

N/A

0.534DataRank · unranked

19 citations

Meagan Hamblin, Miranda L Coldren, Barry Li, Gautam Mereddy, Mustafa Shaikh +9 more

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes

Science(2025)10.1126/science.adi8577

N/A

0.490DataRank · unranked

22 citations

Charlotte Nesbitt, Samuel A. Miller, Daniel B. Burkhardt, Inna Lipchina, Doris Fu +18 more

RNA-responsive elements for eukaryotic translational control

Nature Biotechnology(2021)10.1038/s41587-021-01068-2

N/A

0DataRank · unranked

103 citations

Angelo S. Mao, Helena de Puig, Kehan Zhang, Nathaniel D. Tippens, Xiao Tan +12 more

Lab-on-a-chip multiplexed electrochemical sensor enables simultaneous detection of SARS-CoV-2 RNA and host antibodies

medRxiv(2021)10.1101/2021.09.01.21262387

N/A

0DataRank · unranked

17 citations

Joshua Rainbow, Sanjay Sharma Timilsina, Pawan Jolly, Helena de Puig, Mohamed Yafia +11 more

A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma

Nature Biomedical Engineering(2022)10.1038/s41551-022-00919-w

N/A

0DataRank · unranked

279 citations

Joshua Rainbow, Sharma T. Sanjay, Pawan Jolly, Helena de Puig, Mohamed Yafia +11 more

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

Molecular Systems Biology(2022)10.15252/msb.202211081

N/A

0DataRank · unranked

271 citations

Aarti Krishnan, Erica J. Zheng, H. Stärk, Abigail L. Manson, Ashlee M. Earl +3 more

The sound of silence: Transgene silencing in mammalian cell engineering

Cell Systems(2022)10.1016/j.cels.2022.11.005

N/A

0DataRank · unranked

205 citations

Hailey I. Edelstein, Fokion Glykofrydis, Kasey S. Love, Sebastian Palacios, Josh Tycko +22 more

Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples

Nature Biomedical Engineering(2022)10.1038/s41551-022-00850-0

N/A

0DataRank · unranked

89 citations

Severino Jefferson Ribeiro da Silva, Yuxiu Guo, Seray Cicek, Larissa Krokovsky, Paige Homme +24 more

Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies

Nature Communications(2022)10.1038/s41467-022-30272-0

N/A

0DataRank · unranked

69 citations

Ian W. Andrews, Alexandra Grote, Abigail L. Manson, Miguel A. Alcantar, Ashlee M. Earl +2 more

Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality

Cell chemical biology(2022)10.1016/j.chembiol.2021.12.010

N/A

0DataRank · unranked

55 citations

Ian W. Andrews, Dana Braff, Caroline B. M. Porter, Arnaud Gutierrez, Yoshikazu Furuta +11 more

Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions

Molecular Cell(2022)10.1016/j.molcel.2022.07.009

N/A

0DataRank · unranked

48 citations

Jonathan Stokes, Sarah C. Bening, Charles Vidoudez, Sunia A. Trauger, James J. Collins +1 more

SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates

Nucleic Acids Research(2022)10.1093/nar/gkac531

N/A

0DataRank · unranked

35 citations

Chadi A. El Farran, Yingying Zeng, Benedict Shao Quan Ho, Qiuye Bao, Zihao Zheng +11 more

Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness

Nano Today(2022)10.1016/j.nantod.2022.101669

N/A

0DataRank · unranked

14 citations

Irene Bosch, Nol Salcedo, James J. Collins, Kimberly Hamad‐Schifferli, Lee Gehrke +1 more

Prediction of intercellular communication networks using CellComm

Research Square(2022)10.21203/rs.3.pex-1843/v1

N/A

0DataRank · unranked

1 citations

Caroline Kubaczka, Wade W. Sugden, Mohamad Najia, Ran Jing, Arianna Markel +7 more

Discovery of a structural class of antibiotics with explainable deep learning

Nature(2023)10.1038/s41586-023-06887-8

N/A

0DataRank · unranked

429 citations

Erica J. Zheng, Jacqueline A. Valeri, Nina M. Donghia, Melis N. Anahtar, Satotaka Omori +16 more

Lateral flow test engineering and lessons learned from COVID-19

Nature Reviews Bioengineering(2023)10.1038/s44222-022-00007-3

N/A

0DataRank · unranked

294 citations

Benjamin S. Miller, Nicole E. Weckman, Dounia Cherkaoui, Da Huang, Alyssa Thomas DeCruz +22 more

Leveraging artificial intelligence in the fight against infectious diseases

Science(2023)10.1126/science.adh1114

N/A

0DataRank · unranked

282 citations

César de la Fuente‐Núñez, James J. Collins, Felix Wong

Discovery of antibiotics that selectively kill metabolically dormant bacteria

Cell chemical biology(2023)10.1016/j.chembiol.2023.10.026

N/A

0DataRank · unranked

53 citations

Jacqueline A. Valeri, Ian W. Andrews, Aarti Krishnan, Parijat Bandyopadhyay, Melis N. Anahtar +9 more

BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences

Cell Systems(2023)10.1016/j.cels.2023.05.007

N/A

0DataRank · unranked

42 citations

Luis R. Soenksen, Katherine M. Collins, Pradeep Ramesh, George Cai, Rani K. Powers +6 more

Autocatalytic base editing for RNA-responsive translational control

Nature Communications(2023)10.1038/s41467-023-36851-z

N/A

0DataRank · unranked

35 citations

Katherine Ilia, Shiva Razavi, Nathaniel D. Tippens, Makoto A. Lalwani, Kehan Zhang +5 more

Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.25.525529

N/A

0DataRank · unranked

8 citations

Nika Shakiba, Trevor Bingham, Ross D. Jones, Michael M. Kaminski, Eliezer Aravera +7 more

Engineering synthetic phosphorylation signaling networks in human cells

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557100

N/A

0DataRank · unranked

8 citations

Jason W. Rocks, Kaiyi Jiang, Andrew J. Walters, Kshitij Rai, Jing Liu +7 more

Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches

medRxiv(2023)10.1101/2023.06.02.23290873

N/A

0DataRank · unranked

5 citations

Anli A. Tang, Amit Eshed, Zackary M. Ticktin, Soma Chaudhary, Duo Ma +11 more

A niche-derived non-ribosomal peptide triggers planarian sexual development

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.06.570471

N/A

0DataRank · unranked

3 citations

Katherine L. Browder, Rui Chen, James J. Collins, Phillip A. Newmark, Melanie Issigonis

Machine learning for antimicrobial peptide identification and design

Nature Reviews Bioengineering(2024)10.1038/s44222-024-00152-x

N/A

0DataRank · unranked

229 citations

Felix Wong, James J. Collins, César de la Fuente‐Núñez, Fang Wan

Accurate RNA 3D structure prediction using a language model-based deep learning approach

Nature Methods(2024)10.1038/s41592-024-02487-0

N/A

0DataRank · unranked

198 citations

Zhihang Hu, Siqi Sun, Di Liu, Felix Wong, Jiuming Wang +12 more

Rapid, multiplexed, and enzyme-free nucleic acid detection using programmable aptamer-based RNA switches

Chem(2024)10.1016/j.chempr.2024.03.015

N/A

0DataRank · unranked

31 citations

Amit Eshed, Anli A. Tang, Nery R. Arevalos, Zachary M. Ticktin, Soma Chaudhary +12 more

An explainable deep learning platform for molecular discovery

Nature Protocols(2024)10.1038/s41596-024-01084-x

N/A

0DataRank · unranked

24 citations

Satotaka Omori, Alicia Li, Aarti Krishnan, Ryan S. Lach, Joseph Rufo +3 more

O-glycosylation contributes to mammalian glycoRNA biogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.28.610074

N/A

0DataRank · unranked

20 citations

Christopher Watkins, Chunsheng Jin, Xixuan Xie, Xiao Tan, Charlotta G. Lebedenko +8 more

Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells

Nature(2015)10.1038/nature14150

N/A

0DataRank · unranked

0 citations

Patrick Cahan, Alex K. Shalek, Rahul Satija, A. Jay DaleyKeyser, Hu Li +12 more

Essay: Using Machine Learning for Antibiotic Discovery

Physical Review Letters(2025)10.1103/y3fg-s9vg

N/A

0DataRank · unranked

9 citations

James J. Collins, César de la Fuente‐Núñez

Cell-free biosensors for rapid detection of water contaminants

Nature Biotechnology(2020)10.1038/s41587-020-0571-7

N/A

0DataRank · unranked

409 citations

Khalid K. Alam, Matthew S. Verosloff, Daiana A. Capdevila, Morgane Desmau, Phillip R. Clauer +9 more

Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway

Nature Communications(2020)10.1038/s41467-020-18018-2

N/A

0DataRank · unranked

31 citations

Ahmed H. Badran, James J. Collins, Chad W. Johnston

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility

Genome Research(2020)10.1101/gr.257840.119

N/A

0DataRank · unranked

73 citations

Chadi A. El Farran, Ying Ying Zeng, Yao Yi, Tushar Warrier, Pradeep Gautam +8 more

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

Science(2021)10.1126/science.aba0862

N/A

0DataRank · unranked

362 citations

Sarah C. Bening, Abigail L. Manson, Jonathan Stokes, Michael A. Kohanski, Ahmed H. Badran +5 more

Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants

Science Advances(2021)10.1126/sciadv.abh2944

N/A

0DataRank · unranked

330 citations

Rose Lee, Devora Najjar, Xiao Tan, Luis R. Soenksen, Nicolaas M. Angenent-Mari +12 more

Deep learning identifies synergistic drug combinations for treating COVID-19

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2105070118

N/A

0DataRank · unranked

174 citations

Jonathan Stokes, Richard T. Eastman, Zina Itkin, Alexey Zakharov, James J. Collins +3 more

Engineering advanced logic and distributed computing in human CAR immune cells

Nature Communications(2021)10.1038/s41467-021-21078-7

N/A

0DataRank · unranked

137 citations

Atsushi Okuma, Katri Sofjan, Seunghee Lee, James J. Collins, Wilson W. Wong +1 more

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics

Cell(2021)10.1016/j.cell.2021.01.017

N/A

0DataRank · unranked

135 citations

Justin H. Letendre, James J. Collins, Wilson W. Wong, Xiao Tan

Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality

Nature Communications(2021)10.1038/s41467-021-22485-6

N/A

0DataRank · unranked

126 citations

Jonathan Stokes, Bernardo Cervantes, Sider Penkov, Jens Friedrichs, Lars D. Renner +2 more