James J. Collins

0000-0002-5560-8246

Gene Regulatory Networkssynthetic biologyModels, GeneticSynthetic BiologyDeep LearningGenetic EngineeringAnti-Bacterial AgentsantibioticsGene Expression RegulationModels, Biological

On Valency

published · living versions

MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

with Yikun Zhang, Xiwei Cheng, Mingze Yuan, Yu Zhang +13

1 version

W_ka3rjr2vv1 · current

Preprints & journals

354 papers in the corpus · 1989–2026

From code to cure: Harnessing AI for antibiotic discovery and design.

Krishnan, Aarti, Cao, Hanqun, Collins, James J et al.

0 citations

428738982026Science translational medicine. 2026;18(871):eaee4629

Deep learning-enabled discovery of antibiotics effective against Neisseria gonorrhoeae.

Anahtar, Melis N, Valeri, Jacqueline A, Modaresi, Seyed Majed et al.

5 citations

423083302026Science translational medicine. 2026;18(854):eads4699

Genetic code expansion enables programmable covalent protein design

de Puig, H., Kuru, E., Moret, M. et al.

0 citations

10.64898/2026.05.15.725538v12026bioRxiv

FATE-MAP predicts teratogenicity and human gastrulation failure modes by integrating deep learning and mechanistic modeling.

Rufo, Joseph, Qiu, Chongxu, Han, Dasol et al.

3 citations

417146222026Nature communications. 2026;17(1)

Generative AI for synthetic biology: Designing biological parts, circuits, and genomes.

Kim, Nayoung, De Carluccio, Giuliano, Zhang, Kehan et al.

5 citations

417134012026Cell systems. 2026;17(2):101533

A field-deployable CRISPR-based biosensing platform for monitoring marine ecosystems.

Kim, Nayoung, Collins, Daniel S, Donghia, Nina M et al.

10 citations

426396302026Nature sustainability. 2026;9(1):51-64

Digital CRISPR-based diagnostics for quantification of Candida auris and resistance mutations.

Rolando, Justin C, Thieme, Anton, Weckman, Nicole E et al.

9 citations

415353882026Nature biomedical engineering. 2026;10(11):2436-2449

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes.

DeMeo, Benjamin, Nesbitt, Charlotte, Miller, Samuel A et al.

55 citations

411296122025Science (New York, N.Y.). 2025;390(6776):eadi8577

Reversing transgene silencing via targeted chromatin editing.

Palacios, Sebastian, Salibi, Elia, Lu, Eric et al.

1 citation

412800192025bioRxiv : the preprint server for biology. 2025

Convergence of nanotechnology and CRISPR-based diagnostics.

Johnston, Midori, Dissanayake-Perera, Schan, Collins, James J et al.

21 citations

410390962025Nature nanotechnology. 2025;20(10):1365-1373

Mitigating antimicrobial resistance by innovative solutions in AI (MARISA): a modified James Lind Alliance analysis.

Waldock, William J, Thould, Hannah, Chindelevitch, Leonid et al.

6 citations

408904552025npj antimicrobials and resistance. 2025;3(1):75

A generative deep learning approach to de novo antibiotic design.

Krishnan, Aarti, Anahtar, Melis N, Valeri, Jacqueline A et al.

102 citations

408162672025Cell. 2025;188(21):5962-5979.e22

Essay: Using Machine Learning for Antibiotic Discovery.

de la Fuente-Nunez, Cesar, Collins, James J

12 citations

407579962025Physical review letters. 2025;135(3):030001

Optogenetics-enabled discovery of integrated stress response modulators.

Wong, Felix, Li, Alicia, Omori, Satotaka et al.

16 citations

406514732025Cell. 2025;188(18):4950-4967.e22

Induction of Multipotential Hematopoietic Progenitors from Human Pluripotent Stem Cells via Respecification of Lineage-Restricted Precursors.

Doulatov, Sergei, Vo, Linda T, Chou, Stephanie S et al.

1 citation

403062772026Cell stem cell. 2025;32(6):1025

Machine learning for synthetic gene circuit engineering.

Palacios, Sebastian, Collins, James J, Del Vecchio, Domitilla

32 citations

398747192025Current opinion in biotechnology. 2025;92:103263

An explainable deep learning platform for molecular discovery.

Wong, Felix, Omori, Satotaka, Li, Alicia et al.

29 citations

396538002025Nature protocols. 2025;20(4):1020-1056

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

Shen, Tao, Hu, Zhihang, Sun, Siqi et al.

281 citations

395727162024Nature methods. 2024;21(12):2287-2298

Deep generative design of RNA aptamers using structural predictions.

Wong, Felix, He, Dongchen, Krishnan, Aarti et al.

86 citations

395060802024Nature computational science. 2024;4(11):829-839

UROPOT: study protocol for a randomized, double-blind phase I/II trial for metabolism-based potentiation of antimicrobial prophylaxis in the urological tract.

Stritt, Kevin, Roth, Beat, Masnada, Audrey et al.

4 citations

394073252024Trials. 2024;25(1):682

Customizable gene sensing and response without altering endogenous coding sequences.

Caliendo, Fabio, Vitu, Elvira, Wang, Junmin et al.

6 citations

392667212025Nature chemical biology. 2025;21(3):348-359

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids.

Kuru, Erkin, Rittichier, Jonathan, de Puig, Helena et al.

10 citations

392374892024Nature communications. 2024;15(1):7531

O-glycosylation contributes to mammalian glycoRNA biogenesis.

Porat, Jennifer, Watkins, Christopher P, Jin, Chunsheng et al.

23 citations

392577762025bioRxiv : the preprint server for biology. 2024

A high-throughput synthetic biology approach for studying combinatorial chromatin-based transcriptional regulation.

Alcantar, Miguel A, English, Max A, Valeri, Jacqueline A et al.

14 citations

389061162024Molecular cell. 2024;84(12):2382-2396.e9

Addendum: Designing microbial consortia with defined social interactions.

Kong, Wentao, Collins, James J, Lu, Ting

1 citation

386494532024Nature chemical biology. 2024;20(6):789-790

Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches.

Yan, Zhaoqing, Eshed, Amit, Tang, Anli A et al.

40 citations

390360672026Chem. 2024;10(7):2220-2244

Machine learning for antimicrobial peptide identification and design.

Wan, Fangping, Wong, Felix, Collins, James J et al.

281 citations

398505162025Nature reviews bioengineering. 2024;2(5):392-407

Discovery of a structural class of antibiotics with explainable deep learning.

Wong, Felix, Zheng, Erica J, Valeri, Jacqueline A et al.

461 citations

381236862024Nature. 2024;626(7997):177-185

Discovery of antibiotics that selectively kill metabolically dormant bacteria.

Zheng, Erica J, Valeri, Jacqueline A, Andrews, Ian W et al.

56 citations

380297562024Cell chemical biology. 2024;31(4):712-728.e9

Engineering synthetic phosphorylation signaling networks in human cells.

Yang, Xiaoyu, Rocks, Jason W, Jiang, Kaiyi et al.

40 citations

377453272026bioRxiv : the preprint server for biology. 2023

KatG catalase deficiency confers bedaquiline hyper-susceptibility to isoniazid resistant Mycobacterium tuberculosis.

Ofori-Anyinam, N, Hamblin, M, Coldren, M L et al.

23 citations

379050732025bioRxiv : the preprint server for biology. 2023

Engineering microbial division of labor for plastic upcycling.

Bao, Teng, Qian, Yuanchao, Xin, Yongping et al.

162 citations

377521192023Nature communications. 2023;14(1):5712

Leveraging artificial intelligence in the fight against infectious diseases.

Wong, Felix, de la Fuente-Nunez, Cesar, Collins, James J

306 citations

374406202023Science (New York, N.Y.). 2023;381(6654):164-170

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

Valeri, Jacqueline A, Soenksen, Luis R, Collins, Katherine M et al.

41 citations

373484662023Cell systems. 2023;14(6):525-542.e9

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

Yan, Zhaoqing, Tang, Anli A, Eshed, Amit et al.

4 citations

373333642024medRxiv : the preprint server for health sciences. 2023

Gaming bacterial metabolism.

Valeri, Jacqueline A, Krishnan, Aarti, Collins, James J

1 citation

372687732023Nature microbiology. 2023;8(6):1004-1005

Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii.

Liu, Gary, Catacutan, Denise B, Rathod, Khushi et al.

360 citations

372312672023Nature chemical biology. 2023;19(11):1342-1350

Discovering small-molecule senolytics with deep neural networks.

Wong, Felix, Omori, Satotaka, Donghia, Nina M et al.

77 citations

371428292023Nature aging. 2023;3(6):734-750

Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.

Phillips, Elizabeth A, Silverman, Adam D, Joneja, Aric et al.

43 citations

371428442023Nature biomedical engineering. 2023;7(12):1571-1582

Controlled Continuous Evolution of Enzymatic Activity Screened at Ultrahigh Throughput Using Drop-Based Microfluidics.

Rosenthal, R G, Diana Zhang, X, Đurđić, K Ilić et al.

31 citations

370198452023Angewandte Chemie (International ed. in English). 2023;62(24):e202303112

A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks.

English, Max A, Alcantar, Miguel A, Collins, James J

15 citations

369708452023Molecular systems biology. 2023;19(6):e11398

Autocatalytic base editing for RNA-responsive translational control.

Gayet, Raphaël V, Ilia, Katherine, Razavi, Shiva et al.

35 citations

369066592023Nature communications. 2023;14(1):1339

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

Ilia, Katherine, Shakiba, Nika, Bingham, Trevor et al.

23 citations

367478132023bioRxiv : the preprint server for biology. 2023

Harnessing synthetic biology to enhance ocean health.

Nguyen, Peter Q, Huang, Xiaoning, Collins, Daniel S et al.

36 citations

366699472023Trends in biotechnology. 2023;41(7):860-874

The sound of silence: Transgene silencing in mammalian cell engineering.

Cabrera, Alan, Edelstein, Hailey I, Glykofrydis, Fokion et al.

201 citations

365492732022Cell systems. 2022;13(12):950-973

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

de Puig, Helena, Bosch, Irene, Salcedo, Nol et al.

15 citations

363487422026Nano today. 2022;47:101669

Enhancing nutritional niche and host defenses by modifying the gut microbiome.

Sun, Qing, Vega, Nic M, Cervantes, Bernardo et al.

15 citations

363777682022Molecular systems biology. 2022;18(11):e9933

Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.

Wong, Felix, Krishnan, Aarti, Zheng, Erica J et al.

283 citations

360658472022Molecular systems biology. 2022;18(9):e11081

Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions.

Wong, Felix, Stokes, Jonathan M, Bening, Sarah C et al.

47 citations

359734272022Molecular cell. 2022;82(18):3499-3512.e10

Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.

Broto, Marta, Kaminski, Michael M, Adrianus, Christopher et al.

253 citations

359273212022Nature nanotechnology. 2022;17(10):1120-1126

Career total: 568 works. 354 are in this corpus.Showing the 50 most recent.

Profile built from the corpus for this byline.

568

works

116K

citations

168

h-index

Corpus papers per year

Corpus papers per year, 1989 to 2026. Busiest year 2014, 25 papers.
Year	Papers
1989	2
1990	1
1991	1
1992	2
1993	1
1994	4
1995	11
1996	7
1997	1
1998	7
1999	9
2000	4
2001	7
2002	11
2003	9
2004	3
2005	5
2006	4
2007	10
2008	4
2009	11
2010	10
2011	13
2012	18
2013	13
2014	25
2015	12
2016	14
2017	14
2018	18
2019	16
2020	15
2021	13
2022	16
2023	17
2024	10
2025	9
2026	7

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