James J. Collins, PhD - Publications

Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Systems Biology, Synthetic Biology

225 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Wong F, Stokes JM, Cervantes B, Penkov S, Friedrichs J, Renner LD, Collins JJ. Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality. Nature Communications. 12: 2321. PMID 33875652 DOI: 10.1038/s41467-021-22485-6  0.6
2021 Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science (New York, N.Y.). 371. PMID 33602825 DOI: 10.1126/science.aba0862  1
2020 Bojar D, Powers RK, Camacho DM, Collins JJ. Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions. Cell Host & Microbe. PMID 33120114 DOI: 10.1016/j.chom.2020.10.004  0.6
2020 Angenent-Mari NM, Garruss AS, Soenksen LR, Church G, Collins JJ. A deep learning approach to programmable RNA switches. Nature Communications. 11: 5057. PMID 33028812 DOI: 10.1038/s41467-020-18677-1  0.32
2020 Zheng EJ, Stokes JM, Collins JJ. Eradicating Bacterial Persisters with Combinations of Strongly and Weakly Metabolism-Dependent Antibiotics. Cell Chemical Biology. PMID 32916087 DOI: 10.1016/J.Chembiol.2020.08.015  0.6
2020 Johnston CW, Badran AH, Collins JJ. Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. Nature Communications. 11: 4202. PMID 32826900 DOI: 10.1038/S41467-020-18018-2  0.6
2020 Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, ... ... Collins JJ, et al. A Deep Learning Approach to Antibiotic Discovery. Cell. 181: 475-483. PMID 32302574 DOI: 10.1016/j.cell.2020.04.001  0.6
2020 Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackerman Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, ... ... Collins JJ, et al. A Deep Learning Approach to Antibiotic Discovery. Cell. 180: 688-702.e13. PMID 32084340 DOI: 10.1016/J.Cell.2020.01.021  0.6
2019 Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ. Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nature Microbiology. PMID 31451773 DOI: 10.1038/S41564-019-0536-0  1
2019 Stokes JM, Lopatkin AJ, Lobritz MA, Collins JJ. Bacterial Metabolism and Antibiotic Efficacy. Cell Metabolism. PMID 31279676 DOI: 10.1016/J.Cmet.2019.06.009  0.6
2019 Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Cell. PMID 31080069 DOI: 10.1016/J.Cell.2019.04.016  0.88
2019 Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, et al. Publisher Correction: Definitions and guidelines for research on antibiotic persistence. Nature Reviews. Microbiology. PMID 31036919 DOI: 10.1038/S41579-019-0207-4  1
2019 Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science (New York, N.Y.). PMID 31000590 DOI: 10.1126/Science.Aau8287  0.64
2019 Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, et al. Definitions and guidelines for research on antibiotic persistence. Nature Reviews. Microbiology. PMID 30980069 DOI: 10.1038/S41579-019-0196-3  1
2019 Stokes JM, Gutierrez A, Lopatkin AJ, Andrews IW, French S, Matic I, Brown ED, Collins JJ. A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria. Nature Methods. PMID 30858599 DOI: 10.1038/S41592-019-0333-Y  0.6
2018 Mao N, Cubillos-Ruiz A, Cameron DE, Collins JJ. Probiotic strains detect and suppress cholera in mice. Science Translational Medicine. 10. PMID 29899022 DOI: 10.1126/Scitranslmed.Aao2586  0.32
2018 Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. Next-Generation Machine Learning for Biological Networks. Cell. 173: 1581-1592. PMID 29887378 DOI: 10.1016/J.Cell.2018.05.015  0.6
2018 Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, ... Collins JJ, et al. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. Bmc Biology. 16: 62. PMID 29871632 DOI: 10.1186/S12915-018-0527-2  0.36
2018 Bashor CJ, Collins JJ. Understanding Biological Regulation Through Synthetic Biology. Annual Review of Biophysics. PMID 29547341 DOI: 10.1146/Annurev-Biophys-070816-033903  0.32
2017 Gutierrez A, Jain S, Bhargava P, Hamblin M, Lobritz MA, Collins JJ. Understanding and Sensitizing Density-Dependent Persistence to Quinolone Antibiotics. Molecular Cell. PMID 29225037 DOI: 10.1016/J.Molcel.2017.11.012  0.48
2017 Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ. Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. Cell Host & Microbe. 22: 757-765.e3. PMID 29199098 DOI: 10.1016/J.Chom.2017.10.020  1
2017 Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology. PMID 29062088 DOI: 10.1038/S41564-017-0043-0  0.48
2017 Yang JH, Bening SC, Collins JJ. Antibiotic efficacy-context matters. Current Opinion in Microbiology. 39: 73-80. PMID 29049930 DOI: 10.1016/J.Mib.2017.09.002  0.88
2017 Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini CN, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ, Walker GC. Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proceedings of the National Academy of Sciences of the United States of America. PMID 28794281 DOI: 10.1073/Pnas.1707466114  1
2017 Meylan S, Porter CB, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM, Collins JJ. Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control. Cell Chemical Biology. PMID 28111098 DOI: 10.1016/J.Chembiol.2016.12.015  0.88
2016 Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ. Portable, On-Demand Biomolecular Manufacturing. Cell. 167: 248-259.e12. PMID 27662092 DOI: 10.1016/J.Cell.2016.09.013  1
2016 Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, de Soysa Y, Cahan P, Theißen J, Tu HC, Han A, Kurek KC, LaPier GS, Osborne JK, ... ... Collins JJ, et al. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature. PMID 27383785 DOI: 10.1038/Nature18632  1
2016 Toh CX, Chan JW, Chong ZS, Wang HF, Guo HC, Satapathy S, Ma D, Goh GY, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins JJ, Daley GQ, Wee KB, et al. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell Reports. 15: 2597-607. PMID 27292646 DOI: 10.1016/J.Celrep.2016.05.049  1
2016 Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. Comparison of Cas9 activators in multiple species. Nature Methods. PMID 27214048 DOI: 10.1038/Nmeth.3871  0.32
2016 Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, ... Collins JJ, et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell. PMID 27160350 DOI: 10.1016/J.Cell.2016.04.059  1
2016 Burrill DR, Vernet A, Collins JJ, Silver PA, Way JC. Targeted erythropoietin selectively stimulates red blood cell expansion in vivo. Proceedings of the National Academy of Sciences of the United States of America. PMID 27114509 DOI: 10.1073/Pnas.1525388113  1
2016 Dy AJ, Collins JJ. Engineering Models to Scale. Cell. 165: 516-7. PMID 27104972 DOI: 10.1016/J.Cell.2016.04.017  1
2016 Braff D, Shis D, Collins JJ. Synthetic biology platform technologies for antimicrobial applications. Advanced Drug Delivery Reviews. PMID 27089812 DOI: 10.1016/J.Addr.2016.04.006  1
2016 Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ. A role for the bacterial GATC methylome in antibiotic stress survival. Nature Genetics. PMID 26998690 DOI: 10.1038/Ng.3530  1
2015 Kim HJ, Li H, Collins JJ, Ingber DE. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proceedings of the National Academy of Sciences of the United States of America. PMID 26668389 DOI: 10.1073/Pnas.1522193112  1
2015 Chan CT, Lee JW, Cameron DE, Bashor CJ, Collins JJ. 'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nature Chemical Biology. PMID 26641934 DOI: 10.1038/Nchembio.1979  1
2015 Slomovic S, Pardee K, Collins JJ. Synthetic biology devices for in vitro and in vivo diagnostics. Proceedings of the National Academy of Sciences of the United States of America. 112: 14429-35. PMID 26598662 DOI: 10.1073/Pnas.1508521112  1
2015 Belenky P, Ye JD, Porter CB, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Reports. 13: 968-980. PMID 26565910 DOI: 10.1016/J.Celrep.2015.09.059  1
2015 Slomovic S, Collins JJ. DNA sense-and-respond protein modules for mammalian cells. Nature Methods. 12: 1085-90. PMID 26389572 DOI: 10.1038/Nmeth.3585  1
2015 Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, ... ... Collins JJ, et al. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell. 163: 230-45. PMID 26365490 DOI: 10.1016/J.Cell.2015.08.037  1
2015 Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, et al. Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods. 12: 1051-4. PMID 26344044 DOI: 10.1038/Nmeth.3580  1
2015 Lobritz MA, Belenky P, Porter CB, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS, Collins JJ. Antibiotic efficacy is linked to bacterial cellular respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100898 DOI: 10.1073/Pnas.1509743112  1
2015 Krom RJ, Bhargava P, Lobritz MA, Collins JJ. Engineered Phagemids for Nonlytic, Targeted Antibacterial Therapies. Nano Letters. 15: 4808-13. PMID 26044909 DOI: 10.1021/Acs.Nanolett.5B01943  1
2015 Keung AJ, Joung JK, Khalil AS, Collins JJ. Chromatin regulation at the frontier of synthetic biology. Nature Reviews. Genetics. 16: 159-71. PMID 25668787 DOI: 10.1038/Nrg3900  1
2015 Bhargava P, Collins JJ. Boosting bacterial metabolism to combat antibiotic resistance. Cell Metabolism. 21: 154-5. PMID 25651168 DOI: 10.1016/J.Cmet.2015.01.012  1
2015 Dwyer DJ, Collins JJ, Walker GC. Unraveling the physiological complexities of antibiotic lethality. Annual Review of Pharmacology and Toxicology. 55: 313-32. PMID 25251995 DOI: 10.1146/Annurev-Pharmtox-010814-124712  1
2014 Cahan P, Morris SA, Collins JJ, Daley GQ. Defining cellular identity through network biology. Cell Cycle (Georgetown, Tex.). 13: 3313-4. PMID 25485572 DOI: 10.4161/15384101.2014.972918  1
2014 Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 516: 56-61. PMID 25471879 DOI: 10.1038/Nature13920  1
2014 Kishony R, Collins JJ. Editorial overview: Antimicrobials: grappling with the complexities of antibiotics and resistance. Current Opinion in Microbiology. 21: v-vi. PMID 25444122 DOI: 10.1016/J.Mib.2014.10.004  1
2014 Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Paper-based synthetic gene networks. Cell. 159: 940-54. PMID 25417167 DOI: 10.1016/j.cell.2014.10.004  1
2014 Green AA, Silver PA, Collins JJ, Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell. 159: 925-39. PMID 25417166 DOI: 10.1016/J.Cell.2014.10.002  1
2014 Cameron DE, Collins JJ. Tunable protein degradation in bacteria. Nature Biotechnology. 32: 1276-81. PMID 25402616 DOI: 10.1038/Nbt.3053  1
2014 Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. The Journal of Clinical Investigation. 124: 4212-8. PMID 25271726 DOI: 10.1172/Jci72333  1
2014 Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. Journal of Immunology (Baltimore, Md. : 1950). 193: 4485-96. PMID 25267973 DOI: 10.4049/Jimmunol.1401280  1
2014 Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ. CellNet: network biology applied to stem cell engineering. Cell. 158: 903-15. PMID 25126793 DOI: 10.1016/J.Cell.2014.07.020  1
2014 Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell. 158: 889-902. PMID 25126792 DOI: 10.1016/J.Cell.2014.07.021  1
2014 Lang AH, Li H, Collins JJ, Mehta P. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. Plos Computational Biology. 10: e1003734. PMID 25122086 DOI: 10.1371/Journal.Pcbi.1003734  1
2014 Keung AJ, Bashor CJ, Kiriakov S, Collins JJ, Khalil AS. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell. 158: 110-20. PMID 24995982 DOI: 10.1016/J.Cell.2014.04.047  1
2014 Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, ... ... Collins JJ, et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology. 32: 1202-12. PMID 24880487 DOI: 10.1038/nbt.2877  1
2014 Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell. 15: 92-101. PMID 24813856 DOI: 10.1016/J.Stem.2014.04.002  1
2014 Collins JJ, Maxon M, Ellington A, Fussenegger M, Weiss R, Sauro H. Synthetic biology: How best to build a cell. Nature. 509: 155-7. PMID 24812682 DOI: 10.1038/509155A  1
2014 Dwyer DJ, Belenky PA, Yang JH, MacDonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, ... ... Collins JJ, et al. Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences of the United States of America. 111: E2100-9. PMID 24803433 DOI: 10.1073/Pnas.1401876111  1
2014 Dusonchet J, Li H, Guillily M, Liu M, Stafa K, Derada Troletti C, Boon JY, Saha S, Glauser L, Mamais A, Citro A, Youmans KL, Liu L, Schneider BL, Aebischer P, ... ... Collins JJ, et al. A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity. Human Molecular Genetics. 23: 4887-905. PMID 24794857 DOI: 10.1093/Hmg/Ddu202  1
2014 Torisawa YS, Spina CS, Mammoto T, Mammoto A, Weaver JC, Tat T, Collins JJ, Ingber DE. Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro. Nature Methods. 11: 663-9. PMID 24793454 DOI: 10.1038/Nmeth.2938  1
2014 Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nature Reviews. Microbiology. 12: 381-90. PMID 24686414 DOI: 10.1038/Nrmicro3239  1
2014 Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ, Lerou PH. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports. 7: 70-8. PMID 24685138 DOI: 10.1016/J.Celrep.2014.03.007  1
2014 Way JC, Collins JJ, Keasling JD, Silver PA. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell. 157: 151-61. PMID 24679533 DOI: 10.1016/J.Cell.2014.02.039  1
2014 Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of Sciences of the United States of America. 111: 4838-43. PMID 24639514 DOI: 10.1073/Pnas.1321321111  1
2014 Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H, Wu Q. Zfp322a Regulates mouse ES cell pluripotency and enhances reprogramming efficiency. Plos Genetics. 10: e1004038. PMID 24550733 DOI: 10.1371/Journal.Pgen.1004038  1
2014 Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. Bmc Genomics. 15: 121. PMID 24511998 DOI: 10.1186/1471-2164-15-121  1
2014 Brock A, Krause S, Li H, Kowalski M, Goldberg MS, Collins JJ, Ingber DE. Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Science Translational Medicine. 6: 217ra2. PMID 24382894 DOI: 10.1126/Scitranslmed.3007048  1
2014 Jasuja R, Costello JC, Singh R, Gupta V, Spina CS, Toraldo G, Jang H, Li H, Serra C, Guo W, Chauhan P, Narula NS, Guarneri T, Ergun A, Travison TG, ... Collins JJ, et al. Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate-sparing anabolic therapy. Aging Cell. 13: 303-10. PMID 24305501 DOI: 10.1111/Acel.12174  1
2013 Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Reply to Blair et al.: Dose-dependent effects and oxidative stress responses in antibiotic tolerance in Salmonella typhimurium. Proceedings of the National Academy of Sciences of the United States of America. 110: E4570. PMID 24422210 DOI: 10.1073/Pnas.1318744110  1
2013 Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports. 1: 266-80. PMID 24319662 DOI: 10.1016/J.Stemcr.2013.07.004  1
2013 Doulatov S, Vo LT, Chou SS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI, Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell. 13: 459-70. PMID 24094326 DOI: 10.1016/J.Stem.2013.09.002  1
2013 Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proceedings of the National Academy of Sciences of the United States of America. 110: 14420-5. PMID 23946425 DOI: 10.1073/Pnas.1308085110  1
2013 Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C. Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences of the United States of America. 110: 14324-9. PMID 23934048 DOI: 10.1073/Pnas.1311839110  1
2013 Kalghatgi S, Spina CS, Costello JC, Liesa M, Morones-Ramirez JR, Slomovic S, Molina A, Shirihai OS, Collins JJ. Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in Mammalian cells. Science Translational Medicine. 5: 192ra85. PMID 23825301 DOI: 10.1126/Scitranslmed.3006055  1
2013 Morones-Ramirez JR, Winkler JA, Spina CS, Collins JJ. Silver enhances antibiotic activity against gram-negative bacteria. Science Translational Medicine. 5: 190ra81. PMID 23785037 DOI: 10.1126/Scitranslmed.3006276  1
2013 Cohen NR, Lobritz MA, Collins JJ. Microbial persistence and the road to drug resistance. Cell Host & Microbe. 13: 632-42. PMID 23768488 DOI: 10.1016/J.Chom.2013.05.009  1
2013 Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 499: 219-22. PMID 23748443 DOI: 10.1038/Nature12212  1
2013 Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C, Best AJ, ... ... Collins J, et al. The transcriptional landscape of αβ T cell differentiation. Nature Immunology. 14: 619-32. PMID 23644507 DOI: 10.1038/Ni.2590  1
2013 Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, ... ... Collins J, et al. Identification of transcriptional regulators in the mouse immune system. Nature Immunology. 14: 633-43. PMID 23624555 DOI: 10.1038/Ni.2587  1
2013 Belenky P, Camacho D, Collins JJ. Fungicidal drugs induce a common oxidative-damage cellular death pathway. Cell Reports. 3: 350-8. PMID 23416050 DOI: 10.1016/J.Celrep.2012.12.021  1
2013 Best JA, Blair DA, Knell J, Yang E, Mayya V, Doedens A, Dustin ML, Goldrath AW. Transcriptional insights into the CD8(+) T cell response to infection and memory T cell formation. Nature Immunology. 14: 404-12. PMID 23396170 DOI: 10.1038/Ni.2536  1
2013 Brynildsen MP, Winkler JA, Spina CS, MacDonald IC, Collins JJ. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nature Biotechnology. 31: 160-5. PMID 23292609 DOI: 10.1038/Nbt.2458  1
2013 Cohen NR, Brennan PJ, Shay T, Watts GF, Brigl M, Kang J, Brenner MB. Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nature Immunology. 14: 90-9. PMID 23202270 DOI: 10.1038/Ni.2490  1
2013 Pérez MC, Fernández MI, Collins J, Rodríguez JA, García R, Delgado JA, Guerra RM, Almirall A, Márquez D, Ortega JJ, Velazco G, García L, Valdes L. Comportamiento óseo de alveolos dentarios implantados con biograft-g®. Evolución de casos a los 6 meses Ifmbe Proceedings. 33: 156-159. DOI: 10.1007/978-3-642-21198-0_40  1
2013 Anseth K, Berry D, Boyden E, Chiang YM, Collins J, Elisseeff J, García-Martínez J, Horvitz E, Ravikant N, Rogers J, Saif U, Vandebroek S, Zhao B, Zohar D, Zolot K. 35 innovators under 35 2013 Technology Review. 116: 26-83.  1
2013 Green AA, Silver P, Collins JJ, Yin P. Highly orthogonal programmable riboregulators for complex digital logic in E. Coli Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 233-234.  1
2012 Collins JJ. Forward engineering. Interview by Kristie Nybo. Biotechniques. 53: 209. PMID 23227477 DOI: 10.2144/000113932  1
2012 Bashor CJ, Collins JJ. Insulating gene circuits from context by RNA processing. Nature Biotechnology. 30: 1061-2. PMID 23138300 DOI: 10.1038/Nbt.2411  1
2012 McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell. 11: 701-14. PMID 23122293 DOI: 10.1016/J.Stem.2012.07.018  1
2012 Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS, Collins JJ. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nature Methods. 9: 1077-80. PMID 23042452 DOI: 10.1038/Nmeth.2205  1
2012 Gautiar EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma'Ayan A, Chua WJ, Hansen TH, Turley SJ, ... ... Collins J, et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages Nature Immunology. 13: 1118-1128. PMID 23023392 DOI: 10.1038/Ni.2419  1
2012 Kwong LN, Costello JC, Liu H, Jiang S, Helms TL, Langsdorf AE, Jakubosky D, Genovese G, Muller FL, Jeong JH, Bender RP, Chu GC, Flaherty KT, Wargo JA, Collins JJ, et al. Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nature Medicine. 18: 1503-10. PMID 22983396 DOI: 10.1038/Nm.2941  1
2012 Fu W, Ergun A, Lu T, Hill JA, Haxhinasto S, Fassett MS, Gazit R, Adoro S, Glimcher L, Chan S, Kastner P, Rossi D, Collins JJ, Mathis D, Benoist C. A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nature Immunology. 13: 972-80. PMID 22961053 DOI: 10.1038/Ni.2420  1
2012 Bezman NA, Kim CC, Sun JC, Min-Oo G, Hendricks DW, Kamimura Y, Best JA, Goldrath AW, Lanier LL. Molecular definition of the identity and activation of natural killer cells. Nature Immunology. 13: 1000-9. PMID 22902830 DOI: 10.1038/Ni.2395  1
2012 Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. A synthetic biology framework for programming eukaryotic transcription functions. Cell. 150: 647-58. PMID 22863014 DOI: 10.1016/J.Cell.2012.05.045  1
2012 Kumar RM, Collins JJ. Making a noisy gene: HDACs turn up the static. Molecular Cell. 47: 151-3. PMID 22840998 DOI: 10.1016/J.Molcel.2012.07.008  1
2012 Miller JC, Brown BD, Shay T, Gautier EL, Jojic V, Cohain A, Pandey G, Leboeuf M, Elpek KG, Helft J, Hashimoto D, Chow A, Price J, Greter M, Bogunovic M, et al. Deciphering the transcriptional network of the dendritic cell lineage. Nature Immunology. 13: 888-99. PMID 22797772 DOI: 10.1038/Ni.2370  1
2012 Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/Nmeth.2016  1
2012 Genovese G, Ergun A, Shukla SA, Campos B, Hanna J, Ghosh P, Quayle SN, Rai K, Colla S, Ying H, Wu CJ, Sarkar S, Xiao Y, Zhang J, Zhang H, ... ... Collins JJ, et al. microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discovery. 2: 736-49. PMID 22750848 DOI: 10.1158/2159-8290.Cd-12-0111  1
2012 Dwyer DJ, Camacho DM, Kohanski MA, Callura JM, Collins JJ. Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Molecular Cell. 46: 561-72. PMID 22633370 DOI: 10.1016/J.Molcel.2012.04.027  1
2012 Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science (New York, N.Y.). 336: 315-9. PMID 22517853 DOI: 10.1126/Science.1219192  1
2012 Narayan K, Sylvia KE, Malhotra N, Yin CC, Martens G, Vallerskog T, Kornfeld H, Xiong N, Cohen NR, Brenner MB, Berg LJ, Kang J. Intrathymic programming of effector fates in three molecularly distinct γδ T cell subtypes. Nature Immunology. 13: 511-8. PMID 22473038 DOI: 10.1038/Ni.2247  1
2012 Malhotra D, Fletcher AL, Astarita J, Lukacs-Kornek V, Tayalia P, Gonzalez SF, Elpek KG, Chang SK, Knoblich K, Hemler ME, Brenner MB, Carroll MC, Mooney DJ, Turley SJ. Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nature Immunology. 13: 499-510. PMID 22466668 DOI: 10.1038/Ni.2262  1
2012 Callura JM, Cantor CR, Collins JJ. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences of the United States of America. 109: 5850-5. PMID 22454498 DOI: 10.1073/Pnas.1203808109  1
2012 Vega NM, Allison KR, Khalil AS, Collins JJ. Signaling-mediated bacterial persister formation. Nature Chemical Biology. 8: 431-3. PMID 22426114 DOI: 10.1038/Nchembio.915  1
2012 Collins J. Synthetic Biology: Bits and pieces come to life Nature. 483: S8-S10. PMID 22378128 DOI: 10.1038/483S8A  1
2012 Collins J. Q&A: Circuit capacity Nature. 483: S11. PMID 22378119 DOI: 10.1038/483S11A  1
2012 Kumar RM, Collins JJ. Cellular signal processing: out of one, many. Molecular Cell. 45: 143-4. PMID 22284673 DOI: 10.1016/J.Molcel.2012.01.004  1
2012 Ferree A, Guillily M, Li H, Smith K, Takashima A, Squillace R, Weigele M, Collins JJ, Wolozin B. Regulation of physiologic actions of LRRK2: focus on autophagy. Neuro-Degenerative Diseases. 10: 238-41. PMID 22204929 DOI: 10.1159/000332599  1
2012 Lee HH, Collins JJ. Microbial environments confound antibiotic efficacy. Nature Chemical Biology. 8: 6-9. PMID 22173343 DOI: 10.1038/Nchembio.740  1
2011 Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology. 29: 1117-9. PMID 22119740 DOI: 10.1038/Nbt.2052  1
2011 Belenky P, Collins JJ. Microbiology. Antioxidant strategies to tolerate antibiotics. Science (New York, N.Y.). 334: 915-6. PMID 22096180 DOI: 10.1126/Science.1214823  1
2011 Collins JJ, Donadio S. Expanding and enhancing our antibacterial arsenal. Current Opinion in Microbiology. 14: 511-2. PMID 21945218 DOI: 10.1016/J.Mib.2011.09.005  1
2011 Allison KR, Brynildsen MP, Collins JJ. Heterogeneous bacterial persisters and engineering approaches to eliminate them. Current Opinion in Microbiology. 14: 593-8. PMID 21937262 DOI: 10.1016/J.Mib.2011.09.002  1
2011 Ruder WC, Lu T, Collins JJ. Synthetic biology moving into the clinic. Science (New York, N.Y.). 333: 1248-52. PMID 21885773 DOI: 10.1126/Science.1206843  1
2011 Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proceedings of the National Academy of Sciences of the United States of America. 108: 15522-7. PMID 21876160 DOI: 10.1073/Pnas.1104318108  1
2011 Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics. 12: 165-85. PMID 21801025 DOI: 10.1146/Annurev-Genom-082410-101506  1
2011 Allison KR, Brynildsen MP, Collins JJ. Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature. 473: 216-20. PMID 21562562 DOI: 10.1038/Nature10069  1
2011 Balázsi G, van Oudenaarden A, Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell. 144: 910-25. PMID 21414483 DOI: 10.1016/J.Cell.2011.01.030  1
2011 Painter MW, Davis S, Hardy RR, Mathis D, Benoist C. Transcriptomes of the B and T lineages compared by multiplatform microarray profiling. Journal of Immunology (Baltimore, Md. : 1950). 186: 3047-57. PMID 21307297 DOI: 10.4049/Jimmunol.1002695  1
2011 O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable signal processing in synthetic MAP kinase cascades. Cell. 144: 119-31. PMID 21215374 DOI: 10.1016/J.Cell.2010.12.014  1
2011 Allison KR, Collins JJ. Bacteria as control engineers. Molecular Cell. 41: 4-5. PMID 21211717 DOI: 10.1016/J.Molcel.2010.12.025  1
2011 Belenky P, Collins JJ. Antioxidant strategies to tolerate antibiotics (Science (915)) Science. 334: 1639. DOI: 10.1126/science.334.6063.1639  1
2010 Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 7: 618-30. PMID 20888316 DOI: 10.1016/J.Stem.2010.08.012  1
2010 Lee HH, Molla MN, Cantor CR, Collins JJ. Bacterial charity work leads to population-wide resistance. Nature. 467: 82-5. PMID 20811456 DOI: 10.1038/Nature09354  1
2010 Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences of the United States of America. 107: 15898-903. PMID 20713708 DOI: 10.1073/Pnas.1009747107  1
2010 Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R, Walker GC. Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 107: 15517-22. PMID 20696893 DOI: 10.1073/Pnas.1005203107  1
2010 Kohanski MA, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nature Reviews. Microbiology. 8: 423-35. PMID 20440275 DOI: 10.1038/Nrmicro2333  1
2010 Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Research. 38: 2712-26. PMID 20211838 DOI: 10.1093/Nar/Gkq091  1
2010 Kohanski MA, DePristo MA, Collins JJ. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Molecular Cell. 37: 311-20. PMID 20159551 DOI: 10.1016/J.Molcel.2010.01.003  1
2009 Lu TK, Khalil AS, Collins JJ. Next-generation synthetic gene networks. Nature Biotechnology. 27: 1139-50. PMID 20010597 DOI: 10.1038/Nbt.1591  1
2009 Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Molecular Cell. 36: 845-60. PMID 20005847 DOI: 10.1016/J.Molcel.2009.11.024  1
2009 Dwyer DJ, Kohanski MA, Collins JJ. Role of reactive oxygen species in antibiotic action and resistance. Current Opinion in Microbiology. 12: 482-9. PMID 19647477 DOI: 10.1016/J.Mib.2009.06.018  1
2009 Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Synthetic gene networks that count. Science (New York, N.Y.). 324: 1199-202. PMID 19478183 DOI: 10.1126/Science.1172005  1
2009 Brynildsen MP, Collins JJ. Systems biology makes it personal. Molecular Cell. 34: 137-8. PMID 19394290 DOI: 10.1016/J.Molcel.2009.04.004  1
2009 Camacho DM, Collins JJ. Systems biology strikes gold. Cell. 137: 24-6. PMID 19345182 DOI: 10.1016/J.Cell.2009.03.032  1
2009 Lu TK, Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences of the United States of America. 106: 4629-34. PMID 19255432 DOI: 10.1073/Pnas.0800442106  1
2009 Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu J, Liu G, Zhang X, Bowers J, Vaziri C, Ott K, Sensinger K, Collins JJ, Brody JS, et al. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences of the United States of America. 106: 2319-24. PMID 19168627 DOI: 10.1073/Pnas.0806383106  1
2009 Lorenz DR, Cantor CR, Collins JJ. A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences of the United States of America. 106: 1145-50. PMID 19164565 DOI: 10.1073/Pnas.0812551106  1
2008 Dwyer DJ, Kohanski MA, Collins JJ. Networking opportunities for bacteria. Cell. 135: 1153-6. PMID 19109881 DOI: 10.1016/J.Cell.2008.12.016  1
2008 Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G, Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell. 135: 679-90. PMID 19013277 DOI: 10.1016/J.Cell.2008.09.038  1
2008 Heng TS, Painter MW. The Immunological Genome Project: networks of gene expression in immune cells. Nature Immunology. 9: 1091-4. PMID 18800157 DOI: 10.1038/Ni1008-1091  1
2008 Kohanski MA, Collins JJ. Rewiring bacteria, two components at a time. Cell. 133: 947-8. PMID 18555769 DOI: 10.1016/J.Cell.2008.05.035  1
2008 Collins J. Review: What is Life? by Ed Regis New Scientist. 198: 47. DOI: 10.1016/S0262-4079(08)61106-9  1
2007 Guido NJ, Lee P, Wang X, Elston TC, Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal. 93: L55-7. PMID 17890398 DOI: 10.1529/Biophysj.107.118687  1
2007 Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell. 130: 797-810. PMID 17803904 DOI: 10.1016/J.Cell.2007.06.049  1
2007 Deans TL, Cantor CR, Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell. 130: 363-72. PMID 17662949 DOI: 10.1016/J.Cell.2007.05.045  1
2007 Murphy KF, Balázsi G, Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences of the United States of America. 104: 12726-31. PMID 17652177 DOI: 10.1073/Pnas.0608451104  1
2007 Lu TK, Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences of the United States of America. 104: 11197-202. PMID 17592147 DOI: 10.1073/Pnas.0704624104  1
2007 Collins JJ, Bukowski JA, Weed DL, Brent RL, Klein P, Boerstoel-Streefland M, Sprafka JM, Williams AL, Holsapple MP. Evaluating emerging issues in epidemiology. Regulatory Toxicology and Pharmacology : Rtp. 48: 296-307. PMID 17543434 DOI: 10.1016/J.Yrtph.2007.04.002  1
2007 Nelson AL, Collins J, Knibbe H, Cookson K, de Castro AB, Whipple KL. Safer patient handling. Nursing Management. 38: 26-32; quiz 32-3. PMID 17473792 DOI: 10.1097/01.NUMA.0000262923.39562.0e  1
2007 Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Molecular Systems Biology. 3: 91. PMID 17353933 DOI: 10.1038/Msb4100135  1
2007 Ergün A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Molecular Systems Biology. 3: 82. PMID 17299418 DOI: 10.1038/Msb4100125  1
2007 Hayete B, Gardner TS, Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology. 3: 77. PMID 17299414 DOI: 10.1038/Msb4100118  1
2007 Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. Plos Biology. 5: e8. PMID 17214507 DOI: 10.1371/Journal.Pbio.0050008  1
2006 Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell. 24: 853-65. PMID 17189188 DOI: 10.1016/J.Molcel.2006.11.003  1
2006 Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nature Biotechnology. 24: 545-54. PMID 16680139 DOI: 10.1038/Nbt1208  1
2006 Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ. A bottom-up approach to gene regulation. Nature. 439: 856-60. PMID 16482159 DOI: 10.1038/Nature04473  1
2006 Priplata AA, Patritti BL, Niemi JB, Hughes R, Gravelle DC, Lipsitz LA, Veves A, Stein J, Bonato P, Collins JJ. Noise-enhanced balance control in patients with diabetes and patients with stroke. Annals of Neurology. 59: 4-12. PMID 16287079 DOI: 10.1002/Ana.20670  1
2005 Kirman CR, Gargas ML, Marsh GM, Strother DE, Klaunig JE, Collins JJ, Deskin R. Cancer dose--response assessment for acrylonitrile based upon rodent brain tumor incidence: use of epidemiologic, mechanistic, and pharmacokinetic support for nonlinearity. Regulatory Toxicology and Pharmacology : Rtp. 43: 85-103. PMID 16099568 DOI: 10.1016/J.Yrtph.2005.06.007  1
2005 Blake WJ, Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell. 122: 147-9. PMID 16051138 DOI: 10.1016/J.Cell.2005.07.006  1
2005 Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews. Genetics. 6: 451-64. PMID 15883588 DOI: 10.1038/Nrg1615  1
2005 Isaacs FJ, Blake WJ, Collins JJ. Molecular biology. Signal processing in single cells. Science (New York, N.Y.). 307: 1886-8. PMID 15790834 DOI: 10.1126/Science.1110797  1
2005 di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology. 23: 377-83. PMID 15765094 DOI: 10.1038/Nbt1075  1
2004 Starr TB, Gause C, Youk AO, Stone R, Marsh GM, Collins JJ. A risk assessment for occupational acrylonitrile exposure using epidemiology data. Risk Analysis : An Official Publication of the Society For Risk Analysis. 24: 587-601. PMID 15209932 DOI: 10.1111/J.0272-4332.2004.00461.X  1
2004 Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology. 22: 841-7. PMID 15208640 DOI: 10.1038/Nbt986  1
2004 Casanova M, Cole P, Collins JJ, Conolly R, Delzell E, Heck Hd Hd, Leonard R, Lewis R, Marsh GM, Ott MG, Sorahan T, Axten CW. Re: Mortality from lymphohematopoietic malignancies among workers in formaldehyde industries. Journal of the National Cancer Institute. 96: 966-7; author reply . PMID 15199116 DOI: 10.1093/Jnci/Djh176  1
2004 Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ. Programmable cells: interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences of the United States of America. 101: 8414-9. PMID 15159530 DOI: 10.1073/Pnas.0402940101  1
2004 Di Bernardo D, Gardner TS, Collins JJ. Robust identification of large genetic networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 486-97. PMID 14992527  1
2003 Laughton CA, Slavin M, Katdare K, Nolan L, Bean JF, Kerrigan DC, Phillips E, Lipsitz LA, Collins JJ. Aging, muscle activity, and balance control: physiologic changes associated with balance impairment. Gait & Posture. 18: 101-8. PMID 14654213 DOI: 10.1016/S0966-6362(02)00200-X  1
2003 Priplata AA, Niemi JB, Harry JD, Lipsitz LA, Collins JJ. Vibrating insoles and balance control in elderly people. Lancet. 362: 1123-4. PMID 14550702 DOI: 10.1016/S0140-6736(03)14470-4  1
2003 Kaern M, Blake WJ, Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering. 5: 179-206. PMID 14527313 DOI: 10.1146/Annurev.Bioeng.5.040202.121553  1
2003 Collins JJ, Ireland B, Buckley CF, Shepperly D. Lymphohaematopoeitic cancer mortality among workers with benzene exposure. Occupational and Environmental Medicine. 60: 676-9. PMID 12937190 DOI: 10.1136/Oem.60.9.676  1
2003 Hsiao-Wecksler ET, Katdare K, Matson J, Liu W, Lipsitz LA, Collins JJ. Predicting the dynamic postural control response from quiet-stance behavior in elderly adults. Journal of Biomechanics. 36: 1327-33. PMID 12893041 DOI: 10.1016/S0021-9290(03)00153-2  1
2003 Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science (New York, N.Y.). 301: 102-5. PMID 12843395 DOI: 10.1126/Science.1081900  1
2003 Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences of the United States of America. 100: 7714-9. PMID 12808135 DOI: 10.1073/Pnas.1332628100  1
2003 Collins JJ, Priplata AA, Gravelle DC, Niemi J, Harry J, Lipsitz LA. Noise-enhanced human sensorimotor function. Ieee Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society. 22: 76-83. PMID 12733463 DOI: 10.1109/Memb.2003.1195700  1
2003 Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences of the United States of America. 100: 5944-9. PMID 12730377 DOI: 10.1073/Pnas.0933416100  1
2003 Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 422: 633-7. PMID 12687005 DOI: 10.1038/Nature01546  1
2002 Scinicariello AP, Inglis JT, Collins JJ. The effects of stochastic monopolar galvanic vestibular stimulation on human postural sway. Journal of Vestibular Research : Equilibrium & Orientation. 12: 77-85. PMID 12867666  1
2002 Priplata A, Niemi J, Salen M, Harry J, Lipsitz LA, Collins JJ. Noise-enhanced human balance control. Physical Review Letters. 89: 238101. PMID 12485044 DOI: 10.1103/Physrevlett.89.238101  1
2002 Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 420: 224-30. PMID 12432407 DOI: 10.1038/Nature01257  1
2002 Gravelle DC, Laughton CA, Dhruv NT, Katdare KD, Niemi JB, Lipsitz LA, Collins JJ. Noise-enhanced balance control in older adults. Neuroreport. 13: 1853-6. PMID 12395078 DOI: 10.1097/00001756-200210280-00004  1
2002 Hasty J, Collins JJ. Translating the noise. Nature Genetics. 31: 13-4. PMID 11984558 DOI: 10.1038/Ng0502-13  1
2002 Yeung MK, Tegnér J, Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences of the United States of America. 99: 6163-8. PMID 11983907 DOI: 10.1073/Pnas.092576199  1
2002 Dhruv NT, Niemi JB, Harry JD, Lipsitz LA, Collins JJ. Enhancing tactile sensation in older adults with electrical noise stimulation. Neuroreport. 13: 597-600. PMID 11973453 DOI: 10.1097/00001756-200204160-00012  1
2002 Hasty J, Dolnik M, Rottschäfer V, Collins JJ. Synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters. 88: 148101. PMID 11955179 DOI: 10.1103/Physrevlett.88.148101  1
2002 Liu W, Lipsitz LA, Montero-Odasso M, Bean J, Kerrigan DC, Collins JJ. Noise-enhanced vibrotactile sensitivity in older adults, patients with stroke, and patients with diabetic neuropathy. Archives of Physical Medicine and Rehabilitation. 83: 171-6. PMID 11833019 DOI: 10.1053/Apmr.2002.28025  1
2002 McMillen D, Kopell N, Hasty J, Collins JJ. Synchronizing genetic relaxation oscillators by intercell signaling. Proceedings of the National Academy of Sciences of the United States of America. 99: 679-84. PMID 11805323 DOI: 10.1073/Pnas.022642299  1
2001 Hasty J, Isaacs F, Dolnik M, McMillen D, Collins JJ. Designer gene networks: Towards fundamental cellular control. Chaos (Woodbury, N.Y.). 11: 207-220. PMID 12779454 DOI: 10.1063/1.1345702  1
2001 Hasty J, Collins JJ, Wiesenfeld K, Grigg P. Wavelets of excitability in sensory neurons. Journal of Neurophysiology. 86: 2097-101. PMID 11600664 DOI: 10.1152/Jn.2001.86.4.2097  1
2001 Collins JJ, Ness R, Tyl RW, Krivanek N, Esmen NA, Hall TA. A review of adverse pregnancy outcomes and formaldehyde exposure in human and animal studies. Regulatory Toxicology and Pharmacology : Rtp. 34: 17-34. PMID 11502153 DOI: 10.1006/Rtph.2001.1486  1
2001 Scinicariello AP, Eaton K, Inglis JT, Collins JJ. Enhancing human balance control with galvanic vestibular stimulation. Biological Cybernetics. 84: 475-80. PMID 11417059 DOI: 10.1007/Pl00007991  1
2001 Hasty J, Collins JJ. Protein interactions. Unspinning the web. Nature. 411: 30-1. PMID 11333958 DOI: 10.1038/35075182  1
2001 Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nature Reviews. Genetics. 2: 268-79. PMID 11283699 DOI: 10.1038/35066056  1
2001 Marsh GM, Youk AO, Collins JJ. Reevaluation of lung cancer risk in the acrylonitrile cohort study of the National Cancer Institute and the National Institute for Occupational Safety and Health. Scandinavian Journal of Work, Environment & Health. 27: 5-13. PMID 11266147 DOI: 10.5271/Sjweh.581  1
2001 Collins JJ, Esmen NA, Hall TA. A review and meta-analysis of formaldehyde exposure and pancreatic cancer. American Journal of Industrial Medicine. 39: 336-45. PMID 11241567 DOI: 10.1002/1097-0274(200103)39:3<336::AID-AJIM1022>3.0.CO;2-K  1
2000 Gardner TS, Collins JJ. Neutralizing noise in gene networks. Nature. 405: 520-1. PMID 10850696 DOI: 10.1038/35014708  1
2000 Collins JJ, Barbela T, Huebner WW, Divine BJ, Schnatter AR, Carpenter AV, Hearne FT, Raabe GK, Fayerweather W. A framework for addressing health issues in or near a manufacturing facility. Journal of Occupational and Environmental Medicine / American College of Occupational and Environmental Medicine. 42: 163-70. PMID 10693077  1
2000 Hasty J, Pradines J, Dolnik M, Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences of the United States of America. 97: 2075-80. PMID 10681449 DOI: 10.1073/Pnas.040411297  1
2000 Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 403: 339-42. PMID 10659857 DOI: 10.1038/35002131  1
1999 Nozaki D, Collins JJ, Yamamoto Y. Mechanism of stochastic resonance enhancement in neuronal models driven by 1/f noise. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 4637-44. PMID 11970325 DOI: 10.1103/Physreve.60.4637  1
1999 Neiman A, Schimansky-Geier L, Moss F, Shulgin B, Collins JJ. Synchronization of noisy systems by stochastic signals. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 284-92. PMID 11969761 DOI: 10.1103/Physreve.60.284  1
1999 Collins JJ, Strauss ME, Riordan SG. Mortalities of workers at the Nitro plant with exposure to 2-mercaptobenzothialzole. Occupational and Environmental Medicine. 56: 667-71. PMID 10658544 DOI: 10.1136/Oem.56.10.667  1
1999 Mar DJ, Chow CC, Gerstner W, Adams RW, Collins JJ. Noise shaping in populations of coupled model neurons. Proceedings of the National Academy of Sciences of the United States of America. 96: 10450-5. PMID 10468629 DOI: 10.1073/Pnas.96.18.10450  1
1999 Lauk M, Chow CC, Lipsitz LA, Mitchell SL, Collins JJ. Assessing muscle stiffness from quiet stance in Parkinson's disease. Muscle & Nerve. 22: 635-9. PMID 10331364 DOI: 10.1002/(Sici)1097-4598(199905)22:5<635::Aid-Mus13>3.0.Co;2-0  1
1998 Chow CC, Imhoff TT, Collins JJ. Enhancing aperiodic stochastic resonance through noise modulation. Chaos (Woodbury, N.Y.). 8: 616-620. PMID 12779765 DOI: 10.1063/1.166343  1
1998 Richardson KA, Imhoff TT, Grigg P, Collins JJ. Using electrical noise to enhance the ability of humans to detect subthreshold mechanical cutaneous stimuli. Chaos (Woodbury, N.Y.). 8: 599-603. PMID 12779763 DOI: 10.1063/1.166341  1
1998 Gardner TS, Dolnik M, Collins JJ. A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 95: 14190-5. PMID 9826676 DOI: 10.1073/Pnas.95.24.14190  1
1998 Collins JJ, Chow CC. It's a small world. Nature. 393: 409-10. PMID 9623993 DOI: 10.1038/30835  1
1998 Suki B, Alencar AM, Sujeer MK, Lutchen KR, Collins JJ, Andrade JS, Ingenito EP, Zapperi S, Stanley HE. Life-support system benefits from noise [3] Nature. 393: 127-128. PMID 9603516 DOI: 10.1038/30130  1
1998 Kerrigan DC, Todd MK, Della Croce U, Lipsitz LA, Collins JJ. Biomechanical gait alterations independent of speed in the healthy elderly: evidence for specific limiting impairments. Archives of Physical Medicine and Rehabilitation. 79: 317-22. PMID 9523785 DOI: 10.1016/S0003-9993(98)90013-2  1
1997 Christini DJ, Collins JJ. Control of chaos in excitable physiological systems: A geometric analysis. Chaos (Woodbury, N.Y.). 7: 544-549. PMID 12779680 DOI: 10.1063/1.166279  1
1997 Christini DJ, Collins JJ. Real-time, adaptive, model-independent control of low-dimensional chaotic and nonchaotic dynamical systems Ieee Transactions On Circuits and Systems I: Fundamental Theory and Applications. 44: 1027-1030. DOI: 10.1109/81.633896  1
1995 Cohn LH, Rizzo RJ, Adams DH, Couper GS, Sullivan TE, Collins JJ, Aranki SF. The effect of pathophysiology on the surgical treatment of ischemicmitral regurgitation: operative and late risks of repair versusreplacement European Journal of Cardio-Thoracic Surgery. 9: 568-574. PMID 8562102 DOI: 10.1016/S1010-7940(05)80008-9  1
1995 Collins JJ, Chow CC, Imhoff TT. Stochastic resonance without tuning. Nature. 376: 236-8. PMID 7617033 DOI: 10.1038/376236A0  1
1994 Rosenstein MT, Collins JJ, De Luca CJ. Reconstruction expansion as a geometry-based framework for choosing proper delay times Physica D: Nonlinear Phenomena. 73: 82-98. DOI: 10.1016/0167-2789(94)90226-7  1
1993 Rosenstein MT, Collins JJ, De Luca CJ. A practical method for calculating largest Lyapunov exponents from small data sets Physica D: Nonlinear Phenomena. 65: 117-134. DOI: 10.1016/0167-2789(93)90009-P  1
1989 Collins JJ, Whittle MW. Influence of gait parameters on the loading of the lower limb Journal of Biomedical Engineering. 11: 409-412. PMID 2796321 DOI: 10.1016/0141-5425(89)90105-2  1
1989 Collins JJ, Whittle MW. Impulsive forces during walking and their clinical implications Clinical Biomechanics. 4: 179-187. DOI: 10.1016/0268-0033(89)90023-5  1
1977 Norwood WI, Cohn LH, Collins JJ. Results of reoperation for recurrent angina pectoris Annals of Thoracic Surgery. 23: 9-13. PMID 299807 DOI: 10.1016/S0003-4975(10)64060-X  1
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