Collins Lab, MIT
Collins Lab, MIT
Synthetic Biology | Systems Biology | Antibiotics

 PUBLICATIONS

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2024

  1. Discovery of antibiotics that selectively kill metabolically dormant bacteria.
    Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S and Collins JJ.
    Cell Chemical Biology 31: 712-728 (2024).
  1. Rapid, multiplexed, and enzyme-free nucleic acid detection using programmable aptamer-based RNA switches.
    Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P and Green AA.
    Chem: published online (2024).
  1. Machine learning for antimicrobial peptide identification and design.
    Wan F, Wong F, Collins JJ and de la Fuente-Nunez C.
    Nature Reviews Bioengineering: published online (2024).
  1. Discovery of a structural class of antibiotics with explainable deep learning.
    Wong F, Zheng EJ, Valeri JA, Donghia NM, Anahtar MN, Omori S, Li A, Cubillos-Ruiz A, Krishnan A, Jin W, Manson AL, Friedrichs J, Helbig R, Hajian B, Fiejtek DK, Wagner FF, Soutter HH, Earl AM, Stokes JM, Renner LD and Collins JJ.
    Nature: 626: 177-185 (2024).
 

2023

  1. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts.
    Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D and Schlaeger TM.
    Science Advances 9: eadg8495 (2023).
  1. Engineering microbial division of labor for plastic upcycling.
    Bao T, Qian Y, Xin Y, Collins JJ and Lu T.
    Nature Communications 14: 5712 (2023).
  1. Leveraging artificial intelligence in the fight against infectious diseases.
    Wong F, de la Fuente-Nunez C and Collins JJ.
    Science 381: 164-170 (2023).
  1. BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences.
    Valeri JA, Soenksen LR, Collins KM, Ramesh P, Cai G, Powers R, Angenent-Mari NM, Camacho DM, Wong F, Lu TK and Collins JJ.
    Cell Systems 14: 525–542 (2023).
  1. Controlled continuous evolution of enzymatic activity screened at ultrahigh throughput using drop-based microfluidics.
    Rosenthal RG, Zhang XD, Ilić Đurđić K, Collins JJ and Weitz DA.
    Angewandte Chemie 62: e202303112 (2023).
  1. Gaming bacterial metabolism.
    Valeri JA, Krishnan A and Collins  JJ.
    Nature Microbiology 8: 1004-1005 (2023).
  1. Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii.
    Liu G, Catacutan DB, Rathod K, Swanson  K, Jin W, Mohammed JC, Chiappino-Pepe A, Syed SA, Fragis M, Rachwalski K, Magolan  J, Surette MG, Coombes  BK, Jaakkola T, Barzilay R, Collins  JJ and Stokes JM.
    Nature Chemical Biology 19: 1342-1350 (2023).
  1. Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.
    Phillips EA, Silverman AD, Joneja A, Liu M, Brown C, Carlson P, Coticchia C, Shytle K, Larsen A, Goyal, Cai V, Huang J, Hickey JE , Ryan E, Acheampong J, Ramesh P, Collins JJ  and Blake WJ.
    Nature Biomedical Engineering 7: 1571-1582 (2023).
  1. Discovering small-molecule senolytics with deep neural networks.
    Wong F, Omori S, Donghia NM, Zheng EJ and Collins JJ.
    Nature Aging 3: 734-750 (2023).
  1. A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks.
    English MA, Alcantar MA and Collins JJ.
    Molecular Systems Biology 19: e11398 (2023).
  1. Harnessing synthetic biology to enhance ocean health.
    Nguyen PQ, Huang X, Collins DS, Collins JJ and Lu T.
    Trends in Biotechnology 41: 860-874 (2023).
  1. Autocatalytic base editing for RNA-responsive translational control.
    Gayet RV, Ilia K, Razavi S, Tippens ND, Lalwani MA, Zhang K, Chen JX, Chen JC, Vargas-Asencio J and Collins JJ.
    Nature Communications 14: 1339 (2023).
  1. Lateral flow test engineering and lessons learned from COVID-19.
    Budd J, Miller BS, Weckman NE, Cherkaoui D, Huang D, Decruz AT, Fongwen N, Han G, Broto M, Estcourt CS, Gibbs J, Pillay D, Sonnenberg P, Meurant R, Thomas MR, Keegan N, Stevens MM, Nastouli E, Topo EJ, Johnson AM, Shahmanesh M, Ozcan A, Collins JJ, Suarez MF, Rodriguez B, Peeling RW and McKendry RA.
    Nature Reviews Bioengineering 1: 13-31 (2023).
 

2022

  1. The sound of silence: Transgene silencing in mammalian cell engineering.
    Cabera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE and Deans TL.
    Cell Systems 13: 950-973 (2022).
  1. Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness.
    de Puig H, Bosch I, Salcedo N, Collins JJ, Hamad-Schifferli K and Gehrke L.
    Nano Today 47: e101669 (2022).
  1. Enhancing nutritional niche and host defenses by modifying the gut microbiome.
    Sun Q, Vega NM, Cervantes B, Mancuso CP, Mao N, Taylor MN, Collins JJ, Khalil AS, Gore J and Lu TK.
    Molecular Systems Biology 18: e9933 (2022).
  1. End-to-end design of wearable sensors.
    Ates HC, Nguyen PQ, Gonzalez-Macia L, Morales-Narváez E, Güder F, Collins JJ and Dincer C.
    Nature Reviews Materials 7: 887–907 (2022).
  1. Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
    Broto F, Kaminski MM, Adrianus C, Kim N, Greensmith R, Dissanayake-Perera S, Schubert AJ, Tan X, Kim H, Dighe AS, Collins JJ and Stevens MM.
    Nature Nanotechnology 17: 1120–1126 (2022).
  1. Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions.
    Wong F, Stokes JM, Bening SC, Vidoudez C, Trauger SA and Collins JJ.
    Molecular Cell 82: 3499-3512 (2022).
  1. Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.
    Wong F, Krishnan A, Zheng EJ, Stark H, Manson AL, Earl AM, Jaakkola T and Collins JJ.
    Molecular Systems Biology 18: e11081 (2022). Primary screen dataset available here and benchmarking dataset available here.
  1. 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.
    Najjar D, Rainbow J, Sharma Timilsina S, Jolly P, de Puig H, Yafia M, Durr N, Sallum H, Alter G, Li JZ, Yu XG, Walt DR, Paradiso JA, Estrela P, Collins JJ and Ingber DE.
    Nature Biomedical Engineering 6: 968–978 (2022).
  1. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates.
    Warrier T, El Farran C, Zeng Y, Ho BSQ, Bao Q, Zheng ZH, Bi X, Ng HH, Ong DST, Chu JJH, Sanyal A, Fullwood MJ, Collins JJ, Li H, Xu J and Loh Y-H.
    Nucleic Acids Research 50: 7326–7349 (2022).
  1. An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis.
    Cubillos-Ruiz A, Alcantar MA, Donghia NM, Cárdenas P, Avila-Pacheco J and Collins JJ.
    Nature Biomedical Engineering 6: 910-921 (2022).
  1. Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies.
    Zheng EJ, Andrews IW, Grote AT, Manson AL, Alcantar MA, Earl AM and Collins JJ.
    Nature Communications 13: 2525 (2022).
  1. CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development.
    da Rocha EL, Kubaczka C, Sugden WW, Najia MA, Jing R, Markel A, LeBlanc ZC, dos Santos Peixoto R, Falchetti M, Collins JJ, North TE and Daley GQ.
    Nature Cell Biology 24: 579-589 (2022).
  1. RNA-responsive elements for eukaryotic translational control.
    Zhao EM, Mao AS, de Puig H, Zhang K, Tippens ND, Tan X, Ran FA, Han I, Nguyen PQ, Chory EJ, Hua TY, Ramesh P, Thompson DB, Oh CY, Zigon ES, English MA and Collins JJ.
    Nature Biotechnology 40: 539-545 (2022).
  1. Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples.
    Karlikow M , Yuxiu Guo SJR, Cicek S, Krokovsky L, Homme P, Xiong Y, Xu T, Calderón-Peláez MG, Camacho-Ortega S, Ma D, Ferraz de Magalhães JJ, Fernandes Souza BNR, de Albuquerque Cabral DG, Jaenes K, Sutyrina P, Ferrante T, Benitez AD, Nipaz V, Ponce P, Rackus DG, Collins JJ, Paiva M, Castellanos JE, Cevallos V, Green AA, Ayres C, Pena L and Pardee K.
    Nature Biomedical Engineering 6: 246-256 (2022).
  1. Increased energy demand from anabolic-catabolic processes drives beta-lactam antibiotic lethality.
    Lobritz MA, Andrews IA, Braff D, Porter CB, Gutierrez A, Furuta Y, Cortes LB, Ferrante T, Bening SC, Wong F, Gruber C, Bakerlee CW, Lambert G, Walker GC, Dwyer DJ and Collins JJ.
    Cell Chemical Biology 29: 276-286 (2022).

2021

  1. Engineering living therapeutics with synthetic biology.
    Cubillos-Ruiz A, Guo T, Sokolovska A, Miller PF, Collins JJ, Lu TK and Lora JM.
    Nature Reviews Drug Discovery 20: 941-960 (2021).
  1. Deep learning identifies synergistic drug combinations for treating COVID-19.
    Jin W, Stokes JM, Eastman RT, Itkin Z, Zakharov AV, Collins JJ, Jaakkola TS and Barzilay R.
    Proceedings of the National Academy of Sciences USA 118: e2105070118 (2021).
  1. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants.
    de Puig H, Lee RA, Najjar D, Tan X, Soekensen LR, Angenent-Mari NM, Donghia NM, Weckman NE, Ory A, Ng CF, Nguyen PQ, Mao AS, Ferrante TC, Lansberry G, Sallum H, Niemi J and Collins JJ.
    Science Advances 7: eabh2944 (2021).
  1. CRISPR-based diagnostics.
    Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F and Collins JJ.
    Nature Biomedical Engineering 5: 643-656 (2021).
  1. Wearable materials with embedded synthetic biology sensors for biomolecule detection.
    Nguyen PQ, Soenksen LR, Donghia NM, Angenent-Mari NM, de Puig H, Huang A, Lee R, Slomovic S, Galbersanini T, Lansberry G, Sallum HM, Zhao EM, Niemi JB and Collins JJ.
    Nature Biotechnology 39: 1366–1374 (2021).
  1. Designing biological circuits: synthetic biology within the operon model and beyond.
    English MA, Gayet RV and Collins JJ.
    Annual Review of Biochemistry 90: 221-244 (2021).
  1. Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality.
    Wong F, Stokes JM, Cervantes B, Penkov S, Friedrichs J, Renner LD and Collins JJ.
    Nature Communications 12: 2321 (2021).
  1. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics.
    Tan X, Letendre JH, Collins JJ and Wong WW.
    Cell 184: 881-898 (2021).
  1. Clinically relevant mutations in core metabolic genes confer antibiotic resistance.
    Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH and Collins JJ.
    Science 371: eaba0862 (2021).
  1. Using deep learning for dermatologist-level detection of suspicious pigmented skin lesions from wide-field images.
    Soenksen LR, Kassis T, Conover ST, Marti-Fuster B, Birkenfeld JS, Tucker-Schwartz J, Naseem A, Stavert RR, Kim CC, Senna MM, Avilés-Izquierdo J, Collins JJ, Barzilay R and Gray ML.
    Science Translational Medicine 13: eabb3652 (2021).
  1. Engineering advanced logic and distributed computing in human CAR immune cells.
    Cho JH, Okuma A, Sofjan K, Lee S, Collins JJ and Wong WW.
    Nature Communications 12: 792 (2021).
  1. Anomalous COVID-19 tests hinder researchers.
    Robinson-McCarthy LR, Mijalis AJ, Filsinger GT, de Puig H, Donghia NM, Schaus TE, Rasmussen RA, Ferreira R, Lunshof JE, Chao G, Ter-Ovanesyan D, Dodd O, Kuru E, Sesay AM, Rainbow J, Pawlowski AC, Wannier TM, Yin P, Collins JJ, Ingber DE, Church GM and Tam JM.
    Science 371: 244-245 (2021).
  1. Deep-learning resources for studying glycan-mediated host-microbe interactions.
    Bojar D, Powers RK, Camacho DM and Collins JJ.
    Cell Host & Microbe 29: 132-144 (2021).

2020

  1. Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria.
    Lee RA, De Puig H, Nguyen PQ, Angenent-Mari NM, Donghia NM, McGee JP, Dvorin JD, Klapperich CM, Pollock NR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 117: 25722-25731 (2020).
  1. Cell-free biosensors for rapid detection of water contaminants.
    Jung JK, Alam KK, Verosloff MS, Capdevila DA, Desmau M, Clauer PR, Lee JW , Nguyen PQ, Pastén PA, Matiasek SJ, Gaillard JF, Giedroc DP, Collins JJ and Lucks JB.
    Nature Biotechnology 38: 1451–1459 (2020).
  1. Evidence that coronavirus superspreading is fat-tailed.
    Wong F and Collins JJ.
    Proceedings of the National Academy of Sciences USA 117: 29416-29418 (2020).
  1. A deep learning approach to programmable RNA switches.
    Angenent-Mari NM, Garruss AS, Soenksen LR, Church G and Collins JJ.
    Nature Communications 11: 5057 (2020).
  1. Sequence-to-function deep learning frameworks for engineered riboregulators.
    Valeri JA, Collins KM, Ramesh P, Alcantar MA, Lepe BA, Lu TK and Camacho DM.
    Nature Communications 11: 5058 (2020).
  1. Eradicating bacterial persisters with combinations of strongly and weakly metabolism-dependent antibiotics.
    Zheng EJ, Stokes JM and Collins JJ.
    Cell Chemical Biology 27: 1544-1552 (2020).
  1. Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release.
    Gayet RV, de Puig H, English MA, Soenksen LR, Nguyen PQ, Mao AS, Angenent-Mari NM and Collins JJ.
    Nature Protocols 15: 3030-3063 (2020).
  1. Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway.
    Johnston CW, Badran AH and Collins JJ.
    Nature Communications 11: 4202 (2020).
  1. Predictive biology: modelling, understanding and harnessing microbial complexity.
    Lopatkin AJ and Collins JJ.
    Nature Reviews Microbiology 18: 507-520 (2020).
  1. A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection.
    Kaminski MM, Alcantar MA, Lape IT, Greensmith R, Huske AC, Valeri JA, Marty FM, Klämbt V, Azzi J, Akalin E, Riella LV and Collins JJ.
    Nature Biomedical Engineering 4: 601-609 (2020).
  1. Point-of-care devices to detect Zika and other emerging viruses.
    de Puig H, Bosch I, Collins JJ and Gehrke L.
    Annual Reviews in Biomedical Engineering 22: 371-386 (2020).
  1. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing.
    Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CXD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF and Loh YH.
    Science Advances 6: eaba1190 (2020).
  1. Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility.
    Xing QR, Farran CA El, Zeng YY, Yi Y, Warrier T, Gautam P, Collins JJ, Xu J, Dröge P, Koh C-G, Li H, Zhang L-F and Loh Y-H.
    Genome Research 30: 1027-1039 (2020).
  1. A deep learning approach to antibiotic discovery.
    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, Church GM, Brown ED, Jaakkola TS, Barzilay R and Collins JJ.
    Cell 180: 688-702 (2020). Primary screen dataset available here.

2019

  1. A systems biology pipeline identifies regulatory networks for stem cell engineering.
    Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong K, Collins JJ, Cahan P, North TE, Lauffenburger DA and Daley GQ.
    Nature Biotechnology 37: 810-818 (2019).
  1. De novo-designed translation-repressing riboregulators for multi-input cellular logic.
    Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P and Green AA.
    Nature Chemical Biology 15: 1173-1182 (2019).
  1. Engineering microbial peer pressure.
    Johnston CW and Collins JJ.
    Science 365: 986-987 (2019).
  1. Programmable CRISPR-responsive smart materials.
    English MA, Soenksen LR, Gayet RV, Puig H De, Angenent-mari NM, Mao AS, Nguyen PQ and Collins JJ.
    Science 365: 780-785 (2019).
  1. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies.
    Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ and Khalil AS.
    Science 364: 593-597 (2019).
  1. Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.
    Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L and Collins JJ.
    Nature Microbiology 4: 2109-2117 (2019).
  1. Bacterial metabolism and antibiotic efficacy.
    Stokes JM, Lopatkin AJ, Lobritz MA and Collins JJ.
    Cell Metabolism 30: 251-259 (2019).
  1. Definitions and guidelines for research on antibiotic persistence.
    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, Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van Melderen L and Zinkernagel A.
    Nature Reviews Microbiology 17: 441-448 (2019).
  1. Complex host-microbe-antibiotic interactions.
    Collins JJ.
    Cell Host & Microbe 26: 8 (2019).
  1. A white-box machine learning approach for revealing antibiotic mechanisms of action.
    Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC and Collins JJ.
    Cell 177: 1649-1661 (2019).
  1. Altered metabolic states.
    Collins JJ.
    Cell Metabolism 29: 509 (2019).
  1. A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria.
    Stokes JM, Gutierrez A, Lopatkin AJ, Andrews IW, French S, Matic I, Brown ED and Collins JJ.
    Nature Methods 16: 303-306 (2019).

2018

  1. Designing microbial consortia with defined social interactions.
    Kong W, Meldgin DR, Collins JJ and Lu T.
    Nature Chemical Biology 14: 821-829 (2018).
  1. An enhanced CRISPR repressor for targeted mammalian gene regulation.
    Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo C, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S and Church GM.
    Nature Methods 15: 611-616 (2018).
  1. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.
    Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A and Collins JJ.
    Nature Communications 9: 3347 (2018).
  1. BioBits Explorer: A modular synthetic biology education kit.
    Huang A, Nguyen PQ, Stark JC, Takahashi MK, Donghia N, Ferrante T, Dy AJ, Hsu KJ, Dubner RS, Pardee K, Jewett MC and Collins JJ.
    Science Advances 4: eaat5105 (2018).
  1. BioBits Bright: A fluorescent synthetic biology education kit.
    Stark JC, Huang A, Nguyen PQ, Dubner RS, Hsu KJ, Ferrante TC, Anderson M, Kanapskyte A, Mucha Q, Packett JS, Patel P, Patel R, Qaq D, Zondor T, Burke J, Martinez T, Miller-Berry A, Puppala A, Reichert K, Schmid M, Brand L, Hill LR, Chellaswamy JF, Faheem N, Fetherling S, Gong E, Gonzalzles EM, Granito T, Koritsaris J, Nguyen B, Ottman S, Palffy C, Patel A, Skweres S, Slaton A, Woods T, Donghia N, Pardee K, Collins JJ and Jewett MC.
    Science Advances 4: eaat5107 (2018).
  1. Next-generation machine learning for biological networks.
    Camacho DM, Collins KM, Powers RK, Costello JC and Collins JJ.
    Cell 173: 1581-1592 (2018).
  1. Probiotic strains detect and suppress cholera in mice.
    Mao N, Cubillos-Ruiz A, Cameron DE and Collins JJ.
    Science Translational Medicine 10: eaao2586 (2018).
  1. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast.
    Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, Cecchi R, Lopez Garnier S, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ and Church GM.
    Nature Biotechnology 36: 540-549 (2018).
  1. Universal chimeric antigen receptors for multiplexed and logical control of T cell responses.
    Cho JH, Collins JJ and Wong WW.
    Cell 173: 1426-1438 (2018).
  1. Understanding biological regulation through synthetic biology.
    Bashor CJ and Collins JJ.
    Annual Review of Biophysics 47: 399-423 (2018).
  1. Next-generation biocontainment systems for engineered organisms.
    Lee JW, Chan CTY, Slomovic S and Collins JJ.
    Nature Chemical Biology 14: 530-537 (2018).
  1. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms.
    Shapiro RS, Chavez A and Collins JJ.
    Nature Reviews Microbiology 16: 333-339 (2018).
  1. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6.
    Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ and Zhang F.
    Science 360: 439-444 (2018).
  1. Precise Cas9 targeting enables genomic mutation prevention.
    Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ and Church GM.
    Proceedings of the National Academy of Sciences USA 115: 3669-3673 (2018).
  1. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans.
    Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM and Collins JJ.
    Nature Microbiology 2: 73-82 (2018).
  1. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.
    Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth II MH, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK and Karp JM.
    BMC Biology 16: 62 (2018).
  1. Targeting antibiotic tolerance, pathogen by pathogen.
    Meylan S, Andrews IW and Collins JJ.
    Cell 172: 1228-1238 (2018).
  1. Reconstruction of complex single-cell trajectories using CellRouter.
    Lummertz da Rocha E, Rowe RG, Lundin V, Malleshaiah M, Jha DK, Rambo CR, Li H, North TE, Collins JJ and Daley GQ.
    Nature Communications 9: 892 (2018).

2017

  1. Using engineered bacteria to characterize infection dynamics and antibiotic effects in vivo.
    Certain LK, Way JC, Pezone AJ and Collins JJ.
    Cell Host & Microbe 22: 263-268 (2017).
  1. Complex cellular logic computation using ribocomputing devices.
    Green AA, Kim J, Ma D, Silver PA, Collins JJ and Yin P.
    Nature 548: 117-121 (2017).
  1. Biophysical constraints arising from compositional context in synthetic gene networks.
    Yeung E, Dy AJ, Martin KB, Beck JL, Collins JJ and Murray RM.
    Cell Systems 5: 11-24, e1-e12 (2017).
  1. Nucleic acid detection with CRISPR-Cas13a/C2c2.
    Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ and Zhang F.
    Science 356: 438-442 (2017).
  1. A blueprint for a synthetic genetic feedback controller to reprogram cell fate.
    Del Vecchio D, Abdallah H, Qian Y and Collins JJ.
    Cell Systems 4: 109-120 (2017).
  1. Understanding and sensitizing density-dependent persistence to quinolone antibiotics.
    Gutierrez A, Jain S, Bhargava P, Hamblin M, Lobritz MA and Collins JJ.
    Molecular Cell 68: 1019-1021 (2017).
  1. Antibiotic-induced changes to the host metabolic environment inhibit drug efficacy and alter immune function.
    Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO and Collins JJ.
    Cell Host & Microbe 22: 757-765 (2017).
  1. Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling.
    Chandrasekaran S, Zhang J, Sun Z, Li H, Daley G and Collins JJ.
    Cell Reports 21: 2965-2977 (2017).
  1. Antibiotic efficacy - context matters.
    Yang JH, Bening SC and Collins JJ.
    Current Opinion in Microbiology 39: 73-80 (2017).
  1. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors.
    Skamagki M, Correia C, Yeung P, Baslan T, Beck S, Zhang C, Ross CA, Dang L, Liu Z, Giunta S, Chang TP, Wang J, Ananthanarayanan A, Bohndorf M, Bosbach B, Adjaye J, Funabiki H, Kim J, Lowe S, Collins JJ, Lu CW, Li H, Zhao R and Kim K.
    Nature Cell Biology 19: 1037-1048 (2017).
  1. Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality.
    Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini CN, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ and Walker GC.
    Proceedings of the National Academy of Sciences USA 114: 9164-9169 (2017).
  1. Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via tricarboxylic acid cycle control.
    Meylan S, Porter CBM, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM and Collins JJ.
    Cell Chemical Biology 24: 195-206 (2017).
  1. Engineering models to scale.
    Dy AJ and Collins JJ.
    Cell 165: 516-517 (2017).

2016

  1. Portable, on-demand biomolecular manufacturing.
    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 and Collins JJ.
    Cell 167: 248-259 (2016).
  1. Creating single-copy genetic circuits.
    Lee JW, Gyorgy A, Cameron DE, Pyenson N, Choi KR, Way JC, Silver PA, Del Vecchio D and Collins JJ.
    Molecular Cell 63: 329-336 (2016).
  1. Comparison of Cas9 activators in multiple species.
    Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJK, Buchthal J, Housden BE, Perrimon N, Collins JJ and Church G.
    Nature Methods 13: 563-567 (2016).
  1. Synthetic biology platform technologies for antimicrobial applications.
    Braff D, Shis D and Collins JJ.
    Advanced Drug Delivery Reviews 105: 35-43 (2016).
  1. Targeted erythropoietin selectively stimulates blood cell expansion in vivo.
    Burrill DR, Vernet A, Collins JJ, Silver PA and Way JC.
    Proceedings of the National Academy of Sciences USA 113: 5245-5250 (2016).
  1. Rapid, low-cost detection of Zika virus using programmable biomolecular components.
    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 and Collins JJ.
    Cell 165: 1255-1266 (2016).
  1. 'Deadman' and 'Passcode' microbial kill switches for bacterial containment.
    Chan CTY, Lee JW, Cameron DE, Bashor CJ and Collins JJ.
    Nature Chemical Biology 12: 82-86 (2016).
  1. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip.
    Kim HJ, Li H, Collins JJ and Ingber DE.
    Proceedings of the National Academy of Sciences USA 113: 7-15 (2016).
  1. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma.
    Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, Soysa Y, Cahan P, Theißen J, Tu H, Han A, Kurek KC, LaPier GS, Osborne JK, Ross SJ, Cesana M, Collins JJ, Berthold F and Daley GQ.
    Nature 535: 246-251 (2016).
  1. LIN28 regulates stem cell metabolism and conversion to primed pluripotency.
    Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ and Daley GQ.
    Cell Stem Cell 19: 66-80 (2016).
  1. RNAi reveals phase-specific global regulators of human somatic cell reprogramming.
    Toh CXD, Chan JW, Chong ZS, Wang HF, Guo HC, Satapathy S, Ma D, Goh GYL, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins JJ, Daley GQ, Wee KB, Farran CAE, Li H, Lim YP, Bard FA and Loh YH.
    Cell Reports 15: 2597-2607 (2016).
  1. Chemogenomics and orthology-based design of antibiotic combination therapies.
    Chandrasekaran S, Cokol-Cakmak M, Sahin N, Yilancioglu K, Kazan H, Collins JJ and Cokol M.
    Molecular Systems Biology 12: 1-12 (2016).
  1. A role for the bacterial GATC methylome in antibiotic stress survival.
    Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H and Collins JJ.
    Nature Genetics 48: 581-586 (2016).

2015

  1. Synthetic biology devices for in vitro and in vivo diagnostics.
    Slomovic S, Pardee K and Collins JJ.
    Proceedings of the National Academy of Sciences USA 112: 14429-14435 (2015).
  1. DNA sense-and-respond protein modules for mammalian cells.
    Slomovic S and Collins JJ.
    Nature Methods 12: 1085-1090 (2015).
  1. Cas9 gRNA engineering for genome editing, activation and repression.
    Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJK, Ebrahimkhani MR, Collins JJ, Weiss R and Church GM.
    Nature Methods 12: 1051-1054 (2015).
  1. Engineered phagemids for nonlytic, targeted antibacterial therapies.
    Krom RJ, Bhargava P, Lobritz MA and Collins JJ.
    Nano Letters 15: 4808-4813 (2015).
  1. Highly efficient Cas9-mediated transcriptional programming.
    Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, Iyer EPR, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ and Church GM.
    Nature Methods 12: 326-328 (2015).
  1. Chromatin regulation at the frontier of synthetic biology.
    Keung AJ, Joung JK, Khalil AS and Collins JJ.
    Nature Reviews Genetics 16: 159-171 (2015).
  1. Bactericidal antibiotics induce toxic metabolic perturbations that lead to cellular damage.
    Belenky P, Ye JD, Porter CBM, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC and Collins JJ.
    Cell Reports 13: 968-980 (2015).
  1. Systematic identification of factors for provirus silencing in embryonic stem cells.
    Yang BX, EL Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YFS, Goh GYL, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA and Loh YH.
    Cell 163: 230-245 (2015).
  1. Antibiotic efficacy is linked to bacterial cellular respiration.
    Lobritz MA, Belenky P, Porter CBM, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS and Collins JJ.
    Proceedings of the National Academy of Sciences USA 112: 8173-8180 (2015).
  1. Boosting bacterial metabolism to combat antibiotic resistance.
    Bhargava P and Collins JJ.
    Cell Metabolism 21: 154-155 (2015).
  1. Unraveling the physiological complexities of antibiotic lethality.
    Dwyer DJ, Collins JJ and Walker GC.
    Annual Review of Pharmacology and Toxicology 55: 313-312 (2015).
 

2014

  1. Tunable protein degradation in bacteria.
    Cameron DE and Collins JJ.
    Nature Biotechnology 32: 1276-1281 (2014).
  1. Paper-based synthetic gene networks.
    Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P and Collins JJ.
    Cell 159: 940-954 (2014).
  1. Toehold switches: de-novo-designed regulators of gene expression.
    Green AA, Silver PA, Collins JJ and Yin P.
    Cell 159: 925-939 (2014).
  1. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation.
    Keung AJ, Bashor CJ, Kiriakov S, Collins JJ and Khalil AS.
    Cell 158: 110-120 (2014).
  1. Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro.
    Torisawa Y, Spina CS, Mammoto T, Mammoto A, Weaver JC, Tat T, Collins JJ and Ingber DE.
    Nature Methods 11: 663-669 (2014).
  1. Syntrophic exchange in synthetic microbial communities.
    Mee MT, Collins JJ, Church GM and Wang HH.
    Proceedings of the National Academy of Sciences USA 111: E2149-E2156 (2014).
  1. Synthetic biology: How best to build a cell.
    Collins JJ, Maxon M, Ellington A, Fussenegger M, Weiss R and Sauro H.
    Nature 509: 155-157 (2014).
  1. A brief history of synthetic biology.
    Cameron DE, Bashor CJ and Collins JJ.
    Nature Reviews Microbiology 12: 381-390 (2014).
  1. Programmable bacteria detect and record an environmental signal in the mammalian gut.
    Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC and Silver PA.
    Proceedings of the National Academy of Sciences USA 111: 4838-4843 (2014).
  1. Integrating biological redesign: where synthetic biology came from and where it needs to go.
    Way JC, Collins JJ, Keasling JD, Silver PA.
    Cell 157: 151-161 (2014).
  1. Deconstructing transcriptional heterogeneity in pluripotent stem cells.
    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 and Collins JJ.
    Nature 516: 56-61 (2014).
  1. A community effort to assess and improve drug sensitivity prediction algorithms.
    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, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW and Stolovitzky G.
    Nature Biotechnology 32: 1202-1212 (2014).
  1. Defining cellular identity through network biology.
    Cahan P, Morris SA, Collins JJ and Daley GQ.
    Cell Cycle 13: 3313-3314 (2014).
  1. Editorial overview: Antimicrobials: Grappling with the complexities of antibiotics and resistance.
    Collins JJ and Kishony R.
    Current Opinion in Microbiology 21: v-vi (2014).
  1. Antibiotics and the gut microbiota.
    Modi SR, Collins JJ and Relman DA.
    Journal of Clinical Investigation 124: 4212-4218 (2014).
  1. A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity.
    Dusonchet J, Li H, Guillily M, Liu M, Stafa K, Troletii CD, Boon JY, Saha S, Mamais A, Citro A, Youmans KL, Liu L, Schneider BL, Aebischer P, Yue Z, Bandopadhyay R, Glicksman MA, Moore DJ, Collins JJ and Wolozin B.
    Human Molecular Genetics 23: 4887-4905 (2014).
  1. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes.
    Lang AH, Li H, Collins JJ and Mehta PJ.
    PLOS Computational Biology 10: e1003734 (2014).
  1. CellNet: network biology applied to stem cell engineering.
    Cahan P, Li H, Morris SA, da Rocha EL, Daley GQ and Collins JJ.
    Cell 158: 903-915 (2014).
  1. Dissecting engineered cell types and enhancing cell fate conversion via CellNet.
    Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ and Daley GQ.
    Cell 158: 889-902 (2014).
  1. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells.
    Lu Y, Loh Y, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CD, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ and Marto JA.
    Cell Stem Cell 15: 92-101 (2014).
  1. Antibiotics induce redox-related physiological alterations as part of their lethality.
    Dwyer DJ, Belenky PA, Yang JH, MacDonald IC, Martell JD, Takahashi N, Chan CTY, Lobritz MA, Braff D, Schwarz E, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, Khalil AS, Ting AY, Walker GC and Collins JJ.
    Proceedings of the National Academy of Sciences USA 111: E2100-E2109 (2014).
  1. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming.
    Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ and Lerou PH.
    Cell Reports 7: 70-78 (2014).
  1. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria.
    Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ and Walker GC.
    BMC Genomics 15: 121 (2014).
  1. Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency.
    Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H and Wu Q.
    PLOS Genetics 10: e1004038 (2014).
  1. Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice.
    Brock A, Krause S, Li H, Kowalski M, Goldberg MS, Collins JJ and Ingber DE.
    Science Translational Medicine 6: 217ra2 (2014).
 

2013

  1. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors.
    Doulatov S, Vo LT, Chou sS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI and Daley GQ.
    Cell Stem Cell 13: 459-470 (2013).
  1. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells.
    Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ and The Immunological Genome Project Consortium.
    Stem Cell Reports 1: 266-280 (2013).
  1. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance.
    Vega NM, Allison KR, Samuels AN, Klempner MS and Collins JJ.
    Proceedings of the National Academy of Sciences USA 110: 14420-14425 (2013).
  1. Differential splicing across immune system lineages.
    Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C and ImmGen Consortium.
    Proceedings of the National Academy of Sciences USA 110: 14324-14329 (2013).
  1. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome.
    Modi SR, Lee HH, Spina CS and Collins JJ.
    Nature 499: 219-222 (2013).
  1. Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in mammalian cells.
    Kalghatgi S, Spina CS, Costello JC, Liesa M, Morones-Ramirez JR, Slomovic S, Molina A, Shirihai OS and Collins JJ.
    Science Translational Medicine 5: 192ra85 (2013).
  1. Silver enhances antibiotic activity against Gram-negative bacteria.
    Morones-Ramirez JR, Winkler JA, Spina CS and Collins JJ.
    Science Translational Medicine 5: 190ra81 (2013).
  1. Introduction to Focus Issue: Quantitative approaches to genetic networks.
    Albert R, Collins JJ and Glass L.
    Chaos 23: 25001 (2013).
  1. Microbial persistence and the road to drug resistance.
    Cohen NR, Lobritz MA and Collins JJ.
    Cell Host & Microbe 13: 632-642 (2013).
  1. Fungicidal drugs induce a common oxidative-damage cellular death pathway.
    Belenky P, Camacho D and Collins JJ.
    Cell Reports 3: 350-358 (2013).
  1. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production.
    Brynildsen MP, Winkler JA, Spina CS, MacDonald CI and Collins JJ.
    Nature Biotechnology 31: 160-165 (2013).
 

2012

  1. Insulating gene circuits from context by RNA processing.
    Bashor CJ and Collins JJ.
    Nature Biotechnology 30: 1061-1062 (2012).
  1. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks.
    Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS and Collins JJ.
    Nature Methods 9: 1077-1080 (2012).
  1. A synthetic biology framework for programming eukaryotic transcription functions.
    Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK and Collins JJ.
    Cell 150: 647-658 (2012).
  1. Genetic switchboard for synthetic biology applications.
    Callura JM, Cantor CR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 109: 5850-5855 (2012).
  1. Synthetic biology: bits and pieces come to life.
    Collins JJ.
    Nature 483: S8-S10 (2012).109: 5850-5855 (2012).
  1. The transcriptional landscape of hematopoietic stem cell ontogeny.
    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 and Daley GQ.
    Cell Stem Cell 11: 701-714 (2012).
  1. A multiply redundant genetic switch "locks in" the transcriptional signature of regulatory T cells.
    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 and Benoist C.
    Nature Immunology 13: 972-980 (2012).
  1. Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma.
    Kwong LN, Costello JC, Huiyun L, Jiang S, Helms TL, Langsdorf AE, Jakubosky D, Genovese G, Muller FL, Jeong JH, Bender RP, Chu GC, Flaherty KT, Wargo JA, Collins JJ and Chin L.
    Nature Medicine 18: 1503-1510 (2012).
  1. microRNA regulatory network inference identifies miR-34a as a novel regulator of TFG-ß signaling in glioblastoma.
    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, Kwong L, Dunn K, Wiedemeyer WR, Brennan C, Zheng H, Rimm DL, Collins JJ and Chin L.
    Cancer Discovery 2: 736-749 (2012).
  1. Wisdom of crowds for robust gene network inference.
    Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, The Dream5 Consortium, Kellis M, Collins JJ and Stolovitzky G.
    Nature Methods 9: 796-804 (2012).
  1. Making a noisy gene: HDACs turn up the static.
    Kumar RM and Collins JJ.
    Molecular Cell 47: 151-153 (2012).
  1. Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis.
    Dwyer DJ, Camacho DM, Kohanski MA, Callura JM and Collins JJ.
    Molecular Cell 46: 561-572 (2012).
  1. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics.
    Foti JJ, Devadoss B, Winkler JA, Collins JJ and Walker GC.
    Science 336: 315-319 (2012).
  1. Signaling-mediated bacterial persister formation.
    Vega NM, Allison KR, Khalil AS and Collins JJ.
    Nature Chemical Biology 8: 431-433 (2012).
  1. Cellular signal processing: out of one, many.
    Kumar RM and Collins JJ.
    Molecular Cell 45: 143-144 (2012).
  1. Microbial environments confound antibiotic efficacy.
    Lee HH and Collins JJ.
    Nature Chemical Biology 8: 6-9 (2012).
 

2011

  1. Synthetic biology moving into the clinic.
    Ruder WC, Lu T and Collins JJ.
    Science 333: 1248-1252 (2011).
  1. Tunable signal processing in synthetic MAP kinase cascades.
    O'Shaughnessy EC, Palani S, Collins JJ and Sarkar CA.
    Cell 144: 119-131 (2011).
  1. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells.
    Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Hongguang H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP and Daley GQ.
    Nature Biotechnology 29: 1117-1119 (2011).
  1. Antioxidant strategies to tolerate antibiotics.
    Belenky P and Collins JJ.
    Science 334: 915-916 (2011).
  1. Heterogeneous bacterial persisters and engineering approaches to eliminate them.
    Allison KR, Brynildsen MP and Collins JJ.
    Current Opinion in Microbiology 14: 593-598 (2011).
  1. Genomic approaches to deconstruct pluripotency.
    Loh YH, Yang L, Yang CY, Li H, Collins JJ and Daley GQ.
    Annual Review of Genomics and Human Genetics 12: 165-185 (2011).
  1. Functional characterization of bacterial sRNAs using a network biology approach.
    Modi SR, Camacho DM, Kohanski MA, Walker GC and Collins JJ.
    Proceedings of the National Academy of Sciences USA 108: 15522-15527 (2011).
  1. Metabolite-enabled eradication of bacterial persisters by aminoglycosides.
    Allison KR, Brynildsen MP and Collins JJ.
    Nature 473: 216-220 (2011).
  1. Cellular decision making and biological noise: from microbes to mammals.
    Balázsi G, van Oudenaarden A and Collins JJ.
    Cell 144: 910-925 (2011).
  1. Bacteria as control engineers.
    Allison KR and Collins JJ.
    Molecular Cell 41: 4-5 (2011).
 

2010

  1. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA.
    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 and Rossi DJ.
    Cell Stem Cell 7: 618-630 (2010).
  1. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators.
    Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 107: 15898-15903 (2010).
  1. Synthetic biology: applications come of age.
    Khalil AS and Collins JJ.
    Nature Reviews Genetics 11: 367-379 (2010).
  1. Tuning and controlling gene expression noise in synthetic gene networks.
    Murphy KF, Adams RM, Wang X, Balazsi G and Collins JJ.
    Nucleic Acids Research 38:2712-2726 (2010).
  1. Bacterial charity work leads to population-wide resistance.
    Lee HH, Molla MN, Cantor CR and Collins JJ.
    Nature 467: 82-86 (2010).
  1. Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli.
    Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R and Walker GC.
    Proceedings of the National Academy of Sciences USA 107: 15517-15522 (2010).
  1. Reprogramming of T cells from human peripheral blood.
    Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault, F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S and Daley GQ.
    Cell Stem Cell 7: 15-19 (2010).
  1. How antibiotics kill bacteria: from targets to networks.
    Kohanski MA, Dwyer DJ and Collins JJ.
    Nature Reviews Microbiology 8: 423-435 (2010).
  1. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis.
    Kohanski MA, DePristo MA and Collins JJ.
    Molecular Cell 37: 311-320 (2010).

2009

  1. Next-generation synthetic gene networks.
    Lu TK, Khalil AS and Collins JJ.
    Nature Biotechnology 27:1139-1150 (2009).
  1. Synthetic gene networks that count.
    Friedland AE, Lu TK, Wang X, Shi D, Church G and Collins JJ.
    Science 324: 1199-1202 (2009).
  1. Diversity-based, model-guided construction of synthetic gene networks with predicted functions.
    Ellis T, Wang X and Collins JJ.
    Nature Biotechnology 27: 465-471 (2009).
  1. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.
    Lu TK and Collins JJ.
    Proceedings of the National Academy of Sciences USA 106: 4629-4634 (2009).
  1. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli.
    Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ and Walker GC.
    Molecular Cell 36: 845-860 (2009).
  1. Role of reactive oxygen species in antibiotic action and resistance.
    Dwyer DJ, Kohanski MA and Collins JJ.
    Current Opinion in Microbiology 12; 482-489 (2009).
  1. Systems biology makes it personal.
    Brynildsen MP and Collins JJ.
    Molecular Cell 34: 137-138 (2009).
  1. Systems biology strikes gold.
    Camacho DM and Collins JJ.
    Cell 137: 24-26 (2009).
  1. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium.
    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, Getts R, Lenburg ME and Spira A.
    Proceedings of the National Academy of Sciences USA 106: 2319-2324 (2009).
  1. A network biology approach to aging in yeast.
    Lorenz DR, Cantor CR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 106: 1145-1150 (2009).
 

2008

  1. Rewiring bacteria, two components at a time.
    Kohanski MA and Collins JJ.
    Cell 133: 947-948 (2008).
  1. Networking opportunities for bacteria.
    Dwyer DJ, Kohanski MA and Collins JJ.
    Cell 135: 1153-1156 (2008).
  1. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death.
    Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G and Collins JJ.
    Cell 135: 679-690 (2008).
  1. The Immunological Genome Project: networks of gene expression in immune cells.
    Heng TS, Painter MW, Elpek K, Lukacs-Kornek V, Mauermann N, Turley SJ, Koller D, Kim FS, Wagers AJ, Asinovski N, Davis S, Fassett M, Feuerer M, Gray DH, Haxhinasto S, Hill JA, Hyatt G, Laplace C, Leatherbee K, Mathis D, Benoist C, Jianu R, Laidlaw DH, Best JA, Knell J, Goldrath AW, Jarjoura J, Sun JC, Zhu Y, Lanier LL, Ergun A, Li Z, Collins JJ, Shinton SA, Hardy RR, Friedline R, Sylvia K and Kang J.
    Nature Immunology 9: 1091-1094 (2008).
  1. Gene regulation: hacking the network on a sugar high.
    Ellis T, Wang X and Collins JJ.
    Molecular Cell 30: 1-2 (2008).
 

2007

  1. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase.
    Guido NJ, Lee P, Wang X, Elston TC and Collins JJ.
    Biophysical Journal 93: L55-L57 (2007).
  1. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells.
    Deans TL, Cantor CR and Collins JJ.
    Cell 130: 363-372 (2007).
  1. Combinatorial promoter design for engineering noisy gene expression.
    Murphy KF, Balazsi G and Collins JJ.
    Proceedings of the National Academy of Sciences USA 104: 12726-12731 (2007).
  1. Dispersing biofilms with engineered enzymatic bacteriophage.
    Lu TK and Collins JJ.
    Proceedings of the National Academy of Sciences USA 104: 11197-11202 (2007).
  1. Taking the inventory inside single cells.
    Balazsi G and Collins JJ.
    Nature Chemical Biology 3: 141-142 (2007).
  1. A common mechanism of cellular death induced by bactericidal antibiotics.
    Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA and Collins JJ.
    Cell 130: 797-810 (2007).
  1. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli.
    Dwyer DJ, Kohanski MA, Hayete B and Collins JJ.
    Molecular Systems Biology 3: 91 (2007).
  1. A network biology approach to prostate cancer.
    Ergun A, Lawrence CA, Kohanski MA, Brennan TA and Collins JJ.
    Molecular Systems Biology 3: 82 (2007).
  1. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
    Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS.
    PLOS Biology 5(1): e8 (2007).
  1. Size matters: network inference tackles the genome scale.
    Hayete B, Gardner TS and Collins JJ.
    Molecular Systems Biology 3: 77 (2007).
 

2006

  1. Phenotypic consequences of promoter-mediated transcriptional noise.
    Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR and Collins JJ.
    Molecular Cell 24: 853-865 (2006).
  1. Engineering life: building a FAB for biology.
    Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C and Weiss R.
    Scientific American 294: 44-51 (2006).
  1. RNA synthetic biology.
    Isaacs FJ, Dwyer DJ and Collins JJ.
    Nature Biotechnology 24: 545-554 (2006).
  1. A bottom-up approach to gene regulation.
    Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins JJ.
    Nature 439: 856-860 (2006).
 

2005

  1. And the noise played on: stochastic gene expression and HIV-1 infection.
    Blake WJ and Collins JJ.
    Cell 122: 147-155 (2005).
  1. Stochasticity in gene expression: from theories to phenotypes.
    Kaern M, Elston TC, Blake WJ, and Collins JJ.
    Nature Reviews Genetics 6: 451-464 (2005).
  1. Signal processing in single cells.
    Isaacs FJ, Blake WJ and Collins JJ.
    Science 307: 1886-1888 (2005).
  1. Plug-and-play with RNA.
    Isaacs FJ and Collins JJ.
    Nature Biotechnology 23: 306-307 (2005).
  1. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks.
    di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ.
    Nature Biotechnology 23: 377-383 (2005).

2004

  1. Engineered riboregulators enable post-transcriptional control of gene expression.
    Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR and Collins JJ.
    Nature Biotechnology 22: 841-847 (2004).
  1. Programmable cells: Interfacing natural and engineered gene networks.
    Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 101: 8414-8419 (2004).
  1. Evolving complex dynamics in electronic models of genetic networks.
    Mason J, Linsay P, Collins JJ and Glass L.
    Chaos 14: 707-715 (2004).
  1. Inferring microbial genetic networks.
    Gardner TS, Shimer S and Collins JJ.
    ASM News 70: 121-126 (2004).
 

2003

  1. Prediction and measurement of an autoregulatory genetic module.
    Isaacs FJ, Hasty J, Cantor CR and Collins JJ.
    Proceedings of the National Academy of Sciences USA 100: 7714-7719 (2003).
  1. Noise in eukaryotic gene expression.
    Blake WJ, Kaern M, Cantor CR and Collins JJ.
    Nature 422: 633-637 (2003).
  1. The engineering of gene regulatory networks.
    Kaern M, Blake WJ and Collins JJ.
    Annual Review of Biomedical Engineering 5: 179-206 (2003).
  1. Inferring genetic networks and identifying compound mode of action via expression profiling.
    Gardner TS, Bernardo D, Lorenz D and Collins JJ.
    Science 301: 102-105 (2003).
  1. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling.
    Tegner J, Yeung MKS, Hasty J and Collins JJ.
    Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003).
 

2002

  1. Engineered gene circuits.
    Hasty J, McMillen D and Collins JJ.
    Nature 420: 224-230 (2002).
  1. A synthetic gene network for entraining and amplifying cellular oscillations.
    Hasty J, Dolnik M, Rottschafer V and Collins JJ.
    Physical Review Letters 88: 148101 (2002).
  1. Synchronizing genetic relaxation oscillators with intercell signaling.
    McMillen D, Kopell N, Hasty J and Collins JJ.
    Proceedings of the National Academy of Sciences USA 99: 679-684 (2002).
  1. Translating the noise.
    Hasty J and Collins JJ.
    Nature Genetics 31: 13-14 (2002).
  1. Reverse engineering gene networks using singular value decomposition and robust regression.
    Yeung MKS, Tegner J and Collins JJ.
    Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002).
 

2001

  1. Computational studies of gene regulatory networks: In numero molecular biology.
    Hasty J, McMillen D, Isaacs F and Collins JJ.
    Nature Reviews Genetics 2: 268-279 (2001).
  1. Designer gene networks: Towards fundamental cellular control.
    Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ.
    Chaos 11: 207-220 (2001).
  1. Protein interactions: unspinning the web.
    Hasty J and Collins JJ.
    Nature 411: 30-31 (2001).
 

2000

  1. Neutralizing noise in gene networks.
    Gardner TS and Collins JJ.
    Nature 405: 520-521 (2000).
  1. Noise-based switches and amplifiers for gene expression.
    Hasty J, Pradines J, Dolnik M and Collins JJ.
    Proceedings of the National Academy of Sciences USA 97: 2075-2080 (2000).
  1. Construction of a genetic toggle switch in Escherichia coli.
    Gardner TS, Cantor CR and Collins JJ.
    Nature 403: 339-342 (2000).