1. Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA. De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology 15: 1173-1182 (2019). [pdf file]

  2. Johnston CW, Collins JJ. Engineering microbial peer pressure. Science 365: 986-987 (2019). [pdf file]

  3. English MA, Soenksen LR, Gayet RV, Puig H De, Angenent-mari NM, Mao AS, Nguyen PQ, Collins JJ. Programmable CRISPR-responsive smart materials. Science 365: 780-785 (2019). [pdf file]

  4. Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ and Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science 364: 593-597 (2019). [pdf file]

  5. Kong W, Meldgin DR, Collins JJ and Lu T. Designing microbial consortia with defined social interactions. Nature Chemical Biology 14: 821-829 (2018). [pdf file]

  6. 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. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods 15: 611-616 (2018). [pdf file]

  7. Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A and Collins JJ. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nature Communications 9: 3347 (2018). [pdf file]

  8. 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. BioBits Explorer: A modular synthetic biology education kit. Science Advances 4: eaat5105 (2018). [pdf file]

  9. 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. BioBits Bright: A flourescent synthetic biology education kit. Science Advances 4: eaat5107 (2018). [pdf file]

  10. Camacho DM, Collins KM, Powers RK, Costello JC and Collins JJ. Next-generation machine learning for biological networks. Cell 173: 1581-1592 (2018). [pdf file]

  11. Mao N, Cubillos-Ruiz A, Cameron DE and Collins JJ. Probiotic strains detect and suppress cholera in mice. Science Translational Medicine 10: eaao2586 (2018). [pdf file]

  12. 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. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nature Biotechnology 36: 540-549 (2018). [pdf file]

  13. Cho JH, Collins JJ and Wong WW. Universal chimeric antigen receptors for multiplexed and logical control of T cell responses. Cell 173: 1426-1438 (2018). [pdf file]

  14. Bashor CJ and Collins JJ. Understanding biological regulation through synthetic biology. Annual Review of Biophysics 47: 399-423 (2018). [pdf file]

  15. Lee JW, Chan CTY, Slomovic S and Collins JJ. Next-generation biocontainment systems for engineered organisms. Nature Chemical Biology 14: 530-537 (2018). [pdf file]

  16. Shapiro RS, Chavez A and Collins JJ. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nature Reviews Microbiology 16: 333-339 (2018). [pdf file]

  17. Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ and Zhang F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360: 439-444 (2018). [pdf file]

  18. Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ and Church GM. Precise Cas9 targeting enables genomic mutation prevention. Proceedings of the National Academy of Sciences USA 115: 3669-3673 (2018). [pdf file]

  19. Shapiro SS, 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. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology 2: 73-82 (2018). [pdf file]

  20. Certain LK, Way JC, Pezone AJ and Collins JJ. Using engineered bacteria to characterize infection dynamics and antibiotic effects in vivo. Cell Host & Microbe 22: 263-268 (2017). [pdf file]

  21. Green AA, Kim J, Ma D, Silver PA, Collins JJ and Yin, P. Complex cellular logic computation using ribocomputing devices. Nature 548: 117-121 (2017). [pdf file]

  22. Yeung E, Dy AJ, Martin KB, Beck JL, Collins JJ and Murray, RM. Biophysical constraints arising from compositional context in synthetic gene networks. Cell Systems 5: 11-24, e1-e12 (2017). [pdf file]

  23. 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. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356: 438-442 (2017). [pdf file]

  24. Del Vecchio D, Abdallah H, Qian Y and Collins JJ. A blueprint for a synthetic genetic feedback controller to reprogram cell fate. Cell Systems 4: 109-120 (2017). [pdf file]

  25. 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. Portable, on-demand biomolecular manufacturing. Cell 167: 248-259 (2016). [pdf file]

  26. Lee JW, Gyorgy A, Cameron DE, Pyenson N, Choi KR, Way JC, Silver PA, Del Vecchio D and Collins JJ. Creating single-copy genetic circuits. Molecular Cell 63: 329-336 (2016). [pdf file]

  27. 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. Comparison of Cas9 activators in multiple species. Nature Methods 13: 563-567 (2016). [pdf file]

  28. Braff D, Shis D and Collins JJ. Synthetic biology platform technologies for antimicrobial applications. Advanced Drug Delivery Reviews 105: 35-43 (2016). [pdf file]

  29. Burrill DR, Vernet A, Collins JJ, Silver PA and Way JC. Targeted erythropoietin selectively stimulates blood cell expansion in vivo. Proceedings of the National Academy of Sciences USA 113: 5245-5250 (2016). [pdf file]

  30. 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. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165: 1255-1266 (2016). [pdf file]

  31. Chan CTY, Lee JW, Cameron DE, Bashor CJ and Collins JJ. 'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nature Chemical Biology 12: 82-86 (2016). [pdf file]

  32. Kim HJ, Li H, Collins JJ and 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 USA 113: 7-15 (2016). [pdf file]

  33. Slomovic S, Pardee K and Collins JJ. Synthetic biology devices for in vitro and in vivo diagnostics. Proceedings of the National Academy of Sciences USA 112: 14429-14435 (2015). [pdf file]

  34. Slomovic S and Collins JJ. DNA sense-and-respond protein modules for mammalian cells. Nature Methods 12: 1085-1090 (2015). [pdf file]

  35. 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 G. Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods 12: 1051-1054 (2015). [pdf file]

  36. Krom RJ, Bhargava P, Lobritz MA and Collins JJ. Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Letters 15: 4808-4813 (2015). [pdf file]

  37. 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. Highly efficient Cas9-mediated transcriptional programming. Nature Methods 12: 326-328 (2015). [pdf file]

  38. Keung AJ, Joung JK, Khalil AS and Collins JJ. Chromatin regulation at the frontier of synthetic biology. Nature Reviews Genetics 16: 159-171 (2015). [pdf file]

  39. Cameron DE and Collins JJ. Tunable protein degradation in bacteria. Nature Biotechnology 32: 1276-1281 (2014). [pdf file]

  40. Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P and Collins JJ. Paper-based synthetic gene networks. Cell 159: 940-954 (2014). [pdf file]

  41. Green AA, Silver PA, Collins JJ and Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell 159: 925-939 (2014). [pdf file]

  42. Keung AJ, Bashor CJ, Kiriakov S, Collins JJ and Khalil AS. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158: 110-120 (2014). [pdf file]

  43. Torisawa Y, Spina CS, Mammoto T, Mammoto A, Weaver JC, Tat T, Collins JJ and Ingber DE. Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro. Nature Methods 11: 663-669 (2014). [pdf file]

  44. Mee MT, Collins JJ, Church GM and Wang HH. Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences USA 111: E2149-E2156 (2014). [pdf file]

  45. Collins JJ, Maxon M, Ellington A, Fussenegger M, Weiss R and Sauro H. Synthetic biology: How best to build a cell. Nature 509: 155-157 (2014). [pdf file]

  46. Cameron DE, Bashor CJ and Collins JJ. A brief history of synthetic biology. Nature Reviews Microbiology 12: 381-390 (2014). [pdf file]

  47. Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC and Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of Sciences USA 111: 4838-4843 (2014). [pdf file]

  48. Way JC, Collins JJ, Keasling JD, Silver PA. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157: 151-161 (2014). [pdf file]

  49. Albert R, Collins JJ and Glass L. Introduction to Focus Issue: Quantitative approaches to genetic networks. Chaos 23: 25001 (2013). [pdf file]

  50. Bashor CJ and Collins JJ. Insulating gene circuits from context by RNA processing. Nature Biotechnology 30: 1061-1062 (2012). [pdf file]

  51. Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS and Collins JJ. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nature Methods 9: 1077-1080 (2012). [pdf file]

  52. Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK and Collins JJ. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150: 647-658 (2012). [pdf file]

  53. Callura JM, Cantor CR and Collins JJ. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences USA 109: 5850-5855 (2012). [pdf file]

  54. Collins JJ. Synthetic biology: bits and pieces come to life. Nature 483: S8-S10 (2012). [pdf file]

  55. Ruder WC, Lu T and Collins JJ. Synthetic biology moving into the clinic. Science 333: 1248-1252 (2011). [pdf file]

  56. O'Shaughnessy EC, Palani S, Collins JJ and Sarkar CA. Tunable signal processing in synthetic MAP kinase cascades. Cell 144: 119-131 (2011). [pdf file]

  57. 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. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7: 618-630 (2010). [pdf file]

  58. Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR and Collins JJ. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences USA 107: 15898-15903 (2010). [pdf file]

  59. Khalil AS and Collins JJ. Synthetic biology: applications come of age. Nature Reviews Genetics 11: 367-379 (2010). [pdf file]

  60. Murphy KF, Adams RM, Wang X, Balazsi G and Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Research 38:2712-2726 (2010). [pdf file]

  61. Lu TK, Khalil AS and Collins JJ. Next-generation synthetic gene networks. Nature Biotechnology 27:1139-1150 (2009). [pdf file]

  62. Friedland AE, Lu TK, Wang X, Shi D, Church G and Collins JJ. Synthetic gene networks that count. Science 324: 1199-1202 (2009). [pdf file]

  63. Ellis T, Wang X and Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009). [pdf file]

  64. Lu TK and Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences USA 106: 4629-4634 (2009). [pdf file]

  65. Kohanski MA and Collins JJ. Rewiring bacteria, two components at a time. Cell 133: 947-948 (2008). [pdf file]

  66. Guido NJ, Lee P, Wang X, Elston TC and Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal 93: L55-L57 (2007). [pdf file]

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  1. Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ (2019) Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nature Microbiology 4: 2109-2117 (2019). [pdf file]

  2. Stokes JM, Lopatkin AJ, Lobritz MA and Collins JJ. Bacterial Metabolism and Antibiotic Efficacy. Cell Metabolism 30: 251-259 (2019). [pdf file]

  3. 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, Zinkernagel A. Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology 17: 441-448 (2019). [pdf file]

  4. Collins JJ. Complex host-microbe-antibiotic interactions. Cell Host & Microbe 26: 8 (2019). [pdf file]

  5. 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. A white-box machine learning approach for revealing antibiotic mechanisms of action. Cell 177: 1649-1661 (2019). [pdf file]

  6. Collins JJ. Altered metabolic states. Cell Metabolism 29:509 (2019). [pdf file]

  7. Stokes JM, Gutierrez A, Lopatkin AJ, Andrews IW, French S, Matic I, Brown ED and Collins JJ. A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria. Nature Methods 16: 303-306 (2019). [pdf file]

  8. 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. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biology 16: 62 (2018). [pdf file]

  9. Meylan S, Andrews IW and Collins JJ. Targeting antibiotic tolerance, pathogen by pathogen. Cell 172: 1228-1238 (2018). [pdf file]

  10. Lummertz da Rocha E, Rowe RG, Lundin V, Malleshaiah M, Jha DK, Rambo CR, Li H, North TE, Collins JJ and Daley GQ. Reconstruction of complex single-cell trajectories using CellRouter. Nature Communications 9: 892 (2018). [pdf file]

  11. Gutierrez A, Jain S, Bhargava P, Hamblin M, Lobritz MA and Collins JJ. Understanding and sensitizing density-dependent persistence to quinolone antibiotic. Molecular Cell 68: 1019-1021 (2017). [pdf file]

  12. Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO and Collins JJ. Antibiotic-induced changes to the host metabolic environment inhibit drug efficacy and alter immune function. Cell Host & Microbe 22: 757-765 (2017). [pdf file]

  13. Chandrasekaran S, Zhang J, Sun Z, Li H, Daley G and Collins JJ. Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling. Cell Reports 21: 2965-2977 (2017). [pdf file]

  14. Yang JH, Bening SC and Collins JJ. Antibiotic efficacy - context matters. Current Opinion in Microbiology 39: 73-80 (2017). [pdf file]

  15. 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. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology 19: 1037-1048 (2017). [pdf file]

  16. Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini CN, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ and Walker GC. Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proceedings of the National Academy of Sciences USA 114: 9164-9169 (2017). [pdf file]

  17. Meylan S, Porter CBM, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM and Collins JJ. Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via tricarboxylic acid cycle control. Cell Chemical Biology 24: 195-206 (2017). [pdf file]

  18. 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. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature 535: 246-251 (2016). [pdf file]

  19. 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. LIN28 regulates stem cell metabolism and conversion to primed pluripotency. Cell Stem Cell 19: 66-80 (2016). [pdf file]

  20. 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 . RNAi reveals phase-specific global regulators of human somatic cell reprogramming. Cell Reports 15: 2597-2607 (2016). [pdf file]

  21. Chandrasekaran S, Cokol-Cakmak M, Sahin N, Yilancioglu K, Kazan H, Collins JJ and Cokol M. Chemogenomics and orthology-based design of antibiotic combination therapies. Molecular Systems Biology 12: 1-12 (2016). [pdf file]

  22. Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H and Collins JJ. A role for the bacterial GATC methylome in antibiotic stress sruvival. Nature Genetics 48: 581-586 (2016). [pdf file]

  23. Belenky P, Ye JD, Porter CBM, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC and Collins JJ. Bactericidal antibiotics induce toxic metabolic perturbations that lead to cellular damage. Cell Reports 13: 968-980 (2015). [pdf file]

  24. 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. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell 163: 230-245 (2015). [pdf file]

  25. Lobritz MA, Belenky P, Porter CBM, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS and Collins JJ. Antibiotic efficacy is linked to bacterial cellular respiration. Proceedings of the National Academy of Sciences USA 112: 8173-8180 (2015). [pdf file]

  26. Bhargava P and Collins JJ. Boosting bacterial metabolism to combat antibiotic resistance. Cell Metabolism 21: 154-155 (2015). [pdf file]

  27. Dwyer DJ, Collins JJ and Walker GC. Unraveling the physiological complexities of antibiotic lethality. Annual Review of Pharmacology and Toxicology 55: 313-312 (2015). [pdf file]

  28. 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. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516: 56-61 (2014). [pdf file]

  29. 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. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology 32: 1202-1212 (2014). [pdf file]

  30. Cahan P, Morris SA, Collins JJ and Daley GQ. Defining cellular identity through network biology. Cell Cycle 13: 3313-3314 (2014). [pdf file]

  31. Collins JJ and Kishony R. Editorial overview: Antimicrobials: Grappling with the complexities of antibiotics and resistance. Current Opinion in Microbiology 21: v-vi (2014). [pdf file]

  32. Modi SR, Collins JJ and Relman DA. Antibiotics and the gut microbiota. The Journal of Clinical Investigation 124: 4212-4218 (2014). [pdf file]

  33. 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. 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: 4887-4905 (2014). [pdf file]

  34. Lang AH, Li H, Collins JJ and Mehta PJ. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLOS Computational Biology 10: e1003734 (2014). [pdf file]

  35. Cahan P, Li H, Morris SA, da Rocha EL, Daley GQ and Collins JJ. CellNet: network biology applied to stem cell engineering. Cell 158: 903-915 (2014). [pdf file]

  36. Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ and Daley GQ. Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell 158: 889-902 (2014). [pdf file]

  37. 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. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 15: 92-101 (2014). [pdf file]

  38. 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. Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences USA 111: E2100-E2109 (2014). [pdf file]

  39. Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ and Lerou PH. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports 7: 70-78 (2014). [pdf file]

  40. Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ and Walker GC. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15: 121 (2014). [pdf file]

  41. Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H and Wu Q. Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency. PLOS Genetics 10: e1004038 (2014). [pdf file]

  42. Brock A, Krause S, Li H, Kowalski M, Goldberg MS, Collins JJ and Ingber DE. Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Science Translational Medicine 6: 217ra2 (2014). [pdf file]

  43. Doulatov S, Vo LT, Chou sS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI and Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell 13: 459-470 (2013). [pdf file]

  44. 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. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports 1: 266-280 (2013). [pdf file]

  45. Vega NM, Allison KR, Samuels AN, Klempner MS and Collins JJ. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proceedings of the National Academy of Sciences USA 110: 14420-14425 (2013). [pdf file]

  46. Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C and ImmGen Consortium. Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences USA 110: 14324-14329 (2013). [pdf file]

  47. Modi SR, Lee HH, Spina CS and Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499: 219-222 (2013). [pdf file]

  48. 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 (2013). [pdf file]

  49. Morones-Ramirez JR, Winkler JA, Spina CS and Collins JJ. Silver enhances antibiotic activity against Gram-negative bacteria. Science Translational Medicine 5: 190ra81 (2013). [pdf file]

  50. Cohen NR, Lobritz MA and Collins JJ. Microbial persistence and the road to drug resistance. Cell Host & Microbe 13: 632-642 (2013). [pdf file]

  51. Belenky P, Camacho D and Collins JJ. Fungicidal drugs induce a common oxidative-damage cellular death pathway. Cell Reports 3: 350-358 (2013). [pdf file]

  52. Brynildsen MP, Winkler JA, Spina CS, MacDonald CI and Collins JJ. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nature Biotechnology 31: 160-165 (2013). [pdf file]

  53. 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. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell 11: 701-714 (2012). [pdf file]

  54. 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. A multiply redundant genetic switch ‘locks in’ the transcriptional signature of regulatory T cells. Nature Immunology 13: 972-980 (2012). [pdf file]

  55. 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. Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nature Medicine 18: 1503-1510 (2012). [pdf file]

  56. 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. microRNA regulatory network inference identifies miR-34a as a novel regulator of TFG-ß signaling in glioblastoma. Cancer Discovery 2: 736-749 (2012). [pdf file]

  57. Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, The Dream5 Consortium, Kellis M, Collins JJ and Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods 9: 796-804 (2012).[pdf file]

  58. Kumar RM and Collins JJ. Making a noisy gene: HDACs turn up the static. Molecular Cell 47: 151-153 (2012). [pdf file]

  59. Dwyer DJ, Camacho DM, Kohanski MA, Callura JM and Collins JJ. Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Molecular Cell 46: 561-572 (2012). [pdf file]

  60. Foti JJ, Devadoss B, Winkler JA, Collins JJ and Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science 336: 315-319 (2012). [pdf file]

  61. Vega NM, Allison KR, Khalil AS and Collins JJ. Signaling-mediated bacterial persister formation. Nature Chemical Biology 8: 431-433 (2012). [pdf file]

  62. Kumar RM and Collins JJ. Cellular signal processing: out of one, many. Molecular Cell 45: 143-144 (2012). [pdf file]

  63. Lee HH and Collins JJ. Microbial environments confound antibiotic efficacy. Nature Chemical Biology 8: 6-9 (2012). [pdf file]

  64. 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. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology 29: 1117-1119 (2011). [pdf file]

  65. Belenky P and Collins JJ. Antioxidant strategies to tolerate antibiotics. Science 334: 915-916 (2011). [pdf file]

  66. Allison KR, Brynildsen MP and Collins JJ. Heterogeneous bacterial persisters and engineering approaches to eliminate them. Current Opinion in Microbiology 14: 593-598 (2011). [pdf file]

  67. Loh YH, Yang L, Yang CY, Li H, Collins JJ and Daley GQ. Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics 12: 165-185 (2011). [pdf file]

  68. Modi SR, Camacho DM, Kohanski MA, Walker GC and Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proceedings of the National Academy of Sciences USA 108: 15522-15527 (2011). [pdf file]

  69. Allison KR, Brynildsen MP and Collins JJ. Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature 473: 216-220 (2011). [pdf file]

  70. Balázsi G, van Oudenaarden A and Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell 144: 910-925 (2011). [pdf file]

  71. Allison KR and Collins JJ. Bacteria as control engineers. Molecular Cell 41: 4-5 (2011). [pdf file]

  72. Lee HH, Molla MN, Cantor CR and Collins JJ. Bacterial charity work leads to population-wide resistance. Nature 467: 82-86 (2010). [pdf file]

  73. Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R and 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 USA 107: 15517-15522 (2010). [pdf file]

  74. 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. Reprogramming of T cells from human peripheral blood. Cell Stem Cell 7: 15-19 (2010). [pdf file]

  75. Kohanski MA, Dwyer DJ and Collins JJ. How antibiotics kill bacteria: from targets to networks. Nature Reviews Microbiology 8: 423-435 (2010). [pdf file]

  76. Kohanski MA, DePristo MA and Collins JJ. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Molecular Cell 37: 311-320 (2010). [pdf file]

  77. Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ and Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Molecular Cell 36: 845-860 (2009). [pdf file]

  78. Dwyer DJ, Kohanski MA and Collins JJ. Role of reactive oxygen species in antibiotic action and resistance. Current Opinion in Microbiology 12; 482-489 (2009). [pdf file]

  79. Brynildsen MP and Collins JJ. Systems biology makes it personal. Molecular Cell 34: 137-138 (2009). [pdf file]

  80. Camacho DM and Collins JJ. Systems biology strikes gold. Cell 137: 24-26 (2009). [pdf file]

  81. 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. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences USA 106: 2319-2324 (2009). [pdf file]

  82. Lorenz DR, Cantor CR and Collins JJ. A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences USA 106: 1145-1150 (2009). [pdf file]

  83. Dwyer DJ, Kohanski MA and Collins JJ. Networking opportunities for bacteria. Cell 135: 1153-1156 (2008). [pdf file]

  84. Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G and Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135: 679-690 (2008). [pdf file]

  85. 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. The Immunological Genome Project: networks of gene expression in immune cells.  Nature Immunolology 9: 1091-1094 (2008). [pdf file]

  86. Ellis T, Wang X and Collins JJ. Gene regulation: hacking the network on a sugar high. Molecular Cell 30: 1-2 (2008). [pdf file]

  87. Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA and Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130: 797-810 (2007). [pdf file]

  88. Dwyer DJ, Kohanski MA, Hayete B and Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Molecular Systems Biology 3: 91 (2007). [pdf file]

  89. Ergun A, Lawrence CA, Kohanski MA, Brennan TA and Collins JJ. A network biology approach to prostate cancer. Molecular Systems Biology 3: 82 (2007). [pdf file]

  90. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLOS Biology 5(1): e8 (2007). [pdf file]

  91. Hayete B, Gardner TS and Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology 3: 77 (2007). [pdf file]

  92. di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005). [pdf file]

  93. Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [pdf file]

  94. Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [pdf file]

  95. Tegner J, Yeung MKS, Hasty J and Collins JJ. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003). [pdf file]

  96. Yeung MKS, Tegner J and Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002). [pdf file]

  97. Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [pdf file]

  1. Priplata AA, Patritti BL, Niemi JB, Hughes R, Gravelle DC, Lipsitz LA, Veves A, Stein J, Bonato P and Collins JJ. Noise-enhanced balance control in patients with diabetes and patients with stroke. Annals of Neurology 59: 4-12 (2006). [pdf file]

  2. Harry JD, Niemi JB, Priplata AA and Collins JJ. Balancing act. IEEE Spectrum, April: 36-41 (2005). [pdf file]

  3. Priplata AA, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Vibrating insoles and balance control in elderly people. The Lancet 362: 1123-1124 (2003). [pdf file]

  4. Collins JJ, Priplata AA, Gravelle DC, Niemi J, Harry J and Lipsitz LA. Noise-enhanced human sensorimotor function. IEEE Engineering in Medicine and Biology Magazine 22: 76-83 (2003). [pdf file]

  5. Priplata AA, Niemi J, Salen M, Harry J, Lipsitz LA and Collins JJ. Noise-enhanced human balance control. Physical Review Letters 89: 238101 (2002). [pdf file]

  6. Gravelle DC, Laughton CA, Dhruv NT, Katdare KD, Niemi JB, Lipsitz LA and Collins JJ. Noise-enhanced balance control in older adults. Neuroreport 13: 1853-1856 (2002). [pdf file]

  7. Dhruv NT, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Enhancing tactile sensation in older adults with electrical noise stimulation. Neuroreport 13: 597-600 (2002). [pdf file]

  8. Liu W, Lipsitz LA, Montero-Odasso M, Bean J, Kerrigan DC and Collins JJ. Noise-enhanced vibrotactile sensitivity in older adults and patients with stroke and patients with diabetic neuropathy. Archives of Physical Medicine and Rehabilitation 83: 171-176 (2002). [pdf file]

  9. Nozaki D, Collins JJ and Yamamoto Y. Mechanism of stochastic resonance enhancement in neuronal models driven by 1/f noise. Physical Review E 60: 4637-4644 (1999). [pdf file]

  10. Pradines JR, Osipov GV and Collins JJ. Coherence resonance in excitable and oscillatory systems: the essential role of slow and fast dynamics.  Physical Review E 60: 6407-6410 (1999). [pdf file]

  11. Neiman A, Schimansky-Geier L, Moss F, Shulgin B and Collins JJ. Synchronization of noisy systems by stochastic signals. Physical Review E 60: 284-292 (1999). [pdf file]

  12. Nozaki D, Mar DJ, Grigg P and Collins JJ. Effects of colored noise on stochastic resonance in sensory neurons. Physical Review Letters 82: 2402-2405 (1999). [pdf file]

  13. Collins JJ. Fishing for function in noise. Nature 402: 241-242 (1999). [pdf file]

  14. Suki B, Alencar AM, Sujeer MK, Lutchen KR, Collins JJ, Andrade JS, Ingenito EP, Zapperi S and Stanley HE. Life-support system benefits from noise. Nature 393: 127-128 (1998). [pdf file]

  15. Richardson KA, Imhoff TT, Grigg P and Collins JJ. Using electrical noise to enhance the ability of humans to detect subthreshold mechanical cutaneous stimuli. CHAOS 8: 599-603 (1998). [pdf file]

  16. Chow CC, Imhoff TT and Collins JJ. Enhancing aperiodic stochastic resonance through noise modulation. CHAOS 8: 616-620 (1998). [pdf file]

  17. Gailey PC, Neiman A, Collins JJ and Moss F. Stochastic resonance in ensembles of nondynamical elements: the role of internal noise. Physical Review Letters 79: 4701-4704 (1997). [pdf file]

  18. Collins JJ, Imhoff TT and Grigg P. Noise-mediated enhancements and decrements in human tactile sensation. Physical Review E 56: 923-926 (1997). [pdf file]

  19. Cordo P, Inglis JT, Verschueren S, Collins JJ, Merfeld DM, Rosenblum S, Buckley S and Moss F. Noise in human muscle spindles. Nature 383: 769-770 (1996). [pdf file]

  20. Collins JJ, Imhoff TT and Grigg P. Noise-enhanced tactile sensation. Nature 383: 770 (1996). [pdf file]

  21. Collins JJ, Imhoff TT and Grigg P. Noise-enhanced information transmission in rat SA1 cutaneous mechanoreceptors via aperiodic stochastic resonance. Journal of Neurophysiology 76: 642-645 (1996). [pdf file]

  22. Collins JJ, Chow CC, Capela AC and Imhoff TT. Aperiodic stochastic resonance. Physical Review E 54: 5575-5584 (1996). [pdf file]

  23. Heneghan C, Chow CC, Collins JJ, Imhoff TT, Lowen SB and Teich MC. Information measures quantifying aperiodic stochastic resonance. Physical Review E 54: R2228-R2231 (1996). [pdf file]

  24. Collins JJ, Chow CC and Imhoff TT. Aperiodic stochastic resonance in excitable systems. Physical Review E 52: R3321-R3324 (1995). [pdf file]

  25. Collins JJ, Chow CC and Imhoff TT. Stochastic resonance without tuning. Nature 376: 236-238 (1995). [pdf file]
+ Coupled Neural Oscillators
+ Human Balance Control and Locomotion
+ Dynamical Control of Biological Systems
+ Nonlinear Time Series Analysis