James J. Collins, PhD - Publications

Affiliations: 
Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
Systems Biology, Synthetic Biology
Website:
http://collinslab.mit.edu/

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

Year Citation  Score
2022 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, et al. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Research. PMID 35776115 DOI: 10.1093/nar/gkac531  0.408
2022 Lummertz da Rocha E, Kubaczka C, Sugden WW, Najia MA, Jing R, Markel A, LeBlanc ZC, Dos Santos Peixoto R, Falchetti M, Collins JJ, North TE, Daley GQ. CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development. Nature Cell Biology. PMID 35414020 DOI: 10.1038/s41556-022-00884-1  0.44
2021 Lobritz MA, Andrews IW, Braff D, Porter CBM, Gutierrez A, Furuta Y, Cortes LBG, Ferrante T, Bening SC, Wong F, Gruber C, Bakerlee CW, Lambert G, Walker GC, Dwyer DJ, ... Collins JJ, et al. Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality. Cell Chemical Biology. PMID 34990601 DOI: 10.1016/j.chembiol.2021.12.010  0.535
2021 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, ... ... Collins JJ, et al. RNA-responsive elements for eukaryotic translational control. Nature Biotechnology. PMID 34711989 DOI: 10.1038/s41587-021-01068-2  0.751
2021 Cubillos-Ruiz A, Guo T, Sokolovska A, Miller PF, Collins JJ, Lu TK, Lora JM. Engineering living therapeutics with synthetic biology. Nature Reviews. Drug Discovery. PMID 34616030 DOI: 10.1038/s41573-021-00285-3  0.537
2021 Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science (New York, N.Y.). 371. PMID 33602825 DOI: 10.1126/science.aba0862  0.7
2021 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, ... ... Collins JJ, et al. Anomalous COVID-19 tests hinder researchers. Science (New York, N.Y.). 371: 244-245. PMID 33446547 DOI: 10.1126/science.abf8873  0.307
2020 Angenent-Mari NM, Garruss AS, Soenksen LR, Church G, Collins JJ. A deep learning approach to programmable RNA switches. Nature Communications. 11: 5057. PMID 33028812 DOI: 10.1038/s41467-020-18677-1  0.394
2020 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, Loh YH. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Science Advances. 6. PMID 32917699 DOI: 10.1126/Sciadv.Aba1190  0.595
2020 Zheng EJ, Stokes JM, Collins JJ. Eradicating Bacterial Persisters with Combinations of Strongly and Weakly Metabolism-Dependent Antibiotics. Cell Chemical Biology. PMID 32916087 DOI: 10.1016/J.Chembiol.2020.08.015  0.317
2020 Johnston CW, Badran AH, Collins JJ. Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. Nature Communications. 11: 4202. PMID 32826900 DOI: 10.1038/S41467-020-18018-2  0.329
2020 Xing QR, El Farran CA, Zeng YY, Yi Y, Warrier T, Gautam P, Collins JJ, Xu J, Dröge P, Koh CG, Li H, Zhang LF, Loh YH. Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Research. PMID 32699019 DOI: 10.1101/Gr.257840.119  0.469
2020 Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, ... ... Collins JJ, et al. A Deep Learning Approach to Antibiotic Discovery. Cell. 181: 475-483. PMID 32302574 DOI: 10.1016/j.cell.2020.04.001  0.757
2020 Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackerman Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, ... ... Collins JJ, et al. A Deep Learning Approach to Antibiotic Discovery. Cell. 180: 688-702.e13. PMID 32084340 DOI: 10.1016/J.Cell.2020.01.021  0.784
2019 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. PMID 31686032 DOI: 10.1038/S41589-019-0388-1  0.306
2019 Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ. Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nature Microbiology. PMID 31451773 DOI: 10.1038/S41564-019-0536-0  0.57
2019 Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ. Author Correction: A systems biology pipeline identifies regulatory networks for stem cell engineering. Nature Biotechnology. PMID 31312048 DOI: 10.1038/S41587-019-0212-1  0.452
2019 Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ. A systems biology pipeline identifies regulatory networks for stem cell engineering. Nature Biotechnology. 37: 810-818. PMID 31267104 DOI: 10.1038/S41587-019-0159-2  0.534
2019 Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Cell. PMID 31080069 DOI: 10.1016/J.Cell.2019.04.016  0.648
2019 Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, et al. Publisher Correction: Definitions and guidelines for research on antibiotic persistence. Nature Reviews. Microbiology. PMID 31036919 DOI: 10.1038/S41579-019-0207-4  0.608
2019 Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science (New York, N.Y.). PMID 31000590 DOI: 10.1126/Science.Aau8287  0.309
2019 Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, et al. Definitions and guidelines for research on antibiotic persistence. Nature Reviews. Microbiology. PMID 30980069 DOI: 10.1038/S41579-019-0196-3  0.652
2019 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, ... ... Collins JJ, et al. Author Correction: ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology. PMID 30643186 DOI: 10.1038/S41556-018-0269-Y  0.399
2018 Nageshwaran S, Chavez A, Cher Yeo N, Guo X, Lance-Byrne A, Tung A, Collins JJ, Church GM. CRISPR Guide RNA Cloning for Mammalian Systems. Journal of Visualized Experiments : Jove. PMID 30346403 DOI: 10.3791/57998  0.447
2018 Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, ... ... Collins JJ, et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods. PMID 30013045 DOI: 10.1038/S41592-018-0048-5  0.484
2018 Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, Cecchi R, Garnier SL, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ, Church GM. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nature Biotechnology. PMID 29786095 DOI: 10.1038/Nbt.4147  0.467
2018 Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM. Precise Cas9 targeting enables genomic mutation prevention. Proceedings of the National Academy of Sciences of the United States of America. PMID 29555762 DOI: 10.1073/Pnas.1718148115  0.447
2018 Bashor CJ, Collins JJ. Understanding Biological Regulation Through Synthetic Biology. Annual Review of Biophysics. PMID 29547341 DOI: 10.1146/Annurev-Biophys-070816-033903  0.333
2018 Meylan S, Andrews IW, Collins JJ. Targeting Antibiotic Tolerance, Pathogen by Pathogen. Cell. 172: 1228-1238. PMID 29522744 DOI: 10.1016/J.Cell.2018.01.037  0.312
2018 Lummertz da Rocha E, Rowe RG, Lundin V, Malleshaiah M, Jha DK, Rambo CR, Li H, North TE, Collins JJ, Daley GQ. Reconstruction of complex single-cell trajectories using CellRouter. Nature Communications. 9: 892. PMID 29497036 DOI: 10.1038/S41467-018-03214-Y  0.587
2017 Gutierrez A, Jain S, Bhargava P, Hamblin M, Lobritz MA, Collins JJ. Understanding and Sensitizing Density-Dependent Persistence to Quinolone Antibiotics. Molecular Cell. PMID 29225037 DOI: 10.1016/J.Molcel.2017.11.012  0.47
2017 Chandrasekaran S, Zhang J, Sun Z, Zhang L, Ross CA, Huang YC, Asara JM, Li H, Daley GQ, Collins JJ. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling. Cell Reports. 21: 2965-2977. PMID 29212039 DOI: 10.1016/J.Celrep.2017.07.048  0.544
2017 Chandrasekaran S, Zhang J, Sun Z, Zhang L, Ross CA, Huang YC, Asara JM, Li H, Daley GQ, Collins JJ. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling. Cell Reports. 21: 2965-2977. PMID 29212039 DOI: 10.1016/J.Celrep.2017.07.048  0.544
2017 Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ. Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. Cell Host & Microbe. 22: 757-765.e3. PMID 29199098 DOI: 10.1016/J.Chom.2017.10.020  0.577
2017 Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology. PMID 29062088 DOI: 10.1038/S41564-017-0043-0  0.588
2017 Yang JH, Bening SC, Collins JJ. Antibiotic efficacy-context matters. Current Opinion in Microbiology. 39: 73-80. PMID 29049930 DOI: 10.1016/J.Mib.2017.09.002  0.598
2017 Certain LK, Way JC, Pezone MJ, Collins JJ. Using Engineered Bacteria to Characterize Infection Dynamics and Antibiotic Effects In Vivo. Cell Host & Microbe. PMID 28867388 DOI: 10.1016/J.Chom.2017.08.001  0.309
2017 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, ... ... Collins JJ, et al. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology. PMID 28846095 DOI: 10.1038/Ncb3598  0.439
2017 Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini CN, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ, Walker GC. Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proceedings of the National Academy of Sciences of the United States of America. PMID 28794281 DOI: 10.1073/Pnas.1707466114  0.59
2017 Yeung E, Dy AJ, Martin KB, Ng AH, Del Vecchio D, Beck JL, Collins JJ, Murray RM. Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks. Cell Systems. PMID 28734826 DOI: 10.1016/J.Cels.2017.06.001  0.326
2017 Meylan S, Porter CB, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM, Collins JJ. Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control. Cell Chemical Biology. PMID 28111098 DOI: 10.1016/J.Chembiol.2016.12.015  0.585
2017 Del Vecchio D, Abdallah H, Qian Y, Collins JJ. A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate. Cell Systems. PMID 28065574 DOI: 10.1016/J.Cels.2016.12.001  0.339
2016 Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, de Soysa Y, Cahan P, Theißen J, Tu HC, Han A, Kurek KC, LaPier GS, Osborne JK, ... ... Collins JJ, et al. Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature. PMID 27383785 DOI: 10.1038/Nature18632  0.732
2016 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, ... ... Collins JJ, et al. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. PMID 27320042 DOI: 10.1016/J.Stem.2016.05.009  0.577
2016 Toh CX, Chan JW, Chong ZS, Wang HF, Guo HC, Satapathy S, Ma D, Goh GY, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins JJ, Daley GQ, Wee KB, et al. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell Reports. 15: 2597-607. PMID 27292646 DOI: 10.1016/J.Celrep.2016.05.049  0.606
2016 Chandrasekaran S, Cokol-Cakmak M, Sahin N, Yilancioglu K, Kazan H, Collins JJ, Cokol M. Chemogenomics and orthology-based design of antibiotic combination therapies. Molecular Systems Biology. 12: 872. PMID 27222539 DOI: 10.15252/Msb.20156777  0.324
2016 Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. Comparison of Cas9 activators in multiple species. Nature Methods. PMID 27214048 DOI: 10.1038/Nmeth.3871  0.489
2016 Braff D, Shis D, Collins JJ. Synthetic biology platform technologies for antimicrobial applications. Advanced Drug Delivery Reviews. PMID 27089812 DOI: 10.1016/J.Addr.2016.04.006  0.313
2016 Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ. A role for the bacterial GATC methylome in antibiotic stress survival. Nature Genetics. PMID 26998690 DOI: 10.1038/Ng.3530  0.464
2015 Kim HJ, Li H, Collins JJ, Ingber DE. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proceedings of the National Academy of Sciences of the United States of America. PMID 26668389 DOI: 10.1073/Pnas.1522193112  0.436
2015 Chan CT, Lee JW, Cameron DE, Bashor CJ, Collins JJ. 'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nature Chemical Biology. PMID 26641934 DOI: 10.1038/Nchembio.1979  0.324
2015 Belenky P, Ye JD, Porter CB, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Reports. 13: 968-980. PMID 26565910 DOI: 10.1016/J.Celrep.2015.09.059  0.31
2015 Slomovic S, Collins JJ. DNA sense-and-respond protein modules for mammalian cells. Nature Methods. 12: 1085-90. PMID 26389572 DOI: 10.1038/Nmeth.3585  0.312
2015 Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, ... ... Collins JJ, et al. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell. 163: 230-45. PMID 26365490 DOI: 10.1016/J.Cell.2015.08.037  0.576
2015 Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, et al. Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods. 12: 1051-4. PMID 26344044 DOI: 10.1038/Nmeth.3580  0.477
2015 Lobritz MA, Belenky P, Porter CB, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS, Collins JJ. Antibiotic efficacy is linked to bacterial cellular respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100898 DOI: 10.1073/Pnas.1509743112  0.716
2015 Krom RJ, Bhargava P, Lobritz MA, Collins JJ. Engineered Phagemids for Nonlytic, Targeted Antibacterial Therapies. Nano Letters. 15: 4808-13. PMID 26044909 DOI: 10.1021/Acs.Nanolett.5B01943  0.314
2015 Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, ... ... Collins JJ, et al. Highly efficient Cas9-mediated transcriptional programming. Nature Methods. 12: 326-8. PMID 25730490 DOI: 10.1038/Nmeth.3312  0.493
2015 Keung AJ, Joung JK, Khalil AS, Collins JJ. Chromatin regulation at the frontier of synthetic biology. Nature Reviews. Genetics. 16: 159-71. PMID 25668787 DOI: 10.1038/Nrg3900  0.311
2015 Dwyer DJ, Collins JJ, Walker GC. Unraveling the physiological complexities of antibiotic lethality. Annual Review of Pharmacology and Toxicology. 55: 313-32. PMID 25251995 DOI: 10.1146/Annurev-Pharmtox-010814-124712  0.608
2015 Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ. Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells Nature. 519: 118-118. DOI: 10.1038/Nature14150  0.545
2014 Cahan P, Morris SA, Collins JJ, Daley GQ. Defining cellular identity through network biology. Cell Cycle (Georgetown, Tex.). 13: 3313-4. PMID 25485572 DOI: 10.4161/15384101.2014.972918  0.449
2014 Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 516: 56-61. PMID 25471879 DOI: 10.1038/Nature13920  0.598
2014 Green AA, Silver PA, Collins JJ, Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell. 159: 925-39. PMID 25417166 DOI: 10.1016/J.Cell.2014.10.002  0.345
2014 Cameron DE, Collins JJ. Tunable protein degradation in bacteria. Nature Biotechnology. 32: 1276-81. PMID 25402616 DOI: 10.1038/Nbt.3053  0.31
2014 Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. The Journal of Clinical Investigation. 124: 4212-8. PMID 25271726 DOI: 10.1172/Jci72333  0.583
2014 Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ. CellNet: network biology applied to stem cell engineering. Cell. 158: 903-15. PMID 25126793 DOI: 10.1016/J.Cell.2014.07.020  0.601
2014 Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell. 158: 889-902. PMID 25126792 DOI: 10.1016/J.Cell.2014.07.021  0.603
2014 Lang AH, Li H, Collins JJ, Mehta P. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. Plos Computational Biology. 10: e1003734. PMID 25122086 DOI: 10.1371/Journal.Pcbi.1003734  0.483
2014 Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell. 15: 92-101. PMID 24813856 DOI: 10.1016/J.Stem.2014.04.002  0.587
2014 Dwyer DJ, Belenky PA, Yang JH, MacDonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, ... ... Collins JJ, et al. Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences of the United States of America. 111: E2100-9. PMID 24803433 DOI: 10.1073/Pnas.1401876111  0.797
2014 Dusonchet J, Li H, Guillily M, Liu M, Stafa K, Derada Troletti C, Boon JY, Saha S, Glauser L, Mamais A, Citro A, Youmans KL, Liu L, Schneider BL, Aebischer P, ... ... Collins JJ, et al. A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity. Human Molecular Genetics. 23: 4887-905. PMID 24794857 DOI: 10.1093/Hmg/Ddu202  0.458
2014 Torisawa YS, Spina CS, Mammoto T, Mammoto A, Weaver JC, Tat T, Collins JJ, Ingber DE. Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro. Nature Methods. 11: 663-9. PMID 24793454 DOI: 10.1038/Nmeth.2938  0.677
2014 Mee MT, Collins JJ, Church GM, Wang HH. Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 111: E2149-56. PMID 24778240 DOI: 10.1073/Pnas.1405641111  0.461
2014 Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ, Lerou PH. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports. 7: 70-8. PMID 24685138 DOI: 10.1016/J.Celrep.2014.03.007  0.424
2014 Way JC, Collins JJ, Keasling JD, Silver PA. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell. 157: 151-61. PMID 24679533 DOI: 10.1016/J.Cell.2014.02.039  0.307
2014 Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H, Wu Q. Zfp322a Regulates mouse ES cell pluripotency and enhances reprogramming efficiency. Plos Genetics. 10: e1004038. PMID 24550733 DOI: 10.1371/Journal.Pgen.1004038  0.486
2014 Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. Bmc Genomics. 15: 121. PMID 24511998 DOI: 10.1186/1471-2164-15-121  0.72
2014 Brock A, Krause S, Li H, Kowalski M, Goldberg MS, Collins JJ, Ingber DE. Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Science Translational Medicine. 6: 217ra2. PMID 24382894 DOI: 10.1126/Scitranslmed.3007048  0.459
2014 Jasuja R, Costello JC, Singh R, Gupta V, Spina CS, Toraldo G, Jang H, Li H, Serra C, Guo W, Chauhan P, Narula NS, Guarneri T, Ergun A, Travison TG, ... Collins JJ, et al. Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate-sparing anabolic therapy. Aging Cell. 13: 303-10. PMID 24305501 DOI: 10.1111/Acel.12174  0.762
2013 Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Reply to Blair et al.: Dose-dependent effects and oxidative stress responses in antibiotic tolerance in Salmonella typhimurium. Proceedings of the National Academy of Sciences of the United States of America. 110: E4570. PMID 24422210 DOI: 10.1073/Pnas.1318744110  0.77
2013 Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports. 1: 266-80. PMID 24319662 DOI: 10.1016/J.Stemcr.2013.07.004  0.317
2013 Doulatov S, Vo LT, Chou SS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI, Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell. 13: 459-70. PMID 24094326 DOI: 10.1016/J.Stem.2013.09.002  0.563
2013 Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proceedings of the National Academy of Sciences of the United States of America. 110: 14420-5. PMID 23946425 DOI: 10.1073/Pnas.1308085110  0.78
2013 Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C. Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences of the United States of America. 110: 14324-9. PMID 23934048 DOI: 10.1073/Pnas.1311839110  0.595
2013 Wang B, Collins JJ, Newmark PA. Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni. Elife. 2: e00768. PMID 23908765 DOI: 10.7554/Elife.00768  0.303
2013 Kalghatgi S, Spina CS, Costello JC, Liesa M, Morones-Ramirez JR, Slomovic S, Molina A, Shirihai OS, Collins JJ. Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in Mammalian cells. Science Translational Medicine. 5: 192ra85. PMID 23825301 DOI: 10.1126/Scitranslmed.3006055  0.712
2013 Albert R, Collins JJ, Glass L. Introduction to focus issue: quantitative approaches to genetic networks. Chaos (Woodbury, N.Y.). 23: 025001. PMID 23822498 DOI: 10.1063/1.4810923  0.368
2013 Morones-Ramirez JR, Winkler JA, Spina CS, Collins JJ. Silver enhances antibiotic activity against gram-negative bacteria. Science Translational Medicine. 5: 190ra81. PMID 23785037 DOI: 10.1126/Scitranslmed.3006276  0.786
2013 Cohen NR, Lobritz MA, Collins JJ. Microbial persistence and the road to drug resistance. Cell Host & Microbe. 13: 632-42. PMID 23768488 DOI: 10.1016/J.Chom.2013.05.009  0.315
2013 Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 499: 219-22. PMID 23748443 DOI: 10.1038/Nature12212  0.799
2013 Collins JJ, Wang B, Lambrus BG, Tharp ME, Iyer H, Newmark PA. Adult somatic stem cells in the human parasite Schistosoma mansoni. Nature. 494: 476-9. PMID 23426263 DOI: 10.1038/Nature11924  0.301
2013 Brynildsen MP, Winkler JA, Spina CS, MacDonald IC, Collins JJ. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nature Biotechnology. 31: 160-5. PMID 23292609 DOI: 10.1038/Nbt.2458  0.784
2012 McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell. 11: 701-14. PMID 23122293 DOI: 10.1016/J.Stem.2012.07.018  0.589
2012 Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS, Collins JJ. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nature Methods. 9: 1077-80. PMID 23042452 DOI: 10.1038/Nmeth.2205  0.775
2012 Fu W, Ergun A, Lu T, Hill JA, Haxhinasto S, Fassett MS, Gazit R, Adoro S, Glimcher L, Chan S, Kastner P, Rossi D, Collins JJ, Mathis D, Benoist C. A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nature Immunology. 13: 972-80. PMID 22961053 DOI: 10.1038/Ni.2420  0.578
2012 Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. A synthetic biology framework for programming eukaryotic transcription functions. Cell. 150: 647-58. PMID 22863014 DOI: 10.1016/J.Cell.2012.05.045  0.573
2012 Kumar RM, Collins JJ. Making a noisy gene: HDACs turn up the static. Molecular Cell. 47: 151-3. PMID 22840998 DOI: 10.1016/J.Molcel.2012.07.008  0.305
2012 Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/Nmeth.2016  0.791
2012 Genovese G, Ergun A, Shukla SA, Campos B, Hanna J, Ghosh P, Quayle SN, Rai K, Colla S, Ying H, Wu CJ, Sarkar S, Xiao Y, Zhang J, Zhang H, ... ... Collins JJ, et al. microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discovery. 2: 736-49. PMID 22750848 DOI: 10.1158/2159-8290.Cd-12-0111  0.576
2012 Dwyer DJ, Camacho DM, Kohanski MA, Callura JM, Collins JJ. Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Molecular Cell. 46: 561-72. PMID 22633370 DOI: 10.1016/J.Molcel.2012.04.027  0.778
2012 Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science (New York, N.Y.). 336: 315-9. PMID 22517853 DOI: 10.1126/Science.1219192  0.651
2012 Callura JM, Cantor CR, Collins JJ. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences of the United States of America. 109: 5850-5. PMID 22454498 DOI: 10.1073/Pnas.1203808109  0.791
2012 Vega NM, Allison KR, Khalil AS, Collins JJ. Signaling-mediated bacterial persister formation. Nature Chemical Biology. 8: 431-3. PMID 22426114 DOI: 10.1038/Nchembio.915  0.779
2012 Ferree A, Guillily M, Li H, Smith K, Takashima A, Squillace R, Weigele M, Collins JJ, Wolozin B. Regulation of physiologic actions of LRRK2: focus on autophagy. Neuro-Degenerative Diseases. 10: 238-41. PMID 22204929 DOI: 10.1159/000332599  0.431
2012 Lee HH, Collins JJ. Microbial environments confound antibiotic efficacy. Nature Chemical Biology. 8: 6-9. PMID 22173343 DOI: 10.1038/Nchembio.740  0.583
2012 Brock A, Li H, Krause S, Kowalski M, Collins JJ, Ingber DE. Abstract 4920: Gene network models identify targets for mammary tumor normalization Cancer Research. 72: 4920-4920. DOI: 10.1158/1538-7445.Am2012-4920  0.478
2012 Powers J, Spina C, Collins J, Daley G. Abstract 2948: The role of the RNA binding protein LIN28B in neuroblastoma Cancer Research. 72: 2948-2948. DOI: 10.1158/1538-7445.Am2012-2948  0.738
2012 Brock A, Krause S, Li H, Kowalski M, Collins J, Ingber D. Abstract P5-05-04: Intraductal delivery of RNAi-based therapeutics to gene targets identified through computational systems modeling Cancer Research. 72. DOI: 10.1158/0008-5472.Sabcs12-P5-05-04  0.438
2012 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, Daley GQ. Erratum: Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells (Nature Biotechnology (2011) 29 (1117-1119)) Nature Biotechnology. 30. DOI: 10.1038/Nbt0112-112B  0.556
2011 Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology. 29: 1117-9. PMID 22119740 DOI: 10.1038/Nbt.2052  0.554
2011 Allison KR, Brynildsen MP, Collins JJ. Heterogeneous bacterial persisters and engineering approaches to eliminate them. Current Opinion in Microbiology. 14: 593-8. PMID 21937262 DOI: 10.1016/J.Mib.2011.09.002  0.768
2011 Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proceedings of the National Academy of Sciences of the United States of America. 108: 15522-7. PMID 21876160 DOI: 10.1073/Pnas.1104318108  0.738
2011 Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics. 12: 165-85. PMID 21801025 DOI: 10.1146/Annurev-Genom-082410-101506  0.58
2011 Allison KR, Brynildsen MP, Collins JJ. Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature. 473: 216-20. PMID 21562562 DOI: 10.1038/Nature10069  0.772
2011 O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable signal processing in synthetic MAP kinase cascades. Cell. 144: 119-31. PMID 21215374 DOI: 10.1016/J.Cell.2010.12.014  0.77
2011 Allison KR, Collins JJ. Bacteria as control engineers. Molecular Cell. 41: 4-5. PMID 21211717 DOI: 10.1016/J.Molcel.2010.12.025  0.654
2011 Brock A, Li H, Krause S, Collins JJ, Ingber DE. Abstract 4924: Gene network inference models reveal novel key mediators of mammary tumorigenesis Cancer Research. 71: 4924-4924. DOI: 10.1158/1538-7445.Am2011-4924  0.504
2010 Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 7: 618-30. PMID 20888316 DOI: 10.1016/J.Stem.2010.08.012  0.577
2010 Lee HH, Molla MN, Cantor CR, Collins JJ. Bacterial charity work leads to population-wide resistance. Nature. 467: 82-5. PMID 20811456 DOI: 10.1038/Nature09354  0.543
2010 Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences of the United States of America. 107: 15898-903. PMID 20713708 DOI: 10.1073/Pnas.1009747107  0.797
2010 Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R, Walker GC. Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 107: 15517-22. PMID 20696893 DOI: 10.1073/Pnas.1005203107  0.615
2010 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, et al. Reprogramming of T cells from human peripheral blood. Cell Stem Cell. 7: 15-9. PMID 20621044 DOI: 10.1016/J.Stem.2010.06.004  0.619
2010 Bedau M, Church G, Rasmussen S, Caplan A, Benner S, Fussenegger M, Collins J, Deamer D. Life after the synthetic cell. Nature. 465: 422-4. PMID 20495545 DOI: 10.1038/465422A  0.46
2010 Kohanski MA, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nature Reviews. Microbiology. 8: 423-35. PMID 20440275 DOI: 10.1038/Nrmicro2333  0.743
2010 Collins JJ, Endy D, Hutchison CA, Roberts RJ. Editorial-synthetic biology. Nucleic Acids Research. 38: 2513. PMID 20423911 DOI: 10.1093/Nar/Gkq221  0.315
2010 Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Research. 38: 2712-26. PMID 20211838 DOI: 10.1093/Nar/Gkq091  0.575
2010 Kohanski MA, DePristo MA, Collins JJ. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Molecular Cell. 37: 311-20. PMID 20159551 DOI: 10.1016/J.Molcel.2010.01.003  0.626
2010 Wolozin B, Guillily M, Ferree A, Li H, Pyenson N, Smith K, Saha S, Ebata A, Gabel CV, Collins JJ. C. elegans models of Alzheimer's disease and Parkinson's disease: Systems biology identifies an interaction between tau and LRRK2 Alzheimers & Dementia. 6. DOI: 10.1016/J.Jalz.2010.05.232  0.392
2009 Lu TK, Khalil AS, Collins JJ. Next-generation synthetic gene networks. Nature Biotechnology. 27: 1139-50. PMID 20010597 DOI: 10.1038/Nbt.1591  0.58
2009 Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Molecular Cell. 36: 845-60. PMID 20005847 DOI: 10.1016/J.Molcel.2009.11.024  0.754
2009 Dwyer DJ, Kohanski MA, Collins JJ. Role of reactive oxygen species in antibiotic action and resistance. Current Opinion in Microbiology. 12: 482-9. PMID 19647477 DOI: 10.1016/J.Mib.2009.06.018  0.733
2009 Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Synthetic gene networks that count. Science (New York, N.Y.). 324: 1199-202. PMID 19478183 DOI: 10.1126/Science.1172005  0.787
2009 Brynildsen MP, Collins JJ. Systems biology makes it personal. Molecular Cell. 34: 137-8. PMID 19394290 DOI: 10.1016/J.Molcel.2009.04.004  0.645
2009 Ellis T, Wang X, Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology. 27: 465-71. PMID 19377462 DOI: 10.1038/Nbt.1536  0.343
2009 Camacho DM, Collins JJ. Systems biology strikes gold. Cell. 137: 24-6. PMID 19345182 DOI: 10.1016/J.Cell.2009.03.032  0.313
2009 Lu TK, Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences of the United States of America. 106: 4629-34. PMID 19255432 DOI: 10.1073/Pnas.0800442106  0.598
2009 Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu J, Liu G, Zhang X, Bowers J, Vaziri C, Ott K, Sensinger K, Collins JJ, Brody JS, et al. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences of the United States of America. 106: 2319-24. PMID 19168627 DOI: 10.1073/Pnas.0806383106  0.552
2009 Lorenz DR, Cantor CR, Collins JJ. A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences of the United States of America. 106: 1145-50. PMID 19164565 DOI: 10.1073/Pnas.0812551106  0.721
2009 McKinney-Freeman S, Li H, Curran M, Loewer S, Spina C, Naveiras O, Collins JJ, Daley GQ. A Systems Biology Approach to Study the Acquisition of Adult Repopulating Potential During Hematopoietic Stem Cell Ontogeny. Blood. 114: 1479-1479. DOI: 10.1182/Blood.V114.22.1479.1479  0.769
2009 Wang X, Ellis T, Collins JJ. Diversity-Based Design of Synthetic Gene Networks with Desired Functions Biophysical Journal. 96: 7a. DOI: 10.1016/J.Bpj.2008.12.930  0.339
2008 Dwyer DJ, Kohanski MA, Collins JJ. Networking opportunities for bacteria. Cell. 135: 1153-6. PMID 19109881 DOI: 10.1016/J.Cell.2008.12.016  0.732
2008 Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G, Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell. 135: 679-90. PMID 19013277 DOI: 10.1016/J.Cell.2008.09.038  0.733
2008 Kohanski MA, Collins JJ. Rewiring bacteria, two components at a time. Cell. 133: 947-8. PMID 18555769 DOI: 10.1016/J.Cell.2008.05.035  0.6
2008 Ellis T, Wang X, Collins JJ. Gene regulation: hacking the network on a sugar high. Molecular Cell. 30: 1-2. PMID 18406319 DOI: 10.1016/J.Molcel.2008.03.005  0.349
2007 Guido NJ, Lee P, Wang X, Elston TC, Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal. 93: L55-7. PMID 17890398 DOI: 10.1529/Biophysj.107.118687  0.777
2007 Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell. 130: 797-810. PMID 17803904 DOI: 10.1016/J.Cell.2007.06.049  0.781
2007 Deans TL, Cantor CR, Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell. 130: 363-72. PMID 17662949 DOI: 10.1016/J.Cell.2007.05.045  0.752
2007 Murphy KF, Balázsi G, Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences of the United States of America. 104: 12726-31. PMID 17652177 DOI: 10.1073/Pnas.0608451104  0.574
2007 Lu TK, Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences of the United States of America. 104: 11197-202. PMID 17592147 DOI: 10.1073/Pnas.0704624104  0.561
2007 Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Molecular Systems Biology. 3: 91. PMID 17353933 DOI: 10.1038/Msb4100135  0.775
2007 Ergün A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Molecular Systems Biology. 3: 82. PMID 17299418 DOI: 10.1038/Msb4100125  0.723
2007 Hayete B, Gardner TS, Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology. 3: 77. PMID 17299414 DOI: 10.1038/Msb4100118  0.796
2007 Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. Plos Biology. 5: e8. PMID 17214507 DOI: 10.1371/Journal.Pbio.0050008  0.781
2006 Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell. 24: 853-65. PMID 17189188 DOI: 10.1016/J.Molcel.2006.11.003  0.791
2006 Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. Engineering life: Building a FAB for biology Scientific American. 294: 44-51. PMID 16711359 DOI: 10.1038/Scientificamerican0606-44  0.415
2006 Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nature Biotechnology. 24: 545-54. PMID 16680139 DOI: 10.1038/Nbt1208  0.742
2006 Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ. A bottom-up approach to gene regulation. Nature. 439: 856-60. PMID 16482159 DOI: 10.1038/Nature04473  0.795
2006 Priplata AA, Patritti BL, Niemi JB, Hughes R, Gravelle DC, Lipsitz LA, Veves A, Stein J, Bonato P, Collins JJ. Noise-enhanced balance control in patients with diabetes and patients with stroke. Annals of Neurology. 59: 4-12. PMID 16287079 DOI: 10.1002/Ana.20670  0.742
2006 Priplata AA, Patritti BL, Rosengarten A, Meister JM, Niemi JB, Lipsitz LA, Collins JJ. Enhancing Human Balance Control by Apply Random Vibrations to the Ankle Tendons Medicine & Science in Sports & Exercise. 38: S440. DOI: 10.1249/00005768-200605001-02726  0.738
2005 Blake WJ, Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell. 122: 147-9. PMID 16051138 DOI: 10.1016/J.Cell.2005.07.006  0.696
2005 Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews. Genetics. 6: 451-64. PMID 15883588 DOI: 10.1038/Nrg1615  0.715
2005 Isaacs FJ, Blake WJ, Collins JJ. Molecular biology. Signal processing in single cells. Science (New York, N.Y.). 307: 1886-8. PMID 15790834 DOI: 10.1126/Science.1110797  0.791
2005 di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology. 23: 377-83. PMID 15765094 DOI: 10.1038/Nbt1075  0.634
2005 Isaacs FJ, Collins JJ. Plug-and-play with RNA. Nature Biotechnology. 23: 306-7. PMID 15765083 DOI: 10.1038/Nbt0305-306  0.606
2004 Mason J, Linsay PS, Collins JJ, Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos (Woodbury, N.Y.). 14: 707-15. PMID 15446982 DOI: 10.1063/1.1786683  0.307
2004 Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology. 22: 841-7. PMID 15208640 DOI: 10.1038/Nbt986  0.751
2004 Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ. Programmable cells: interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences of the United States of America. 101: 8414-9. PMID 15159530 DOI: 10.1073/Pnas.0402940101  0.642
2004 Di Bernardo D, Gardner TS, Collins JJ. Robust identification of large genetic networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 486-97. PMID 14992527  0.609
2004 Priplata AA, Niemi JB, Veves A, Lipsitz LA, Collins JJ. Vibrating Insoles Improve Balance in Diabetic Patients with Peripheral Neuropathy Medicine & Science in Sports & Exercise. 36: S6. DOI: 10.1097/00005768-200405001-00028  0.727
2004 Priplata AA, Niemi JB, Harry JD, Lipsitz LA, Collins JJ. Tactile stimulation of insoles and balance control in elderly people The Lancet. 363: 85-86. DOI: 10.1016/S0140-6736(03)15214-2  0.728
2003 Priplata AA, Niemi JB, Harry JD, Lipsitz LA, Collins JJ. Vibrating insoles and balance control in elderly people. Lancet. 362: 1123-4. PMID 14550702 DOI: 10.1016/S0140-6736(03)14470-4  0.741
2003 Kaern M, Blake WJ, Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering. 5: 179-206. PMID 14527313 DOI: 10.1146/Annurev.Bioeng.5.040202.121553  0.716
2003 Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science (New York, N.Y.). 301: 102-5. PMID 12843395 DOI: 10.1126/Science.1081900  0.791
2003 Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences of the United States of America. 100: 7714-9. PMID 12808135 DOI: 10.1073/Pnas.1332628100  0.689
2003 Collins JJ, Priplata AA, Gravelle DC, Niemi J, Harry J, Lipsitz LA. Noise-enhanced human sensorimotor function. Ieee Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society. 22: 76-83. PMID 12733463 DOI: 10.1109/Memb.2003.1195700  0.75
2003 Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences of the United States of America. 100: 5944-9. PMID 12730377 DOI: 10.1073/Pnas.0933416100  0.347
2003 Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 422: 633-7. PMID 12687005 DOI: 10.1038/Nature01546  0.713
2002 Scinicariello AP, Inglis JT, Collins JJ. The effects of stochastic monopolar galvanic vestibular stimulation on human postural sway. Journal of Vestibular Research : Equilibrium & Orientation. 12: 77-85. PMID 12867666  0.761
2002 Priplata A, Niemi J, Salen M, Harry J, Lipsitz LA, Collins JJ. Noise-enhanced human balance control. Physical Review Letters. 89: 238101. PMID 12485044 DOI: 10.1103/Physrevlett.89.238101  0.749
2002 Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 420: 224-30. PMID 12432407 DOI: 10.1038/Nature01257  0.365
2002 Yeung MK, Tegnér J, Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences of the United States of America. 99: 6163-8. PMID 11983907 DOI: 10.1073/Pnas.092576199  0.314
2002 McMillen D, Kopell N, Hasty J, Collins JJ. Synchronizing genetic relaxation oscillators by intercell signaling. Proceedings of the National Academy of Sciences of the United States of America. 99: 679-84. PMID 11805323 DOI: 10.1073/Pnas.022642299  0.359
2001 Hasty J, Isaacs F, Dolnik M, McMillen D, Collins JJ. Designer gene networks: Towards fundamental cellular control. Chaos (Woodbury, N.Y.). 11: 207-220. PMID 12779454 DOI: 10.1063/1.1345702  0.673
2001 Scinicariello AP, Eaton K, Inglis JT, Collins JJ. Enhancing human balance control with galvanic vestibular stimulation. Biological Cybernetics. 84: 475-80. PMID 11417059 DOI: 10.1007/Pl00007991  0.762
2001 Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nature Reviews. Genetics. 2: 268-79. PMID 11283699 DOI: 10.1038/35066056  0.669
2001 Richardson KA, Collins JJ. Chapter 1 Electrical stimulation of the somatosensory system Handbook of Biological Physics. 4: 1-22. DOI: 10.1016/S1383-8121(01)80004-X  0.465
2000 Gardner TS, Collins JJ. Neutralizing noise in gene networks. Nature. 405: 520-1. PMID 10850696 DOI: 10.1038/35014708  0.624
2000 Hasty J, Pradines J, Dolnik M, Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences of the United States of America. 97: 2075-80. PMID 10681449 DOI: 10.1073/Pnas.040411297  0.361
2000 Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 403: 339-42. PMID 10659857 DOI: 10.1038/35002131  0.636
1999 Nozaki D, Collins JJ, Yamamoto Y. Mechanism of stochastic resonance enhancement in neuronal models driven by 1/f noise. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 4637-44. PMID 11970325 DOI: 10.1103/Physreve.60.4637  0.633
1999 Nozaki D, Mar DJ, Grigg P, Collins JJ. Effects of Colored Noise on Stochastic Resonance in Sensory Neurons Physical Review Letters. 82: 2402-2405. DOI: 10.1103/PhysRevLett.82.2402  0.46
1999 Nozaki D, Mar DJ, Grigg P, Collins JJ. Effects of Colored Noise on Stochastic Resonance in Sensory Neurons Physical Review Letters. 82: 2402-2405. DOI: 10.1103/Physrevlett.82.2402  0.527
1999 Dolnik M, Gardner TS, Epstein IR, Collins JJ. Frequency Control of an Oscillatory Reaction by Reversible Binding of an Autocatalyst Physical Review Letters. 82: 1582-1585. DOI: 10.1103/Physrevlett.82.1582  0.577
1998 Richardson KA, Imhoff TT, Grigg P, Collins JJ. Using electrical noise to enhance the ability of humans to detect subthreshold mechanical cutaneous stimuli. Chaos (Woodbury, N.Y.). 8: 599-603. PMID 12779763 DOI: 10.1063/1.166341  0.558
1998 Gardner TS, Dolnik M, Collins JJ. A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 95: 14190-5. PMID 9826676 DOI: 10.1073/Pnas.95.24.14190  0.609
1998 Golubitsky M, Stewart I, Buono P, Collins J. A modular network for legged locomotion Physica D: Nonlinear Phenomena. 115: 56-72. DOI: 10.1016/S0167-2789(97)00222-4  0.304
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