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Items: 1 to 50 of 745

1.

Engineering microbial peer pressure.

Johnston CW, Collins JJ.

Science. 2019 Sep 6;365(6457):986-987. doi: 10.1126/science.aay3157. No abstract available.

PMID:
31488676
2.

Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.

Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ.

Nat Microbiol. 2019 Aug 26. doi: 10.1038/s41564-019-0536-0. [Epub ahead of print]

PMID:
31451773
3.

Programmable CRISPR-responsive smart materials.

English MA, Soenksen LR, Gayet RV, de Puig H, Angenent-Mari NM, Mao AS, Nguyen PQ, Collins JJ.

Science. 2019 Aug 23;365(6455):780-785. doi: 10.1126/science.aaw5122.

PMID:
31439791
4.

Author Correction: A systems biology pipeline identifies regulatory networks for stem cell engineering.

Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ.

Nat Biotechnol. 2019 Aug;37(8):962. doi: 10.1038/s41587-019-0212-1.

PMID:
31312048
5.

Evaluation of potential health effects associated with occupational and environmental exposure to styrene - an update.

Banton MI, Bus JS, Collins JJ, Delzell E, Gelbke HP, Kester JE, Moore MM, Waites R, Sarang SS.

J Toxicol Environ Health B Crit Rev. 2019;22(1-4):1-130. doi: 10.1080/10937404.2019.1633718. Epub 2019 Jul 8.

PMID:
31284836
6.

Bacterial Metabolism and Antibiotic Efficacy.

Stokes JM, Lopatkin AJ, Lobritz MA, Collins JJ.

Cell Metab. 2019 Aug 6;30(2):251-259. doi: 10.1016/j.cmet.2019.06.009. Epub 2019 Jul 3. Review.

PMID:
31279676
7.

A systems biology pipeline identifies regulatory networks for stem cell engineering.

Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ.

Nat Biotechnol. 2019 Jul;37(7):810-818. doi: 10.1038/s41587-019-0159-2. Epub 2019 Jul 1. Erratum in: Nat Biotechnol. 2019 Aug;37(8):962.

PMID:
31267104
8.

Severe maternal morbidity during delivery hospitalisation in a large international administrative database, 2008-2013: a retrospective cohort.

Lipkind HS, Zuckerwise LC, Turner EB, Collins JJ, Campbell KH, Reddy UM, Illuzi JL, Merriam AA.

BJOG. 2019 Sep;126(10):1223-1230. doi: 10.1111/1471-0528.15818. Epub 2019 Jun 20.

PMID:
31100201
9.

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, Collins JJ.

Cell. 2019 May 30;177(6):1649-1661.e9. doi: 10.1016/j.cell.2019.04.016. Epub 2019 May 9.

PMID:
31080069
10.

Systematically improved in vitro culture conditions reveal new insights into the reproductive biology of the human parasite Schistosoma mansoni.

Wang J, Chen R, Collins JJ 3rd.

PLoS Biol. 2019 May 8;17(5):e3000254. doi: 10.1371/journal.pbio.3000254. eCollection 2019 May.

11.

Key paediatric messages from the 2018 European Respiratory Society International Congress.

Nenna R, Hunt KA, Dassios T, Collins JJP, Rottier RJ, Liu NM, Rottier B, Goutaki M, Karadag B, Prayle A, Fernandes RM, Parisi GF, Barben J, Rubbo B, Snijders D, Makrinioti H, Hall G, Pijnenburg MW, Grigg J.

ERJ Open Res. 2019 Apr 29;5(2). pii: 00241-2018. doi: 10.1183/23120541.00241-2018. eCollection 2019 Apr.

12.

Publisher Correction: 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, Zinkernagel A.

Nat Rev Microbiol. 2019 Jul;17(7):460. doi: 10.1038/s41579-019-0207-4.

PMID:
31036919
13.

Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies.

Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS.

Science. 2019 May 10;364(6440):593-597. doi: 10.1126/science.aau8287. Epub 2019 Apr 18.

14.

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, Zinkernagel A.

Nat Rev Microbiol. 2019 Jul;17(7):441-448. doi: 10.1038/s41579-019-0196-3. Review. Erratum in: Nat Rev Microbiol. 2019 Apr 29;:.

PMID:
30980069
15.

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, Collins JJ.

Nat Methods. 2019 Apr;16(4):303-306. doi: 10.1038/s41592-019-0333-y. Epub 2019 Mar 11.

PMID:
30858599
16.

Author Correction: 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, Kim K.

Nat Cell Biol. 2019 Apr;21(4):531-532. doi: 10.1038/s41556-018-0269-y.

PMID:
30643186
17.

A meta-analysis of epidemiologic studies of occupationally exposed styrene workers and micronuclei levels.

Collins JJ, Moore M.

Mutat Res Genet Toxicol Environ Mutagen. 2019 Jan;837:15-28. doi: 10.1016/j.mrgentox.2018.08.011. Epub 2018 Sep 21.

PMID:
30595205
18.

CRISPR Guide RNA Cloning for Mammalian Systems.

Nageshwaran S, Chavez A, Cher Yeo N, Guo X, Lance-Byrne A, Tung A, Collins JJ, Church GM.

J Vis Exp. 2018 Oct 2;(140). doi: 10.3791/57998.

PMID:
30346403
19.

Cohort study of workers at a New Zealand agrochemical plant to assess the effect of dioxin exposure on mortality.

McBride DI, Collins JJ, Bender TJ, Bodner KM, Aylward LL.

BMJ Open. 2018 Oct 17;8(10):e019243. doi: 10.1136/bmjopen-2017-019243.

20.

Early Career Members at the ERS Lung Science Conference: cell-matrix interactions in lung disease and regeneration: Early career forum.

Almendros I, Alsafadi HN, Bölükbas D, Collins JJP, Duch P, Garrido-Martin EM, Kahn N, Karampitsakos T, Mahmutovic Persson I, Tzouvelekis A, Uhl FE, Bartel S.

Breathe (Sheff). 2018 Jun;14(2):e78-e83. doi: 10.1183/20734735.016818.

21.

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, Collins JJ.

Nat Commun. 2018 Aug 21;9(1):3347. doi: 10.1038/s41467-018-05864-4.

22.

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, Jewett MC.

Sci Adv. 2018 Aug 1;4(8):eaat5107. doi: 10.1126/sciadv.aat5107. eCollection 2018 Aug.

23.

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, Collins JJ.

Sci Adv. 2018 Aug 1;4(8):eaat5105. doi: 10.1126/sciadv.aat5105. eCollection 2018 Aug.

24.

An enhanced CRISPR repressor for targeted mammalian gene regulation.

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, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM.

Nat Methods. 2018 Aug;15(8):611-616. doi: 10.1038/s41592-018-0048-5. Epub 2018 Jul 16.

25.

Impaired Angiogenic Supportive Capacity and Altered Gene Expression Profile of Resident CD146+ Mesenchymal Stromal Cells Isolated from Hyperoxia-Injured Neonatal Rat Lungs.

Collins JJP, Lithopoulos MA, Dos Santos CC, Issa N, Möbius MA, Ito C, Zhong S, Vadivel A, Thébaud B.

Stem Cells Dev. 2018 Aug 15;27(16):1109-1124. doi: 10.1089/scd.2017.0145. Epub 2018 Jun 29.

PMID:
29957134
26.

Designing microbial consortia with defined social interactions.

Kong W, Meldgin DR, Collins JJ, Lu T.

Nat Chem Biol. 2018 Aug;14(8):821-829. doi: 10.1038/s41589-018-0091-7. Epub 2018 Jun 25.

PMID:
29942078
27.

Probiotic strains detect and suppress cholera in mice.

Mao N, Cubillos-Ruiz A, Cameron DE, Collins JJ.

Sci Transl Med. 2018 Jun 13;10(445). pii: eaao2586. doi: 10.1126/scitranslmed.aao2586.

PMID:
29899022
28.

Next-Generation Machine Learning for Biological Networks.

Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ.

Cell. 2018 Jun 14;173(7):1581-1592. doi: 10.1016/j.cell.2018.05.015. Epub 2018 Jun 7. Review.

29.

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 MH 2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM.

BMC Biol. 2018 Jun 5;16(1):62. doi: 10.1186/s12915-018-0527-2.

30.

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, Garnier SL, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ, Church GM.

Nat Biotechnol. 2018 Jul;36(6):540-546. doi: 10.1038/nbt.4147. Epub 2018 May 21.

31.

Next-generation biocontainment systems for engineered organisms.

Lee JW, Chan CTY, Slomovic S, Collins JJ.

Nat Chem Biol. 2018 Jun;14(6):530-537. doi: 10.1038/s41589-018-0056-x. Epub 2018 May 16.

PMID:
29769737
32.

Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses.

Cho JH, Collins JJ, Wong WW.

Cell. 2018 May 31;173(6):1426-1438.e11. doi: 10.1016/j.cell.2018.03.038. Epub 2018 Apr 26.

33.

CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms.

Shapiro RS, Chavez A, Collins JJ.

Nat Rev Microbiol. 2018 Jun;16(6):333-339. doi: 10.1038/s41579-018-0002-7. Review.

PMID:
29599458
34.

A systematic review of epidemiologic studies of styrene and cancer.

Collins JJ, Delzell E.

Crit Rev Toxicol. 2018 Jul;48(6):443-470. doi: 10.1080/10408444.2018.1445700. Epub 2018 Mar 28.

PMID:
29589466
35.

Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni.

Wendt GR, Collins JN, Pei J, Pearson MS, Bennett HM, Loukas A, Berriman M, Grishin NV, Collins JJ 3rd.

Elife. 2018 Mar 20;7. pii: e33221. doi: 10.7554/eLife.33221.

36.

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, Church GM.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3669-3673. doi: 10.1073/pnas.1718148115. Epub 2018 Mar 19.

37.

Understanding Biological Regulation Through Synthetic Biology.

Bashor CJ, Collins JJ.

Annu Rev Biophys. 2018 May 20;47:399-423. doi: 10.1146/annurev-biophys-070816-033903. Epub 2018 Mar 16. Review.

PMID:
29547341
38.

Targeting Antibiotic Tolerance, Pathogen by Pathogen.

Meylan S, Andrews IW, Collins JJ.

Cell. 2018 Mar 8;172(6):1228-1238. doi: 10.1016/j.cell.2018.01.037. Review.

39.

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, Daley GQ.

Nat Commun. 2018 Mar 1;9(1):892. doi: 10.1038/s41467-018-03214-y.

40.

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6.

Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F.

Science. 2018 Apr 27;360(6387):439-444. doi: 10.1126/science.aaq0179. Epub 2018 Feb 15.

41.

Understanding and Sensitizing Density-Dependent Persistence to Quinolone Antibiotics.

Gutierrez A, Jain S, Bhargava P, Hamblin M, Lobritz MA, Collins JJ.

Mol Cell. 2017 Dec 21;68(6):1147-1154.e3. doi: 10.1016/j.molcel.2017.11.012. Epub 2017 Dec 7.

42.

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling.

Chandrasekaran S, Zhang J, Sun Z, Zhang L, Ross CA, Huang YC, Asara JM, Li H, Daley GQ, Collins JJ.

Cell Rep. 2017 Dec 5;21(10):2965-2977. doi: 10.1016/j.celrep.2017.07.048.

43.

Longitudinal and Cross-sectional Analyses of Lung Function in Toluene Diisocyanate Production Workers.

Wang ML, Storey E, Cassidy LD, Doney B, Conner PR, Collins JJ, Carson M, Molenaar D.

J Occup Environ Med. 2017 Dec;59 Suppl 12:S28-S35. doi: 10.1097/JOM.0000000000001124.

44.

Incidence of Occupational Asthma and Exposure to Toluene Diisocyanate in the United States Toluene Diisocyanate Production Industry.

Collins JJ, Anteau S, Conner PR, Cassidy LD, Doney B, Wang ML, Kurth L, Carson M, Molenaar D, Redlich CA, Storey E.

J Occup Environ Med. 2017 Dec;59 Suppl 12:S22-S27. doi: 10.1097/JOM.0000000000000890.

45.

Medical Monitoring for Occupational Asthma Among Toluene Diisocyanate Production Workers in the United States.

Cassidy LD, Doney B, Wang ML, Kurth L, Conner PR, Collins JJ, Carson M, Molenaar D, Redlich CA, Storey E.

J Occup Environ Med. 2017 Dec;59 Suppl 12:S13-S21. doi: 10.1097/JOM.0000000000001197.

46.

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, Collins JJ.

Cell Host Microbe. 2017 Dec 13;22(6):757-765.e3. doi: 10.1016/j.chom.2017.10.020. Epub 2017 Nov 30.

47.

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, Collins JJ.

Nat Microbiol. 2018 Jan;3(1):73-82. doi: 10.1038/s41564-017-0043-0. Epub 2017 Oct 23.

48.

Human induced pluripotent stem cell-derived lung progenitor and alveolar epithelial cells attenuate hyperoxia-induced lung injury.

Shafa M, Ionescu LI, Vadivel A, Collins JJP, Xu L, Zhong S, Kang M, de Caen G, Daneshmand M, Shi J, Fu KZ, Qi A, Wang Y, Ellis J, Stanford WL, Thébaud B.

Cytotherapy. 2018 Jan;20(1):108-125. doi: 10.1016/j.jcyt.2017.09.003. Epub 2017 Oct 20.

PMID:
29056548
49.

Antibiotic efficacy-context matters.

Yang JH, Bening SC, Collins JJ.

Curr Opin Microbiol. 2017 Oct;39:73-80. doi: 10.1016/j.mib.2017.09.002. Epub 2017 Oct 16. Review.

50.

Using Engineered Bacteria to Characterize Infection Dynamics and Antibiotic Effects In Vivo.

Certain LK, Way JC, Pezone MJ, Collins JJ.

Cell Host Microbe. 2017 Sep 13;22(3):263-268.e4. doi: 10.1016/j.chom.2017.08.001. Epub 2017 Aug 31.

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