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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 Feb 15. pii: eaaq0179. doi: 10.1126/science.aaq0179. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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. 2017 Sep;19(9):1037-1048. doi: 10.1038/ncb3598. Epub 2017 Aug 28.


Challenges and Opportunities for Occupational Epidemiology in the Twenty-first Century.

Stayner LT, Collins JJ, Guo YL, Heederik D, Kogevinas M, Steenland K, Wesseling C, Demers PA.

Curr Environ Health Rep. 2017 Sep;4(3):319-324. doi: 10.1007/s40572-017-0154-z. Review.


Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality.

Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini CN, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ, Walker GC.

Proc Natl Acad Sci U S A. 2017 Aug 9. pii: 201707466. doi: 10.1073/pnas.1707466114. [Epub ahead of print]


Profile of children with developmental disabilities attending a complex pain clinic of a children's hospital in Australia.

Garg P, Haynes N, De Lima J, Collins JJ.

J Paediatr Child Health. 2017 Dec;53(12):1186-1191. doi: 10.1111/jpc.13633. Epub 2017 Aug 8.


Complex cellular logic computation using ribocomputing devices.

Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P.

Nature. 2017 Aug 3;548(7665):117-121. doi: 10.1038/nature23271. Epub 2017 Jul 26.


Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.

Yeung E, Dy AJ, Martin KB, Ng AH, Del Vecchio D, Beck JL, Collins JJ, Murray RM.

Cell Syst. 2017 Jul 26;5(1):11-24.e12. doi: 10.1016/j.cels.2017.06.001. Epub 2017 Jul 19.


The Future of Bronchopulmonary Dysplasia: Emerging Pathophysiological Concepts and Potential New Avenues of Treatment.

Collins JJP, Tibboel D, de Kleer IM, Reiss IKM, Rottier RJ.

Front Med (Lausanne). 2017 May 22;4:61. doi: 10.3389/fmed.2017.00061. eCollection 2017. Review.


MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.

Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M.

PLoS Negl Trop Dis. 2017 May 23;11(5):e0005559. doi: 10.1371/journal.pntd.0005559. eCollection 2017 May.


Nucleic acid detection with CRISPR-Cas13a/C2c2.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F.

Science. 2017 Apr 28;356(6336):438-442. doi: 10.1126/science.aam9321. Epub 2017 Apr 13.


Human Umbilical Cord Mesenchymal Stromal Cells Improve Survival and Bacterial Clearance in Neonatal Sepsis in Rats.

Zhu Y, Xu L, Collins JJP, Vadivel A, Cyr-Depauw C, Zhong S, Mense L, Möbius MA, Thébaud B.

Stem Cells Dev. 2017 Jul 15;26(14):1054-1064. doi: 10.1089/scd.2016.0329. Epub 2017 May 17.



Collins JJ 3rd.

Curr Biol. 2017 Apr 3;27(7):R252-R256. doi: 10.1016/j.cub.2017.02.016.


Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control.

Meylan S, Porter CBM, Yang JH, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim SH, Moskowitz SM, Collins JJ.

Cell Chem Biol. 2017 Feb 16;24(2):195-206. doi: 10.1016/j.chembiol.2016.12.015. Epub 2017 Jan 19.


A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate.

Del Vecchio D, Abdallah H, Qian Y, Collins JJ.

Cell Syst. 2017 Jan 25;4(1):109-120.e11. doi: 10.1016/j.cels.2016.12.001. Epub 2017 Jan 5.


Mortality risk among workers with exposure to dioxins.

Collins JJ, Bodner KM, Aylward LL, Bender TJ, Anteau S, Wilken M, Bodnar CM.

Occup Med (Lond). 2016 Dec;66(9):706-712. Epub 2016 Dec 7.


Tissue Degeneration following Loss of Schistosoma mansoni cbp1 Is Associated with Increased Stem Cell Proliferation and Parasite Death In Vivo.

Collins JN, Collins JJ 3rd.

PLoS Pathog. 2016 Nov 3;12(11):e1005963. doi: 10.1371/journal.ppat.1005963. eCollection 2016 Nov.


Methods for Studying the Germline of the Human Parasite Schistosoma mansoni.

Collins JN, Collins JJ 3rd.

Methods Mol Biol. 2017;1463:35-47.


Portable, On-Demand Biomolecular Manufacturing.

Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ.

Cell. 2016 Sep 22;167(1):248-259.e12. doi: 10.1016/j.cell.2016.09.013.


Creating Single-Copy Genetic Circuits.

Lee JW, Gyorgy A, Cameron DE, Pyenson N, Choi KR, Way JC, Silver PA, Del Vecchio D, Collins JJ.

Mol Cell. 2016 Jul 21;63(2):329-336. doi: 10.1016/j.molcel.2016.06.006. Epub 2016 Jul 14.


Schistosomiasis as a disease of stem cells.

Wendt GR, Collins JJ 3rd.

Curr Opin Genet Dev. 2016 Oct;40:95-102. doi: 10.1016/j.gde.2016.06.010. Epub 2016 Jul 5. Review.


Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma.

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, Ross SJ, Cesana M, Collins JJ, Berthold F, Daley GQ.

Nature. 2016 Jul 14;535(7611):246-51. doi: 10.1038/nature18632. Epub 2016 Jul 6.


Isolation of CD146+ Resident Lung Mesenchymal Stromal Cells from Rat Lungs.

Collins JJ, Möbius MA, Thébaud B.

J Vis Exp. 2016 Jun 17;(112). doi: 10.3791/53782.


LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.

Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ.

Cell Stem Cell. 2016 Jul 7;19(1):66-80. doi: 10.1016/j.stem.2016.05.009. Epub 2016 Jun 16.


NF-YB Regulates Spermatogonial Stem Cell Self-Renewal and Proliferation in the Planarian Schmidtea mediterranea.

Iyer H, Collins JJ 3rd, Newmark PA.

PLoS Genet. 2016 Jun 15;12(6):e1006109. doi: 10.1371/journal.pgen.1006109. eCollection 2016 Jun.


RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming.

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, Farran CA, Li H, Lim YP, Bard FA, Loh YH.

Cell Rep. 2016 Jun 21;15(12):2597-607. doi: 10.1016/j.celrep.2016.05.049. Epub 2016 Jun 9.


Chemogenomics and orthology-based design of antibiotic combination therapies.

Chandrasekaran S, Cokol-Cakmak M, Sahin N, Yilancioglu K, Kazan H, Collins JJ, Cokol M.

Mol Syst Biol. 2016 May 24;12(5):872. doi: 10.15252/msb.20156777.


Comparison of Cas9 activators in multiple species.

Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJK, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G.

Nat Methods. 2016 Jul;13(7):563-567. doi: 10.1038/nmeth.3871. Epub 2016 May 23.


Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ.

Cell. 2016 May 19;165(5):1255-1266. doi: 10.1016/j.cell.2016.04.059. Epub 2016 May 6.


Targeted erythropoietin selectively stimulates red blood cell expansion in vivo.

Burrill DR, Vernet A, Collins JJ, Silver PA, Way JC.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5245-50. doi: 10.1073/pnas.1525388113. Epub 2016 Apr 25.


Engineering Models to Scale.

Dy AJ, Collins JJ.

Cell. 2016 Apr 21;165(3):516-7. doi: 10.1016/j.cell.2016.04.017.


Synthetic biology platform technologies for antimicrobial applications.

Braff D, Shis D, Collins JJ.

Adv Drug Deliv Rev. 2016 Oct 1;105(Pt A):35-43. doi: 10.1016/j.addr.2016.04.006. Epub 2016 Apr 18. Review.


Identification of new markers for the Schistosoma mansoni vitelline lineage.

Wang J, Collins JJ 3rd.

Int J Parasitol. 2016 Jun;46(7):405-10. doi: 10.1016/j.ijpara.2016.03.004. Epub 2016 Apr 4.


Stem cell progeny contribute to the schistosome host-parasite interface.

Collins JJ 3rd, Wendt GR, Iyer H, Newmark PA.

Elife. 2016 Mar 22;5:e12473. doi: 10.7554/eLife.12473.


A role for the bacterial GATC methylome in antibiotic stress survival.

Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ.

Nat Genet. 2016 May;48(5):581-6. doi: 10.1038/ng.3530. Epub 2016 Mar 21.


Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea.

Ong TH, Romanova EV, Roberts-Galbraith RH, Yang N, Zimmerman TA, Collins JJ 3rd, Lee JE, Kelleher NL, Newmark PA, Sweedler JV.

J Biol Chem. 2016 Apr 8;291(15):8109-20. doi: 10.1074/jbc.M115.709196. Epub 2016 Feb 16.


Hypophosphatemic rickets and craniosynostosis: a multicenter case series.

Vega RA, Opalak C, Harshbarger RJ, Fearon JA, Ritter AM, Collins JJ, Rhodes JL.

J Neurosurg Pediatr. 2016 Jun;17(6):694-700. doi: 10.3171/2015.10.PEDS15273. Epub 2016 Jan 29.


Propofol administration to the fetal-maternal unit reduces cardiac oxidative stress in preterm lambs subjected to prenatal asphyxia and cardiac arrest.

Seehase M, Houthuizen P, Collins JJ, Zimmermann LJ, Kramer BW.

Pediatr Res. 2016 May;79(5):748-53. doi: 10.1038/pr.2016.10. Epub 2016 Jan 13.


Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip.

Kim HJ, Li H, Collins JJ, Ingber DE.

Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E7-15. doi: 10.1073/pnas.1522193112. Epub 2015 Dec 14.


'Deadman' and 'Passcode' microbial kill switches for bacterial containment.

Chan CT, Lee JW, Cameron DE, Bashor CJ, Collins JJ.

Nat Chem Biol. 2016 Feb;12(2):82-6. doi: 10.1038/nchembio.1979. Epub 2015 Dec 7.


Synthetic biology devices for in vitro and in vivo diagnostics.

Slomovic S, Pardee K, Collins JJ.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14429-35. doi: 10.1073/pnas.1508521112. Review.

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