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1.

A male-derived nonribosomal peptide pheromone controls female schistosome development.

Chen, Rui; Wang, Jipeng; Gradinaru, Irina; Vu, Hieu S; Geboers, Sophie; Naidoo, Jacinth; Ready, Joseph M; Williams, Noelle S; DeBerardinis, Ralph J; Ross, Elliott M; Collins, James J.

Cell ; 185(9): 1506-1520.e17, 2022 04 28.

Artículo en Inglés | MEDLINE | ID: mdl-35385687

2.

Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond.

English, Max A; Gayet, Raphaël V; Collins, James J.

Annu Rev Biochem ; 90: 221-244, 2021 06 20.

Artículo en Inglés | MEDLINE | ID: mdl-33784178

3.

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics.

Tan, Xiao; Letendre, Justin H; Collins, James J; Wong, Wilson W.

Cell ; 184(4): 881-898, 2021 02 18.

Artículo en Inglés | MEDLINE | ID: mdl-33571426

4.

A Deep Learning Approach to Antibiotic Discovery.

Stokes, Jonathan M; Yang, Kevin; Swanson, Kyle; Jin, Wengong; Cubillos-Ruiz, Andres; Donghia, Nina M; MacNair, Craig R; French, Shawn; Carfrae, Lindsey A; Bloom-Ackermann, Zohar; Tran, Victoria M; Chiappino-Pepe, Anush; Badran, Ahmed H; Andrews, Ian W; Chory, Emma J; Church, George M; Brown, Eric D; Jaakkola, Tommi S; Barzilay, Regina; Collins, James J.

Cell ; 180(4): 688-702.e13, 2020 02 20.

Artículo en Inglés | MEDLINE | ID: mdl-32084340

5.

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Yang, Jason H; Wright, Sarah N; Hamblin, Meagan; McCloskey, Douglas; Alcantar, Miguel A; Schrübbers, Lars; Lopatkin, Allison J; Satish, Sangeeta; Nili, Amir; Palsson, Bernhard O; Walker, Graham C; Collins, James J.

Cell ; 177(6): 1649-1661.e9, 2019 05 30.

Artículo en Inglés | MEDLINE | ID: mdl-31080069

6.

Targeting Antibiotic Tolerance, Pathogen by Pathogen.

Meylan, Sylvain; Andrews, Ian W; Collins, James J.

Cell ; 172(6): 1228-1238, 2018 03 08.

Artículo en Inglés | MEDLINE | ID: mdl-29522744

7.

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

Cho, Jang Hwan; Collins, James J; Wong, Wilson W.

Cell ; 173(6): 1426-1438.e11, 2018 05 31.

Artículo en Inglés | MEDLINE | ID: mdl-29706540

8.

Next-Generation Machine Learning for Biological Networks.

Camacho, Diogo M; Collins, Katherine M; Powers, Rani K; Costello, James C; Collins, James J.

Cell ; 173(7): 1581-1592, 2018 06 14.

Artículo en Inglés | MEDLINE | ID: mdl-29887378

9.

Engineering Models to Scale.

Dy, Aaron J; Collins, James J.

Cell ; 165(3): 516-7, 2016 Apr 21.

Artículo en Inglés | MEDLINE | ID: mdl-27104972

10.

Portable, On-Demand Biomolecular Manufacturing.

Pardee, Keith; Slomovic, Shimyn; Nguyen, Peter Q; Lee, Jeong Wook; Donghia, Nina; Burrill, Devin; Ferrante, Tom; McSorley, Fern R; Furuta, Yoshikazu; Vernet, Andyna; Lewandowski, Michael; Boddy, Christopher N; Joshi, Neel S; Collins, James J.

Cell ; 167(1): 248-259.e12, 2016 Sep 22.

Artículo en Inglés | MEDLINE | ID: mdl-27662092

11.

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

Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J.

Cell ; 165(5): 1255-1266, 2016 May 19.

Artículo en Inglés | MEDLINE | ID: mdl-27160350

12.

A Deep Learning Approach to Antibiotic Discovery.

Stokes, Jonathan M; Yang, Kevin; Swanson, Kyle; Jin, Wengong; Cubillos-Ruiz, Andres; Donghia, Nina M; MacNair, Craig R; French, Shawn; Carfrae, Lindsey A; Bloom-Ackermann, Zohar; Tran, Victoria M; Chiappino-Pepe, Anush; Badran, Ahmed H; Andrews, Ian W; Chory, Emma J; Church, George M; Brown, Eric D; Jaakkola, Tommi S; Barzilay, Regina; Collins, James J.

Cell ; 181(2): 475-483, 2020 Apr 16.

Artículo en Inglés | MEDLINE | ID: mdl-32302574

13.

Systematic identification of factors for provirus silencing in embryonic stem cells.

Yang, Bin Xia; El Farran, Chadi A; Guo, Hong Chao; Yu, Tao; Fang, Hai Tong; Wang, Hao Fei; Schlesinger, Sharon; Seah, Yu Fen Samantha; Goh, Germaine Yen Lin; Neo, Suat Peng; Li, Yinghui; Lorincz, Matthew C; Tergaonkar, Vinay; Lim, Tit-Meng; Chen, Lingyi; Gunaratne, Jayantha; Collins, James J; Goff, Stephen P; Daley, George Q; Li, Hu; Bard, Frederic A; Loh, Yuin-Han.

Cell ; 163(1): 230-45, 2015 Sep 24.

Artículo en Inglés | MEDLINE | ID: mdl-26365490

14.

Discovery of a structural class of antibiotics with explainable deep learning.

Wong, Felix; Zheng, Erica J; Valeri, Jacqueline A; Donghia, Nina M; Anahtar, Melis N; Omori, Satotaka; Li, Alicia; Cubillos-Ruiz, Andres; Krishnan, Aarti; Jin, Wengong; Manson, Abigail L; Friedrichs, Jens; Helbig, Ralf; Hajian, Behnoush; Fiejtek, Dawid K; Wagner, Florence F; Soutter, Holly H; Earl, Ashlee M; Stokes, Jonathan M; Renner, Lars D; Collins, James J.

Nature ; 626(7997): 177-185, 2024 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-38123686

15.

Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions.

Wong, Felix; Stokes, Jonathan M; Bening, Sarah C; Vidoudez, Charles; Trauger, Sunia A; Collins, James J.

Mol Cell ; 82(18): 3499-3512.e10, 2022 09 15.

Artículo en Inglés | MEDLINE | ID: mdl-35973427

16.

Toehold switches: de-novo-designed regulators of gene expression.

Green, Alexander A; Silver, Pamela A; Collins, James J; Yin, Peng.

Cell ; 159(4): 925-39, 2014 Nov 06.

Artículo en Inglés | MEDLINE | ID: mdl-25417166

17.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A.

Cell ; 157(1): 151-61, 2014 Mar 27.

Artículo en Inglés | MEDLINE | ID: mdl-24679533

18.

Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation.

Keung, Albert J; Bashor, Caleb J; Kiriakov, Szilvia; Collins, James J; Khalil, Ahmad S.

Cell ; 158(1): 110-20, 2014 Jul 03.

Artículo en Inglés | MEDLINE | ID: mdl-24995982

19.

Paper-based synthetic gene networks.

Pardee, Keith; Green, Alexander A; Ferrante, Tom; Cameron, D Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

Cell ; 159(4): 940-54, 2014 Nov 06.

Artículo en Inglés | MEDLINE | ID: mdl-25417167

20.

CellNet: network biology applied to stem cell engineering.

Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J.

Cell ; 158(4): 903-915, 2014 Aug 14.

Artículo en Inglés | MEDLINE | ID: mdl-25126793

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A male-derived nonribosomal peptide pheromone controls female schistosome development.

Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond.

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics.

A Deep Learning Approach to Antibiotic Discovery.

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Targeting Antibiotic Tolerance, Pathogen by Pathogen.

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

Next-Generation Machine Learning for Biological Networks.

Engineering Models to Scale.

Portable, On-Demand Biomolecular Manufacturing.

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

A Deep Learning Approach to Antibiotic Discovery.

Systematic identification of factors for provirus silencing in embryonic stem cells.

Discovery of a structural class of antibiotics with explainable deep learning.

Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions.

Toehold switches: de-novo-designed regulators of gene expression.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation.

Paper-based synthetic gene networks.

CellNet: network biology applied to stem cell engineering.