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1.

Problem choice and decision trees in science and engineering.

Fischbach, Michael A.

Cell ; 187(8): 1828-1833, 2024 Apr 11.

Article in English | MEDLINE | ID: mdl-38608651

2.

Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.

Wang, Min; Osborn, Lucas J; Jain, Sunit; Meng, Xiandong; Weakley, Allison; Yan, Jia; Massey, William J; Varadharajan, Venkateshwari; Horak, Anthony; Banerjee, Rakhee; Allende, Daniela S; Chan, E Ricky; Hajjar, Adeline M; Wang, Zeneng; Dimas, Alejandra; Zhao, Aishan; Nagashima, Kazuki; Cheng, Alice G; Higginbottom, Steven; Hazen, Stanley L; Brown, J Mark; Fischbach, Michael A.

Cell ; 186(13): 2839-2852.e21, 2023 06 22.

Article in English | MEDLINE | ID: mdl-37352836

3.

Design, construction, and in vivo augmentation of a complex gut microbiome.

Cheng, Alice G; Ho, Po-Yi; Aranda-Díaz, Andrés; Jain, Sunit; Yu, Feiqiao B; Meng, Xiandong; Wang, Min; Iakiviak, Mikhail; Nagashima, Kazuki; Zhao, Aishan; Murugkar, Pallavi; Patil, Advait; Atabakhsh, Katayoon; Weakley, Allison; Yan, Jia; Brumbaugh, Ariel R; Higginbottom, Steven; Dimas, Alejandra; Shiver, Anthony L; Deutschbauer, Adam; Neff, Norma; Sonnenburg, Justin L; Huang, Kerwyn Casey; Fischbach, Michael A.

Cell ; 185(19): 3617-3636.e19, 2022 09 15.

Article in English | MEDLINE | ID: mdl-36070752

4.

Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota.

Lima-Junior, Djalma S; Krishnamurthy, Siddharth R; Bouladoux, Nicolas; Collins, Nicholas; Han, Seong-Ji; Chen, Erin Y; Constantinides, Michael G; Link, Verena M; Lim, Ai Ing; Enamorado, Michel; Cataisson, Christophe; Gil, Louis; Rao, Indira; Farley, Taylor K; Koroleva, Galina; Attig, Jan; Yuspa, Stuart H; Fischbach, Michael A; Kassiotis, George; Belkaid, Yasmine.

Cell ; 184(14): 3794-3811.e19, 2021 07 08.

Article in English | MEDLINE | ID: mdl-34166614

5.

A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors.

Nemet, Ina; Saha, Prasenjit Prasad; Gupta, Nilaksh; Zhu, Weifei; Romano, Kymberleigh A; Skye, Sarah M; Cajka, Tomas; Mohan, Maradumane L; Li, Lin; Wu, Yuping; Funabashi, Masanori; Ramer-Tait, Amanda E; Naga Prasad, Sathyamangla Venkata; Fiehn, Oliver; Rey, Federico E; Tang, W H Wilson; Fischbach, Michael A; DiDonato, Joseph A; Hazen, Stanley L.

Cell ; 180(5): 862-877.e22, 2020 03 05.

Article in English | MEDLINE | ID: mdl-32142679

6.

Microbiome: Focus on Causation and Mechanism.

Fischbach, Michael A.

Cell ; 174(4): 785-790, 2018 08 09.

Article in English | MEDLINE | ID: mdl-30096310

7.

Mapping the Genetic Landscape of Human Cells.

Horlbeck, Max A; Xu, Albert; Wang, Min; Bennett, Neal K; Park, Chong Y; Bogdanoff, Derek; Adamson, Britt; Chow, Eric D; Kampmann, Martin; Peterson, Tim R; Nakamura, Ken; Fischbach, Michael A; Weissman, Jonathan S; Gilbert, Luke A.

Cell ; 174(4): 953-967.e22, 2018 08 09.

Article in English | MEDLINE | ID: mdl-30033366

8.

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Guo, Chun-Jun; Chang, Fang-Yuan; Wyche, Thomas P; Backus, Keriann M; Acker, Timothy M; Funabashi, Masanori; Taketani, Mao; Donia, Mohamed S; Nayfach, Stephen; Pollard, Katherine S; Craik, Charles S; Cravatt, Benjamin F; Clardy, Jon; Voigt, Christopher A; Fischbach, Michael A.

Cell ; 168(3): 517-526.e18, 2017 01 26.

Article in English | MEDLINE | ID: mdl-28111075

9.

Signaling in Host-Associated Microbial Communities.

Fischbach, Michael A; Segre, Julia A.

Cell ; 164(6): 1288-1300, 2016 Mar 10.

Article in English | MEDLINE | ID: mdl-26967294

10.

A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.

Donia, Mohamed S; Cimermancic, Peter; Schulze, Christopher J; Wieland Brown, Laura C; Martin, John; Mitreva, Makedonka; Clardy, Jon; Linington, Roger G; Fischbach, Michael A.

Cell ; 158(6): 1402-1414, 2014 Sep 11.

Article in English | MEDLINE | ID: mdl-25215495

11.

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.

Cimermancic, Peter; Medema, Marnix H; Claesen, Jan; Kurita, Kenji; Wieland Brown, Laura C; Mavrommatis, Konstantinos; Pati, Amrita; Godfrey, Paul A; Koehrsen, Michael; Clardy, Jon; Birren, Bruce W; Takano, Eriko; Sali, Andrej; Linington, Roger G; Fischbach, Michael A.

Cell ; 158(2): 412-421, 2014 Jul 17.

Article in English | MEDLINE | ID: mdl-25036635

12.

Mapping the T cell repertoire to a complex gut bacterial community.

Nagashima, Kazuki; Zhao, Aishan; Atabakhsh, Katayoon; Bae, Minwoo; Blum, Jamie E; Weakley, Allison; Jain, Sunit; Meng, Xiandong; Cheng, Alice G; Wang, Min; Higginbottom, Steven; Dimas, Alex; Murugkar, Pallavi; Sattely, Elizabeth S; Moon, James J; Balskus, Emily P; Fischbach, Michael A.

Nature ; 621(7977): 162-170, 2023 Sep.

Article in English | MEDLINE | ID: mdl-37587342

13.

A gut-derived metabolite alters brain activity and anxiety behaviour in mice.

Needham, Brittany D; Funabashi, Masanori; Adame, Mark D; Wang, Zhuo; Boktor, Joseph C; Haney, Jillian; Wu, Wei-Li; Rabut, Claire; Ladinsky, Mark S; Hwang, Son-Jong; Guo, Yumei; Zhu, Qiyun; Griffiths, Jessica A; Knight, Rob; Bjorkman, Pamela J; Shapiro, Mikhail G; Geschwind, Daniel H; Holschneider, Daniel P; Fischbach, Michael A; Mazmanian, Sarkis K.

Nature ; 602(7898): 647-653, 2022 02.

Article in English | MEDLINE | ID: mdl-35165440

14.

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.

Han, Shuo; Van Treuren, Will; Fischer, Curt R; Merrill, Bryan D; DeFelice, Brian C; Sanchez, Juan M; Higginbottom, Steven K; Guthrie, Leah; Fall, Lalla A; Dodd, Dylan; Fischbach, Michael A; Sonnenburg, Justin L.

Nature ; 595(7867): 415-420, 2021 07.

Article in English | MEDLINE | ID: mdl-34262212

15.

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians.

Sato, Yuko; Atarashi, Koji; Plichta, Damian R; Arai, Yasumichi; Sasajima, Satoshi; Kearney, Sean M; Suda, Wataru; Takeshita, Kozue; Sasaki, Takahiro; Okamoto, Shoki; Skelly, Ashwin N; Okamura, Yuki; Vlamakis, Hera; Li, Youxian; Tanoue, Takeshi; Takei, Hajime; Nittono, Hiroshi; Narushima, Seiko; Irie, Junichiro; Itoh, Hiroshi; Moriya, Kyoji; Sugiura, Yuki; Suematsu, Makoto; Moritoki, Nobuko; Shibata, Shinsuke; Littman, Dan R; Fischbach, Michael A; Uwamino, Yoshifumi; Inoue, Takashi; Honda, Akira; Hattori, Masahira; Murai, Tsuyoshi; Xavier, Ramnik J; Hirose, Nobuyoshi; Honda, Kenya.

Nature ; 599(7885): 458-464, 2021 11.

Article in English | MEDLINE | ID: mdl-34325466

16.

A metabolic pathway for bile acid dehydroxylation by the gut microbiome.

Funabashi, Masanori; Grove, Tyler L; Wang, Min; Varma, Yug; McFadden, Molly E; Brown, Laura C; Guo, Chunjun; Higginbottom, Steven; Almo, Steven C; Fischbach, Michael A.

Nature ; 582(7813): 566-570, 2020 06.

Article in English | MEDLINE | ID: mdl-32555455

17.

Author Correction: Bile acid metabolites control T_H17 and T_reg cell differentiation.

Hang, Saiyu; Paik, Donggi; Yao, Lina; Kim, Eunha; Trinath, Jamma; Lu, Jingping; Ha, Soyoung; Nelson, Brandon N; Kelly, Samantha P; Wu, Lin; Zheng, Ye; Longman, Randy S; Rastinejad, Fraydoon; Devlin, A Sloan; Krout, Michael R; Fischbach, Michael A; Littman, Dan R; Huh, Jun R.

Nature ; 579(7798): E7, 2020 03.

Article in English | MEDLINE | ID: mdl-32094662

18.

A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.

Sharma, Sreenath V; Lee, Diana Y; Li, Bihua; Quinlan, Margaret P; Takahashi, Fumiyuki; Maheswaran, Shyamala; McDermott, Ultan; Azizian, Nancy; Zou, Lee; Fischbach, Michael A; Wong, Kwok-Kin; Brandstetter, Kathleyn; Wittner, Ben; Ramaswamy, Sridhar; Classon, Marie; Settleman, Jeff.

Cell ; 141(1): 69-80, 2010 Apr 02.

Article in English | MEDLINE | ID: mdl-20371346

19.

Bile acid metabolites control T_H17 and T_reg cell differentiation.

Hang, Saiyu; Paik, Donggi; Yao, Lina; Kim, Eunha; Trinath, Jamma; Lu, Jingping; Ha, Soyoung; Nelson, Brandon N; Kelly, Samantha P; Wu, Lin; Zheng, Ye; Longman, Randy S; Rastinejad, Fraydoon; Devlin, A Sloan; Krout, Michael R; Fischbach, Michael A; Littman, Dan R; Huh, Jun R.

Nature ; 576(7785): 143-148, 2019 12.

Article in English | MEDLINE | ID: mdl-31776512

20.

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes.

Scharschmidt, Tiffany C; Vasquez, Kimberly S; Truong, Hong-An; Gearty, Sofia V; Pauli, Mariela L; Nosbaum, Audrey; Gratz, Iris K; Otto, Michael; Moon, James J; Liese, Jan; Abbas, Abul K; Fischbach, Michael A; Rosenblum, Michael D.

Immunity ; 43(5): 1011-21, 2015 Nov 17.

Article in English | MEDLINE | ID: mdl-26588783

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