faculty
Roger Brent
rbrent@fredhutch.org
Professor
Fred Hutch
Cell Signaling & Cell/Environment Interactions
Computational Biology
Genetics, Genomics & Evolution
Ways to make biomedical research go faster
Faculty Contact Information
Research Summary
One project draws on tenets of control theory from human engineering to develop “expression clamped” controllers of mammalian gene expression. The idea is to allow researchers to understand the effects of small differences in protein dosage on phenotype. A second uses digital technology and machine learning to help Augmented Reality (AR) systems provide guidance to researchers performing lab procedures. Both projects further the lab mission of “epistemic support”, to develop tools and methods to accelerate the pace of scientific discovery over the course of the 21st century.
DEI Statement
I grew up in Hattiesburg, Mississippi, in the 1960s. There, I saw enough racism to last a lifetime, and formed political beliefs that have served me well as an adult. The lab has always been woman friendly. Since about 2000, a significant part of lab effort has been outreach to under-represented minority researchers and aggressive attempts to recruit and mentor such persons, while educating everybody about the social structures in which science is embedded. Most of this work has been at the postdoctoral level or higher but we have had PhD students and we now have undergraduates.
Training Summary
I lack formal training in either DEI or mentoring. For DEI, I may (perhaps) partly make up for lack of training by sincerity of deeply held political beliefs and (many) years experience in trying to do the work. For mentoring, I try hard to get people to develop into their best selves intellectually by doing the best science they can.
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Publications
The following publications were retrieved from PubMed:
Azizoglu A, Brent R, Rudolf F.
Elife. 2021 Aug 3; (10)
Chaperone biomarkers of lifespan and penetrance track the dosages of many other proteins.
Burnaevskiy N, Sands B, Yun S, Tedesco PM, Johnson TE, Kaeberlein M, Brent R, Mendenhall A.
Nat Commun. 2019 Dec 16; 1(10)5725
Crane MM, Sands B, Battaglia C, Johnson B, Yun S, Kaeberlein M, Brent R, Mendenhall A.
Sci Rep. 2019 Jun 24; 1(9)9192
Recipes and Tools for Culture of Escherichia coli.
Elbing KL, Brent R.
Curr Protoc Mol Biol. 2019 Jan; 1(125)e83
Deep learning to predict microscope images.
Brent R, Boucheron L.
Nat Methods. 2018 Nov; 11(15)868-870
Transferring information without distortion.
Andrews SS, Brent R, Balázsi G.
Elife. 2018 Oct 25; (7)
Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling.
Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R.
Mol Syst Biol. 2018 Apr 4; 4(14)e7390
Environmental Canalization of Life Span and Gene Expression in Caenorhabditis elegans.
Mendenhall A, Crane MM, Leiser S, Sutphin G, Tedesco PM, Kaeberlein M, Johnson TE, Brent R.
J Gerontol A Biol Sci Med Sci. 2017 Aug 1; 8(72)1033-1037
Mendenhall A, Crane MM, Tedesco PM, Johnson TE, Brent R.
J Gerontol A Biol Sci Med Sci. 2017 Oct 1; 10(72)1305-1310
Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs.
Andrews SS, Peria WJ, Yu RC, Colman-Lerner A, Brent R.
Cell Syst. 2016 Nov 23; 5(3)444-455.e2
Phasor plotting with frequency-domain flow cytometry.
Cao R, Jenkins P, Peria W, Sands B, Naivar M, Brent R, Houston JP.
Opt Express. 2016 Jun 27; 13(24)14596-607
Overview of Post Cohen-Boyer Methods for Single Segment Cloning and for Multisegment DNA Assembly.
Sands B, Brent R.
Curr Protoc Mol Biol. 2016 Jan; 1(113)3.26.1-3.26.20
Using measures of single-cell physiology and physiological state to understand organismic aging.
Mendenhall A, Driscoll M, Brent R.
Aging Cell. 2016 Feb; 1(15)4-13
Mendenhall AR, Tedesco PM, Sands B, Johnson TE, Brent R.
PLoS One. 2015; 5(10)e0124289
Sands B, Jenkins P, Peria WJ, Naivar M, Houston JP, Brent R.
PLoS One. 2014; 10(9)e109940
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A.
Proc Natl Acad Sci U S A. 2014 Sep 16; 37(111)E3860-9
Pincus D, Ryan CJ, Smith RD, Brent R, Resnekov O.
PLoS One. 2013; 3(8)e56544
Multiplex protein detection with DNA readout via mass spectrometry.
Flanigon J, Kamali-Moghaddam M, Burbulis I, Annink C, Steffen M, Oeth P, Brent R, van den Boom D, Landegren U, Cantor C.
N Biotechnol. 2013 Jan 25; 2(30)153-8
Interaction trap/two-hybrid system to identify interacting proteins.
Golemis EA, Serebriiskii I, Finley RL Jr, Kolonin MG, Gyuris J, Brent R.
Curr Protoc Cell Biol. 2011 Dec; (Chapter 17)Unit 17.3.
Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range.
Thomson TM, Benjamin KR, Bush A, Love T, Pincus D, Resnekov O, Yu RC, Gordon A, Colman-Lerner A, Endy D, Brent R.
Proc Natl Acad Sci U S A. 2011 Dec 13; 50(108)20265-70
Interaction trap/two-hybrid system to identify interacting proteins.
Golemis EA, Serebriiskii I, Finley RL Jr, Kolonin MG, Gyuris J, Brent R.
Curr Protoc Neurosci. 2011 Apr; (Chapter 4)Unit 4.4
Detailed simulations of cell biology with Smoldyn 2.1.
Andrews SS, Addy NJ, Brent R, Arkin AP.
PLoS Comput Biol. 2010 Mar 12; 3(6)e1000705
Cell signaling: what is the signal and what information does it carry?
Brent R
FEBS Lett. 2009 Dec 17; 24(583)4019-24
Interaction trap/two-hybrid system to identify interacting proteins.
Golemis EA, Serebriiskii I, Finley RL Jr, Kolonin MG, Gyuris J, Brent R.
Curr Protoc Protein Sci. 2009 Aug; (Chapter 19)Unit19.2
Negative feedback that improves information transmission in yeast signalling.
Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, Brent R.
Nature. 2008 Dec 11; 7223(456)755-61
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.
Nat Biotechnol. 2008 Oct; 10(26)1155-60
Interaction trap/two-hybrid system to identify interacting proteins.
Golemis EA, Serebriiskii I, Finley RL Jr, Kolonin MG, Gyuris J, Brent R.
Curr Protoc Mol Biol. 2008 Apr; (Chapter 20)Unit 20.1
Selected topics from classical bacterial genetics.
Raleigh EA, Elbing K, Brent R.
Curr Protoc Mol Biol. 2002 Aug; (Chapter 1)Unit 1.4
Media preparation and bacteriological tools.
Elbing K, Brent R.
Curr Protoc Mol Biol. 2002 Aug; (Chapter 1)Unit 1.1
Quantifying small numbers of antibodies with a 'near-universal' protein-DNA chimera.
Burbulis I, Yamaguchi K, Yu R, Resnekov O, Brent R.
Nat Methods. 2007 Dec; 12(4)1011-3
Single-cell quantification of molecules and rates using open-source microscope-based cytometry.
Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu RC, Brent R.
Nat Methods. 2007 Feb; 2(4)175-81
2020 computing: can computers help to explain biology?
Brent R, Bruck J.
Nature. 2006 Mar 23; 7083(440)416-7
Regulated cell-to-cell variation in a cell-fate decision system.
Colman-Lerner A, Gordon A, Serra E, Chin T, Resnekov O, Endy D, Pesce CG, Brent R.
Nature. 2005 Sep 29; 7059(437)699-706
Cell biology. A fishing buddy for hypothesis generators.
Brent R, Lok L.
Science. 2005 Apr 22; 5721(308)504-6
Using protein-DNA chimeras to detect and count small numbers of molecules.
Burbulis I, Yamaguchi K, Gordon A, Carlson R, Brent R.
Nat Methods. 2005 Jan; 1(2)31-7
Automatic generation of cellular reaction networks with Moleculizer 1.0.
Lok L, Brent R.
Nat Biotechnol. 2005 Jan; 1(23)131-6
Building an artificial regulatory system to understand a natural one.
Brent R
Cell. 2004 Jan 23; 2 Suppl(116)S73-4, 1 p following S76
Cyclin D3 activates Caspase 2, connecting cell proliferation with cell death.
Mendelsohn AR, Hamer JD, Wang ZB, Brent R.
Proc Natl Acad Sci U S A. 2002 May 14; 10(99)6871-6
Accepting Students For:
Rotation, Summer
Lab Information
Location: Fred Hutch
Building: Weintraub
Room: B2-201
Box: A2-205
Building: Weintraub
Room: B2-201
Box: A2-205