Publications

Johnson J -T Wang, Jacob L Steenwyk, Rachel B Brem. (2024). “Natural trait variation across Saccharomycotina species.” FEMS Yeast Research.

Taekyu Kang, Emily C. Moore, Emily E. K. Kopania, Christina D. King, Birgit 4 Schilling, Judith Campisi, Jeffrey M. Good, and Rachel B. Brem. (2023). “A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence.” G3.

Wang W, Flury AG, Rodriguez AT, Garrison JL, Brem RB. (2023). “A role for worm cutl-24 in background- and parent-of-origin-dependent ER stress resistance.” BMC Genomics.

Arputhasamy C, Foulger AC, Lucanic M, Rane A, Schmidt M, Garrett T, Broussalian M, Battistoni E, Brem RB, Lithgow GJ, Chamoli M, Andersen JK. (2023). “Potassium-chelating drug sodium polystyrene sulfonate enhances lysosomal function and suppresses proteotoxicity.” Geroscience.

Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. (2022). “Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii.” J Fungi (Basel).

Jin K, Wilson KA, Beck JN, Nelson CS, Brownridge GW 3rd, Harrison BR, Djukovic D, Raftery D, Brem RB, Yu S, Drton M, Shojaie A, Kapahi P, Promislow D. (2022). “Correction: Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila.” PLoS Genetics.

Hilsabeck TAU, Liu-Bryan R, Guo T, Wilson KA, Bose N, Raftery D, Beck JN, Lang S, Jin K, Nelson CS, Oron T, Stoller M, Promislow D, Brem RB, Terkeltaub R, Kapahi P. (2022). “A fly GWAS for purine metabolites identifies human FAM214 homolog medusa, which acts in a conserved manner to enhance hyperuricemia-driven pathologies by modulating purine metabolism and the inflammatory response.” Geroscience.

Marcus de Melo Teixeira, Jason E. Stajich, Jason W. Sahl, George R. Thompson, Rachel B. Brem, Claire A. Dubin, Austin V. Blackmon, Heather L. Mead, Paul Keim, Bridget M. Barker. (2022). “A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain “Silveira”.” G3 (Bethesda).

Melanie B. Abrams, Julie N. Chuong, Faisal AlZaben, Claire A. Dubin, Jeffrey M. Skerker, Rachel B. Brem. (2022). “Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance.” G3 (Bethesda). 12:2 jkab412.

Khanna A, Sellegounder D, Kumar J, Chamoli M, Vargas M, Chinta SJ, Rane A, Nelson C, Peiris TH, Brem R, Andersen J, Lithgow G, Kapahi P. (2021). “Trimethylamine modulates dauer formation, neurodegeneration, and lifespan through tyra-3/daf-11 signaling in Caenorhabditis elegans.” Aging Cell. 17:9 e1009793.

Faisal AlZaben, Julie N. Chuong, Melanie B. Abrams, Rachel B. Brem. (2021). “Joint effects of genes underlying a temperature specialization tradeoff in yeast.” PLoS Genet. 17:9 e1009793.

Wenke Wang, Anna G. Flury, Jennifer L. Garrison, Rachel B. Brem (2021). “Cold survival and its molecular mechanisms in a locally adapted nematode population.” GBE. 13:9 evab188.

Melanie B. Abrams, Claire A. Dubin, Faisal AlZaben, Juan Bravo, Pierre M. Joubert, Carly V. Weiss, Rachel B. Brem (2021). “Population and comparative genetics of thermotolerance divergence between yeast species.” G3 (Bethesda). 11:7 jkab139.

Amit Sharma, Kazutaka Akagi, Blaine Pattavina, Kenneth A. Wilson, Christopher Nelson, Mark Watson, Elie Maksoud, Ayano Harata, Mauricio Ortega, Rachel B. Brem & Pankaj Kapahi (2020). “Musashi expression in intestinal stem cells attenuates radiation-induced decline in intestinal permeability and survival in Drosophila.” Sci.Rep. 10:1 19080.

Ke Zou, Silvia Rouskin, Kevin Dervishi, Mark A. McCormick, Arjun Sasikumar, Changhui Deng, Zhibing Chen, Matt Kaeberlein, Rachel B. Brem, Michael Polymenis, Brian K. Kennedy, Jonathan S. Weissman, Jiashun Zheng, Qi Ouyang, Hao Li (2020). “Life span extension by glucose restriction is abrogated by methionine supplementation: Cross-talk between glucose and methionine and implication of methionine as a key regulator of life span.” Sci.Adv. 6:32 eaba1306.

Kelly Jin, Kenneth A. Wilson, Jennifer N. Beck, Christopher S. Nelson, George W. Brownridge III, Benjamin R. Harrison, Danijel Djukovic, Daniel Raftery, Rachel B. Brem, Shiqing Yu, Mathias Drton, Ali Shojaie, Pankaj Kapahi, Daniel Promislow (2020). “Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila.” PLoS Genet. 16:7 e1008835.

Kenneth A. Wilson, Jennifer N. Beck, Christopher S. Nelson, Tyler A. Hilsabeck, Daniel Promislow, Rachel B. Brem, Pankaj Kapahi (2020). “GWAS for Lifespan and Decline in Climbing Ability in Flies upon Dietary Restriction Reveal decima as a Mediator of Insulin-like Peptide Production.” Curr.Biol. 30:14 2749-2760.

Claire A. Dubin, Jeremy I. Roop, Rachel B. Brem (2020). “Divergence of Peroxisome Membrane Gene Sequence and Expression Between Yeast Species.” G3 (Bethesda). 10:6 2079-2085.

Carolyn M. Walsh, Rose Z. Hill, Jamie Schwendinger-Schreck, Jacques Deguine, Emily C. Brock, Natalie Kucirek, Ziad Rifi, Jessica Wei, Karsten Gronert, Rachel B. Brem, Gregory M. Barton, Diana M. Bautista (2019). “Neutrophils promote CXCR3-dependent itch in the development of atopic dermatitis.” eLife. 8:e48448.

Carly V. Weiss, Rachel B. Brem (2019). “Dissecting Trait Variation Across Species Barriers.” Trends Ecol. Evol. 34:12 1131-1136.

Carly V. Weiss, Julie N. Chuong, Rachel B. Brem (2019). “Genetic Mapping of Thermotolerance Difference Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis.” J. Vis. Exp. 150.

Arjun J Sasikumar, David W Kililea, Brian K Kennedy, Rachel B Brem (2019). “Potassium restriction boosts vacuolar acidity and extends lifespan in yeast.” Exp. Gerontol. 120 101-106.

Monica R Sanchez, Celia Payen, Frances Cheong, Blake T Hovde1, Sarah Bissonnette, Adam P Arkin, Jeffrey M Skerker, Rachel B Brem, Amy A Caudy, Maitreya J Dunham (2019). “Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes.” Genome Res. 29:3 396-406.

Rachel B Brem (2019). “Evolution: The Genetics of Milk Champagne Yeast.” Curr. Biol. 29:7 1126-1136.

Carly Weiss, Jeremy I Roop, Rylee Hackley, Julie Chuong, Igor V Grigoriev, Adam P Arkin, Jeff M Skerker, Rachel B Brem (2018). “Genetic dissection of interspecific differences in yeast thermotolerance.” Nat. Genetics 50:11 1501-1504.

Rose Z Hill, Benjamin U Hoffman, Takeshi Morita, Stephanie M Campos, Ellen A Lumpkin, Rachel B Brem, Diana M Bautista (2018) “The signaling lipid sphingosine 1-phosphate regulates mechanical pain.” Elife, 7

Rose Z Hill, Takeshi Morita, Rachel B Brem, Diana M Bautista (2018) “S1PR3 Mediates Itch and Pain via Distinct TRP Channel-Dependent Pathways.” J. Neurosci, 38:36 7833-7843.

Rachael A Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K Ghalambor, Jesse R Lasky, Rachel B Brem, Stephen R Palumbi, Peter Ralph (2017) “Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures.”Am. Nat., 189:5 463-473

Yulia Mostovoy, Alexander Thiemicke, Tiffany Y Hsu, Rachel B Brem (2016) “The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast.” Genome Biol Evol, 8:6 1748-61

Jeremy I Roop, Kyu Chul Chang, Rachel B Brem (2016) “Polygenic evolution of a sugar specialization trade-off in yeast.” Nature, 530:7590 336-9

Karla A Mark, Kathleen J Dumas, Dipa Bhaumik, Birgit Schilling, Sonnet Davis, Tal Ronnen Oron, Dylan J Sorensen, Mark Lucanic, Rachel B Brem, Simon Melov, Arvind Ramanathan, Bradford W Gibson, Gordon J Lithgow (2016) “Vitamin D Promotes Protein Homeostasis and Longevity via the Stress Response Pathway Genes skn-1, ire-1, and xbp-1.” Cell Rep, 17:5 1227-1237

Christopher S Nelson, Jennifer N Beck, Kenneth A Wilson, Elijah R Pilcher, Pankaj Kapahi, Rachel B Brem (2016) “Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila.” BMC Genomics, 17:1 867

Takeshi Morita, Shannan P McClain, Lyn M Batia, Maurizio Pellegrino, Sarah R Wilson, Michael A Kienzler, Kyle Lyman, Anne Sofie Braun Olsen, Justin F Wong, Cheryl L Stucky, Rachel B Brem, Diana M Bautista (2015) “HTR7 Mediates Serotonergic Acute and Chronic Itch.”Neuron, 87:1 124-38

Mark A McCormick, Joe R Delaney, Mitsuhiro Tsuchiya, Scott Tsuchiyama, Anna Shemorry, Sylvia Sim, Annie Chia-Zong Chou, Umema Ahmed, Daniel Carr, Christopher J Murakami, Jennifer Schleit, George L Sutphin, Brian M Wasko, Christopher F Bennett, Adrienne M Wang, Brady Olsen, Richard P Beyer, Theodor K Bammler, Donna Prunkard, Simon C Johnson, Juniper K Pennypacker, Elroy An, Arieanna Anies, Anthony S Castanza, Eunice Choi, Nick Dang, Shiena Enerio, Marissa Fletcher, Lindsay Fox, Sarani Goswami, Se (2015) “A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging.” Cell Metab., 22:5 895-906

Subhash D Katewa, Kazutaka Akagi, Neelanjan Bose, Kuntol Rakshit, Timothy Camarella, Xiangzhong Zheng, David Hall, Sonnet Davis, Christopher S Nelson, Rachel B Brem, Arvind Ramanathan, Amita Sehgal, Jadwiga M Giebultowicz, Pankaj Kapahi (2015) “Peripheral Circadian Clocks Mediate Dietary Restriction-Dependent Changes in Lifespan and Fat Metabolism in Drosophila.” Cell Metab., 23:1 143-154

Ellison CE, Kowbel D, Glass NL, Taylor JW, Brem RB (2014) “Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates” mBio, American Society for Microbiology

Christopher E Ellison, David Kowbel, N Louise Glass, John W Taylor, Rachel B Brem (2014) “Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates.” mBio, 5:2

Valerie L Wong, Christopher E Ellison, Michael B Eisen, Lior Pachter, Rachel B Brem (2014) “Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum.” PLoS ONE, 9:5 e96784

Ronny Kellner, Amitava Bhattacharyya, Stephan Poppe, Tiffany Y Hsu, Rachel B Brem, Eva H Stukenbrock (2014) “Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs.” Genome Biol Evol, 6:6 1353-65

Hana N Lee, Yulia Mostovoy, Tiffany Y Hsu, Amanda H Chang, Rachel B Brem (2013) “Divergence of iron metabolism in wild Malaysian yeast.” G3 (Bethesda), 3:12 2187-94

Joshua G Schraiber, Yulia Mostovoy, Tiffany Y Hsu, Rachel B Brem (2013) “Inferring evolutionary histories of pathway regulation from transcriptional profiling data.” PLoS Comput. Biol., 9:10 e1003255

Javier Palma-Guerrero, Charles R Hall, David Kowbel, Juliet Welch, John W Taylor, Rachel B Brem, N Louise Glass (2013) “Genome wide association identifies novel loci involved in fungal communication.”PLoS Genet., 9:8 e1003669

Jeremy I Roop, Rachel B Brem (2013) “Rare variants in hypermutable genes underlie common morphology and growth traits in wild Saccharomyces paradoxus.” Genetics, 195:2 513-25

Kristin A Gerhold, Maurizio Pellegrino, Makoto Tsunozaki, Takeshi Morita, Duncan B Leitch, Pamela R Tsuruda, Rachel B Brem, Kenneth C Catania, Diana M Bautista (2013) “The star-nosed mole reveals clues to the molecular basis of mammalian touch.” PLoS ONE, 8:1 e55001

Paul A Jenkins, Yun S Song, Rachel B Brem (2012) “Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.” PLoS ONE, 7:11 e46947

Oh Kyu Yoon, Tiffany Y Hsu, Joo Hyun Im, Rachel B Brem (2012) “Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells.” PLoS Genet., 8:8 e1002882

Jun Zhu, Pavel Sova, Qiuwei Xu, Kenneth M Dombek, Ethan Y Xu, Heather Vu, Zhidong Tu, Rachel B Brem, Roger E Bumgarner, Eric E Schadt (2012) “Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation.” PLoS Biol., 10:4 e1001301

Charles M Denby, Joo Hyun Im, Richard C Yu, C Gustavo Pesce, Rachel B Brem (2012) “Negative feedback confers mutational robustness in yeast transcription factor regulation.” Proc. Natl. Acad. Sci. U.S.A., 109:10 3874-8

Hilary C Martin, Jeremy I Roop, Joshua G Schraiber, Tiffany Y Hsu, Rachel B Brem (2012) “Evolution of a membrane protein regulon in Saccharomyces.” Mol. Biol. Evol., 29:7 1747-56

Hana N Lee, Paul M Magwene, Rachel B Brem (2011) “Natural variation in CDC28 underlies morphological phenotypes in an environmental yeast isolate.” Genetics, 188:3 723-30

Christopher E Ellison, Charles Hall, David Kowbel, Juliet Welch, Rachel B Brem, N L Glass, John W Taylor (2011) “Population genomics and local adaptation in wild isolates of a model microbial eukaryote.” Proc. Natl. Acad. Sci. U.S.A., 108:7 2831-6

Tera C Levin, Andrew M Glazer, Lior Pachter, Rachel B Brem, Michael B Eisen (2010) “Exploring the genetic basis of variation in gene predictions with a synthetic association study.” PLoS ONE, 5:7 e11645

Oh Kyu Yoon, Rachel B Brem (2010) “Noncanonical transcript forms in yeast and their regulation during environmental stress.” RNA, 16:6 1256-67

James H Bullard, Yulia Mostovoy, Sandrine Dudoit, Rachel B Brem (2010) “Polygenic and directional regulatory evolution across pathways in Saccharomyces.” Proc. Natl. Acad. Sci. U.S.A., 107:11 5058-63

Lazar N Dimitrov, Rachel B Brem, Leonid Kruglyak, Daniel E Gottschling (2009) “Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strains.” Genetics, 183:1 365-83

Jun Zhu, Bin Zhang, Erin N Smith, Becky Drees, Rachel B Brem, Leonid Kruglyak, Roger E Bumgarner, Eric E Schadt (2008) “Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.” Nat. Genet., 40:7 854-61

James Ronald, Hua Tang, Rachel B Brem (2006) “Genomewide evolutionary rates in laboratory and wild yeast.” Genetics, 174:1 541-4

James Ronald, Rachel B Brem, Jacqueline Whittle, Leonid Kruglyak (2005) “Local regulatory variation in Saccharomyces cerevisiae.” PLoS Genet., 1:2 e25

Rachel B Brem, John D Storey, Jacqueline Whittle, Leonid Kruglyak (2005) “Genetic interactions between polymorphisms that affect gene expression in yeast.” Nature, 436:7051 701-3

Rachel B Brem, Leonid Kruglyak (2005) “The landscape of genetic complexity across 5,700 gene expression traits in yeast.” Proc. Natl. Acad. Sci. U.S.A., 102:5 1572-7

Gaël Yvert, Rachel B Brem, Jacqueline Whittle, Joshua M Akey, Eric Foss, Erin N Smith, Rachel Mackelprang, Leonid Kruglyak (2003) “Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.” Nat. Genet., 35:1 57-64

Rachel B Brem, Gaël Yvert, Rebecca Clinton, Leonid Kruglyak (2002) “Genetic dissection of transcriptional regulation in budding yeast.”Science, 296:5568 752-5

R Brem, K A Dill (1999) “The effect of multiple binding modes on empirical modeling of ligand docking to proteins.” Protein Sci., 8:5 1134-43

J S Finer-Moore, L Liu, D L Birdsall, R Brem, J Apfeld, D V Santi, R M Stroud (1998) “Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase.” J. Mol. Biol., 276:1 113-29

S Sun, R Brem, H S Chan, K A Dill (1995) “Designing amino acid sequences to fold with good hydrophobic cores.” Protein Eng., 8:12 1205-13

S G Robbins, R B Brem, D J Wilson, L M O’Rourke, J E Robertson, I Westra, S R Planck, J T Rosenbaum (1994) “Immunolocalization of integrins in proliferative retinal membranes.” Invest. Ophthalmol. Vis. Sci., 35:9 3475-85

R B Brem, S G Robbins, D J Wilson, L M O’Rourke, R N Mixon, J E Robertson, S R Planck, J T Rosenbaum (1994) “Immunolocalization of integrins in the human retina.” Invest. Ophthalmol. Vis. Sci., 35:9 3466-74