faculty
Aimee Dudley
adudley@pnri.org
Professor
Pacific Northwest Research Institute
Gene Expression, Cell Cycle & Chromosome Biology
Microbiology, Infection & Immunity
Genetics and genomics in yeast
Faculty Contact Information
Building: 720 Broadway
Box: 720 Broadway
Phone: 206-726-1237
https://www.pnri.org/research/labs/dudley-lab/
Research Summary
The genotype-phenotype problem is among the most fundamental in biology. Given the complete genome sequence of an individual, can we predict what traits they will exhibit? We approach this problem using a combination of genetics, genomics, and synthetic biology. We are currently using “The Awesome Power of Yeast Genetics” to analyze the functional impact of natural variation in human genes and to develop powerful experimental and statistical resources for delineating the genetic architecture of complex, quantitative traits in S. cerevisiae.
DEI Statement
Every scientific breakthrough starts with someone asking a question that they find personally interesting and important. By increasing the participation of individuals with diverse backgrounds and experiences in biomedical research, we expand the range of questions that get asked, and consequently, the discoveries that get made. Our lab strives to be an inclusive environment because science benefits when individuals from all communities and backgrounds bring their talents and perspectives to the pursuit of discovery. In addition to promoting diversity and inclusion in my own lab, I play an active role at the institutional level. As PNRI’s Director of Educational Outreach, I lead the institute’s initiative to recruit trainees from communities that are underrepresented in STEM and to establish partnerships with DEI-focused nonprofit organizations.
Training Summary
Rainier Scholars Internship Supervisor Training: Best Practices for Supporting BIPOC and First-Gen Students in the Workplace – 2022
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&query_key=1&WebEnv=MCID_63915bfe395e202f1245c49c&retmode=json
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Publications
The following publications were retrieved from PubMed:
Sirr A, Timour MS, Cromie GA, Tang M, Dudley AM.
Yeast. 2022 Jun; 6-7(39)354-362
Quantifying yeast colony morphologies with feature engineering from time-lapse photography.
Goldschmidt A, Kunert-Graf J, Scott AC, Tan Z, Dudley AM, Kutz JN.
Sci Data. 2022 May 17; 1(9)216
Maddirevula S, Shamseldin HE, Sirr A, AlAbdi L, Lo RS, Ewida N, Al-Qahtani M, Hashem M, Abdulwahab F, Aboyousef O, Kaya N, Monies D, Salem MH, Al Harbi N, Aldhalaan HM, Alzaidan H, Almanea HM, Alsalamah AK, Al Mutairi F, Ismail S, Abdel-Salam GMH, Alhashem A, Asery A, Faqeih E, AlQassmi A, Al-Hamoudi W, Algoufi T, Shagrani M, Dudley AM, Alkuraya FS.
Front Genet. 2020; (11)580484
Sirr A, Lo RS, Cromie GA, Scott AC, Ashmead J, Heyesus M, Dudley AM.
J Inherit Metab Dis. 2020 Jul; 4(43)758-769
Intosalmi J, Scott AC, Hays M, Flann N, Yli-Harja O, Lähdesmäki H, Dudley AM, Skupin A.
BMC Mol Cell Biol. 2019 Dec 19; 1(20)59
Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies.
Sakhanenko NA, Cromie GA, Dudley AM, Galas DJ.
G3 (Bethesda). 2019 Jul 9; 7(9)2071-2088
Forche A, Solis NV, Swidergall M, Thomas R, Guyer A, Beach A, Cromie GA, Le GT, Lowell E, Pavelka N, Berman J, Dudley AM, Selmecki A, Filler SG.
PLoS Genet. 2019 May; 5(15)e1008137
A polyploid admixed origin of beer yeasts derived from European and Asian wine populations.
Fay JC, Liu P, Ong GT, Dunham MJ, Cromie GA, Jeffery EW, Ludlow CL, Dudley AM.
PLoS Biol. 2019 Mar; 3(17)e3000147
Forche A, Cromie G, Gerstein AC, Solis NV, Pisithkul T, Srifa W, Jeffery E, Abbey D, Filler SG, Dudley AM, Berman J.
Genetics. 2018 Jul; 3(209)725-741
Sirr A, Scott AC, Cromie GA, Ludlow CL, Ahyong V, Morgan TS, Gilbert T, Dudley AM.
G3 (Bethesda). 2018 Jan 4; 1(8)239-251
Jarosz D, Dudley AM.
G3 (Bethesda). 2017 Aug 16; 10(7)3237-41
Cromie GA, Tan Z, Hays M, Sirr A, Jeffery EW, Dudley AM.
G3 (Bethesda). 2017 Aug 7; 8(7)2845-2854
The State of Systems Genetics in 2017.
Baliga NS, Björkegren JL, Boeke JD, Boutros M, Crawford NP, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC.
Cell Syst. 2017 Jan 25; 1(4)7-15
Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch.
Cromie GA, Tan Z, Hays M, Jeffery EW, Dudley AM.
G3 (Bethesda). 2017 Jan 5; 1(7)233-246
Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.
Ludlow CL, Cromie GA, Garmendia-Torres C, Sirr A, Hays M, Field C, Jeffery EW, Fay JC, Dudley AM.
Curr Biol. 2016 Apr 4; 7(26)965-71
Cary GA, Vinh DB, May P, Kuestner R, Dudley AM.
G3 (Bethesda). 2015 Sep 21; 11(5)2497-511
Allelic variation, aneuploidy, and nongenetic mechanisms suppress a monogenic trait in yeast.
Sirr A, Cromie GA, Jeffery EW, Gilbert TL, Ludlow CL, Scott AC, Dudley AM.
Genetics. 2015 Jan; 1(199)247-62
Unidirectional P-body transport during the yeast cell cycle.
Garmendia-Torres C, Skupin A, Michael SA, Ruusuvuori P, Kuwada NJ, Falconnet D, Cary GA, Hansen C, Wiggins PA, Dudley AM.
PLoS One. 2014; 6(9)e99428
BEST: barcode enabled sequencing of tetrads.
Scott AC, Ludlow CL, Cromie GA, Dudley AM.
J Vis Exp. 2014 May 1; 87
Cary GA, Yoon SH, Torres CG, Wang K, Hays M, Ludlow C, Goodlett DR, Dudley AM.
Yeast. 2014 May; 5(31)167-78
Quantitative analysis of colony morphology in yeast.
Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.
Biotechniques. 2014 Jan; 1(56)18-27
POMO--Plotting Omics analysis results for Multiple Organisms.
Lin J, Kreisberg R, Kallio A, Dudley AM, Nykter M, Shmulevich I, May P, Autio R.
BMC Genomics. 2013 Dec 24; (14)918
Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.
Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC.
G3 (Bethesda). 2013 Dec 9; 12(3)2163-71
Aneuploidy underlies a multicellular phenotypic switch.
Tan Z, Hays M, Cromie GA, Jeffery EW, Scott AC, Ahyong V, Sirr A, Skupin A, Dudley AM.
Proc Natl Acad Sci U S A. 2013 Jul 23; 30(110)12367-72
High-throughput tetrad analysis.
Ludlow CL, Scott AC, Cromie GA, Jeffery EW, Sirr A, May P, Lin J, Gilbert TL, Hays M, Dudley AM.
Nat Methods. 2013 Jul; 7(10)671-5
Sípová H, Zhang S, Dudley AM, Galas D, Wang K, Homola J.
Anal Chem. 2010 Dec 15; 24(82)10110-5
Ruusuvuori P, Aijö T, Chowdhury S, Garmendia-Torres C, Selinummi J, Birbaumer M, Dudley AM, Pelkmans L, Yli-Harja O.
BMC Bioinformatics. 2010 May 13; (11)248
Learning a prior on regulatory potential from eQTL data.
Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D.
PLoS Genet. 2009 Jan; 1(5)e1000358
Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segrè D.
Genome Biol. 2008; 9(9)R140
Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.
Proc Natl Acad Sci U S A. 2006 Sep 19; 38(103)14062-7
A global view of pleiotropy and phenotypically derived gene function in yeast.
Dudley AM, Janse DM, Tanay A, Shamir R, Church GM.
Mol Syst Biol. 2005; (1)2005.0001
Clarke AR, Schnieden V, Hamilton BA, Dudley AM, Beard J, Einfeld SL, Buss R, Tobin M, Knowles M, Stevens G, Gibbs N.
Arch Suicide Res. 2004; 2(8)147-52
Predicting phenotype from patterns of annotation.
King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP.
Bioinformatics. 2003; (19 Suppl 1)i183-9
Dudley AM, Aach J, Steffen MA, Church GM.
Proc Natl Acad Sci U S A. 2002 May 28; 11(99)7554-9
Dudley AM, Rougeulle C, Winston F.
Genes Dev. 1999 Nov 15; 22(13)2940-5
Dudley AM, Gansheroff LJ, Winston F.
Genetics. 1999 Apr; 4(151)1365-78
Madison JM, Dudley AM, Winston F.
Mol Cell Biol. 1998 Apr; 4(18)1879-90
T7 RNA polymerase-dependent expression of COXII in yeast mitochondria.
Pinkham JL, Dudley AM, Mason TL.
Mol Cell Biol. 1994 Jul; 7(14)4643-52
Accepting Students For:
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Permanent
Lab Information
Location: Pacific Northwest Research Institute
Building: 720 Broadway
Phone: 206-726-1237
Alt Phone: 206-726-1200
https://www.pnri.org/research/labs/dudley-lab/
Building: 720 Broadway
Phone: 206-726-1237
Alt Phone: 206-726-1200
https://www.pnri.org/research/labs/dudley-lab/