Maddirevula, H. E. Shamseldin, A. Sirr, L. Alabdi, R. S. Lo, M. Hashem, F. Abdulwahab, N. Kaya, D. Monies, M. H. Salem, N. Al Harbi, H. M. Aldhalaan, H. Alzaidan, H. M. Almanea, A. K. Alsalamah, F. Al Mutairi, S. Ismail, G. M. H. Abdel-Salam, A. M. Alhashem, A. Asery, E. Faqeih, W. Al Hamoudi, T. Algoufi, M. Shagrani, A. M. Dudley, F. S. Alkuraya (2020) Exploiting the autozygome to support previously published Mendelian gene-disease associations: An update. Front. Genet.11:580484 PMID: 33456446
Sirr, R. S. Lo, G. A. Cromie, A. C. Scott, J. Ashmead, M. Heyesus, and A. M. Dudley (2020) A yeast-based complementation assay elucidates the functional impact of 200 missense variants in human PSAT1. J Inherit Metab Dis. DOI: 10.1002/jimd.12227 PMID: 32077105
Intosalmi, A. C. Scott, M. Hayes, N. Flann, O. Yli-Harja, H. Lähdesmäki, A. M. Dudley, and A. Skupin (2019) Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies. BMC Mol. Cell Biol. 20:59 PMID: 31856706 [PMCID: PMC6923950]
A. Sakhanenko, G. A. Cromie, A. M. Dudley and D. J. Galas (2019) Computational inference software for tetrad assembly from randomly arrayed yeast colonies. G3 9:2071-2088 PMID: 31109921 [PMCID: PMC6643883]
A. Forche, G. Cromie, A.C. Gerstein, N. V. Solis, T. Pisithkul, W. Srifa, E. Jeffery, D. Abbey, S. G. Filler, A. M. Dudley, J. Berman (2018) Rapid phenotypic and genotypic diversification after exposure to the oral host hiche in Candida albicans. Genetics 209:725-741. PMID: 29724862 [PMCID: PMC6028260]
A. Sirr, A. C. Scott, G. A. Cromie, C. L. Ludlow, V. Ahyong, T. S. Morgan, T. Gilbert, A. M. Dudley (2018) Natural variation in SER1 and ENA6 underlie condition-specific growth defects in S. cerevisiae. G3 8:239-251. PMID: 29138237 [PMCID: PMC5765352]
D. Jarosz and A. M. Dudley (2017) Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems. G3 7: 3237-3241. PMID: 28814445 [PMCID: PMC5633374]
G. A. Cromie, Z. Tan, M. Hays, A. Sirr, E. W. Jeffery, A. M. Dudley (2017) Transcriptional profiling of biofilm regulators identified by an overexpression screen in Saccharomyces cerevisiae. G3 7:2845-2854. PMID: 28673928 [PMCID: PMC5555487]
N. S. Baliga, J. L. Björkegren, J. D. Boeke, M. Boutros, N. P. Crawford, A. M. Dudley, C. R. Farber, A. Jones, A. I. Levey, A. J. Lusis, H. C. Mak, J. H. Nadeau, M. B. Noyes, E. Petretto, N.T. Seyfried, L. M. Steinmetz, S. C. Vonesch (2017) The State of Systems Genetics in 2017. Cell Syst. 4:7-15. PMID: 28125793
G. A. Cromie, Z. Tan, M. Hays, E. W. Jeffery, A. M. Dudley (2017) Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch. G3 7:233-246. PMID: 27836908 [PMCID: PMC5217112]
C. L. Ludlow, G. A. Cromie, C. Garmendia-Torres, A. Sirr, M. Hays, C. Field, E. W. Jeffery, J. C. Fay and A. M. Dudley (2016) Independent origins of yeast associated with coffee and cacao fermentation. Current Biology 26:965-71. PMID: 27020745 [PMCID: PMC4821677]
G. A. Cary, D. B.N. Vinh, P. May, R. Kuestner, and A. M. Dudley (2015) Proteomic analysis of Dhh1 complexes reveals a role for Hsp40 chaperone Ydj1 in yeast P-body assembly. G3 5:2497-511. PMID: 26392412 [PMCID: PMC4632068]
G. A. Cromie and A. M. Dudley (2015) Aneuploidy: Tolerating tolerance. Current Biology 25:R771-3. PMID: 26325142
M. A. Hickman, C. Paulson, A. M. Dudley, and J. Berman (2015) Parasexual ploidy reduction drives population heterogeneity through random and transient aneuploidy in Candida albicans. Genetics 200:781-94. PMID: 25991822 [PMCID: PMC4512543]
A. Sirr, G. A. Cromie, E. W. Jeffery, T. L. Gilbert, C. L. Ludlow, A. C. Scott, and A. M. Dudley (2015) Allelic Variation, Aneuploidy and Non-Genetic Mechanisms Suppress a Monogenic Trait in Yeast. Genetics 199:247-62. PMID: 25398792 [PMCID: PMC4286688]
C. Garmendia-Torres, A. Skupin, S. Michael, P. Ruusuvuori, N. J. Kuwada, D. Falconnet, G. A. Cary, C. Hansen, P. A. Wiggins, and A. M. Dudley (2014) Unidirectional p-body transport during the yeast cell cycle. PLoS One 9:e99428. PMID: 24918601 [PMCID: PMC4053424]
A. C. Scott, C. L. Ludlow, G. A. Cromie, and A. M. Dudley (2014) BEST: Barcode Enabled Sequencing of Tetrads. J. Vis. Exp. doi: 10.3791/51401 PMID: 24836713 [PMCID: PMC4172027]
G. A. Cary, S. H. Yoon, D. R. Goodlett, and A. M. Dudley (2014) Identification and characterization of a drug sensitive strain enables puromycin‐based translational assays in Saccharomyces cerevisiae. Yeast 31:167-78. PMID: 24610064 [PMCID: PMC4013229]
P. Ruusuvuori, J. Lin, Z. Tan, A. C. Scott, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, and A. M. Dudley (2014) Quantitative analysis of yeast colony morphology. Biotechniques 56:18-27. PMID: 24447135 [PMCID: PMC399692]
J. Lin, R. Kreisberg, A. Kallio, A. M. Dudley, M. Nykter, I. Shmulevich, P. May, and R. Autio (2013) POMO: Plotting Omics-associations for Multiple Organisms. BMC Genomics 14:918. PMID: 24365393 [PMCID: PMC3696418]
G. A. Cromie, K. E. Hyma, C. L. Ludlow, C. Garmendia-Torres, T. L. Gilbert, P. May, A. A. Huang, A. M. Dudley, and J. C. Fay (2013) Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq. G3 3:2163-71. PMID: 24122055 [PMCID: PMC3852379]
Z. Tan, M. Hays, G. A. Cromie, E. W. Jeffery, V. Ahyong, A. C. Scott, A. Skupin, A. Sirr, and A. M. Dudley (2013) Aneuploidy as a mechanism for a reversible multicellular phenotypic switch. Proc Natl Acad Sci USA 110:12367-72. PMID: 23812752 [PMCID: PMC3725063]
C. L. Ludlow, A. C. Scott, G. A. Cromie, E. W. Jeffery, A. Sirr, P. May, J. Lin, T. L. Gilbert, M. Hays, and A. M. Dudley (2013) High throughput tetrad analysis. Nat. Methods. 10:671-5. PMID: 23666411 [PMCID: PMC3696418]
J. H. Nadeau and A. M. Dudley (2011) Systems Genetics, Science 331:1015-6. PMID: 21350153
H. Šípová, S. Zhang, A. M. Dudley, D.J. Galas, K. Wang, and J. Homola (2010) Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Analytical Chemistry 82:10110-5. PMID: 21090631 [PMCID: PMC3021551]
P. Ruusuvuori, T. Äijö, S. Chowdhury, C. Garmendia-Torres, J. Selinummi, M. Birbaumer, A. M. Dudley, L. Pelkmans and O. Yli-Harja (2010) Evaluation of methods for detection of fluorescence labeled subcellular objects in micro scope images. BMC Bioinformatics 11:248. PMID: 20465797 [PMCID: PMC3098061]
G. W. Carter and A. M. Dudley (2009) Systems Genetics and Complex Traits. In Encyclopedia of Complexity and Systems Science (Meyers, R. A. Editor) Springer Publishing.
S. I. Lee, Dudley, A. M., D. Drubin, P. A. Silver, N. Krogan, D. Pe’er and D. Koller (2009) Learning a Prior on Regulatory Potential from eQTL Data. PLoS Genet. 5:e1000358. PMID: 19180192 [PMCID: PMC2627940]
E. Snitkin, A. M. Dudley, D. M. Janse, K. Wong, G. M. Church and D. Segrè (2008) Model-driven analysis of experimentally determined growth phenotypes for 465 deletion mutants under 16 different conditions. Genome Biology 9:R140. PMID: 18808699 [PMCID: PMC2592718]Highly Accessed
S. I. Lee, D. Pe’er, A. M. Dudley, G. M. Church and D. Koller (2006) Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. PNAS 103:14062-7. PMID: 16968785 [PMCID: PMC1599912]
A. M. Dudley and D. L. Cardozo (2006) Introduction to biological research: a laboratory course. American Biology Teacher 68: 14-24.
A. M. Dudley, D. M. Janse, A. Tanay, R. Shamir, and G. M. Church (2005) A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Syst. Biol. msb4100004:E1. PMID: 16729036 [PMCID: PMC1681449]
O. D. King, J. C. Lee, A. M. Dudley, D. M. Janse, G. M. Church and F. P. Roth (2003) Predicting phenotype from patterns of annotation. Bioinformatics 19 (Suppl. 1): i183-9. PMID: 12855456
A. M. Dudley, J. Aach, M. A. Steffen and G. M. Church (2002) Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci USA 99:7554-9. PMID: 12032321 [PMCID: PMC124281]
A. M. Dudley, C. Rougeulle and F. Winston (1999) The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes & Dev. 13: 2940-45. PMID: 10580001 [PMCID: PMC317152]
A. M. Dudley, L. J. Gansheroff and F. Winston (1999) Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912δ promoter in Saccharomyces cerevisiae. Genetics 151: 1365-78. PMID: 10101163 [PMCID: PMC1460567]
J. M. Madison, A. M. Dudley and F. Winston (1998) Identification and analysis of MOT3, a zinc finger protein that binds to the retrotransposon Ty long terminal repeat (δ) in Saccharomyces cerevisiae. Mol. Cell. Biol. 18: 1879-90. PMID: 9528759 [PMCID: PMC121417]
J. L. Pinkham, A. M. Dudley and T. L. Mason (1994) T7 RNA polymerase-dependent expression of COXII in yeast mitochondria. Mol. Cell. Biol. 14: 4643-52. PMID: 8007968 [PMCID: PMC358837]
