Alex Nguyen Ba
Assistant Professor
Campus
UTM
CSB Appointment
Full
Research Areas
Bioinformatics / Computational Biology, Biotechnology, Evolutionary Biology, Genetics / Genomics, Quantitative Biology /Modelling, Systems Biology
Education
Ph.D. University of Toronto 2014
B.Sc. University of Toronto 2009
Primary Undergraduate Department
Biology, UTM
Graduate Programs
Cell & Systems Biology
Research Description
We are a group of experimental biologists, computer scientists, and physicists broadly interested in quantitative genetics and evolution. We use high-throughput and high-resolution approaches to tackle the big questions in these fields by building on the latest advances in synthetic biology and computer science. Projects aim to develop new technologies to comprehensively explore the mutational landscape of cells and understand what evolution acts on. We work closely with theorists and statistical biologists to leverage the vast amount of information that can now be produced using high-throughput robotic liquid handling and next-generation sequencing techniques. Our research has implications in precision medicine, vaccine design, and more broadly, microbial evolution.
Contact Information
Office: SB 3016
Lab: SB 3067
Email
Mailing Address
Department of Biology, UTM
3359 Mississauga Road
Mississauga, ON L5L 1C6
Canada
Publications
2022
Idiosyncratic epistasis leads to global fitness–correlated trends
Bakerlee CW, Nguyen Ba AN, Shulgina Y, Rojas Echenique JI, Desai MM
2022, Science, 10.1126/science.abm4774
2020
Chance and necessity in the pleiotropic consequences of adaptation for budding yeast
Jerison ER, Nguyen Ba AN, Desai MM, Kryazhimskiy S
2020, Nature Ecology & Evolution, 10.1038/s41559-020-1128-3
Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials
Zulauf KE, Green AB, Nguyen Ba AN, Jagdish T, Reif D, Seeley R, Dale A, Kirby JE, Bonomo RA
2020, mBio, 10.1128/mBio.00997-20
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu M, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C
2020, Science, 10.1126/science.aaz5667
2019
Modular epistasis and the compensatory evolution of gene deletion mutants
Butler G, Rojas Echenique JI, Kryazhimskiy S, Nguyen Ba AN, Desai MM
2019, PLOS Genetics, 10.1371/journal.pgen.1007958
Evolthon: A community endeavor to evolve lab evolution
Hurst LD, Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y
2019, PLOS Biology, 10.1371/journal.pbio.3000182
Proteome-wide signatures of function in highly diverged intrinsically disordered regions
Zarin T, Strome B, Nguyen Ba AN, Alberti S, Forman-Kay JD, Moses AM
2019, eLife, 10.7554/eLife.46883
High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast
Nguyen Ba AN, Cvijović I, Rojas Echenique JI, Lawrence KR, Rego-Costa A, Liu X, Levy SF, Desai MM
2019, Nature, 10.1038/s41586-019-1749-3
Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes
Pham JY, Ogbunugafor CB, Nguyen Ba AN, Hartl DL
2019, MicrobiologyOpen, 10.1002/mbo3.968
2018
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity
Strome B, Hsu IS, Li Cheong Man M, Zarin T, Nguyen Ba A, Moses AM
2018, BMC Systems Biology, 10.1186/s12918-018-0597-3
Experimental Studies of Evolutionary Dynamics in Microbes
Cvijović I, Nguyen Ba AN, Desai MM
2018, Trends in Genetics, 10.1016/j.tig.2018.06.004
2017
Selection maintains signaling function of a highly diverged intrinsically disordered region
Zarin T, Tsai CN, Nguyen Ba AN, Moses AM
2017, Proceedings of the National Academy of Sciences, 10.1073/pnas.1614787114
Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library
Youn J, Friesen H, Nguyen Ba AN, Liang W, Messier V, Cox MJ, Moses AM, Andrews B
2017, G3: Genes|Genomes|Genetics, 10.1534/g3.116.038471
Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments
Fay JC, Nguyen Ba AN, Strome B, Osman S, Legere E, Zarin T, Moses AM
2017, PLOS Genetics, 10.1371/journal.pgen.1006735
2015
The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism
Tyers M, Gógl G, Schneider KD, Yeh BJ, Alam N, Nguyen Ba AN, Moses AM, Hetényi C, Reményi A, Weiss EL
2015, PLOS Biology, 10.1371/journal.pbio.1002146
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions
Khan T, Douglas GM, Patel P, Nguyen Ba AN, Moses AM
2015, Genome Biology and Evolution, 10.1093/gbe/evv105
2014
A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes
Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G
2014, Molecular Biology and Evolution, 10.1093/molbev/msu037
A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes
Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G
2014, Molecular Biology and Evolution, 10.1093/molbev/msu037
Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
van de Peer Y, Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM
2014, PLoS Computational Biology, 10.1371/journal.pcbi.1003977