Professor Alex Nguyen Ba

Alex Nguyen Ba

Assistant Professor


Campus

UTM

CSB Appointment

Full

Research Areas

Evolutionary Biology, Genetics / Genomics, 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

To what extent can we predict quantitative phenotypes based on genotype? Consider the thousands of mutations that differentiate two individuals in the human population: these at least partly determine heritable phenotypes. Some make families susceptible to disease such as cancer. Mutations affect phenotype by perturbing the underlying cellular network: they can alter 1) enzymatic quality of proteins, 2) gene expression, and 3) protein folding amongst others. We seek to understand how the interconnected network of the cell is affected by small tweaks in the ‘knobs’ that determine differences between individuals and therefore are acted on by evolutionary forces.
Are genetic diseases the collective ‘disarrangement’ of these knobs? Can we understand and predict the effects of mutations at the global scale? Getting at these questions requires comprehensive measurements of the cell at extremely large scale. 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

Lab: DV 4090
Email

Mailing Address

Department of Biology, UTM
3359 Mississauga Road
Mississauga, ON L5L 1C6
Canada

Visit lab’s website


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

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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

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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

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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

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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

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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

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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

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2012

Predicting kinase substrates using conservation of local motif density

Lai ACW, Nguyen Ba AN, Moses AM
2012, Bioinformatics, 10.1093/bioinformatics/bts060

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