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Modular epistasis and the compensatory evolution of gene deletion mutants.
Published in:
PLoS Genetics, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pgen.1007958
By:
- Rojas Echenique, José I.;
- Kryazhimskiy, Sergey;
- Nguyen Ba, Alex N.;
- Desai, Michael M.
Publication type:
Article
Evolthon: A community endeavor to evolve lab evolution.
Published in:
PLoS Biology, 2019, v. 17, n. 3, p. 1, doi. 10.1371/journal.pbio.3000182
By:
- Kaminski Strauss, Sivan;
- Schirman, Dvir;
- Jona, Ghil;
- Brooks, Aaron N.;
- Kunjapur, Aditya M.;
- Nguyen Ba, Alex N.;
- Flint, Alice;
- Solt, Andras;
- Mershin, Andreas;
- Dixit, Atray;
- Yona, Avihu H.;
- Csörgő, Bálint;
- Busby, Bede Phillip;
- Hennig, Bianca P.;
- Pál, Csaba;
- Schraivogel, Daniel;
- Schultz, Daniel;
- Wernick, David G.;
- Agashe, Deepa;
- Levi, Dikla
Publication type:
Article
Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.63910
By:
- Johnson, Milo S.;
- Gopalakrishnan, Shreyas;
- Goyal, Juhee;
- Dillingham, Megan E.;
- Bakerlee, Christopher W.;
- Humphrey, Parris T.;
- Jagdish, Tanush;
- Jerison, Elizabeth R.;
- Kosheleva, Katya;
- Lawrence, Katherine R.;
- Jiseon Min;
- Moulana, Alief;
- Phillips, Angela M.;
- Piper, Julia C.;
- Purkanti, Ramya;
- Rego-Costa, Artur;
- McDonald, Michael J.;
- Nguyen Ba, Alex N.;
- Desai, Michael M.
Publication type:
Article
Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast.
Published in:
eLife, 2022, p. 1, doi. 10.7554/eLife.73983
By:
- Nguyen Ba, Alex N.;
- Lawrence, Katherine R.;
- Rego-Costa, Artur;
- Gopalakrishnan, Shreyas;
- Temko, Daniel;
- Michor, Franziska;
- Desai, Michael M.
Publication type:
Article
Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.70918
By:
- Bakerlee, Christopher W.;
- Phillips, Angela M.;
- Ba, Alex N. Nguyen;
- Desai, Michael M.
Publication type:
Article
A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes.
Published in:
Molecular Biology & Evolution, 2014, v. 31, n. 4, p. 872
By:
- Bergström, Anders;
- Simpson, Jared T.;
- Salinas, Francisco;
- Barré, Benjamin;
- Parts, Leopold;
- Zia, Amin;
- Nguyen Ba, Alex N.;
- Moses, Alan M.;
- Louis, Edward J.;
- Mustonen, Ville;
- Warringer, Jonas;
- Durbin, Richard;
- Liti, Gianni
Publication type:
Article
The genetic basis of differential autodiploidization in evolving yeast populations.
Published in:
G3: Genes | Genomes | Genetics, 2021, v. 11, n. 8, p. 1, doi. 10.1093/g3journal/jkab192
By:
- Tung, Sudipta;
- Bakerlee, Christopher W.;
- Phillips, Angela M.;
- Ba, Alex N. Nguyen;
- Desai, Michael M.
Publication type:
Article
Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library.
Published in:
G3: Genes | Genomes | Genetics, 2017, v. 7, n. 3, p. 911, doi. 10.1534/g3.116.038471
By:
- Ji-Young Youn;
- Friesen, Helena;
- Nguyen Ba, Alex N.;
- Wendy Liang;
- Messier, Vincent;
- Cox, Mike J.;
- Moses, Alan M.;
- Andrews, Brenda
Publication type:
Article
Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences.
Published in:
PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003977
By:
- Nguyen Ba, Alex N.;
- Strome, Bob;
- Hua, Jun Jie;
- Desmond, Jonathan;
- Gagnon-Arsenault, Isabelle;
- Weiss, Eric L.;
- Landry, Christian R.;
- Moses, Alan M.
Publication type:
Article
Minimum information and guidelines for reporting a multiplexed assay of variant effect.
Published in:
Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03223-9
By:
- Claussnitzer, Melina;
- Parikh, Victoria N.;
- Wagner, Alex H.;
- Arbesfeld, Jeremy A.;
- Bult, Carol J.;
- Firth, Helen V.;
- Muffley, Lara A.;
- Nguyen Ba, Alex N.;
- Riehle, Kevin;
- Roth, Frederick P.;
- Tabet, Daniel;
- Bolognesi, Benedetta;
- Glazer, Andrew M.;
- Rubin, Alan F.
Publication type:
Article
A quantitative literature-curated gold standard for kinase-substrate pairs.
Published in:
Genome Biology, 2011, v. 12, n. 4, p. 1, doi. 10.1186/gb-2011-12-4-r39
By:
- Sharifpoor, Sara;
- Nguyen Ba, Alex N.;
- Ji-Young Young;
- Van Dyk, Dewald;
- Friesen, Helena;
- Douglas, Alison C.;
- Kurat, Christoph F.;
- Chong, Yolanda T.;
- Founk, Karen;
- Moses, Alan M.;
- Andrews, Brenda J.
Publication type:
Article
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.
Published in:
Genome Biology & Evolution, 2015, v. 7, n. 6, p. 1815, doi. 10.1093/gbe/evv105
By:
- Khan, Tahsin;
- Douglas, Gavin M.;
- Patel, Priyenbhai;
- Ba, Alex N. Nguyen;
- Moses, Alan M.
Publication type:
Article
Evolution of Characterized Phosphorylation Sites in Budding Yeast.
Published in:
Molecular Biology & Evolution, 2010, v. 27, n. 9, p. 2027, doi. 10.1093/molbev/msq090
By:
- Nguyen Ba, Alex N.;
- Moses, Alan M.
Publication type:
Article
Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes.
Published in:
MicrobiologyOpen, 2020, v. 9, n. 2, p. 1, doi. 10.1002/mbo3.968
By:
- Pham, Jenny Y.;
- Ogbunugafor, C. Brandon;
- Nguyen Ba, Alex N.;
- Hartl, Daniel L.
Publication type:
Article
The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism.
Published in:
PLoS Biology, 2015, v. 13, n. 5, p. 1, doi. 10.1371/journal.pbio.1002146
By:
- Gógl, Gergő;
- Schneider, Kyle D.;
- Yeh, Brian J.;
- Alam, Nashida;
- Nguyen Ba, Alex N.;
- Moses, Alan M.;
- Hetényi, Csaba;
- Reményi, Attila;
- Weiss, Eric L.
Publication type:
Article
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-69
By:
- Liti, Gianni;
- Nguyen Ba, Alex N.;
- Blythe, Martin;
- Müller, Carolin A.;
- Bergström, Anders;
- Cubillos, Francisco A.;
- Dafhnis-Calas, Felix;
- Khoshraftar, Shima;
- Malla, Sunir;
- Mehta, Neel;
- Siow, Cheuk C.;
- Warringer, Jonas;
- Moses, Alan M.;
- Louis, Edward J.;
- Nieduszynski, Conrad A.
Publication type:
Article
Predicting kinase substrates using conservation of local motif density.
Published in:
Bioinformatics, 2012, v. 28, n. 7, p. 962, doi. 10.1093/bioinformatics/bts060
By:
- Lai, Andy C. W.;
- Nguyen Ba, Alex N.;
- Moses, Alan M.
Publication type:
Article
Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions.
Published in:
Science Signaling, 2012, v. 5, n. 215, p. 1, doi. 10.1126/scisignal.2002515
By:
- Ba, Alex N. Nguyen;
- Yeh, Brian J.;
- van Dyk, Dewald;
- Davidson, Alan R.;
- Andrews, Brenda J.;
- Weiss, Eric L.;
- Moses, Alan M.
Publication type:
Article
Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments.
Published in:
PLoS Genetics, 2017, v. 13, n. 4, p. 1, doi. 10.1371/journal.pgen.1006735
By:
- Nguyen Ba, Alex N.;
- Strome, Bob;
- Osman, Selma;
- Legere, Elizabeth-Ann;
- Zarin, Taraneh;
- Moses, Alan M.
Publication type:
Article

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