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1.

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.

Venkataram, Sandeep; Dunn, Barbara; Li, Yuping; Agarwala, Atish; Chang, Jessica; Ebel, Emily R; Geiler-Samerotte, Kerry; Hérissant, Lucas; Blundell, Jamie R; Levy, Sasha F; Fisher, Daniel S; Sherlock, Gavin; Petrov, Dmitri A.

Cell; 166(6): 1585-1596.e22, 2016 Sep 08.

Artículo en Inglés | MEDLINE | ID: mdl-27594428

2.

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.

Li, Weiyi; Miller, Darach; Liu, Xianan; Tosi, Lorenzo; Chkaiban, Lamia; Mei, Han; Hung, Po-Hsiang; Parekkadan, Biju; Sherlock, Gavin; Levy, Sasha F.

Nucleic Acids Res; 52(10): e47, 2024 Jun 10.

Artículo en Inglés | MEDLINE | ID: mdl-38709890

3.

High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast.

Nguyen Ba, Alex N; Cvijovic, Ivana; Rojas Echenique, José I; Lawrence, Katherine R; Rego-Costa, Artur; Liu, Xianan; Levy, Sasha F; Desai, Michael M.

Nature; 575(7783): 494-499, 2019 11.

Artículo en Inglés | MEDLINE | ID: mdl-31723263

4.

Gene Architectures that Minimize Cost of Gene Expression.

Frumkin, Idan; Schirman, Dvir; Rotman, Aviv; Li, Fangfei; Zahavi, Liron; Mordret, Ernest; Asraf, Omer; Wu, Song; Levy, Sasha F; Pilpel, Yitzhak.

Mol Cell; 65(1): 142-153, 2017 Jan 05.

Artículo en Inglés | MEDLINE | ID: mdl-27989436

5.

Gene architectures that minimize cost of gene expression.

Frumkin, Idan; Schirman, Dvir; Rotman, Aviv; Li, Fangfei; Zahavi, Liron; Mordret, Ernest; Asraf, Omer; Wu, Song; Levy, Sasha F; Pilpel, Yitzhak.

Mol Cell; 81(11): 2494, 2021 Jun 03.

Artículo en Inglés | MEDLINE | ID: mdl-34087180

6.

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments.

Jaffe, Mia; Dziulko, Adam; Smith, Justin D; St Onge, Robert P; Levy, Sasha F; Sherlock, Gavin.

Genome Res; 29(4): 668-681, 2019 04.

Artículo en Inglés | MEDLINE | ID: mdl-30782640

7.

The genotype-phenotype landscape of an allosteric protein.

Tack, Drew S; Tonner, Peter D; Pressman, Abe; Olson, Nathan D; Levy, Sasha F; Romantseva, Eugenia F; Alperovich, Nina; Vasilyeva, Olga; Ross, David.

Mol Syst Biol; 17(3): e10179, 2021 03.

Artículo en Inglés | MEDLINE | ID: mdl-33784029

8.

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation.

Lauer, Stephanie; Avecilla, Grace; Spealman, Pieter; Sethia, Gunjan; Brandt, Nathan; Levy, Sasha F; Gresham, David.

PLoS Biol; 16(12): e3000069, 2018 12.

Artículo en Inglés | MEDLINE | ID: mdl-30562346

9.

Quantitative evolutionary dynamics using high-resolution lineage tracking.

Levy, Sasha F; Blundell, Jamie R; Venkataram, Sandeep; Petrov, Dmitri A; Fisher, Daniel S; Sherlock, Gavin.

Nature; 519(7542): 181-6, 2015 Mar 12.

Artículo en Inglés | MEDLINE | ID: mdl-25731169

10.

Bartender: a fast and accurate clustering algorithm to count barcode reads.

Zhao, Lu; Liu, Zhimin; Levy, Sasha F; Wu, Song.

Bioinformatics; 34(5): 739-747, 2018 03 01.

Artículo en Inglés | MEDLINE | ID: mdl-29069318

11.

A method for high-throughput production of sequence-verified DNA libraries and strain collections.

Smith, Justin D; Schlecht, Ulrich; Xu, Weihong; Suresh, Sundari; Horecka, Joe; Proctor, Michael J; Aiyar, Raeka S; Bennett, Richard A O; Chu, Angela; Li, Yong Fuga; Roy, Kevin; Davis, Ronald W; Steinmetz, Lars M; Hyman, Richard W; Levy, Sasha F; St Onge, Robert P.

Mol Syst Biol; 13(2): 913, 2017 02 13.

Artículo en Inglés | MEDLINE | ID: mdl-28193641

12.

The genotype-phenotype landscape of an allosteric protein.

Tack, Drew S; Tonner, Peter D; Pressman, Abe; Olson, Nathan D; Levy, Sasha F; Romantseva, Eugenia F; Alperovich, Nina; Vasilyeva, Olga; Ross, David.

Mol Syst Biol; 17(12): e10847, 2021 Dec.

Artículo en Inglés | MEDLINE | ID: mdl-34913592

13.

Histone variant HTZ1 shows extensive epistasis with, but does not increase robustness to, new mutations.

Richardson, Joshua B; Uppendahl, Locke D; Traficante, Maria K; Levy, Sasha F; Siegal, Mark L.

PLoS Genet; 9(8): e1003733, 2013.

Artículo en Inglés | MEDLINE | ID: mdl-23990806

14.

Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant.

Levy, Sasha F; Ziv, Naomi; Siegal, Mark L.

PLoS Biol; 10(5): e1001325, 2012.

Artículo en Inglés | MEDLINE | ID: mdl-22589700

15.

Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.

Blundell, Jamie R; Levy, Sasha F.

Genomics; 104(6 Pt A): 417-30, 2014 Dec.

Artículo en Inglés | MEDLINE | ID: mdl-25260907

16.

Genome-scale analysis of interactions between genetic perturbations and natural variation.

Hale, Joseph J; Matsui, Takeshi; Goldstein, Ilan; Mullis, Martin N; Roy, Kevin R; Ville, Chris Ne; Miller, Darach; Wang, Charley; Reynolds, Trevor; Steinmetz, Lars M; Levy, Sasha F; Ehrenreich, Ian M.

bioRxiv; 2024 Jan 16.

Artículo en Inglés | MEDLINE | ID: mdl-38293072

17.

Genome-scale analysis of interactions between genetic perturbations and natural variation.

Hale, Joseph J; Matsui, Takeshi; Goldstein, Ilan; Mullis, Martin N; Roy, Kevin R; Ville, Christopher Ne; Miller, Darach; Wang, Charley; Reynolds, Trevor; Steinmetz, Lars M; Levy, Sasha F; Ehrenreich, Ian M.

Nat Commun; 15(1): 4234, 2024 May 18.

Artículo en Inglés | MEDLINE | ID: mdl-38762544

18.

Precision engineering of biological function with large-scale measurements and machine learning.

Tack, Drew S; Tonner, Peter D; Pressman, Abe; Olson, Nathan D; Levy, Sasha F; Romantseva, Eugenia F; Alperovich, Nina; Vasilyeva, Olga; Ross, David.

PLoS One; 18(3): e0283548, 2023.

Artículo en Inglés | MEDLINE | ID: mdl-36989327

19.

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.

Li, Weiyi; Miller, Darach; Liu, Xianan; Tosi, Lorenzo; Chkaiban, Lamia; Mei, Han; Hung, Po-Hsiang; Parekkadan, Biju; Sherlock, Gavin; Levy, Sasha F.

bioRxiv; 2023 Oct 18.

Artículo en Inglés | MEDLINE | ID: mdl-37873145

20.

The robustness continuum.

Levy, Sasha F; Siegal, Mark L.

Adv Exp Med Biol; 751: 431-52, 2012.

Artículo en Inglés | MEDLINE | ID: mdl-22821470

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Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.

High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast.

Gene Architectures that Minimize Cost of Gene Expression.

Gene architectures that minimize cost of gene expression.

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments.

The genotype-phenotype landscape of an allosteric protein.

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation.

Quantitative evolutionary dynamics using high-resolution lineage tracking.

Bartender: a fast and accurate clustering algorithm to count barcode reads.

A method for high-throughput production of sequence-verified DNA libraries and strain collections.

The genotype-phenotype landscape of an allosteric protein.

Histone variant HTZ1 shows extensive epistasis with, but does not increase robustness to, new mutations.

Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant.

Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.

Genome-scale analysis of interactions between genetic perturbations and natural variation.

Genome-scale analysis of interactions between genetic perturbations and natural variation.

Precision engineering of biological function with large-scale measurements and machine learning.

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.

The robustness continuum.