Baryshnikova Lab


 

Publications


 

Main research papers

  1. 2013: Baryshnikova A, Vandersluis B, Costanzo M, Myers CL, Cha RS, Andrews B, Boone C, “Global linkage map connects meiotic centromere function to chromosome size in budding yeast”, G3: Genes, Genomes, Genetics, 3(10):1741-1751
    Pubmed - PDF - Supplementary website - Video (15 min)
  2. 2010: Costanzo M*, Baryshnikova A*, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C, “The genetic landscape of a cell”, Science, 327:425-31
    Pubmed - PDF - Supplementary website
  3. 2010: Baryshnikova A*, Costanzo M*, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL, “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale”, Nat Methods, 7(12):1017-24
    Pubmed - PDF - Supplementary website
* These authors contributed equally to this work.

 

Collaborations

  1. 2014: Rogers JV, McMahon C, Baryshnikova A, Hughson FM, Rose MD, “ER-associated retrograde SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic ER fusion pathway”, Mol Biol Cell, 25(21):3401-3412
    Pubmed
  2. 2013: Vizeacoumar FJ, Arnold R, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J, “A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities”, Mol Syst Biol, 9:696
    Pubmed
  3. 2013: Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone C, Parts L, “SGAtools: one-stop analysis and visualization of array based genetic interaction screens”, Nucleic Acids Research, Epub
  4. 2012: Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin X-Y, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmuller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow N, Costanzo M, Gingras A-C, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C, “Global gene deletion analysis exploring yeast filamentous growth”, Science, 337:1353-1356
    Pubmed
  5. 2012: Cheng E, Vaisica JA, Ou J, Baryshnikova A, Lu Y, Roth FP, Brown GW, “Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae, Genetics, 192(1):147-160
    Pubmed
  6. 2012: Kaluarachchi-Duffy S, Friesen H, Lambert JP, Baryshnikova A, Chong YT, Figeys D, Boone C, Andrews BJ, “Exploring the yeast acetylome using functional genomics”, Cell, 149(4):936-948
    Pubmed
  7. 2012: Tan CM, Therien AG, Lu J, Lee SH, Caron A, Gill CJ, Lebeau-Jacob C, Benton-Perdomo L, Monteiro JM, Pereira PM, Eisen NL, Wu J, Deschamps K, Petcu M, Wong S, Daigneault E, Kramer S, Liang L, Maxwell E, Claveau D, Vaillancourt J, Skorey K, Tam J, Wang H, Meredith TC, Sillaots S, Wang-Jarantow L, Ramtohul Y, Langlois E, Landry F, Reid JC, Parthasarathy G, Sharma S, Baryshnikova A, Lum KJ, Pinho MG, Soisson SM, Roemer T, “Restoring methicillin-resistant Staphylococcus aureus susceptibility to b-lactam antibiotics”, Sci Transl Med, 4(126):126-135
    Pubmed
  8. 2012: Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, VaderSluis B, Myers CL, Papp B, Boone C, Andrews BJ, “Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs”, Genome Res, 22(4):791-801
    Pubmed
  9. 2011: Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP, “Systematic exploration of synergistic drug pairs”, Mol Syst Biol, 7:544
    Pubmed
  10. 2011: Lissina E, Young B, Urbanus ML, Guan XL, Lowenson J, Hoon S, Baryshnikova A, Riezman I, Michaut M, Bader G, Riezman H, Cowen L, Wenk MR, Clarke S, Giaever G, Nislow C, “A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis”, PLoS Genet, 7(10):e1002332
    Pubmed
  11. 2011: Szappanos B, Kovacs K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pal C, Papp B, “An integrated approach to characterize genetic interaction networks in yeast metabolism”, Nat Genet, 43(7):656-662
    Pubmed
  12. 2011: Vaisica JA, Baryshnikova A, Costanzo M, Boone C, Brown GW, “Mms1 and Mms22 stabilize the replisome during replication stress”, Mol Biol Cell, 22(13):2396-2408
    Pubmed
  13. 2011: Magtanong L, Ho CH, Barker SL, Jiao W, Baryshnikova A, Bahr S, Smith AM, Heisler LE, Choy JS, Kuzmin E, Andrusiak K, Kobylianski A, Li Z, Costanzo M, Basrai MA, Giaever G, Nislow C, Andrews B, Boone C, “Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell”, Nat Biotechnol, 29(6):505-511
    Pubmed
  14. 2011: Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C, “Systematic exploration of essential yeast gene function with temperature-sensitive mutants”, Nat Biotechnol, 29(4):361-367
    Pubmed
  15. 2011: Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD, “Protein complexes are central in the yeast genetic landscape”, PLoS Comput Biol, 7(2):e1001092
    Pubmed
  16. 2010: VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL, “Genetic interactions reveal the evolutionary trajectories of duplicate genes”, Mol Syst Biol, 6:429
    Pubmed
  17. 2010: Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C, “DRYGIN: a database of quantitative genetic interaction networks in yeast”, Nucleic Acids Res, 38(Database issue):D502-7
    Pubmed
  18. 2008: Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C, “Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes”, Proc Natl Acad Sci U S A, 105(43):16653-8
    Pubmed
  19. 2007: Chiolo I, Saponaro M, Baryshnikova A, Kim JH, Seo YS, Liberi G, “The human F-Box DNA helicase FBH1 faces Saccharomyces cerevisiae Srs2 and postreplication repair pathway roles”, Mol Cell Biol, 27(21):7439-50
    Pubmed
  20. 2005: Liberi G, Maffioletti G, Lucca C, Chiolo I, Baryshnikova A, Cotta-Ramusino C, Lopes M, Pellicioli A, Haber JE, Foiani M, “Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase”, Genes Dev, 19(3):339-50
    Pubmed

 

Reviews & book chapters

  1. 2014: Kuzmin E, Sharifpoor S, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, “Synthetic genetic array analysis for global mapping of genetic networks in yeast”, Methods Mol Biol, 1205:143-168
    Pubmed
  2. 2013: Baryshnikova A, Costanzo M, Myers CL, Andrews B, Boone C, “Genetic Interaction Networks: Toward an Understanding of Heritability”, Annu Rev Genomics Hum Genet, 14:8.1-8.23
    Pubmed - PDF
  3. 2012: Costanzo M, Baryshnikova A, VanderSluis B, Andrews B, Myers CL, Boone C, “Genetic Networks”, in “Handbook of Systems Biology - Concepts and Insights”, edited by Dekker J, Vidal M, Walhout AJM
    Offline
  4. 2012: Baryshnikova A, Andrews B, “Neighboring-gene effect: a genetic uncertainty principle”, Nat Methods, 9(4):341
    Pubmed - PDF
  5. 2011: Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C, “Charting the genetic interaction map of a cell”, Curr Opin Biotechnol, 22(1):66-74
    Pubmed - PDF
  6. 2011: Ho CH, Piotrowski J, Dixon SJ, Baryshnikova A, Costanzo M, Boone C, “Combining functional genomics and genomical biology to identify targets of bioactive compounds”, Curr Opin Chem Biol, 15(1):66-78
    Pubmed - PDF
  7. 2010: Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C, “Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe, Methods Enzymol, 470:145-179
    Pubmed - PDF
  8. 2009: Costanzo M, Baryshnikova A, Nislow C, Andrews B, Boone C, “You too can play with an edge”, Nat Methods., 6(11):797-8
    Pubmed - PDF
  9. 2009: Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C, “Systematic mapping of genetic interaction networks”, Annu Rev Genet., 43:601-25
    Pubmed - PDF