Franco Vizeacoumar Ph.D.
Guihong Tan at his lab bench.
Matej Usaj in the computer server room..
Front view of the S&P Robotics BioMatrix.
2024
Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle
Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ.
Cell. 2024 Mar 14;187(6):1490-1507.e21. doi: 10.1016/j.cell.2024.02.014. Epub 2024 Mar 6.
K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ).
Garadi Suresh H, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, Masinas MPD, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ.
Mol Cell. 2024 Jun 20;84(12):2337-2352.e9. doi: 10.1016/j.molcel.2024.05.018. Epub 2024 Jun 12.
Expanding TheCellVision.org: a central repository for visualizing and mining high-content cell imaging projects
Myra Paz David Masinas, Athanasios Litsios, Anastasia Razdaibiedina, Matej Usaj, Charles Boone, Brenda J Andrews
Genetics. 2024 May; 227(1): iyae044. Published online 2024 Mar 22. doi: 10.1093/genetics/iyae044
PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data.
Anastasia Razdaibiedina, Alexander Brechalov, Helena Friesen, Mojca Mattiazzi Usaj, Myra Paz David Masinas, Harsha Garadi Suresh, Kyle Wang, Charles Boone, Jimmy Ba, Brenda Andrews
Mol Syst Biol. 2024 May; 20(5): 521–548. Published online 2024 Mar 12. doi: 10.1038/s44320-024-00029-6
A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds.
Lin K, Chang YC, Billmann M, Ward HN, Le K, Hassan AZ, Bhojoo U, Chan K, Costanzo M, Moffat J, Boone C, Bielinsky AK, Myers CL.
Sci Rep. 2024 Jan 30;14(1):2508. doi: 10.1038/s41598-024-51735-y.
Direct structural analysis of a single acyl carrier protein domain in fatty acid synthase from the fungus Saccharomyces cerevisiae.
Samani EK, Chen AC, Lou JW, Dai DL, Keszei AFA, Tan G, Boone C, Grininger M, Mazhab-Jafari MT.
Commun Biol. 2024 Jan 12;7(1):92. doi: 10.1038/s42003-024-05777-7.
2023
N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity.
Varland S, Silva RD, Kjosås I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, Osberg C, Chan K, Zhang X, Tong AHY, Andreazza S, Lee JJ, Nedyalkova L, Ušaj M, Whitworth AJ, Andrews BJ, Moffat J, Myers CL, Gevaert K, Boone C, Martinho RG, Arnesen T.
Nat Commun. 2023 Oct 27;14(1):6774. doi: 10.1038/s41467-023-42342-y.
Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability.
Mishra PK, Au WC, Castineira PG, Ali N, Stanton J, Boeckmann L, Takahashi Y, Costanzo M, Boone C, Bloom KS, Thorpe PH, Basrai MA.
Mol Biol Cell. 2023 Sep 1;34(10):ar99. doi: 10.1091/mbc.E23-03-0108. Epub 2023 Jul 12.
Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity.
Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Fallah S, Sanchez H, Skulska I, Ušaj MM, Safizadeh H, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras AC, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, Cowen LE.
Cell Chem Biol. 2023 Jul 20;30(7):795-810.e8. doi: 10.1016/j.chembiol.2023.06.005. Epub 2023 Jun 26.
Reproducibility metrics for context-specific CRISPR screens.
Billmann M, Ward HN, Aregger M, Costanzo M, Andrews BJ, Boone C, Moffat J, Myers CL.
Cell Syst. 2023 May 17;14(5):418-422.e2. doi: 10.1016/j.cels.2023.04.003.
The proteomic landscape of genome-wide genetic perturbations.
Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Röhl A, Herrera-Domínguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mülleder M, Lilley KS, Boone C, Kustatscher G, Ralser M.
Cell. 2023 Apr 27;186(9):2018-2034.e21. doi: 10.1016/j.cell.2023.03.026. Epub 2023 Apr 19.
2022
Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux.
Masud SN, Chandrashekhar M, Aregger M, Tan G, Zhang X, Mero P, Pirman DA, Zaslaver O, Smolen GA, Lin ZY, Wong CJ, Boone C, Gingras AC, Montenegro-Burke JR, Moffat J.
Nat Chem Biol. 2022 Dec;18(12):1370-1379. doi: 10.1038/s41589-022-01109-0. Epub 2022 Aug 15.
Context-dependent regulation of ferroptosis sensitivity.
Magtanong L, Mueller GD, Williams KJ, Billmann M, Chan K, Armenta DA, Pope LE, Moffat J, Boone C, Myers CL, Olzmann JA, Bensinger SJ, Dixon SJ.
Cell Chem Biol. 2022 Oct 20;29(10):1568. doi: 10.1016/j.chembiol.2022.08.008.
BIONIC: biological network integration using convolutions.
Forster DT, Li SC, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas LAV, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B, Bader GD, Boone C.
Nat Methods. 2022 Oct;19(10):1250-1261. doi: 10.1038/s41592-022-01616-x. Epub 2022 Oct 3.
Repression of essential cell cycle genes increases cellular fitness.
Conti MM, Ghizzoni JM, Gil-Bona A, Wang W, Costanzo M, Li R, Flynn MJ, Zhu LJ, Myers CL, Boone C, Andrews BJ, Benanti JA.
PLoS Genet. 2022 Aug 29;18(8):e1010349. doi: 10.1371/journal.pgen.1010349. eCollection 2022 Aug.
Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG.
Berg MD, Zhu Y, Loll-Krippleber R, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ.
G3 (Bethesda). 2022 Jul 6;12(7):jkac125. doi: 10.1093/g3journal/jkac125.
Phenylboronic Ester-Activated Aryl Iodide-Selective Buchwald-Hartwig-Type Amination toward Bioactivity Assay.
Dhital RN, Sen A, Hu H, Ishii R, Sato T, Yashiroda Y, Kimura H, Boone C, Yoshida M, Futamura Y, Hirano H, Osada H, Hashizume D, Uozumi Y, Yamada YMA.
ACS Omega. 2022 Jul 1;7(28):24184-24189. doi: 10.1021/acsomega.2c01092. eCollection 2022 Jul 19.
High-Throughput Chemical Screen Identifies a 2,5-Disubstituted Pyridine as an Inhibitor of Candida albicans Erg11.
Du Bois AC, Xue A, Pham C, Revie NM, Meyer KJ, Yashiroda Y, Boone C, Nodwell JR, Stogios P, Savchenko A, Robbins N, Iyer KR, Cowen LE.
mSphere. 2022 Jun 29;7(3):e0007522. doi: 10.1128/msphere.00075-22. Epub 2022 May 9.
Targeting fungal membrane homeostasis with imidazopyrazoindoles impairs azole resistance and biofilm formation.
Revie NM, Iyer KR, Maxson ME, Zhang J, Yan S, Fernandes CM, Meyer KJ, Chen X, Skulska I, Fogal M, Sanchez H, Hossain S, Li S, Yashiroda Y, Hirano H, Yoshida M, Osada H, Boone C, Shapiro RS, Andes DR, Wright GD, Nodwell JR, Del Poeta M, Burke MD, Whitesell L, Robbins N, Cowen LE.
Nat Commun. 2022 Jun 25;13(1):3634. doi: 10.1038/s41467-022-31308-1.
Clionamines stimulate autophagy, inhibit Mycobacterium tuberculosis survival in macrophages, and target Pik1.
Persaud R, Li SC, Chao JD, Forestieri R, Donohue E, Balgi AD, Zheng X, Chao JT, Yashiroda Y, Yoshimura M, Loewen CJR, Gingras AC, Boone C, Av-Gay Y, Roberge M, Andersen RJ.
Cell Chem Biol. 2022 May 19;29(5):870-882.e11. doi: 10.1016/j.chembiol.2021.07.017. Epub 2021 Sep 13.
Jerveratrum-Type Steroidal Alkaloids Inhibit β-1,6-Glucan Biosynthesis in Fungal Cell Walls.
Kubo K, Itto-Nakama K, Ohnuki S, Yashiroda Y, Li SC, Kimura H, Kawamura Y, Shimamoto Y, Tominaga KI, Yamanaka D, Adachi Y, Takashima S, Noda Y, Boone C, Ohya Y.
Microbiol Spectr. 2022 Feb 23;10(1):e0087321. doi: 10.1128/spectrum.00873-21. Epub 2022 Jan 12.
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds.
Ohnuki S, Ogawa I, Itto-Nakama K, Lu F, Ranjan A, Kabbage M, Gebre AA, Yamashita M, Li SC, Yashiroda Y, Yoshida S, Usui T, Piotrowski JS, Andrews BJ, Boone C, Brown GW, Ralph J, Ohya Y.
NPJ Syst Biol Appl. 2022 Jan 27;8(1):3. doi: 10.1038/s41540-022-00212-1.
2021
Tubulin isotypes optimize distinct spindle positioning mechanisms during yeast mitosis.
Nsamba ET, Bera A, Costanzo M, Boone C, Gupta ML.
J Cell Biol. 2021 Dec 6;220(12):e202010155. doi: 10.1083/jcb.202010155. Epub 2021 Nov 5.
Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.
Fu C, Zhang X, Veri AO, Iyer KR, Lash E, Xue A, Yan H, Revie NM, Wong C, Lin ZY, Polvi EJ, Liston SD, VanderSluis B, Hou J, Yashiroda Y, Gingras AC, Boone C, O'Meara TR, O'Meara MJ, Noble S, Robbins N, Myers CL, Cowen LE.
Nat Commun. 2021 Nov 11;12(1):6497. doi: 10.1038/s41467-021-26850-3.
The amino acid substitution affects cellular response to mistranslation.
Berg MD, Zhu Y, Ruiz BY, Loll-Krippleber R, Isaacson J, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ.
G3 (Bethesda). 2021 Sep 27;11(10):jkab218. doi: 10.1093/g3journal/jkab218.
Improving Measures of Chemical Structural Similarity Using Machine Learning on Chemical-Genetic Interactions.
Safizadeh H, Simpkins SW, Nelson J, Li SC, Piotrowski JS, Yoshimura M, Yashiroda Y, Hirano H, Osada H, Yoshida M, Boone C, Myers CL.
J Chem Inf Model. 2021 Sep 27;61(9):4156-4172. doi: 10.1021/acs.jcim.0c00993. Epub 2021 Jul 28.
Genome-wide screening of genes associated with momilactone B sensitivity in the fission yeast Schizosaccharomyces pombe.
Tomita K, Yashiroda Y, Matsuo Y, Piotrowski JS, Li SC, Okamoto R, Yoshimura M, Kimura H, Kawamura Y, Kawamukai M, Boone C, Yoshida M, Nojiri H, Okada K.
G3 (Bethesda). 2021 Aug 7;11(8):jkab156. doi: 10.1093/g3journal/jkab156.
A genome-scale yeast library with inducible expression of individual genes.
Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang RY, Climie D, Usaj M, Hotz M, Stoops EH, Baryshnikova A, Boone C, Botstein D, Andrews BJ, McIsaac RS.
Mol Syst Biol. 2021 Jun;17(6):e10207. doi: 10.15252/msb.202110207.
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase.
Kong KE, Fischer B, Meurer M, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M, Khmelinskii A.
Mol Cell. 2021 Jun 3;81(11):2460-2476.e11. doi: 10.1016/j.molcel.2021.04.018. Epub 2021 May 10.
A method for benchmarking genetic screens reveals a predominant mitochondrial bias.
Rahman M, Billmann M, Costanzo M, Aregger M, Tong AHY, Chan K, Ward HN, Brown KR, Andrews BJ, Boone C, Moffat J, Myers CL.
Mol Syst Biol. 2021 May;17(5):e10013. doi: 10.15252/msb.202010013.
Reduced gene dosage of histone H4 prevents CENP-A mislocalization and chromosomal instability in Saccharomyces cerevisiae.
Eisenstatt JR, Ohkuni K, Au WC, Preston O, Gliford L, Suva E, Costanzo M, Boone C, Basrai MA.
Genetics. 2021 May 17;218(1):iyab033. doi: 10.1093/genetics/iyab033.
Environmental robustness of the global yeast genetic interaction network.
Costanzo M, Hou J, Messier V, Nelson J, Rahman M, VanderSluis B, Wang W, Pons C, Ross C, Ušaj M, San Luis BJ, Shuteriqi E, Koch EN, Aloy P, Myers CL, Boone C, Andrews B.
Science. 2021 May 7;372(6542):eabf8424. doi: 10.1126/science.abf8424.
τ-SGA: synthetic genetic array analysis for systematically screening and quantifying trigenic interactions in yeast.
Kuzmin E, Rahman M, VanderSluis B, Costanzo M, Myers CL, Andrews BJ, Boone C.
Nat Protoc. 2021 Feb;16(2):1219-1250. doi: 10.1038/s41596-020-00456-3. Epub 2021 Jan 18.
2020
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects.
Masinas MPD, Usaj MM, Usaj M, Boone C, Andrews BJ.
G3 (Bethesda). 2020 Nov 5;10(11):3969-3976. doi: 10.1534/g3.120.401570.
Genetic profiling of protein burden and nuclear export overload.
Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H.
Elife. 2020 Nov 4;9:e54080. doi: 10.7554/eLife.54080.
Systematic analysis of bypass suppression of essential genes.
van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C.
Mol Syst Biol. 2020 Sep;16(9):e9828. doi: 10.15252/msb.20209828.
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 MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C.
Science. 2020 Jun 26;368(6498):eaaz5667. doi: 10.1126/science.aaz5667.
Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism.
Aregger M, Lawson KA, Billmann M, Costanzo M, Tong AHY, Chan K, Rahman M, Brown KR, Ross C, Usaj M, Nedyalkova L, Sizova O, Habsid A, Pawling J, Lin ZY, Abdouni H, Wong CJ, Weiss A, Mero P, Dennis JW, Gingras AC, Myers CL, Andrews BJ, Boone C, Moffat J.
Nat Metab. 2020 Jun;2(6):499-513. doi: 10.1038/s42255-020-0211-z. Epub 2020 Jun 1.
Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae.
Eisenstatt JR, Boeckmann L, Au WC, Garcia V, Bursch L, Ocampo J, Costanzo M, Weinreich M, Sclafani RA, Baryshnikova A, Myers CL, Boone C, Clark DJ, Baker R, Basrai MA.
G3 (Bethesda). 2020 Jun 1;10(6):2057-2068. doi: 10.1534/g3.120.401131.
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.
Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ.
Mol Syst Biol. 2020 Feb;16(2):e9243. doi: 10.15252/msb.20199243.
Skp, Cullin, F-box (SCF)-Met30 and SCF-Cdc4-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A for Chromosomal Stability in Budding Yeast.
Au WC, Zhang T, Mishra PK, Eisenstatt JR, Walker RL, Ocampo J, Dawson A, Warren J, Costanzo M, Baryshnikova A, Flick K, Clark DJ, Meltzer PS, Baker RE, Myers C, Boone C, Kaiser P, Basrai MA.
PLoS Genet. 2020 Feb 7;16(2):e1008597. doi: 10.1371/journal.pgen.1008597. eCollection 2020 Feb.
2019
Discovering genetic interactions bridging pathways in genome-wide association studies.
Fang G, Wang W, Paunic V, Heydari H, Costanzo M, Liu X, Liu X, VanderSluis B, Oately B, Steinbach M, Van Ness B, Schadt EE, Pankratz ND, Boone C, Kumar V, Myers CL.
Nat Commun. 2019 Sep 19;10(1):4274. doi: 10.1038/s41467-019-12131-7.
Integrating yeast chemical genomics and mammalian cell pathway analysis.
Zhou FL, Li SC, Zhu Y, Guo WJ, Shao LJ, Nelson J, Simpkins S, Yang DH, Liu Q, Yashiroda Y, Xu JB, Fan YY, Yue JM, Yoshida M, Xia T, Myers CL, Boone C, Wang MW.
Acta Pharmacol Sin. 2019 Sep;40(9):1245-1255. doi: 10.1038/s41401-019-0231-y. Epub 2019 May 28.
Functional link between mitochondria and Rnr3, the minor catalytic subunit of yeast ribonucleotide reductase.
Corcoles-Saez I, Ferat JL, Costanzo M, Boone CM, Cha RS.
Microb Cell. 2019 May 20;6(6):286-294. doi: 10.15698/mic2019.06.680.
Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases.
Pascoe N, Seetharaman A, Teyra J, Manczyk N, Satori MA, Tjandra D, Makhnevych T, Schwerdtfeger C, Brasher BB, Moffat J, Costanzo M, Boone C, Sicheri F, Sidhu SS.
J Mol Biol. 2019 Mar 15;431(6):1160-1171. doi: 10.1016/j.jmb.2019.02.007. Epub 2019 Feb 11.
Complex modifier landscape underlying genetic background effects.
Hou J, Tan G, Fink GR, Andrews BJ, Boone C.
Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5045-5054. doi: 10.1073/pnas.1820915116. Epub 2019 Feb 25.
Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments.
Simpkins SW, Deshpande R, Nelson J, Li SC, Piotrowski JS, Ward HN, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.
Nat Protoc. 2019 Feb;14(2):415-440. doi: 10.1038/s41596-018-0099-1.
Identifying Pseudomonas syringae Type III Secreted Effector Function via a Yeast Genomic Screen.
Lee AH, Bastedo DP, Youn JY, Lo T, Middleton MA, Kireeva I, Lee JY, Sharifpoor S, Baryshnikova A, Zhang J, Wang PW, Peisajovich SG, Constanzo M, Andrews BJ, Boone CM, Desveaux D, Guttman DS.
G3 (Bethesda). 2019 Feb 7;9(2):535-547. doi: 10.1534/g3.118.200877.
2018
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions.
Simpkins SW, Nelson J, Deshpande R, Li SC, Piotrowski JS, Wilson EH, Gebre AA, Safizadeh H, Okamoto R, Yoshimura M, Costanzo M, Yashiroda Y, Ohya Y, Osada H, Yoshida M, Boone C, Myers CL.
PLoS Comput Biol. 2018 Oct 30;14(10):e1006532. doi: 10.1371/journal.pcbi.1006532. eCollection 2018 Oct.
A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A.
Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA.
Genetics. 2018 Sep;210(1):203-218. doi: 10.1534/genetics.118.301305. Epub 2018 Jul 16.
Essential Function of Mec1, the Budding Yeast ATM/ATR Checkpoint-Response Kinase, in Protein Homeostasis.
Corcoles-Saez I, Dong K, Johnson AL, Waskiewicz E, Costanzo M, Boone C, Cha RS.
Dev Cell. 2018 Aug 20;46(4):495-503.e2. doi: 10.1016/j.devcel.2018.07.011.
The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion.
Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW.
J Cell Biol. 2018 Jul 2;217(7):2445-2462. doi: 10.1083/jcb.201709009. Epub 2018 Jun 6.
Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs.
Mount HO, Revie NM, Todd RT, Anstett K, Collins C, Costanzo M, Boone C, Robbins N, Selmecki A, Cowen LE.
PLoS Genet. 2018 Apr 27;14(4):e1007319. doi: 10.1371/journal.pgen.1007319. eCollection 2018 Apr.
Systematic analysis of complex genetic interactions.
Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL.
Science. 2018 Apr 20;360(6386):eaao1729. doi: 10.1126/science.aao1729.
Yeast Aim21/Tda2 both regulates free actin by reducing barbed end assembly and forms a complex with Cap1/Cap2 to balance actin assembly between patches and cables.
Shin M, van Leeuwen J, Boone C, Bretscher A.
Mol Biol Cell. 2018 Apr 15;29(8):923-936. doi: 10.1091/mbc.E17-10-0592. Epub 2018 Mar 30.
MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.
Nelson J, Simpkins SW, Safizadeh H, Li SC, Piotrowski JS, Hirano H, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.
Bioinformatics. 2018 Apr 1;34(7):1251-1252. doi: 10.1093/bioinformatics/btx732.
Translocon Declogger Ste24 Protects against IAPP Oligomer-Induced Proteotoxicity.
Kayatekin C, Amasino A, Gaglia G, Flannick J, Bonner JM, Fanning S, Narayan P, Barrasa MI, Pincus D, Landgraf D, Nelson J, Hesse WR, Costanzo M; AMP T2D-GENES Consortium; Myers CL, Boone C, Florez JC, Lindquist S.
Cell. 2018 Mar 22;173(1):62-73.e9. doi: 10.1016/j.cell.2018.02.026. Epub 2018 Mar 8.
2017
Pathway-based discovery of genetic interactions in breast cancer.
Wang W, Xu ZZ, Costanzo M, Boone C, Lange CA, Myers CL.
PLoS Genet. 2017 Sep 28;13(9):e1006973. doi: 10.1371/journal.pgen.1006973. eCollection 2017 Sep.
Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping.
Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA.
Cell Rep. 2017 Sep 12;20(11):2735-2748. doi: 10.1016/j.celrep.2017.08.074.
The Candida albicans transcription factor Cas5 couples stress responses, drug resistance and cell cycle regulation.
Xie JL, Qin L, Miao Z, Grys BT, Diaz JC, Ting K, Krieger JR, Tong J, Tan K, Leach MD, Ketela T, Moran MF, Krysan DJ, Boone C, Andrews BJ, Selmecki A, Ho Wong K, Robbins N, Cowen LE.
Nat Commun. 2017 Sep 11;8(1):499. doi: 10.1038/s41467-017-00547-y.
Functional annotation of chemical libraries across diverse biological processes.
Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.
Nat Chem Biol. 2017 Sep;13(9):982-993. doi: 10.1038/nchembio.2436. Epub 2017 Jul 24.
Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens.
Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J.
G3 (Bethesda). 2017 Aug 7;7(8):2719-2727. doi: 10.1534/g3.117.041277.
Identifying pathogenicity of human variants via paralog-based yeast complementation.
Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, Roth FP.
PLoS Genet. 2017 May 25;13(5):e1006779. doi: 10.1371/journal.pgen.1006779. eCollection 2017 May.
TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.
Usaj M, Tan Y, Wang W, VanderSluis B, Zou A, Myers CL, Costanzo M, Andrews B, Boone C.
G3 (Bethesda). 2017 May 5;7(5):1539-1549. doi: 10.1534/g3.117.040220.
Automated analysis of high-content microscopy data with deep learning.
Kraus OZ, Grys BT, Ba J, Chong Y, Frey BJ, Boone C, Andrews BJ.
Mol Syst Biol. 2017 Apr 18;13(4):924. doi: 10.15252/msb.20177551.
2016
Exploring genetic suppression interactions on a global scale.
van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C.
Science. 2016 Nov 4;354(6312).
A global genetic interaction network maps a wiring diagram of cellular function.
Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.
Science. 2016 Sep 23;353(6306).
Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.
Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone C, Andrews BJ.
Cell Syst. 2016 Sep 28;3(3):264-277.e10.
Direct and Indirect Targeting of PP2A by Conserved Bacterial Type-III Effector Proteins.
Jin L, Ham JH, Hage R, Zhao W, Soto-Hernández J, Lee SY, Paek SM, Kim MG, Boone C, Coplin DL, Mackey D.
PLoS Pathog. 2016 May 18;12(5):e1005609. doi: 10.1371/journal.ppat.1005609. eCollection 2016 May.
An extended set of yeast-based functional assays accurately identifies human disease mutations.
Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP.
Genome Res. 2016 May;26(5):670-80. doi: 10.1101/gr.192526.115. Epub 2016 Mar 14.
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Wanamaker SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.
Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.
2015
Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis.
Chong YT, Koh JL, Friesen H, Duffy SK, Cox MJ, Moses A, Moffat J, Boone C, Andrews BJ.
Cell. 2015 Jun 4;161(6):1413-24.
2014
Heritability and genetic basis of protein level variation in an outbred population.
Parts L, Liu YC, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP.
Genome Res. 2014 Aug;24(8):1363-70.
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities.
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.
Mol Syst Biol. 2013 Oct 8;9:696.
Global linkage map connects meiotic centromere function to chromosome size in budding yeast.
Baryshnikova A, VanderSluis B, Costanzo M, Myers CL, Cha RS, Andrews B, Boone C.
G3 (Bethesda). 2013 Oct 3;3(10):1741-51.
2013
SH3 interactome conserves general function over specific form.
Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD.
Mol Syst Biol. 2013;9:652.
2012
Global gene deletion analysis exploring yeast filamentous growth.
Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmüller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C.
Science. 2012 Sep 14;337(6100):1353-6.
2011
Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell.
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.
Nat Biotechnol. 2011
Systematic exploration of essential yeast gene function with temperature-sensitive mutants.
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, et al.
Nat Biotechnol. 2011
Bringing order to protein disorder through comparative genomics and genetic interactions.
Bellay J, Han S, Michaut M, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM.
Genome Biol. 2011 Feb 16;12(2):R14
Combining functional genomics and chemical biology to identify targets of bioactive compounds.
Ho CH, Piotrowski J, Dixon SJ, Baryshnikova A, Costanzo M, Boone C.
Curr Opin Chem Biol. 2011 Feb;15(1):66-78
Charting the genetic interaction map of a cell.
Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C.
Curr Opin Biotechnol. 2011 Feb;22(1):66-74
Microarray-based target identification using drug hypersensitive fission yeast expressing ORFeome.
Arita Y, Nishimura S, Matsuyama A, Yashiroda Y, Usui T, Boone C, Yoshida M.
Mol Biosyst. 2011 Feb 22
2010
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.
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.
Nat Methods. 2010 Dec;7(12):1017-24
The genetic landscape of a cell.
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, et al.
Science. 2010 Jan 22;327(5964):425-31
DRYGIN: a database of quantitative genetic interaction networks in yeast.
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C.
Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7
Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis.
Vizeacoumar FJ, van Dyk N, Vizeacoumar FS, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ.
J Cell Biol. 2010 Jan 11;188(1):69-81
Genotype to phenotype: a complex problem.
Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C.
Science. 2010 Apr 23;328(5977):469
Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe.
Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C.
Methods Enzymol. 2010;470:145-79
Genetic interactions reveal the evolutionary trajectories of duplicate genes.
VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL.
Mol Syst Biol. 2010 Nov 16;6:429
2009
A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.
Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C.
Nat Biotechnol. 2009 Apr;27(4):369-77
Systematic mapping of genetic interaction networks.
Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C.
Annu Rev Genet. 2009;43:601-25. Review.
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C.
PLoS Biol. 2009 Oct;7(10):e1000218
2008
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.
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.
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8
2007
Exploring genetic interactions and networks with yeast.
Boone C, Bussey H, Andrews BJ.
Nat Rev Genet. 2007 Jun;8(6):437-49. Review.
2006
Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.
Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, et al.
Cell. 2006 Aug 11;126(3):611-25
2004
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.
Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C.
Nat Biotechnol. 2004 Jan;22(1):62-9
Global mapping of the yeast genetic interaction network.
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, et al.
Science. 2004 Feb 6;303(5659):808-13
2002
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.
Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G.
Science. 2002 Jan 11;295(5553):321-4
2001
Systematic genetic analysis with ordered arrays of yeast deletion mutants.
Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C.
Science. 2001 Dec 14;294(5550):2364-8
