IRIC

Publications — IRIC August 1, 2019

Gene Information eXtension (GIX): effortless retrieval of gene product information on any website.

Knight JDR, Samavarchi-Tehrani P, Tyers M, Gingras AC
Nat. Methods 2019-08-01 ;16( 8 ):665-666.

Publications — IRIC July 8, 2019

Mubritinib Targets the Electron Transport Chain Complex I and Reveals the Landscape of OXPHOS Dependency in Acute Myeloid Leukemia.

Baccelli I, Gareau Y, Lehnertz B, Gingras S, Spinella JF, Corneau S, Mayotte N, Girard S, Frechette M, Blouin-Chagnon V, Leveillé K, Boivin I, MacRae T, Krosl J, Thiollier C, Lavallée VP, Kanshin E, Bertomeu T, Coulombe-Huntington J, St-Denis C, Bordeleau ME, Boucher G, Roux PP, Lemieux S, Tyers M, Thibault P, Hébert J, Marinier A, Sauvageau G
Cancer Cell 2019-07-08 ;36( 1 ):84-99.e8.

Publications — IRIC April 1, 2019

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.

Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ
Plant Physiol. 2019-04-01 ;179( 4 ):1893-1907.

Publications — IRIC March 28, 2019

The p38/HOG stress-activated protein kinase network couples growth to division in Candida albicans.

Sellam A, Chaillot J, Mallick J, Tebbji F, Richard Albert J, Cook MA, Tyers M
PLoS Genet. 2019-03-28 ;15( 3 ):e1008052.

Publications — IRIC March 1, 2019

Drug combinations: a strategy to extend the life of antibiotics in the 21st century.

Tyers M, Wright GD
Nat. Rev. Microbiol. 2019-03-01 ;17( 3 ):141-155.

Publications — IRIC January 8, 2019

The BioGRID interaction database: 2019 update.

Oughtred R, Stark C, Breitkreutz BJ, Rust J, Boucher L, Chang C, Kolas N, O'Donnell L, Leung G, McAdam R, Zhang F, Dolma S, Willems A, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M
Nucleic Acids Res. 2019-01-08 ;47( D1 ):D529-D541.

Publications — IRIC September 7, 2018

Combined Enrichment/Enzymatic Approach To Study Tightly Clustered Multisite Phosphorylation on Ser-Rich Domains.

Kanshin E, Pascariu M, Tyers M, D'Amours D, Thibault P
J. Proteome Res. 2018-09-07 ;17( 9 ):3050-3060.

Publications — IRIC August 10, 2018

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay.

Koszela J, Pham NT, Evans D, Mann S, Perez-Pi I, Shave S, Ceccarelli DFJ, Sicheri F, Tyers M, Auer M
BMC Biol. 2018-08-10 ;16( 1 ):88.

Publications — IRIC June 27, 2018

Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability.

Palou R, Dhanaraman T, Marrakchi R, Pascariu M, Tyers M, D'Amours D
PLoS Biol. 2018-06-27 ;16( 6 ):e2003980.

Publications — IRIC May 23, 2018

G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast.

Dorsey S, Tollis S, Cheng J, Black L, Notley S, Tyers M, Royer CA
Cell Syst 2018-05-23 ;6( 5 ):539-554.e11.

Publications — IRIC May 17, 2018

At Long Last, a C-Terminal Bookend for the Ubiquitin Code.

Chatr-Aryamontri A, van der Sloot A, Tyers M
Mol. Cell 2018-05-17 ;70( 4 ):568-571.

Publications — IRIC February 15, 2018

Cdc48/VCP Promotes Chromosome Morphogenesis by Releasing Condensin from Self-Entrapment in Chromatin.

Thattikota Y, Tollis S, Palou R, Vinet J, Tyers M, D'Amours D
Mol. Cell 2018-02-15 ;69( 4 ):664-676.e5.

Publications — IRIC January 2, 2018

Multivalent Interactions with Fbw7 and Pin1 Facilitate Recognition of c-Jun by the SCFFbw7 Ubiquitin Ligase.

Csizmok V, Montecchio M, Lin H, Tyers M, Sunnerhagen M, Forman-Kay JD
Structure 2018-01-02 ;26( 1 ):28-39.e2.

Publications — IRIC January 1, 2018

A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.

Bertomeu T, Coulombe-Huntington J, Chatr-Aryamontri A, Bourdages KG, Coyaud E, Raught B, Xia Y, Tyers M
Mol. Cell. Biol. 2018-01-01 ;38( 1 ):.

Publications — IRIC November 1, 2017

WD40 repeat domain proteins: a novel target class?

Schapira M, Tyers M, Torrent M, Arrowsmith CH
Nat Rev Drug Discov 2017-11-01 ;16( 11 ):773-786.

Publications — IRIC October 17, 2017

Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer.

Li Y, Sahni N, Pancsa R, McGrail DJ, Xu J, Hua X, Coulombe-Huntington J, Ryan M, Tychhon B, Sudhakar D, Hu L, Tyers M, Jiang X, Lin SY, Babu MM, Yi S
Cell Rep 2017-10-17 ;21( 3 ):798-812.

Publications — IRIC July 7, 2017

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

Courcelles M, Coulombe-Huntington J, Cossette É, Gingras AC, Thibault P, Tyers M
J. Proteome Res. 2017-07-07 ;16( 7 ):2645-2652.

Publications — IRIC May 18, 2017

Synthetic Genomics: Rewriting the Genome Chromosome by Chromosome.

van der Sloot A, Tyers M
Mol. Cell 2017-05-18 ;66( 4 ):441-443.

Publications — IRIC May 1, 2017

Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.

Kanshin E, Giguère S, Jing C, Tyers M, Thibault P
Mol. Cell Proteomics 2017-05-01 ;16( 5 ):786-798.

Publications — IRIC January 10, 2017

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.

Islamaj Doğan R, Kim S, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Wilbur WJ, Comeau DC, Dolinski K, Tyers M
Database (Oxford) 2017-01-10 ;2017:.

Publications — IRIC January 4, 2017

The BioGRID interaction database: 2017 update.

Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O'Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M
Nucleic Acids Res. 2017-01-04 ;45( D1 ):D369-D379.

Publications — IRIC January 3, 2017

An allosteric conduit facilitates dynamic multisite substrate recognition by the SCF(Cdc4) ubiquitin ligase.

Csizmok V, Orlicky S, Cheng J, Song J, Bah A, Delgoshaie N, Lin H, Mittag T, Sicheri F, Chan HS, Tyers M, Forman-Kay JD
Nat Commun 2017-01-03 ;8:13943.

Publications — IRIC November 22, 2016

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism.

Wildenhain J, Spitzer M, Dolma S, Jarvik N, White R, Roy M, Griffiths E, Bellows DS, Wright GD, Tyers M
Sci Data 2016-11-22 ;3:160095.

Publications — IRIC November 17, 2016

Discovery of Ibomycin, a Complex Macrolactone that Exerts Antifungal Activity by Impeding Endocytic Trafficking and Membrane Function.

Robbins N, Spitzer M, Wang W, Waglechner N, Patel DJ, O'Brien JS, Ejim L, Ejim O, Tyers M, Wright GD
Cell Chem Biol 2016-11-17 ;23( 11 ):1383-1394.

Publications — IRIC October 21, 2016

Data Independent Acquisition analysis in ProHits 4.0.

Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC
J Proteomics 2016-10-21 ;149:64-68.

Publications — IRIC September 26, 2016

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons.

Drouin A, Giguère S, Déraspe M, Marchand M, Tyers M, Loo VG, Bourgault AM, Laviolette F, Corbeil J
BMC Genomics 2016-09-26 ;17( 1 ):754.

Publications — IRIC September 1, 2016

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

Kim S, Islamaj Doğan R, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S, Santos A, Campos D, Oliveira JL, Singh O, Jonnagaddala J, Dai HJ, Su EC, Chang YC, Su YC, Chu CH, Chen CC, Hsu WL, Peng Y, Arighi C, Wu CH, Vijay-Shanker K, Aydın F, Hüsünbeyi ZM, Özgür A, Shin SY, Kwon D, Dolinski K, Tyers M, Wilbur WJ, Comeau DC
Database (Oxford) 2016-09-01 ;2016:baw121.

Publications — IRIC June 13, 2016

Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells.

Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, Voisin V, Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, Clarke ID, Bader G, Harrington L, Brumell JH, Tyers M, Dirks PB
Cancer Cell 2016-06-13 ;29( 6 ):859-73.

Publications — IRIC March 29, 2016

Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.

Gorelik M, Orlicky S, Sartori MA, Tang X, Marcon E, Kurinov I, Greenblatt JF, Tyers M, Moffat J, Sicheri F, Sidhu SS
Proc. Natl. Acad. Sci. U.S.A. 2016-03-29 ;113( 13 ):3527-32.

Publications — IRIC January 1, 2016

BioGRID: A Resource for Studying Biological Interactions in Yeast.

Oughtred R, Chatr-Aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M
Cold Spring Harb Protoc 2016-01-01 ;2016( 1 ):pdb.top080754.

Publications — IRIC January 1, 2016

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.

Oughtred R, Chatr-Aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M
Cold Spring Harb Protoc 2016-01-01 ;2016( 1 ):pdb.prot088880.

Publications — IRIC December 23, 2015

Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning.

Wildenhain J, Spitzer M, Dolma S, Jarvik N, White R, Roy M, Griffiths E, Bellows DS, Wright GD, Tyers M
Cell Syst 2015-12-23 ;1( 6 ):383-95.

Publications — IRIC November 17, 2015

An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity against Diverse Fungal Pathogens.

Robbins N, Spitzer M, Yu T, Cerone RP, Averette AK, Bahn YS, Heitman J, Sheppard DC, Tyers M, Wright GD
Cell Rep 2015-11-17 ;13( 7 ):1481-92.

Publications — IRIC July 2, 2015

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics.

Kanshin E, Tyers M, Thibault P
J. Proteome Res. 2015-07-02 ;14( 7 ):2998-3004.

Publications — IRIC June 25, 2015

Caenorhabditis elegans is a useful model for anthelmintic discovery.

Burns AR, Luciani GM, Musso G, Bagg R, Yeo M, Zhang Y, Rajendran L, Glavin J, Hunter R, Redman E, Stasiuk S, Schertzberg M, Angus McQuibban G, Caffrey CR, Cutler SR, Tyers M, Giaever G, Nislow C, Fraser AG, MacRae CA, Gilleard J, Roy PJ
Nat Commun 2015-06-25 ;6:7485.

Publications — IRIC February 15, 2015

Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing.

Castonguay E, White SA, Kagansky A, St-Cyr DJ, Castillo AG, Brugger C, White R, Bonilla C, Spitzer M, Earnshaw WC, Schalch T, Ekwall K, Tyers M, Allshire RC
Mol. Cell. Biol. 2015-02-15 ;35( 4 ):662-74.

Publications — IRIC January 28, 2015

The BioGRID interaction database: 2015 update.

Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M
Nucleic Acids Res. 2015-01-28 ;43( Database issue ):D470-8.

Publications — IRIC November 12, 2014

Targeting the INCENP IN-box-Aurora B interaction to inhibit CPC activity in vivo.

Gohard FH, St-Cyr DJ, Tyers M, Earnshaw WC
Open Biol 2014-11-12 ;4( 11 ):.

Publications — IRIC July 15, 2014

Structural basis for the recruitment of glycogen synthase by glycogenin.

Zeqiraj E, Tang X, Hunter RW, García-Rocha M, Judd A, Deak M, von Wilamowitz-Moellendorff A, Kurinov I, Guinovart JJ, Tyers M, Sakamoto K, Sicheri F
Proc. Natl. Acad. Sci. U.S.A. 2014-07-15 ;111( 28 ):E2831-40.

Publications — IRIC June 5, 2014

A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference.

Beard PM, Griffiths SJ, Gonzalez O, Haga IR, Pechenick Jowers T, Reynolds DK, Wildenhain J, Tekotte H, Auer M, Tyers M, Ghazal P, Zimmer R, Haas J
PLoS ONE 2014-06-05 ;9( 6 ):e98431.

Publications — IRIC May 9, 2014

Regulation of the histone deacetylase Hst3 by cyclin-dependent kinases and the ubiquitin ligase SCFCdc4.

Delgoshaie N, Tang X, Kanshin ED, Williams EC, Rudner AD, Thibault P, Tyers M, Verreault A
J. Biol. Chem. 2014-05-09 ;289( 19 ):13186-96.

Publications — IRIC February 1, 2014

E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.

Huang H, Ceccarelli DF, Orlicky S, St-Cyr DJ, Ziemba A, Garg P, Plamondon S, Auer M, Sidhu S, Marinier A, Kleiger G, Tyers M, Sicheri F
Nat. Chem. Biol. 2014-02-01 ;10( 2 ):156-63.

Publications — IRIC February 1, 2014

Structure of an SspH1-PKN1 Complex Reveals the Basis for Host Substrate Recognition and Mechanism of Activation for a Bacterial E3 Ubiquitin Ligase.

Keszei AF, Tang X, McCormick C, Zeqiraj E, Rohde JR, Tyers M, Sicheri F
Mol. Cell. Biol. 2014-02-01 ;34( 3 ):362-73.

Publications — IRIC January 30, 2014

BoxPlotR: a web tool for generation of box plots.

Spitzer M, Wildenhain J, Rappsilber J, Tyers M
Nat. Methods 2014-01-30 ;11( 2 ):121-2.

Publications — IRIC March 21, 2013

A yeast chemical genetic screen identifies inhibitors of human telomerase.

Wong LH, Unciti-Broceta A, Spitzer M, White R, Tyers M, Harrington L
Chem. Biol. 2013-03-21 ;20( 3 ):333-40.

Publications — IRIC February 1, 2013

A strategy for modulation of enzymes in the ubiquitin system.

Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P, Persaud A, Walker JR, Neculai AM, Neculai D, Vorobyov A, Garg P, Beatty L, Chan PK, Juang YC, Landry MC, Yeh C, Zeqiraj E, Karamboulas K, Allali-Hassani A, Vedadi M, Tyers M, Moffat J, Sicheri F, Pelletier L, Durocher D, Raught B, Rotin D, Yang J, Moran MF, Dhe-Paganon S, Sidhu SS
Science 2013-02-01 ;339( 6119 ):590-5.

Publications — IRIC January 1, 2013

Systematic curation of protein and genetic interaction data for computable biology.

Dolinski K, Chatr-Aryamontri A, Tyers M
BMC Biol. 2013-01-01 ;11:43.

Publications — IRIC January 1, 2013

The BioGRID interaction database: 2013 update.

Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust J, Livstone M, Oughtred R, Dolinski K, Tyers M
Nucleic Acids Res. 2013-01-01 ;41( Database issue ):D816-23.

Publications — IRIC January 1, 2013

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.

Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M
Database (Oxford) 2013-01-01 ;2013( 0 ):bat026.

Publications — IRIC September 1, 2012

Analyzing Protein-Protein Interactions from Affinity Purification-Mass Spectrometry Data with SAINT.

Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI
Curr Protoc Bioinformatics 2012-09-01 ;Chapter 8:Unit8.15.

Search

Gene Information eXtension (GIX): effortless retrieval of gene product information on any website.

Mubritinib Targets the Electron Transport Chain Complex I and Reveals the Landscape of OXPHOS Dependency in Acute Myeloid Leukemia.

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.

The p38/HOG stress-activated protein kinase network couples growth to division in Candida albicans.

Drug combinations: a strategy to extend the life of antibiotics in the 21st century.

The BioGRID interaction database: 2019 update.

Combined Enrichment/Enzymatic Approach To Study Tightly Clustered Multisite Phosphorylation on Ser-Rich Domains.

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay.

Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability.

G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast.

At Long Last, a C-Terminal Bookend for the Ubiquitin Code.

Cdc48/VCP Promotes Chromosome Morphogenesis by Releasing Condensin from Self-Entrapment in Chromatin.

Multivalent Interactions with Fbw7 and Pin1 Facilitate Recognition of c-Jun by the SCFFbw7 Ubiquitin Ligase.

A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.

WD40 repeat domain proteins: a novel target class?

Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

Synthetic Genomics: Rewriting the Genome Chromosome by Chromosome.

Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.

The BioGRID interaction database: 2017 update.

An allosteric conduit facilitates dynamic multisite substrate recognition by the SCF(Cdc4) ubiquitin ligase.

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism.

Discovery of Ibomycin, a Complex Macrolactone that Exerts Antifungal Activity by Impeding Endocytic Trafficking and Membrane Function.

Data Independent Acquisition analysis in ProHits 4.0.

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells.

Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.

BioGRID: A Resource for Studying Biological Interactions in Yeast.

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.

Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning.

An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity against Diverse Fungal Pathogens.

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics.

Caenorhabditis elegans is a useful model for anthelmintic discovery.

Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing.

The BioGRID interaction database: 2015 update.

Targeting the INCENP IN-box-Aurora B interaction to inhibit CPC activity in vivo.

Structural basis for the recruitment of glycogen synthase by glycogenin.

A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference.

Regulation of the histone deacetylase Hst3 by cyclin-dependent kinases and the ubiquitin ligase SCFCdc4.

E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.

Structure of an SspH1-PKN1 Complex Reveals the Basis for Host Substrate Recognition and Mechanism of Activation for a Bacterial E3 Ubiquitin Ligase.

BoxPlotR: a web tool for generation of box plots.

A yeast chemical genetic screen identifies inhibitors of human telomerase.

A strategy for modulation of enzymes in the ubiquitin system.

Systematic curation of protein and genetic interaction data for computable biology.

The BioGRID interaction database: 2013 update.

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.

Analyzing Protein-Protein Interactions from Affinity Purification-Mass Spectrometry Data with SAINT.

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