Publications


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Current CEGS publications here
For previous CEGS publications click CEGS I Pubs

 
Celaj A, Schlecht U, Smith J, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP† and St. Onge RP†.
Quantitative analysis of protein interaction network dynamics in yeast.
Mol Syst Biol 2017;accepted
 
Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC†, Roth FP†, and Suk K†.
Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target.
Genome Res 2017;Epub ahead of print.
 
Perrino C, Barabási A-L, Condorelli G, Davidson SM, De Windt L, Dimmeler S, Engel FB, Hausenloy DJ, Hill JA, Van Laake LW, Lecour S, Leor J, Madonna R, Mayr M, Prunier F, Sluijter JPG, Schulz R, Thum T, Ytrehus K, and Ferdinandy P.
Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart.
Cardiovasc Res 2017;113(7):725-36.

 
Yang F, Sun S, Tan G, Costanzo M, Hill DE, Vidal M, Andrews BJ, Boone C, and Roth FP.
Identifying pathogenicity of human variants via paralog-based yeast complementation.
PLoS Genet 2017;13(5):e1006779.

 
Luck K†, Sheynkman GM†, Zhang I, and Vidal M.
Proteome-Scale Human Interactomics.
Trends Biochem Sci 2017;42(5):342-54.

 
Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ†, and Roth FP†.
A common class of transcripts with 5′-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.
RNA 2017;23(3):270-83.

 
Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, and Russell RB.
HSP90 Systematic identification of phosphorylation-mediated protein interaction switches.
PLoS Comput Biol 2017;13(3):e1005462.

 
Karras GI†, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D’Andrea AD, Whitesell L†, and Lindquist S.
HSP90 Shapes the Consequences of Human Genetic Variation.
Cell 2017;168(5):856-66 e12.

 
Khurana V†, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schondorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E†, Berger B†, and Lindquist S†.
Genome-Scale Networks Link Neurodegenerative Disease Genes to alpha-Synuclein through Specific Molecular Pathways.
Cell Syst 2017;4(2):157-70 e14.

 
van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Usaj MM, Pechlaner M, Takar M, Usaj 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†, and Boone C†.
Exploring genetic suppression interactions on a global scale.
Science 2016;354(6312).

 
Kitsak M, Sharma A, Menche J, Guney E, Ghiassian SD, Loscalzo J, and Barabási A-L.
Tissue Specificity of Human Disease Module.
Sci Rep 2016;6:35241.

 
Basler G, Nikoloski Z, Larhlimi A, Barabási A-L, and Liu YY.
Control of fluxes in metabolic networks.
Genome Res 2016;26(7):956-68.

 
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, and Roth FP.
An extended set of yeast-based functional assays accurately identifies human disease mutations.
Genome Res 2016;26(5):670-80.

 
Ghiassian SD, Menche J, Chasman DI, Giulianini F, Wang R, Ricchiuto P, Aikawa M, Iwata H, Muller C, Zeller T, Sharma A, Wild P, Lackner K, Singh S, Ridker PM, Blankenberg S, Barabási A-L and Loscalzo J.
Endophenotype Network Models: Common Core of Complex Diseases.
Sci Rep 2016; 6:27414.

 
Vinayagam A, Gibson TE, Lee HJ, Yilmazel B, Roesel C, Hu Y, Kwon Y, Sharma A, Liu YY, Perrimon N and Barabási A-L.
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.
Proc Natl Acad Sci U S A 2016; 113:4976-81.

 
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, Trigg 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 and Vidal M.
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
Cell 2016; 164:805-17.

 
Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M and Roth FP.
Pooled-matrix protein interaction screens using Barcode Fusion Genetics.
Mol Syst Biol 2016; 12:863.

 
Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y and Yu H.
A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
Cell 2016; 164:310-23.

 
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 and Roth FP.
An extended set of yeast-based functional assays accurately identifies human disease mutations.
Genome Res 2016; 26:670-80.

 
Guney E, Menche J, Vidal M and Barabási A-L.
Network-based in silico drug efficacy screening.
Nat Commun 2016; 7:10331.

 
Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordan R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE and Bulyk ML.
Survey of variation in human transcription factors reveals prevalent DNA binding changes.
Science 2016; 351:1450-4.

 
Sharma A, Menche J, Huang CC, Ort T, Zhou X, Kitsak M, Sahni N, Thibault D, Voung L, Guo F, Ghiassian SD, Gulbahce N, Baribaud F, Tocker J, Dobrin R, Barnathan E, Liu H, Panettieri RA, Jr., Tantisira KG, Qiu W, Raby BA, Silverman EK, Vidal M, Weiss ST and Barabási A-L.
A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma.
Hum. Mol. Genet. 2015; 24:3005-20.

 
Petsalaki E, Helbig AO, Gopal A, Pasculescu A, Roth FP and Pawson T.
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets.
Nucleic Acids Res. 2015. DOI: 10.1093/nar/gkv459.

 
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási A-L, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJ, Lindquist S and Vidal M.
Widespread macromolecular interaction perturbations in human genetic disorders.
Cell 2015; 161:647-60.

 
Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M and Walhout AJ.
Human gene-centered transcription factor networks for enhancers and disease variants.
Cell 2015; 161:661-73.

 
Ghiassian SD, Menche J and Barabási A-L.
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.
PLoS Comput. Biol. 2015; 11:e1004120.

 
Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M and Roth FP.
Protein domain-level landscape of cancer-type-specific somatic mutations.
PLoS Comput. Biol. 2015; 11:e1004147.

 
Menche J, Sharma A, Kitsak M, Ghiassian SD, Vidal M, Loscalzo J and Barabási A-L.
Disease networks. Uncovering disease-disease relationships through the incomplete interactome.
Science 2015; 347:1257601.

 
Taşan M, Musso G, Hao T, Vidal M, MacRae CA and Roth FP.
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.
Nat. Methods 2015; 12:154-9.

 
Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O’Hanlon D, Barrios-Rodiles M, Sternberg MJE, Cordes SP, Roth FP, Wrana JL, Geschwind DH and Blencowe BJ.
A highly conserved program of neuronal microexons is misregulated in autistic brains.
Cell 2014; 159:1511-23.

 
Deo RC, Musso G, Taşan M, Tang P, Poon A, Yuan C, Felix JF, Vasan RS, Beroukhim R, De Marco T, Kwok PY, MacRae CA and Roth FP.
Prioritizing causal disease genes using unbiased genomic features.
Genome Biol. 2014; 15:534.

 
Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis A-R, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási A-L, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP and Vidal M.
A proteome-scale map of the human interactome network.
Cell 2014; 159:1212-26.

 
Brehme M, Voisine C, Rolland T, Wachi S, Soper JH, Zhu Y, Orton K, Villella A, Garza D, Vidal M, Ge H and Morimoto RI.
A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.
Cell Rep. 2014; 9:1135-50.

 
Shen HW and Barabási A-L.
Collective credit allocation in science.
Proc. Natl. Acad. Sci. USA 2014; 111:12325-30.

 
Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP and Cokol
M. Target-independent prediction of drug synergies using only drug lipophilicity.
J. Chem. Inf. Model./em>2014; 54:2286-93.

 
Musso G, Tasan M, Mosimann C, Beaver JE, Plovie E, Carr LA, Chua HN, Dunham J, Zuberi K, Rodriguez H, Morris Q, Zon L, Roth FP, MacRae CA.
Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish.
Development 2014; 141:224-35.

 
Wang W, Zhong Q, Teng L, Bhatnagar N, Sharma B, Zhang X, Luther W 2nd, Haynes LP, Burgoyne RD, Vidal M, Volchenboum S, Hill DE, George RE.
Mutations that disrupt PHOXB interaction with the neuronal calcium sensor HPCAL1 impede cellular differentiation in neuroblastoma.
Oncogene 2013; 33:3316-24.

 
Sahni N, Yi S, Zhong Q, Jailkhani N, Charloteaux B, Cusick ME, Vidal M.
Edgotype: a fundamental link between genotype and phenotype.
Curr Opin Genet Dev 2013; 23:649-57.

 
Sunyaev SR, Roth FP
Systems biology and the analysis of genetic variation.
Curr Opin Genet Dev 2013; 23:599-601.

 
Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC.
Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.
Nat Methods 2013; 10:1239-45.

 
Mehra A, Zahra A, Thompson V, Sirisaengtaksin N, Wells A, Porto M, Köster S, Penberthy K, Kubota Y, Dricot A, Rogan D, Vidal M, Hill DE, Bean AJ, Philips JA.
Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking.
PLoS Pathog 2013; 9:e1003734.

 

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