Deep learning for protein structure prediction and design-progress and applications.

Jänes J, Beltrao P.

Mol Syst Biol, 2024

doi:10.1038/s44320-024-00016-x.

A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization.

Pacini C, Duncan E, Gonçalves E, Gilbert J, Bhosle S, Horswell S, Karakoc E, Lightfoot H, Curry E, Muyas F, Bouaboula M, Pedamallu CS, Cortes-Ciriano I, Behan FM, Zalmas LP, Barthorpe A, Francies H, Rowley S, Pollard J, Beltrao P, Parts L, Iorio F, Garnett MJ.

Cancer Cell, 2024

doi:10.1016/j.ccell.2023.12.016.

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer.

Memon D, Schoenfeld AJ, Ye D, Fromm G, Rizvi H, Zhang X, Keddar MR, Mathew D, Yoo KJ, Qiu J, Lihm J, Miriyala J, Sauter JL, Luo J, Chow A, Bhanot UK, McCarthy C, Vanderbilt CM, Liu C, Abu-Akeel M, Plodkowski AJ, McGranahan N, Łuksza M, Greenbaum BD, Merghoub T, Achour I, Barrett JC, Stewart R, Beltrao P, Schreiber TH, Minn AJ, Miller ML, Hellmann MD.

Cancer Cell, 2024

doi:10.1016/j.ccell.2023.12.013.

SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ.

Cell, 2023

doi:10.1016/j.cell.2023.08.026.

Clustering predicted structures at the scale of the known protein universe.

Barrio-Hernandez I, Yeo J, Jänes J, Mirdita M, Gilchrist CLM, Wein T, Varadi M, Velankar S, Beltrao P, Steinegger M.

Nature, 2023

doi:10.1038/s41586-023-06510-w.

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.

Blood, 2023

doi:10.1182/blood.2023020118.

Highlights from the 1st European cancer dependency map symposium and workshop.

Trastulla L, Savino A, Beltrao P, Ciriano IC, Fenici P, Garnett MJ, Guerini I, Bigas NL, Mattaj I, Petsalaki E, Riva L, Tape CJ, Leeuwen JV, Sharma S, Vazquez F, Iorio F.

FEBS Lett, 2023

doi:10.1002/1873-3468.14699.

A human proteogenomic-cellular framework identifies KIF5A as a modulator of astrocyte process integrity with relevance to ALS.

Szebényi K, Barrio-Hernandez I, Gibbons GM, Biasetti L, Troakes C, Beltrao P, Lakatos A.

Commun Biol, 2023

doi:10.1038/s42003-023-05041-4.

High-throughput deep learning variant effect prediction with Sequence UNET.

Dunham AS, Beltrao P, AlQuraishi M.

Genome Biol, 2023

doi:10.1186/s13059-023-02948-3.

Network expansion of genetic associations defines a pleiotropy map of human cell biology.

Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, Del-Toro N, Gonzalez A, Zhang Q, Mountjoy E, Suveges D, Ochoa D, Ghoussaini M, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P.

Nat Genet, 2023

doi:10.1038/s41588-023-01327-9.

Towards a structurally resolved human protein interaction network.

Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A.

Nat Struct Mol Biol, 2023

doi:10.1038/s41594-022-00910-8.

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.

Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P.

Mol Syst Biol, 2023

doi:10.15252/msb.202110631.

Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization.

King GA, Wettstein R, Varberg JM, Chetlapalli K, Walsh ME, Gillet LCJ, Hernández-Armenta C, Beltrao P, Aebersold R, Jaspersen SL, Matos J, Ünal E.

J Cell Biol, 2023

doi:10.1083/jcb.202204039.

A structural biology community assessment of AlphaFold2 applications.

Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

Nat Struct Mol Biol, 2022

doi:10.1038/s41594-022-00849-w.

Network analysis of genome-wide association studies for drug target prioritisation.

Barrio-Hernandez I, Beltrao P.

Curr Opin Chem Biol, 2022

doi:10.1016/j.cbpa.2022.102206.

Systematic discovery of biomolecular condensate-specific protein phosphorylation.

Sridharan S, Hernandez-Armendariz A, Kurzawa N, Potel CM, Memon D, Beltrao P, Bantscheff M, Huber W, Cuylen-Haering S, Savitski MM.

Nat Chem Biol, 2022

doi:10.1038/s41589-022-01062-y.

Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling.

Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ.

Cell Rep, 2022

doi:10.1016/j.celrep.2022.110690.

Evolution of enhanced innate immune evasion by SARS-CoV-2.

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ.

Nature, 2022

doi:10.1038/s41586-021-04352-y.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P.

Nat Biotechnol, 2022

doi:10.1038/s41587-021-01051-x.

Exploring amino acid functions in a deep mutational landscape.

Dunham AS, Beltrao P.

Mol Syst Biol, 2021

doi:10.15252/msb.202110305.

Network expansion of genetic associations defines a pleiotropy map of human cell biology

Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, del-Toro N, Zhang Q, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P.

2021

doi:10.1101/2021.07.19.452924.

Individual COVID-19 disease trajectories revealed by plasma proteomics.

Memon D, Barrio-Hernandez I, Beltrao P.

EMBO Mol Med, 2021

doi:10.15252/emmm.202114532.

Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.

Memon D, Gill MB, Papachristou EK, Ochoa D, D'Santos CS, Miller ML, Beltrao P.

Cell Rep, 2021

doi:10.1016/j.celrep.2021.109155.

Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.

Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Gustincich S, Tartaglia GG, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Angelantonio ED, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O'Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Beltrao P, Danesh J, Hung AM, Chang KM, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP, VA Million Veteran Program COVID-19 Science Initiative.

Nat Med, 2021

doi:10.1038/s41591-021-01310-z.

Author Correction: Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.

Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A.

Nat Genet, 2021

doi:10.1038/s41588-021-00822-1.

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM.

Mol Syst Biol, 2021

doi:10.15252/msb.202010188.

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.

Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A.

Nat Genet, 2021

doi:10.1038/s41588-020-00776-w.

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.

Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J.

Mol Syst Biol, 2021

doi:10.15252/msb.20209730.

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases.

Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P.

Cell Rep, 2021

doi:10.1016/j.celrep.2020.108602.

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study.

Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E.

PLoS Genet, 2020

doi:10.1371/journal.pgen.1009065.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ.

Science, 2020

doi:10.1126/science.abe9403.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ.

Cell, 2020

doi:10.1016/j.cell.2020.06.034.

Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.

Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski MM, Latz E, Hardt WD, Krijgsveld J, Typas A.

Nat Microbiol, 2020

doi:10.1038/s41564-020-0736-7.

Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy.

Jiménez-Sánchez A, Cybulska P, Mager KL, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa RE, Soslow RA, Walther T, Shen R, Chi DS, Park KJ, Hollmann T, Reis-Filho JS, Markowetz F, Beltrao P, Vargas HA, Zamarin D, Brenton JD, Snyder A, Weigelt B, Sala E, Miller ML.

Nat Genet, 2020

doi:10.1038/s41588-020-0630-5.

Prediction of Signed Protein Kinase Regulatory Circuits.

Invergo BM, Petursson B, Akhtar N, Bradley D, Giudice G, Hijazi M, Cutillas P, Petsalaki E, Beltrao P.

Cell Syst, 2020

doi:10.1016/j.cels.2020.04.005.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ.

Nature, 2020

doi:10.1038/s41586-020-2286-9.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P.

Nat Biotechnol, 2020

doi:10.1038/s41587-019-0344-3.

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.

Galardini M, Busby BP, Vieitez C, Dunham AS, Typas A, Beltrao P.

Mol Syst Biol, 2019

doi:10.15252/msb.20198831.

Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.

Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M.

Nat Immunol, 2019

doi:10.1038/s41590-019-0471-5.

Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.

Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P.

Mol Cell Proteomics, 2019

doi:10.1074/mcp.ra118.001280.

Evolution of protein kinase substrate recognition at the active site.

Bradley D, Beltrao P.

PLoS Biol, 2019

doi:10.1371/journal.pbio.3000341.

Conserved phosphorylation hotspots in eukaryotic protein domain families.

Strumillo MJ, Oplová M, Viéitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P.

Nat Commun, 2019

doi:10.1038/s41467-019-09952-x.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun, 2019

doi:10.1038/s41467-019-08814-w.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Hermjakob H, Orchard S, Porras P.

Nat Commun, 2019

doi:10.1038/s41467-018-07709-6.

iProteinDB: An Integrative Database of <i>Drosophila</i> Post-translational Modifications.

Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N.

G3 (Bethesda), 2019

doi:10.1534/g3.118.200637.

A resource of variant effect predictions of single nucleotide variants in model organisms.

Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P.

Mol Syst Biol, 2018

doi:10.15252/msb.20188430.

Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.

Invergo BM, Beltrao P.

Essays Biochem, 2018

doi:10.1042/ebc20180019.

Evolution, dynamics and dysregulation of kinase signalling.

Ochoa D, Bradley D, Beltrao P.

Curr Opin Struct Biol, 2018

doi:10.1016/j.sbi.2017.12.008.

Phenotype inference in an <i>Escherichia coli</i> strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.

Elife, 2017

doi:10.7554/elife.31035.

Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.

Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O.

Cell Rep, 2017

doi:10.1016/j.celrep.2017.10.071.

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.

Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P.

Cell Syst, 2017

doi:10.1016/j.cels.2017.08.013.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell Rep, 2017

doi:10.1016/j.celrep.2017.08.010.

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y.

J Proteome Res, 2017

doi:10.1021/acs.jproteome.7b00087.

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P.

Bioinformatics, 2017

doi:10.1093/bioinformatics/btx082.

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.

PLoS Comput Biol, 2017

doi:10.1371/journal.pcbi.1005297.

An atlas of human kinase regulation.

Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P.

Mol Syst Biol, 2016

doi:10.15252/msb.20167295.

Evolution of protein phosphorylation across 18 fungal species.

Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.

Science, 2016

doi:10.1126/science.aaf2144.

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.

Wagih O, Sugiyama N, Ishihama Y, Beltrao P.

Mol Cell Proteomics, 2016

doi:10.1074/mcp.m115.052357.

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.

PLoS Comput Biol, 2015

doi:10.1371/journal.pcbi.1004362.

Towards the computational design of protein post-translational regulation.

Strumillo M, Beltrao P.

Bioorg Med Chem, 2015

doi:10.1016/j.bmc.2015.04.056.

Differential genetic interactions of yeast stress response MAPK pathways.

Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.

Mol Syst Biol, 2015

doi:10.15252/msb.20145606.

Kinase-two-hybrid: towards the conditional interactome.

Ochoa D, Beltrao P.

Mol Syst Biol, 2015

doi:10.15252/msb.20156107.

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T.

J Am Soc Nephrol, 2014

doi:10.1681/asn.2013070760.

Evolution and functional cross-talk of protein post-translational modifications.

Beltrao P, Bork P, Krogan NJ, van Noort V.

Mol Syst Biol, 2013

doi:10.1002/msb.201304521.

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.

Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.

Nat Methods, 2013

doi:10.1038/nmeth.2519.

Systematic functional prioritization of protein posttranslational modifications.

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ.

Cell, 2012

doi:10.1016/j.cell.2012.05.036.

Hierarchical modularity and the evolution of genetic interactomes across species.

Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ.

Mol Cell, 2012

doi:10.1016/j.molcel.2012.05.028.

Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.

Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ.

Proc Natl Acad Sci U S A, 2011

doi:10.1073/pnas.1019735108.

Phenotypic landscape of a bacterial cell.

Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA.

Cell, 2011

doi:10.1016/j.cell.2010.11.052.

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.

Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ.

Mol Syst Biol, 2010

doi:10.1038/msb.2010.107.

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.

Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A.

Mol Syst Biol, 2010

doi:10.1038/msb.2010.31.

Quantitative genetic interactions reveal biological modularity.

Beltrao P, Cagney G, Krogan NJ.

Cell, 2010

doi:10.1016/j.cell.2010.05.019.

ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs.

Encinar JA, Fernandez-Ballester G, Sánchez IE, Hurtado-Gomez E, Stricher F, Beltrao P, Serrano L.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp424.

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ.

PLoS Biol, 2009

doi:10.1371/journal.pbio.1000134.

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.

Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, Valencia A, Serrano L.

J Mol Biol, 2009

doi:10.1016/j.jmb.2009.03.038.

Microblogging the ISMB: a new approach to conference reporting.

Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S.

PLoS Comput Biol, 2009

doi:10.1371/journal.pcbi.1000263.

Evolvability and hierarchy in rewired bacterial gene networks.

Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L.

Nature, 2008

doi:10.1038/nature06847.

Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.

Sánchez IE, Beltrao P, Stricher F, Schymkowitz J, Ferkinghoff-Borg J, Rousseau F, Serrano L.

PLoS Comput Biol, 2008

doi:10.1371/journal.pcbi.1000052.

Analyzing protein interaction networks using structural information.

Kiel C, Beltrao P, Serrano L.

Annu Rev Biochem, 2008

doi:10.1146/annurev.biochem.77.062706.133317.

Structures in systems biology.

Beltrao P, Kiel C, Serrano L.

Curr Opin Struct Biol, 2007

doi:10.1016/j.sbi.2007.05.005.

A genome-wide Ras-effector interaction network.

Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L.

J Mol Biol, 2007

doi:10.1016/j.jmb.2007.05.015.

Specificity and evolvability in eukaryotic protein interaction networks.

Beltrao P, Serrano L.

PLoS Comput Biol, 2007

doi:10.1371/journal.pcbi.0030025.

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.

Syst Biol (Stevenage), 2004

doi:10.1049/sb:20045017.

Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp.

Massey SE, Moura G, Beltrão P, Almeida R, Garey JR, Tuite MF, Santos MA.

Genome Res, 2003

doi:10.1101/gr.811003.