Publications

Publications

2020

*
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. Nature genetics (2020) DOI: 10.1038/s41588-020-0630-5
*
Exploring amino acid functions in a deep mutational landscape
Dunham A, Beltrao P. Preprint DOI: 10.1101/2020.05.26.116756
*
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, Huettenhain 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 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
*
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O’Meara MJ, 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, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJ, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, Zastrow Mv, Taunton J, Schwartz O, Vignuzzi M, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. Preprint DOI: 10.1101/2020.03.22.002386
*
Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica.
Nieman DC, Groen AJ, Pugachev A, Simonson AJ, Polley K, James K, El-Khodor BF, Varadharaj S, Hernández-Armenta C. Proteomes Volume 8 (2020) DOI: 10.3390/proteomes8010004
*
Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer's disease risk genes
Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A. Preprint DOI: 10.1101/2020.01.22.20018424
*
Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex During Red Blood Cell Invasion by Plasmodium falciparum Merozoites
More KR, Kaur I, Gianetto QG, Invergo BM, Chaze T, Jain R, Huon C, Gutenbrunner P, Weisser H, Matondo M, Choudhary JS, Langsley G, Singh S, Chitnis CE. Preprint DOI: 10.1101/2020.01.17.911107
*
A draft genome sequence of the elusive giant squid, Architeuthis dux.
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP. GigaScience Volume 9 (2020) DOI: 10.1093/gigascience/giz152

2019

*
Publisher Correction: In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.
Memon D, Bi J, Miller CJ. Scientific reports Volume 9 (2019) p.20211 DOI: 10.1038/s41598-019-55753-z
*
Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells.
Barrio-Hernandez I, Jafari A, Rigbolt KTG, Hallenborg P, Sanchez-Quiles V, Skovrind I, Akimov V, Kratchmarova I, Dengjel J, Kassem M, Blagoev B. Genome research Volume 30 (2020) p.127-137 DOI: 10.1101/gr.248286.119
*
Towards a systematic map of the functional role of protein phosphorylation
Viéitez C, Busby BP, Ochoa D, Mateus A, Galardini M, Jawed A, Memon D, Potel CM, Vonesch SC, Tu CS, Shahraz M, Stein F, Steinmetz LM, Savitski MM, Typas A, Beltrao P. Preprint DOI: 10.1101/872770
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. Nature biotechnology Volume 38 (2020) p.365-373 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. Molecular systems biology Volume 15 (2019) p.e8831 DOI: 10.15252/msb.20198831
*
Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions
Lees JA, Tien Mai T, Galardini M, Wheeler NE, Corander J. Preprint DOI: 10.1101/852426
*
Population Structure, Stratification and Introgression of Human Structural Variation
Almarri MA, Bergström A, Prado-Martinez J, Yang F, Fu B, Dunham AS, Chen Y, Hurles ME, Tyler-Smith C, Xue Y. Preprint DOI: 10.1101/746172
*
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. Nature immunology Volume 20 (2019) p.1372-1380 DOI: 10.1038/s41590-019-0471-5
*
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. Preprint DOI: 10.1101/712034
*
Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status.
Dueñas M, Pérez-Figueroa A, Oliveira C, Suárez-Cabrera C, Sousa A, Oliveira P, Villacampa F, Paramio JM, Martínez-Fernández M. Scientific reports Volume 9 (2019) p.10362 DOI: 10.1038/s41598-019-46652-4
*
Proteome-wide inference of protein kinase regulatory circuits
Invergo BM, Petursson B, Bradley D, Giudice G, Petsalaki E, Beltrao P. Preprint DOI: 10.1101/703157
*
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.
Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. Molecular & cellular proteomics : MCP Volume 18 (2019) p.S114-S125 DOI: 10.1074/mcp.ra118.001280
Evolution of protein kinase substrate recognition at the active site.
Bradley D, Beltrao P. PLoS biology Volume 17 (2019) p.e3000341 DOI: 10.1371/journal.pbio.3000341
*
In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.
Memon D, Bi J, Miller CJ. Scientific reports Volume 9 (2019) p.7372 DOI: 10.1038/s41598-019-43758-7
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. Nature communications Volume 10 (2019) p.1977 DOI: 10.1038/s41467-019-09952-x
*
Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.
Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J. Systems medicine (New Rochelle, N.Y.) Volume 2 (2019) p.1-9 DOI: 10.1089/sysm.2018.0013
*
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. Nature communications Volume 10 (2019) p.1098 DOI: 10.1038/s41467-019-08814-w
*
CDH1 somatic alterations in Mexican patients with diffuse and mixed sporadic gastric cancer.
Bustos-Carpinteyro AR, Oliveira C, Sousa A, Oliveira P, Pinheiro H, Carvalho J, Magaña-Torres MT, Flores-Miramontes MG, Aguilar-Lemarroy A, Jave-Suárez LF, Peregrina-Sandoval J, Cruz-Ramos JA, Sánchez-López JY. BMC cancer Volume 19 (2019) p.69 DOI: 10.1186/s12885-019-5294-0
*
iProteinDB: An Integrative Database of Drosophila 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, Md.) Volume 9 (2019) p.1-11 DOI: 10.1534/g3.118.200637
*
Copy number aberrations drive kinase re-wiring leading to genetic vulnerabilities in cancer
Memon D, Gill MG, Papachristou E, Ochoa D, D'Santos C, Miller ML, Beltrao P. Preprint DOI: 10.1101/515932
*
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. Nature communications Volume 10 (2019) p.10 DOI: 10.1038/s41467-018-07709-6

2018

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. Molecular systems biology Volume 14 (2018) p.e8430 DOI: 10.15252/msb.20188430
*
Predicting eukaryotic protein secretion without signals.
Nielsen H, Petsalaki EI, Zhao L, Stühler K. Biochimica et biophysica acta. Proteins and proteomics Volume 1867 (2019) p.140174 DOI: 10.1016/j.bbapap.2018.11.011
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.
Invergo BM, Beltrao P. Essays in biochemistry Volume 62 (2018) p.525-534 DOI: 10.1042/ebc20180019
*
Chromatin accessibility dynamics across C. elegans development and ageing.
Jänes J, Dong Y, Schoof M, Serizay J, Appert A, Cerrato C, Woodbury C, Chen R, Gemma C, Huang N, Kissiov D, Stempor P, Steward A, Zeiser E, Sauer S, Ahringer J. eLife Volume 7 (2018) DOI: 10.7554/elife.37344
*
Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma.
Bennett L, Howell M, Memon D, Smowton C, Zhou C, Miller CJ. Scientific reports Volume 8 (2018) p.14830 DOI: 10.1038/s41598-018-33276-3
*
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. Preprint DOI: 10.1101/391185
*
UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.
Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B. Nature structural & molecular biology Volume 25 (2018) p.631-640 DOI: 10.1038/s41594-018-0084-y
*
Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium Curators, del Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong L, Jurisica I, Hermjakob H, Orchard S, Porras P. Preprint DOI: 10.1101/346833
*
Comprehensive variant effect predictions of single nucleotide variants in model organisms
Wagih O, Busby B, Galardini M, Memon D, Typas A, Beltrao P. Preprint DOI: 10.1101/313031
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nature microbiology Volume 3 (2018) p.514-522 DOI: 10.1038/s41564-018-0123-9
*
Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model.
Nené NR, Dunham AS, Illingworth CJR. Genetics Volume 209 (2018) p.255-264 DOI: 10.1534/genetics.118.300790
*
pyseer: a comprehensive tool for microbial pangenome-wide association studies
Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J. Preprint DOI: 10.1101/266312
*
Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors
Wagih O, Merico D, Delong A, Frey BJ. Preprint DOI: 10.1101/253427
Evolution, dynamics and dysregulation of kinase signalling.
Ochoa D, Bradley D, Beltrao P. Current opinion in structural biology Volume 48 (2018) p.133-140 DOI: 10.1016/j.sbi.2017.12.008

2017

Phenotype inference in an Escherichia coli 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 Volume 6 (2017) DOI: 10.7554/elife.31035
*
StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites.
Akimov V, Olsen LCB, Hansen SVF, Barrio-Hernandez I, Puglia M, Jensen SS, Solov'yov IA, Kratchmarova I, Blagoev B. Journal of proteome research Volume 17 (2018) p.296-304 DOI: 10.1021/acs.jproteome.7b00566
ggseqlogo: a versatile R package for drawing sequence logos.
Wagih O. Bioinformatics (Oxford, England) Volume 33 (2017) p.3645-3647 DOI: 10.1093/bioinformatics/btx469
Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Cell reports Volume 21 (2017) p.2017-2029 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 systems Volume 5 (2017) p.386-398.e4 DOI: 10.1016/j.cels.2017.08.013
*
Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.
Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A. ACS central science Volume 3 (2017) p.1086-1095 DOI: 10.1021/acscentsci.7b00269
*
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.
Jiménez-Sánchez A, Memon D, Pourpe S, Veeraraghavan H, Li Y, Vargas HA, Gill MB, Park KJ, Zivanovic O, Konner J, Ricca J, Zamarin D, Walther T, Aghajanian C, Wolchok JD, Sala E, Merghoub T, Snyder A, Miller ML. Cell Volume 170 (2017) p.927-938.e20 DOI: 10.1016/j.cell.2017.07.025
*
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 reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
*
Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor.
Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B. Molecular & cellular proteomics : MCP Volume 16 (2017) p.1433-1446 DOI: 10.1074/mcp.m116.066423
Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851 DOI: 10.1093/bioinformatics/btx082
*
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. Journal of proteome research Volume 16 (2017) p.1825-1830 DOI: 10.1021/acs.jproteome.7b00087
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 computational biology Volume 13 (2017) p.e1005297 DOI: 10.1371/journal.pcbi.1005297

2016

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. Molecular systems biology Volume 12 (2016) p.888 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 (New York, N.Y.) Volume 354 (2016) p.229-232 DOI: 10.1126/science.aaf2144
*
Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response.
Memon D, Dawson K, Smowton CS, Xing W, Dive C, Miller CJ. NPJ genomic medicine Volume 1 (2016) p.16020 DOI: 10.1038/npjgenmed.2016.20
*
Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
Gonçalves E, Raguz Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. Preprint DOI: 10.1101/057398
*
Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.
Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V. Royal Society open science Volume 3 (2016) p.150484 DOI: 10.1098/rsos.150484

2015

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.
Wagih O, Sugiyama N, Ishihama Y, Beltrao P. Molecular & cellular proteomics : MCP Volume 15 (2016) p.236-245 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 computational biology Volume 11 (2015) p.e1004362 DOI: 10.1371/journal.pcbi.1004362
*
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.
Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D. PloS one Volume 10 (2015) p.e0130600 DOI: 10.1371/journal.pone.0130600
Towards the computational design of protein post-translational regulation.
Strumillo M, Beltrao P. Bioorganic & medicinal chemistry Volume 23 (2015) p.2877-2882 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. Molecular systems biology Volume 11 (2015) p.800 DOI: 10.15252/msb.20145606
Kinase-two-hybrid: towards the conditional interactome.
Ochoa D, Beltrao P. Molecular systems biology Volume 11 (2015) p.798 DOI: 10.15252/msb.20156107
*
Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited.
Rossier BC, Baker ME, Studer RA. Physiological reviews Volume 95 (2015) p.297-340 DOI: 10.1152/physrev.00011.2014

2014

*
Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.
Baker ME, Nelson DR, Studer RA. The Journal of steroid biochemistry and molecular biology Volume 151 (2015) p.12-24 DOI: 10.1016/j.jsbmb.2014.10.020
*
CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. Nucleic acids research Volume 43 (2015) p.D376-81 DOI: 10.1093/nar/gku947
Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.
Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R. Open biology Volume 4 (2014) DOI: 10.1098/rsob.140121
*
Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations.
Rallapalli PM, Orengo CA, Studer RA, Perkins SJ. Molecular biology and evolution Volume 31 (2014) p.3040-3056 DOI: 10.1093/molbev/msu248
*
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. Journal of the American Society of Nephrology : JASN Volume 25 (2014) p.1509-1522 DOI: 10.1681/asn.2013070760
*
Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.
Studer RA, Christin PA, Williams MA, Orengo CA. Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.2223-2228 DOI: 10.1073/pnas.1310811111

2013

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V. Molecular systems biology Volume 9 (2013) p.714 DOI: 10.1002/msb.201304521
*
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA. Nucleic acids research Volume 42 (2014) p.D240-5 DOI: 10.1093/nar/gkt1205
*
Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Nucleic acids research Volume 42 (2014) p.D917-21 DOI: 10.1093/nar/gkt1065
*
Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.
Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L. PLoS genetics Volume 9 (2013) p.e1003730 DOI: 10.1371/journal.pgen.1003730
*
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. Nature methods Volume 10 (2013) p.676-682 DOI: 10.1038/nmeth.2519
*
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes.
Studer RA, Dessailly BH, Orengo CA. The Biochemical journal Volume 449 (2013) p.581-594 DOI: 10.1042/bj20121221

2012

*
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA. Nucleic acids research Volume 41 (2013) p.D490-8 DOI: 10.1093/nar/gks1211