Publications

Publications

2018

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

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

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

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

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

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

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

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

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) p.
DOI: 10.7554/elife.31035

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

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

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

2015

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

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

2014

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

2013

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

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