Publications

Publications

2018

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
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
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
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
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
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
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

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
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

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
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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