Publications

Publications

2018

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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, Pinero J, Kotlyar M, Chiara P, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras Millan P. Preprint DOI: 10.1101/346833
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
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pyseer: a comprehensive tool for microbial pangenome-wide association studies
Lees J, Galardini M, Bentley SD, Weiser JN, Corander J. Preprint DOI: 10.1101/266312
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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
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
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
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
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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

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
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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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
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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
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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
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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
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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

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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