| Year |
Citation |
Score |
| 2020 |
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, et al. Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Briefings in Bioinformatics. PMID 32313939 DOI: 10.1093/Bib/Bbaa046 |
0.314 |
|
| 2020 |
Ducrest AL, Neuenschwander S, Schmid-Siegert E, Pagni M, Train C, Dylus D, Nevers Y, Warwick Vesztrocy A, San-Jose LM, Dupasquier M, Dessimoz C, Xenarios I, Roulin A, Goudet J. New genome assembly of the barn owl (). Ecology and Evolution. 10: 2284-2298. PMID 32184981 DOI: 10.1002/Ece3.5991 |
0.324 |
|
| 2020 |
Bolleman J, de Castro E, Baratin D, Gehant S, Cuche BA, Auchincloss AH, Coudert E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Xenarios I, Redaschi N, Bridge A. HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. Gigascience. 9. PMID 32034905 DOI: 10.1093/Gigascience/Giaa003 |
0.334 |
|
| 2019 |
Famiglietti ML, Estreicher A, Breuza L, Poux S, Redaschi N, Xenarios I, Bridge A. An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. Database : the Journal of Biological Databases and Curation. 2019. PMID 30937429 DOI: 10.1093/Database/Baz040 |
0.352 |
|
| 2018 |
Egli A, Blanc DS, Greub G, Keller PM, Lazarevic V, Lebrand A, Leib S, Neher RA, Perreten V, Ramette A, Schrenzel J, Stephan R, Wagner K, Wuethrich D, Xenarios I. Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss Medical Weekly. 148: w14693. PMID 30552858 DOI: 10.4414/Smw.2018.14693 |
0.333 |
|
| 2018 |
Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A. Updates in Rhea: SPARQLing biochemical reaction data. Nucleic Acids Research. PMID 30272209 DOI: 10.1093/Nar/Gky876 |
0.32 |
|
| 2017 |
Martin Campos T, Mylonas R, Masselot A, Waridel P, Petricevic T, Xenarios I, Quadroni M. MsViz, a graphical software tool for in-depth manual validation and quantitation of post-translational modifications. Journal of Proteome Research. PMID 28636386 DOI: 10.1021/Acs.Jproteome.7B00194 |
0.332 |
|
| 2016 |
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, ... ... Xenarios I, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Research. PMID 27899635 DOI: 10.1093/Nar/Gkw1107 |
0.343 |
|
| 2016 |
Kostyrko K, Neuenschwander S, Junier T, Regamey A, Iseli C, Schmid-Siegert E, Bosshard S, Majocchi S, Le Fourn V, Girod PA, Xenarios I, Mermod N. MAR-mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering. Biotechnology and Bioengineering. PMID 27575535 DOI: 10.1002/Bit.26086 |
0.32 |
|
| 2016 |
Rodius S, Androsova G, Götz L, Liechti R, Crespo I, Merz S, Nazarov PV, de Klein N, Jeanty C, González-Rosa JM, Muller A, Bernardin F, Niclou SP, Vallar L, Mercader N, ... ... Xenarios I, et al. Analysis of the dynamic co-expression network of heart regeneration in the zebrafish. Scientific Reports. 6: 26822. PMID 27241320 DOI: 10.1038/Srep26822 |
0.301 |
|
| 2016 |
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, ... ... Xenarios I, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/Nmeth.3830 |
0.313 |
|
| 2016 |
Crespo I, Doucey MA, Xenarios I. Social networks help to infer causality in the tumor microenvironment. Bmc Research Notes. 9: 168. PMID 26979239 DOI: 10.1186/S13104-016-1976-8 |
0.3 |
|
| 2016 |
Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Methods in Molecular Biology (Clifton, N.J.). 1374: 23-54. PMID 26519399 DOI: 10.1007/978-1-4939-3167-5_2 |
0.35 |
|
| 2016 |
Famiglietti ML, Breuza L, Neto T, Gehant S, Redaschi N, Bougueleret L, Xenarios I, Poux S. Human protein variants in UniProtKB/Swiss-Prot: improving access to knowledge through standardized annotations F1000research. 5. DOI: 10.7490/F1000Research.1111798.1 |
0.302 |
|
| 2015 |
Alfaiz AA, Müller V, Boutry-Kryza N, Ville D, Guex N, de Bellescize J, Rivier C, Labalme A, des Portes V, Edery P, Till M, Xenarios I, Sanlaville D, Herrmann JM, Lesca G, et al. West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1. European Journal of Human Genetics : Ejhg. PMID 26486472 DOI: 10.1038/Ejhg.2015.227 |
0.317 |
|
| 2015 |
Wachowicz P, Chasapi A, Krapp A, Cano Del Rosario E, Schmitter D, Sage D, Unser M, Xenarios I, Rougemont J, Simanis V. Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN. Journal of Cell Science. 128: 741-54. PMID 25501816 DOI: 10.1242/Jcs.160150 |
0.308 |
|
| 2015 |
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, ... ... Xenarios I, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Research. 43: D213-21. PMID 25428371 DOI: 10.1093/Nar/Gku1243 |
0.348 |
|
| 2015 |
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Research. 43: D1064-70. PMID 25348399 DOI: 10.1093/Nar/Gku1002 |
0.332 |
|
| 2014 |
Rausell A, Mohammadi P, McLaren PJ, Bartha I, Xenarios I, Fellay J, Telenti A. Analysis of stop-gain and frameshift variants in human innate immunity genes. Plos Computational Biology. 10: e1003757. PMID 25058640 DOI: 10.1371/Journal.Pcbi.1003757 |
0.32 |
|
| 2014 |
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, ... ... Xenarios I, et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics : McP. 13: 2765-75. PMID 24980485 DOI: 10.1074/Mcp.O113.036681 |
0.303 |
|
| 2014 |
Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. Human Mutation. 35: 927-35. PMID 24848695 DOI: 10.1002/Humu.22594 |
0.332 |
|
| 2014 |
Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M, Deplancke B, Desvergne B, Guex N, Naef F, Rougemont J, ... ... Xenarios I, et al. Quantifying ChIP-seq data: A spiking method providing an internal reference for sample-to-sample normalization Genome Research. 24: 1157-1168. PMID 24709819 DOI: 10.1101/Gr.168260.113 |
0.311 |
|
| 2014 |
Apweiler R, Bateman A, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Alpi E, Antunes R, Arganiska J, Casanova EB, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, ... ... Xenarios I, et al. Activities at the Universal Protein Resource (UniProt) Nucleic Acids Research. 42: D191-D198. PMID 24253303 DOI: 10.1093/Nar/Gkt1140 |
0.326 |
|
| 2014 |
Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics. 15: 123-35. PMID 23172809 DOI: 10.1093/Bib/Bbs058 |
0.302 |
|
| 2013 |
Peterson H, Abu Dawud R, Garg A, Wang Y, Vilo J, Xenarios I, Adjaye J. Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. Frontiers in Physiology. 4: 303. PMID 24194720 DOI: 10.3389/Fphys.2013.00303 |
0.307 |
|
| 2013 |
Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I. Application of text-mining for updating protein post-translational modification annotation in UniProtKB. Bmc Bioinformatics. 14: 104. PMID 23517090 DOI: 10.1186/1471-2105-14-104 |
0.3 |
|
| 2013 |
Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L. pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics (Oxford, England). 29: 1215-7. PMID 23505298 DOI: 10.1093/Bioinformatics/Btt129 |
0.348 |
|
| 2013 |
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Research. 41: D584-9. PMID 23193261 DOI: 10.1093/Nar/Gks1157 |
0.329 |
|
| 2012 |
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, ... ... Xenarios I, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research. 40: W597-603. PMID 22661580 DOI: 10.1093/Nar/Gks400 |
0.317 |
|
| 2012 |
Jungo F, Bougueleret L, Xenarios I, Poux S. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon : Official Journal of the International Society On Toxinology. 60: 551-7. PMID 22465017 DOI: 10.1016/J.Toxicon.2012.03.010 |
0.316 |
|
| 2012 |
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Brinkman F, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, ... ... Xenarios I, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nature Methods. 9: 345-50. PMID 22453911 DOI: 10.1038/Nmeth.1931 |
0.312 |
|
| 2012 |
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, ... ... Xenarios I, et al. The UniProt-GO Annotation database in 2011. Nucleic Acids Research. 40: D565-70. PMID 22123736 DOI: 10.1093/Nar/Gkr1048 |
0.372 |
|
| 2012 |
Garg A, Mohanram K, De Micheli G, Xenarios I. Implicit methods for qualitative modeling of gene regulatory networks. Methods in Molecular Biology (Clifton, N.J.). 786: 397-443. PMID 21938638 DOI: 10.1007/978-1-61779-292-2_22 |
0.336 |
|
| 2011 |
Kapur K, Schüpbach T, Xenarios I, Kutalik Z, Bergmann S. Comparison of strategies to detect epistasis from eQTL data. Plos One. 6: e28415. PMID 22205949 DOI: 10.1371/Journal.Pone.0028415 |
0.326 |
|
| 2011 |
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y. Visualization and quality assessment of de novo genome assemblies. Bioinformatics (Oxford, England). 27: 3425-6. PMID 21994228 DOI: 10.1093/Bioinformatics/Btr569 |
0.651 |
|
| 2011 |
Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C. Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings in Bioinformatics. 12: 423-35. PMID 21737420 DOI: 10.1093/Bib/Bbr034 |
0.371 |
|
| 2011 |
Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Quadroni M, Waridel P, Gaillard M, Pidoux M, Rapin B, Rivolta C, Xenarios I, Simpson AJ, Antonarakis SE, Beckmann JS, et al. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. Plos One. 6: e18369. PMID 21494657 DOI: 10.1371/Journal.Pone.0018369 |
0.339 |
|
| 2011 |
Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, ... ... Xenarios I, et al. The genome of the fire ant Solenopsis invicta. Proceedings of the National Academy of Sciences of the United States of America. 108: 5679-84. PMID 21282665 DOI: 10.1073/Pnas.1009690108 |
0.66 |
|
| 2011 |
Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P. ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Research. 39: D576-82. PMID 20947564 DOI: 10.1093/Nar/Gkq901 |
0.332 |
|
| 2010 |
Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I. Animal Toxins: How is Complexity Represented in Databases? Toxins. 2: 262-82. PMID 22069583 DOI: 10.3390/Toxins2020262 |
0.301 |
|
| 2010 |
Liechti R, Csárdi G, Bergmann S, Schütz F, Sengstag T, Boj SF, Servitja JM, Ferrer J, Van Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL, Marselli L, ... ... Xenarios I, et al. EuroDia: a beta-cell gene expression resource. Database : the Journal of Biological Databases and Curation. 2010: baq024. PMID 20940178 DOI: 10.1093/Database/Baq024 |
0.323 |
|
| 2010 |
Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Le Mercier P, Bairoch A, Xenarios I. OpenFluDB, a database for human and animal influenza virus. Database : the Journal of Biological Databases and Curation. 2010: baq004. PMID 20624713 DOI: 10.1093/Database/Baq004 |
0.318 |
|
| 2010 |
Santuari L, Pradervand S, Amiguet-Vercher AM, Thomas J, Dorcey E, Harshman K, Xenarios I, Juenger TE, Hardtke CS. Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biology. 11: R4. PMID 20067627 DOI: 10.1186/Gb-2010-11-1-R4 |
0.32 |
|
| 2009 |
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E. ENFIN--A European network for integrative systems biology. Comptes Rendus Biologies. 332: 1050-8. PMID 19909926 DOI: 10.1016/J.Crvi.2009.09.003 |
0.308 |
|
| 2009 |
Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M. MIMAS 3.0 is a Multiomics Information Management and Annotation System. Bmc Bioinformatics. 10: 151. PMID 19450266 DOI: 10.1186/1471-2105-10-151 |
0.326 |
|
| 2009 |
Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J. The Microbe browser for comparative genomics Nucleic Acids Research. 37: W296-W299. PMID 19406928 DOI: 10.1093/Nar/Gkp268 |
0.35 |
|
| 2009 |
Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinformatics (Oxford, England). 25: 662-3. PMID 19168913 DOI: 10.1093/Bioinformatics/Btp017 |
0.341 |
|
| 2008 |
Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G. Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics (Oxford, England). 24: 1917-25. PMID 18614585 DOI: 10.1093/Bioinformatics/Btn336 |
0.321 |
|
| 2007 |
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. Bmc Biology. 5: 44. PMID 17925023 DOI: 10.1186/1741-7007-5-44 |
0.319 |
|
| 2007 |
Pasquali C, Bertschy-Meier D, Chabert C, Curchod ML, Arod C, Booth R, Mechtler K, Vilbois F, Xenarios I, Ferguson CG, Prestwich GD, Camps M, Rommel C. A chemical proteomics approach to phosphatidylinositol 3-kinase signaling in macrophages. Molecular & Cellular Proteomics : McP. 6: 1829-41. PMID 17617665 DOI: 10.1074/Mcp.T600066-Mcp200 |
0.304 |
|
| 2004 |
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, ... ... Xenarios I, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/Nbt926 |
0.345 |
|
| 2002 |
Duan XJ, Xenarios I, Eisenberg D. Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Molecular & Cellular Proteomics : McP. 1: 104-16. PMID 12096128 DOI: 10.1074/Mcp.M100026-Mcp200 |
0.334 |
|
| 2002 |
Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research. 30: 303-5. PMID 11752321 DOI: 10.1093/Nar/30.1.303 |
0.328 |
|
| 2001 |
Xenarios I, Eisenberg D. Protein interaction databases. Current Opinion in Biotechnology. 12: 334-9. PMID 11551460 DOI: 10.1016/S0958-1669(00)00224-X |
0.338 |
|
| 2001 |
Kennedy MA, Venkateswaran A, Tarr PT, Xenarios I, Kudoh J, Shimizu N, Edwards PA. Characterization of the human ABCG1 gene: liver X receptor activates an internal promoter that produces a novel transcript encoding an alternative form of the protein. The Journal of Biological Chemistry. 276: 39438-47. PMID 11500512 DOI: 10.1074/Jbc.M105863200 |
0.31 |
|
| 2001 |
Marcotte EM, Xenarios I, Eisenberg D. Mining literature for protein-protein interactions. Bioinformatics (Oxford, England). 17: 359-63. PMID 11301305 DOI: 10.1093/Bioinformatics/17.4.359 |
0.31 |
|
| 2000 |
Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. Localizing proteins in the cell from their phylogenetic profiles. Proceedings of the National Academy of Sciences of the United States of America. 97: 12115-20. PMID 11035803 DOI: 10.1073/Pnas.220399497 |
0.307 |
|
| 2000 |
Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature. 405: 823-6. PMID 10866208 DOI: 10.1038/35015694 |
0.339 |
|
| 2000 |
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Research. 28: 289-91. PMID 10592249 DOI: 10.1093/Nar/28.1.289 |
0.304 |
|
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