| Year |
Citation |
Score |
| 2024 |
Korir PK, Iudin A, Somasundharam S, Weyand S, Salih O, Hartley M, Sarkans U, Patwardhan A, Kleywegt GJ. Ten recommendations for organising bioimaging data for archival. F1000research. 12. PMID 38486614 DOI: 10.12688/f1000research.129720.2 |
0.469 |
|
| 2022 |
Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive - building a home for life-sciences microscopy data. Journal of Molecular Biology. 167505. PMID 35189131 DOI: 10.1016/j.jmb.2022.167505 |
0.395 |
|
| 2020 |
Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A. From ArrayExpress to BioStudies. Nucleic Acids Research. PMID 33211879 DOI: 10.1093/nar/gkaa1062 |
0.523 |
|
| 2020 |
Krebs A, van Vugt-Lussenburg BMA, Waldmann T, Albrecht W, Boei J, Ter Braak B, Brajnik M, Braunbeck T, Brecklinghaus T, Busquet F, Dinnyes A, Dokler J, Dolde X, Exner TE, Fisher C, ... ... Sarkans U, et al. The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods. Archives of Toxicology. PMID 32632539 DOI: 10.1007/S00204-020-02802-6 |
0.363 |
|
| 2018 |
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. A call for public archives for biological image data. Nature Methods. 15: 849-854. PMID 30377375 DOI: 10.1038/S41592-018-0195-8 |
0.454 |
|
| 2018 |
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Research. PMID 30357387 DOI: 10.1093/Nar/Gky964 |
0.527 |
|
| 2018 |
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Publisher Correction: Image Data Resource: a bioimage data integration and publication platform. Nature Methods. PMID 30287931 DOI: 10.1038/S41592-018-0169-X |
0.448 |
|
| 2017 |
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. The BioStudies database-one stop shop for all data supporting a life sciences study. Nucleic Acids Research. PMID 29069414 DOI: 10.1093/Nar/Gkx965 |
0.552 |
|
| 2017 |
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nature Methods. 14: 775-781. PMID 28775673 DOI: 10.1038/Nmeth.4326 |
0.492 |
|
| 2017 |
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, ... ... Sarkans U, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nature Biotechnology. 35: 406-409. PMID 28486464 DOI: 10.1038/Nbt.3790 |
0.454 |
|
| 2017 |
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U. Orchestrating differential data access for translational research: a pilot implementation. Bmc Medical Informatics and Decision Making. 17: 30. PMID 28330491 DOI: 10.1186/S12911-017-0424-6 |
0.498 |
|
| 2017 |
Huerta L, Barrera E, Bazant W, Fonseca NA, Fullgrabe A, Keays M, Mohammed S, Munoz-Pomer A, Tang A, Papatheodorou I, Petryszak R, Sarkans U, Brazma A. Expression Atlas: exploring gene expression results across species under different biological conditions F1000research. 6. DOI: 10.7490/F1000Research.1114619.1 |
0.305 |
|
| 2015 |
McEntyre J, Sarkans U, Brazma A. The BioStudies database. Molecular Systems Biology. 11: 847. PMID 26700850 DOI: 10.15252/Msb.20156658 |
0.484 |
|
| 2015 |
Kirsanova C, Brazma A, Rustici G, Sarkans U. Cellular phenotype database: a repository for systems microscopy data. Bioinformatics (Oxford, England). PMID 25861964 DOI: 10.1093/Bioinformatics/Btv199 |
0.479 |
|
| 2015 |
Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, ... ... Sarkans U, et al. diXa: a data infrastructure for chemical safety assessment. Bioinformatics (Oxford, England). 31: 1505-7. PMID 25505093 DOI: 10.1093/bioinformatics/btu827 |
0.339 |
|
| 2015 |
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, ... ... Sarkans U, et al. ArrayExpress update--simplifying data submissions. Nucleic Acids Research. 43: D1113-6. PMID 25361974 DOI: 10.1093/Nar/Gku1057 |
0.553 |
|
| 2014 |
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H. Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Research. 42: D50-2. PMID 24265224 DOI: 10.1093/Nar/Gkt1081 |
0.484 |
|
| 2014 |
Kirsanova C, Sarkans U, Rustici G, Jupp S, Brazma A. Cellular phenotype database with ontology assisted data browsing F1000research. 5. DOI: 10.7490/F1000Research.1096808.1 |
0.524 |
|
| 2013 |
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, ... ... Sarkans U, et al. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Research. 41: D987-90. PMID 23193272 DOI: 10.1093/Nar/Gks1174 |
0.569 |
|
| 2012 |
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P. graph2tab, a library to convert experimental workflow graphs into tabular formats. Bioinformatics (Oxford, England). 28: 1665-7. PMID 22556367 DOI: 10.1093/Bioinformatics/Bts258 |
0.394 |
|
| 2012 |
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H. The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Research. 40: D64-70. PMID 22096232 DOI: 10.1093/Nar/Gkr937 |
0.444 |
|
| 2011 |
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, et al. ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research. 39: D1002-4. PMID 21071405 DOI: 10.1093/Nar/Gkq1040 |
0.518 |
|
| 2009 |
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, et al. A System for Information Management in BioMedical Studies--SIMBioMS. Bioinformatics (Oxford, England). 25: 2768-9. PMID 19633095 DOI: 10.1093/Bioinformatics/Btp420 |
0.457 |
|
| 2009 |
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, ... ... Sarkans U, et al. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research. 37: D868-72. PMID 19015125 DOI: 10.1093/Nar/Gkn889 |
0.544 |
|
| 2008 |
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A. Data storage and analysis in ArrayExpress and Expression Profiler. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 7.13. PMID 18819076 DOI: 10.1002/0471250953.Bi0713S23 |
0.54 |
|
| 2007 |
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, ... ... Sarkans U, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347 |
0.499 |
|
| 2007 |
Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U. PASSIM--an open source software system for managing information in biomedical studies. Bmc Bioinformatics. 8: 52. PMID 17291344 DOI: 10.1186/1471-2105-8-52 |
0.384 |
|
| 2007 |
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, et al. ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Research. 35: D747-50. PMID 17132828 DOI: 10.1093/Nar/Gkl995 |
0.537 |
|
| 2006 |
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, ... ... Sarkans U, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489 |
0.487 |
|
| 2006 |
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M. Data storage and analysis in ArrayExpress. Methods in Enzymology. 411: 370-86. PMID 16939801 DOI: 10.1016/S0076-6879(06)11020-4 |
0.601 |
|
| 2006 |
Brazma A, Krestyaninova M, Sarkans U. Standards for systems biology. Nature Reviews. Genetics. 7: 593-605. PMID 16847461 DOI: 10.1038/Nrg1922 |
0.431 |
|
| 2006 |
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, ... Sarkans U, et al. Wrestling with SUMO and bio-ontologies. Nature Biotechnology. 24: 21-2; author reply 2. PMID 16404382 DOI: 10.1038/Nbt0106-21A |
0.323 |
|
| 2005 |
Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M. Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress. Plant Physiology. 139: 632-6. PMID 16219923 DOI: 10.1104/Pp.105.063156 |
0.567 |
|
| 2005 |
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, et al. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 33: D553-5. PMID 15608260 DOI: 10.1093/Nar/Gki056 |
0.599 |
|
| 2005 |
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, et al. The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics (Oxford, England). 21: 1495-501. PMID 15564302 DOI: 10.1093/Bioinformatics/Bti157 |
0.496 |
|
| 2004 |
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Research. 32: W465-70. PMID 15215431 DOI: 10.1093/Nar/Gkh470 |
0.527 |
|
| 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, 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 |
0.378 |
|
| 2003 |
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies. 326: 1075-8. PMID 14744115 DOI: 10.1016/J.Crvi.2003.09.026 |
0.6 |
|
| 2003 |
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 31: 68-71. PMID 12519949 DOI: 10.1093/nar/gkg091 |
0.523 |
|
| 2002 |
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K. Microarray data representation, annotation and storage. Advances in Biochemical Engineering/Biotechnology. 77: 113-39. PMID 12227734 DOI: 10.1007/3-540-45713-5_7 |
0.544 |
|
| 2002 |
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 3: RESEARCH0046. PMID 12225585 DOI: 10.1186/Gb-2002-3-9-Research0046 |
0.571 |
|
| 2001 |
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, ... ... Sarkans U, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 29: 365-71. PMID 11726920 DOI: 10.1038/Ng1201-365 |
0.567 |
|
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