Found: 29

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  • Multi-omics HeCaToS dataset of repeated dose toxicity for cardiotoxic & hepatotoxic compounds.

    Published in:
    Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01825-1
    By:
    • Verheijen, Marcha;
    • Sarkans, Ugis;
    • Wolski, Witold;
    • Jennen, Danyel;
    • Caiment, Florian;
    • Kleinjans, Jos;
    • HeCaToS Consortium;
    • Agarkova, Irina;
    • Atkinson, Francis L.;
    • Bachmann, Ivo;
    • Baier, Vanessa;
    • Barel, Gal;
    • Bauer, Chris;
    • van den Beucken, Twan;
    • Boerno, Stefan;
    • Bosc, Nicolas;
    • Carey, Conn;
    • Castell, José V.;
    • Clayton, Olivia;
    • Cordes, Henrik
    Publication type:
    Article

  • ArrayExpress update – from bulk to single-cell expression data.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D711, doi. 10.1093/nar/gky964
    By:
    • Athar, Awais;
    • Füllgrabe, Anja;
    • George, Nancy;
    • Iqbal, Haider;
    • Huerta, Laura;
    • Ali, Ahmed;
    • Snow, Catherine;
    • Fonseca, Nuno A;
    • Petryszak, Robert;
    • Papatheodorou, Irene;
    • Sarkans, Ugis;
    • Brazma, Alvis
    Publication type:
    Article

  • The BioStudies database--one stop shop for all data supporting a life sciences study.

    Published in:
    Nucleic Acids Research, 2018, v. 46, n. D1, p. D1266, doi. 10.1093/nar/gkx965
    By:
    • Sarkans, Ugis;
    • Gostev, Mikhail;
    • Athar, Awais;
    • Behrangi, Ehsan;
    • Melnichuk, Olga;
    • Ali, Ahmed;
    • Minguet, Jasmine;
    • Rada, Juan Camillo;
    • Snow, Catherine;
    • Tikhonov, Andrew
    Publication type:
    Article

  • ArrayExpress update—simplifying data submissions.

    Published in:
    Nucleic Acids Research, 2015, v. 43, n. D1, p. D1113, doi. 10.1093/nar/gku1057
    By:
    • Kolesnikov, Nikolay;
    • Hastings, Emma;
    • Keays, Maria;
    • Melnichuk, Olga;
    • Tang, Y. Amy;
    • Williams, Eleanor;
    • Dylag, Miroslaw;
    • Kurbatova, Natalja;
    • Brandizi, Marco;
    • Burdett, Tony;
    • Megy, Karyn;
    • Pilicheva, Ekaterina;
    • Rustici, Gabriella;
    • Tikhonov, Andrew;
    • Parkinson, Helen;
    • Petryszak, Robert;
    • Sarkans, Ugis;
    • Brazma, Alvis
    Publication type:
    Article

  • Updates to BioSamples database at European Bioinformatics Institute.

    Published in:
    Nucleic Acids Research, 2014, v. 42, n. D1, p. D50, doi. 10.1093/nar/gkt1081
    By:
    • Faulconbridge, Adam;
    • Burdett, Tony;
    • Brandizi, Marco;
    • Gostev, Mikhail;
    • Pereira, Rui;
    • Vasant, Drashtti;
    • Sarkans, Ugis;
    • Brazma, Alvis;
    • Parkinson, Helen
    Publication type:
    Article

  • The BioSample Database (BioSD) at the European Bioinformatics Institute.

    Published in:
    Nucleic Acids Research, 2012, p. D64, doi. 10.1093/nar/gkr937
    By:
    • Gostev, Mikhail;
    • Faulconbridge, Adam;
    • Brandizi, Marco;
    • Fernandez-Banet, Julio;
    • Sarkans, Ugis;
    • Brazma, Alvis;
    • Parkinson, Helen
    Publication type:
    Article

  • ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments.

    Published in:
    Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D1002, doi. 10.1093/nar/gkq1040
    By:
    • Parkinson, Helen;
    • Sarkans, Ugis;
    • Kolesnikov, Nikolay;
    • Abeygunawardena, Niran;
    • Burdett, Tony;
    • Dylag, Miroslaw;
    • Emam, Ibrahim;
    • Farne, Anna;
    • Hastings, Emma;
    • Holloway, Ele;
    • Kurbatova, Natalja;
    • Lukk, Margus;
    • Malone, James;
    • Mani, Roby;
    • Pilicheva, Ekaterina;
    • Rustici, Gabriella;
    • Sharma, Anjan;
    • Williams, Eleanor;
    • Adamusiak, Tomasz;
    • Brandizi, Marco
    Publication type:
    Article

  • Discovering and linking public omics data sets using the Omics Discovery Index.

    Published in:
    Nature Biotechnology, 2017, v. 35, n. 5, p. 406, doi. 10.1038/nbt.3790
    By:
    • Perez-Riverol, Yasset;
    • Bai, Mingze;
    • da Veiga Leprevost, Felipe;
    • Squizzato, Silvano;
    • Park, Young Mi;
    • Haug, Kenneth;
    • Carroll, Adam J;
    • Spalding, Dylan;
    • Paschall, Justin;
    • Wang, Mingxun;
    • del-Toro, Noemi;
    • Ternent, Tobias;
    • Zhang, Peng;
    • Buso, Nicola;
    • Bandeira, Nuno;
    • Deutsch, Eric W;
    • Campbell, David S;
    • Beavis, Ronald C;
    • Salek, Reza M;
    • Sarkans, Ugis
    Publication type:
    Article

  • The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

    Published in:
    Nature Biotechnology, 2007, v. 25, n. 10, p. 1127, doi. 10.1038/nbt1347
    By:
    • Jones, Andrew R.;
    • Miller, Michael;
    • Aebersold, Ruedi;
    • Apweiler, Rolf;
    • Ball, Catherine A.;
    • Brazma, Alvis;
    • DeGreef, James;
    • Hardy, Nigel;
    • Hermjakob, Henning;
    • Hubbard, Simon J.;
    • Hussey, Peter;
    • Igra, Mark;
    • Jenkins, Helen;
    • Julian, Jr., Randall K.;
    • Laursen, Kent;
    • Oliver, Stephen G.;
    • Paton, Norman W.;
    • Sansone, Susanna-Assunta;
    • Sarkans, Ugis;
    • Stoeckert, Jr., Christian J.
    Publication type:
    Article

  • Wrestling with SUMO and bio-ontologies.

    Published in:
    2006
    By:
    • Stoeckert, Christian;
    • Ball, Catherine;
    • Brazma, Alvis;
    • Brinkman, Ryan;
    • Causton, Helen;
    • Fan, Liju;
    • Fostel, Jennifer;
    • Fragoso, Gilberto;
    • Heiskanen, Mervi;
    • Holstege, Frank;
    • Morrison, Norman;
    • Parkinson, Helen;
    • Quackenbush, John;
    • Rocca-Serra, Philippe;
    • Sansone, Susanna-Assunta;
    • Sarkans, Ugis;
    • Sherlock, Gavin;
    • Stevens, Robert;
    • Taylor, Chris;
    • Taylor, Ronald
    Publication type:
    Letter

  • The HUPO PSI's Molecular Interaction format-a community standard for the representation of protein interaction data.

    Published in:
    Nature Biotechnology, 2004, v. 22, n. 2, p. 177, doi. 10.1038/nbt926
    By:
    • Bader, Gary;
    • Wojcik, Jérôme;
    • Salwinski, Lukasz;
    • Ceol, Arnaud;
    • Moore, Susan;
    • Orchard, Sandra;
    • Sarkans, Ugis;
    • von Mering, Christian;
    • Roechert, Bernd;
    • Poux, Sylvain;
    • Jung, Eva;
    • Mersch, Henning;
    • Kersey, Paul;
    • Lappe, Michael;
    • Yixue Li, Michael;
    • Rong Zeng;
    • Rana, Debashis;
    • Nikolski, Macha;
    • Husi, Holger;
    • Brun, Christine
    Publication type:
    Article

  • Minimum information about a microarray experiment (MIAME)?toward standards for microarray data.

    Published in:
    Nature Genetics, 2001, v. 29, n. 4, p. 365, doi. 10.1038/ng1201-365
    By:
    • Brazma, Alvis;
    • Hingamp, Pascal;
    • Quackenbush, John;
    • Sherlock, Gavin;
    • Spellman, Paul;
    • Stoeckert, Chris;
    • Aach, John;
    • Ansorge, Wilhelm;
    • Ball, Catherine A.;
    • Causton, Helen C.;
    • Gaasterland, Terry;
    • Glenisson, Patrick;
    • Holstege, Frank C.P.;
    • Kim, Irene F.;
    • Markowitz, Victor;
    • Matese, John C.;
    • Parkinson, Helen;
    • Robinson, Alan;
    • Sarkans, Ugis
    Publication type:
    Article

  • Orchestrating differential data access for translational research: a pilot implementation.

    Published in:
    2017
    By:
    • Brandizi, Marco;
    • Melnichuk, Olga;
    • Bild, Raffael;
    • Kohlmayer, Florian;
    • Rodriguez-Castro, Benedicto;
    • Spengler, Helmut;
    • Kuhn, Klaus A.;
    • Kuchinke, Wolfgang;
    • Ohmann, Christian;
    • Mustonen, Timo;
    • Linden, Mikael;
    • Nyrönen, Tommi;
    • Lappalainen, Ilkka;
    • Brazma, Alvis;
    • Sarkans, Ugis
    Publication type:
    journal article

  • Standards for systems biology.

    Published in:
    Nature Reviews Genetics, 2006, v. 7, n. 8, p. 593, doi. 10.1038/nrg1922
    By:
    • Brazma, Alvis;
    • Krestyaninova, Maria;
    • Sarkans, Ugis
    Publication type:
    Article

  • PASSIM -- an open source software system for managing information in biomedical studies.

    Published in:
    BMC Bioinformatics, 2007, v. 8, p. 1, doi. 10.1186/1471-2105-8-52
    By:
    • Viksna, Juris;
    • Celms, Edgars;
    • Opmanis, Martins;
    • Podnieks, Karlis;
    • Rucevskis, Peteris;
    • Zarins, Andris;
    • Barrett, Amy;
    • Guha Neogi, Sudeshna;
    • Krestyaninova, Maria;
    • McCarthy, Mark I;
    • Brazma, Alvis;
    • Sarkans, Ugis
    Publication type:
    Article

  • A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

    Published in:
    BMC Bioinformatics, 2006, v. 7, p. 489, doi. 10.1186/1471-2105-7-489
    By:
    • Rayner, Tim F;
    • Rocca-Serra, Philippe;
    • Spellman, Paul T;
    • Causton, Helen C;
    • Farne, Anna;
    • Holloway, Ele;
    • Irizarry, Rafael A;
    • Junmin Liu;
    • Maier, Donald S;
    • Miller, Michael;
    • Petersen, Kjell;
    • Quackenbush, John;
    • Sherlock, Gavin;
    • Stoeckert Jr, Christian J;
    • White, Joseph;
    • Whetzel, Patricia L;
    • Wymore, Farrell;
    • Parkinson, Helen;
    • Sarkans, Ugis;
    • Ball, Catherine A
    Publication type:
    Article

  • Expression Profiler: next generation—an online platform for analysis of microarray data.

    Published in:
    Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w465, doi. 10.1093/nar/gkh470
    By:
    • Kapushesky, Misha;
    • Kemmeren, Patrick;
    • Culhane, Aedín C.;
    • Durinck, Steffen;
    • Ihmels, Jan;
    • Körner, Christine;
    • Kull, Meelis;
    • Torrente, Aurora;
    • Sarkans, Ugis;
    • Vilo, Jaak;
    • Brazma, Alvis
    Publication type:
    Article

  • ArrayExpress—a public repository for microarray gene expression data at the EBI.

    Published in:
    Nucleic Acids Research, 2003, v. 31, n. 1, p. 68, doi. 10.1093/nar/gkg091
    By:
    • Brazma, Alvis;
    • Parkinson, Helen;
    • Sarkans, Ugis;
    • Shojatalab, Mohammadreza;
    • Vilo, Jaak;
    • Abeygunawardena, Niran;
    • Holloway, Ele;
    • Kapushesky, Misha;
    • Kemmeren, Patrick;
    • Lara, Gonzalo Garcia;
    • Oezcimen, Ahmet;
    • Rocca-Serra, Philippe;
    • Sansone, Susanna-Assunta
    Publication type:
    Article

  • The BioStudies database.

    Published in:
    Molecular Systems Biology, 2015, v. 11, n. 12, p. n/a, doi. 10.15252/msb.20156658
    By:
    • McEntyre, Jo;
    • Sarkans, Ugis;
    • Brazma, Alvis
    Publication type:
    Article

  • Human metabolic profiles are stably controlled by genetic and environmental variation.

    Published in:
    Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.57
    By:
    • Nicholson, George;
    • Rantalainen, Mattias;
    • Maher, Anthony D;
    • Li, Jia V;
    • Malmodin, Daniel;
    • Ahmadi, Kourosh R;
    • Faber, Johan H;
    • Hallgrímsdóttir, Ingileif B;
    • Barrett, Amy;
    • Toft, Henrik;
    • Krestyaninova, Maria;
    • Viksna, Juris;
    • Neogi, Sudeshna Guha;
    • Dumas, Marc‐Emmanuel;
    • Sarkans, Ugis;
    • Silverman, Bernard W;
    • Donnelly, Peter;
    • Nicholson, Jeremy K;
    • Allen, Maxine;
    • Zondervan, Krina T
    Publication type:
    Article

  • Providing open imaging data at scale: An EMBL-EBI perspective.

    Published in:
    Histochemistry & Cell Biology, 2023, v. 160, n. 3, p. 211, doi. 10.1007/s00418-023-02216-2
    By:
    • Hartley, Matthew;
    • Iudin, Andrii;
    • Padwardhan, Ardan;
    • Sarkans, Ugis;
    • Yoldaş, Aybüke Küpcü;
    • Kleywegt, Gerard J.
    Publication type:
    Article

  • A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.

    Published in:
    2018
    By:
    • Kuepfer, Lars;
    • Clayton, Olivia;
    • Thiel, Christoph;
    • Cordes, Henrik;
    • Nudischer, Ramona;
    • Blank, Lars M.;
    • Baier, Vanessa;
    • Heymans, Stephane;
    • Caiment, Florian;
    • Roth, Adrian;
    • Fluri, David A.;
    • Kelm, Jens M.;
    • Castell, José;
    • Selevsek, Nathalie;
    • Schlapbach, Ralph;
    • Keun, Hector;
    • Hynes, James;
    • Sarkans, Ugis;
    • Gmuender, Hans;
    • Herwig, Ralf
    Publication type:
    Letter

  • The ArrayExpress gene expression database: a software engineering and implementation perspective.

    Published in:
    Bioinformatics, 2005, v. 21, n. 8, p. 1495, doi. 10.1093/bioinformatics/bti157
    By:
    • Ugis Sarkans
    Publication type:
    Article

  • A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection.

    Published in:
    PLoS Genetics, 2011, v. 7, n. 9, p. 1, doi. 10.1371/journal.pgen.1002270
    By:
    • Nicholson, George;
    • Rantalainen, Mattias;
    • V. Li, Jia;
    • Maher, Anthony D.;
    • Malmodin, Daniel;
    • Ahmadi, Kourosh R.;
    • Faber, Johan H.;
    • Barrett, Amy;
    • Min, Josine L.;
    • Rayner, N. William;
    • Toft, Henrik;
    • Krestyaninova, Maria;
    • Viksna, Juris;
    • Neogi, Sudeshna Guha;
    • Dumas, Marc-Emmanuel;
    • Sarkans, Ugis;
    • Donnelly, Peter;
    • Illig, Thomas;
    • Adamski, Jerzy;
    • Suhre, Karsten
    Publication type:
    Article

  • Biomarkers in autism spectrum disorder: the old and the new.

    Published in:
    Psychopharmacology, 2014, v. 231, n. 6, p. 1201, doi. 10.1007/s00213-013-3290-7
    By:
    • Ruggeri, Barbara;
    • Sarkans, Ugis;
    • Schumann, Gunter;
    • Persico, Antonio
    Publication type:
    Article

  • Cellular phenotype database: a repository for systems microscopy data.

    Published in:
    Bioinformatics, 2015, v. 31, n. 16, p. 2736, doi. 10.1093/bioinformatics/btv199
    By:
    • Kirsanova, Catherine;
    • Brazma, Alvis;
    • Rustici, Gabriella;
    • Sarkans, Ugis
    Publication type:
    Article

  • diXa: a data infrastructure for chemical safety assessment.

    Published in:
    2015
    By:
    • Hendrickx, Diana M.;
    • Aerts, Hugo J. W. L.;
    • Caiment, Florian;
    • Clark, Dominic;
    • Ebbels, Timothy M. D.;
    • Evelo, Chris T.;
    • Gmuender, Hans;
    • Hebels, Dennie G. A. J.;
    • Herwig, Ralf;
    • Hescheler, Jürgen;
    • Jennen, Danyel G. J.;
    • Jetten, Marlon J. A.;
    • Kanterakis, Stathis;
    • Keun, Hector C.;
    • Matser, Vera;
    • Overington, John P.;
    • Pilicheva, Ekaterina;
    • Sarkans, Ugis;
    • Segura-Lepe, Marcelo P.;
    • Sotiriadou, Isaia
    Publication type:
    Product Review

  • graph2tab, a library to convert experimental workflow graphs into tabular formats.

    Published in:
    Bioinformatics, 2012, v. 28, n. 12, p. 1665, doi. 10.1093/bioinformatics/bts258
    By:
    • Brandizi, Marco;
    • Kurbatova, Natalja;
    • Sarkans, Ugis;
    • Rocca-Serra, Philippe
    Publication type:
    Article

  • A System for Information Management in BioMedical Studies—SIMBioMS.

    Published in:
    Bioinformatics, 2009, v. 25, n. 20, p. 2768, doi. 10.1093/bioinformatics/btp420
    By:
    • Krestyaninova, Maria;
    • Zarins, Andris;
    • Viksna, Juris;
    • Kurbatova, Natalja;
    • Rucevskis, Peteris;
    • Neogi, Sudeshna Guha;
    • Gostev, Mike;
    • Perheentupa, Teemu;
    • Knuuttila, Juha;
    • Barrett, Amy;
    • Lappalainen, Ilkka;
    • Rung, Johan;
    • Podnieks, Karlis;
    • Sarkans, Ugis;
    • McCarthy, Mark I.;
    • Brazma, Alvis
    Publication type:
    Article