Found: 23

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  • Wikidata as a knowledge graph for the life sciences.

    Published in:
    eLife, 2020, p. 1, doi. 10.7554/eLife.52614
    By:
    • WAAGMEESTER, ANDRA;
    • STUPP, GREGORY;
    • BURGSTALLER-MUEHLBACHER, SEBASTIAN;
    • GOOD, BENJAMIN M.;
    • GRIFFITH, MALACHI;
    • GRIFFITH, OBI L.;
    • HANSPERS, KRISTINA;
    • HERMJAKOB, HENNING;
    • HUDSON, TOBY S.;
    • HYBISKE, KEVIN;
    • KEATING, SARAH M.;
    • MANSKE, MAGNUS;
    • MAYERS, MICHAEL;
    • MIETCHEN, DANIEL;
    • MITRAKA, ELVIRA;
    • PICO, ALEXANDER R.;
    • PUTMAN, TIMOTHY;
    • RIUTTA, ANDERS;
    • QUERALT-ROSINACH, NURIA;
    • SCHRIML, LYNN M.
    Publication type:
    Article

  • Gene expression profiles during human CD4+ T cell differentiation.

    Published in:
    International Immunology, 2004, v. 16, n. 8, p. 1109, doi. 10.1093/intimm/dxh112
    By:
    • Myeong Sup Lee;
    • Kristina Hanspers;
    • Christopher S. Barker;
    • Abner P. Korn;
    • Joseph M. McCune
    Publication type:
    Article

  • WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

    Published in:
    Nucleic Acids Research, 2018, v. 46, n. D1, p. D661, doi. 10.1093/nar/gkx1064
    By:
    • Slenter, Denise N;
    • Kutmon, Martina;
    • Hanspers, Kristina;
    • Riutta, Anders;
    • Windsor, Jacob;
    • Nunes, Nuno;
    • Mélius, Jonathan;
    • Cirillo, Elisa;
    • Coort, Susan L;
    • Digles, Daniela
    Publication type:
    Article

  • WikiPathways: capturing the full diversity of pathway knowledge.

    Published in:
    Nucleic Acids Research, 2016, v. 44, n. 1, p. D488, doi. 10.1093/nar/gkv1024
    By:
    • Kutmon, Martina;
    • Riutta, Anders;
    • Nunes, Nuno;
    • Hanspers, Kristina;
    • Willighagen, Egon L.;
    • Bohler, Anwesha;
    • Mélius, Jonathan;
    • Waagmeester, Andra;
    • Sinha, Sravanthi R.;
    • Miller, Ryan;
    • Coort, Susan L.;
    • Cirillo, Elisa;
    • Smeets, Bart;
    • Evelo, Chris T.;
    • Pico, Alexander R.
    Publication type:
    Article

  • WikiPathways: building research communities on biological pathways.

    Published in:
    Nucleic Acids Research, 2012, p. D1301, doi. 10.1093/nar/gkr1074
    By:
    • Kelder, Thomas;
    • van Iersel, Martijn P.;
    • Hanspers, Kristina;
    • Kutmon, Martina;
    • Conklin, Bruce R.;
    • Evelo, Chris T.;
    • Pico, Alexander R.
    Publication type:
    Article

  • BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.

    Published in:
    Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad570
    By:
    • Callaghan, Jackson;
    • Xu, Colleen H;
    • Xin, Jiwen;
    • Cano, Marco Alvarado;
    • Riutta, Anders;
    • Zhou, Eric;
    • Juneja, Rohan;
    • Yao, Yao;
    • Narayan, Madhumita;
    • Hanspers, Kristina;
    • Agrawal, Ayushi;
    • Pico, Alexander R;
    • Wu, Chunlei;
    • Su, Andrew I
    Publication type:
    Article

  • Pathway information extracted from 25 years of pathway figures.

    Published in:
    Genome Biology, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02181-2
    By:
    • Hanspers, Kristina;
    • Riutta, Anders;
    • Summer-Kutmon, Martina;
    • Pico, Alexander R.
    Publication type:
    Article

  • Mining Biological Pathways Using WikiPathways Web Services.

    Published in:
    PLoS ONE, 2009, v. 4, n. 7, p. 1, doi. 10.1371/journal.pone.0006447
    By:
    • Kelder, Thomas;
    • Pico, Alexander R.;
    • Hanspers, Kristina;
    • van Iersel, Martijn P.;
    • Evelo, Chris;
    • Conklin, Bruce R.
    Publication type:
    Article

  • Increased DNA microarray hybridization specificity using sscDNA targets.

    Published in:
    BMC Genomics, 2005, v. 6, p. 57, doi. 10.1186/1471-2164-6-57
    By:
    • Barker, Christopher S;
    • Griffin, Chandi;
    • Dolganov, Gregory M;
    • Hanspers, Kristina;
    • Hwa Yang, Jean Yee;
    • Erle, David J
    Publication type:
    Article

  • The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

    Published in:
    BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-5
    By:
    • Iersel, Martijn P van;
    • Pico, Alexander R;
    • Kelder, Thomas;
    • Jianjiong Gao;
    • Ho, Isaac;
    • Hanspers, Kristina;
    • Conklin, Bruce R;
    • Evelo, Chris T
    Publication type:
    Article

  • Presenting and exploring biological pathways with PathVisio.

    Published in:
    2008
    By:
    • van Iersel, Martijn P.;
    • Kelder, Thomas;
    • Pico, Alexander R.;
    • Hanspers, Kristina;
    • Coort, Susan;
    • Conklin, Bruce R.;
    • Evelo, Chris
    Publication type:
    Product Review

  • GenMAPP 2: new features and resources for pathway analysis.

    Published in:
    BMC Bioinformatics, 2007, v. 8, p. 217, doi. 10.1186/1471-2105-8-217
    By:
    • Salomonis, Nathan;
    • Hanspers, Kristina;
    • Zambon, Alexander C;
    • Vranizan, Karen;
    • Lawlor, Steven C;
    • Dahlquist, Kam D;
    • Doniger, Scott W;
    • Stuart, Josh;
    • Conklin, Bruce R;
    • Pico, Alexander R
    Publication type:
    Article

  • Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors.

    Published in:
    PLoS Computational Biology, 2009, v. 5, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000553
    By:
    • Salomonis, Nathan;
    • Nelson, Brandon;
    • Vranizan, Karen;
    • Pico, Alexander R.;
    • Hanspers, Kristina;
    • Kuchinsky, Allan;
    • Ta, Linda;
    • Mercola, Mark;
    • Conklin, Bruce R.
    Publication type:
    Article

  • Ten simple rules for creating reusable pathway models for computational analysis and visualization.

    Published in:
    2021
    By:
    • Hanspers, Kristina;
    • Kutmon, Martina;
    • Coort, Susan L.;
    • Digles, Daniela;
    • Dupuis, Lauren J.;
    • Ehrhart, Friederike;
    • Hu, Finterly;
    • Lopes, Elisson N.;
    • Martens, Marvin;
    • Pham, Nhung;
    • Shin, Woosub;
    • Slenter, Denise N.;
    • Waagmeester, Andra;
    • Willighagen, Egon L.;
    • Winckers, Laurent A.;
    • Evelo, Chris T.;
    • Pico, Alexander R.
    Publication type:
    Editorial

  • A System-Based Approach to Interpret Dose- and Time-Dependent Microarray Data: Quantitative Integration of Gene Ontology Analysis for Risk Assessment.

    Published in:
    Toxicological Sciences, 2006, v. 92, n. 2, p. 560, doi. 10.1093/toxsci/kfj184
    By:
    • Xiaozhong Yu;
    • William C. Griffith;
    • Kristina Hanspers;
    • James F. Dillman;
    • Hansel Ong;
    • Melinda A. Vredevoogd;
    • Elaine M. Faustman
    Publication type:
    Article

  • Reactome from a WikiPathways Perspective.

    Published in:
    PLoS Computational Biology, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004941
    By:
    • Bohler, Anwesha;
    • Wu, Guanming;
    • Kutmon, Martina;
    • Pradhana, Leontius Adhika;
    • Coort, Susan L.;
    • Hanspers, Kristina;
    • Haw, Robin;
    • Pico, Alexander R.;
    • Evelo, Chris T.
    Publication type:
    Article

  • WikiPathways: Pathway Editing for the People.

    Published in:
    PLoS Biology, 2008, v. 6, n. 7, p. e184, doi. 10.1371/journal.pbio.0060184
    By:
    • Pico, Alexander R.;
    • Kelder, Thomas;
    • Van Iersel, Martijn P.;
    • Hanspers, Kristina;
    • Conklin, Bruce R.;
    • Evelo, Chris
    Publication type:
    Article

  • WikiPathways 2024: next generation pathway database.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D679, doi. 10.1093/nar/gkad960
    By:
    • Agrawal, Ayushi;
    • Balcı, Hasan;
    • Hanspers, Kristina;
    • Coort, Susan L;
    • Martens, Marvin;
    • Slenter, Denise N;
    • Ehrhart, Friederike;
    • Digles, Daniela;
    • Waagmeester, Andra;
    • Wassink, Isabel;
    • Abbassi-Daloii, Tooba;
    • Lopes, Elisson N;
    • Iyer, Aishwarya;
    • Acosta, Javier Millán;
    • Willighagen, Lars G;
    • Nishida, Kozo;
    • Riutta, Anders;
    • Basaric, Helena;
    • Evelo, Chris T;
    • Willighagen, Egon L
    Publication type:
    Article

  • WikiPathways: connecting communities.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D613, doi. 10.1093/nar/gkaa1024
    By:
    • Martens, Marvin;
    • Ammar, Ammar;
    • Riutta, Anders;
    • Waagmeester, Andra;
    • Slenter, Denise N;
    • Hanspers, Kristina;
    • A. Miller, Ryan;
    • Digles, Daniela;
    • Lopes, Elisson N;
    • Ehrhart, Friederike;
    • Dupuis, Lauren J;
    • Winckers, Laurent A;
    • Coort, Susan L;
    • Willighagen, Egon L;
    • Evelo, Chris T;
    • Pico, Alexander R;
    • Kutmon, Martina
    Publication type:
    Article

  • Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes.

    Published in:
    2017
    By:
    • Shah, Ravi;
    • Murthy, Venkatesh;
    • Pacold, Michael;
    • Danielson, Kirsty;
    • Tanriverdi, Kahraman;
    • Larson, Martin G.;
    • Hanspers, Kristina;
    • Pico, Alexander;
    • Mick, Eric;
    • Reis, Jared;
    • de Ferranti, Sarah;
    • Freinkman, Elizaveta;
    • Levy, Daniel;
    • Hoffmann, Udo;
    • Osganian, Stavroula;
    • Das, Saumya;
    • Freedman, Jane E.
    Publication type:
    journal article

  • NOA: a cytoscape plugin for network ontology analysis.

    Published in:
    Bioinformatics, 2013, v. 29, n. 16, p. 2066, doi. 10.1093/bioinformatics/btt334
    By:
    • Zhang, Chao;
    • Wang, Jiguang;
    • Hanspers, Kristina;
    • Xu, Dong;
    • Chen, Luonan;
    • Pico, Alexander R.
    Publication type:
    Article

  • GO-Elite: a flexible solution for pathway and ontology over-representation.

    Published in:
    Bioinformatics, 2012, v. 28, n. 16, p. 2209, doi. 10.1093/bioinformatics/bts366
    By:
    • Zambon, Alexander C.;
    • Gaj, Stan;
    • Ho, Isaac;
    • Hanspers, Kristina;
    • Vranizan, Karen;
    • Evelo, Chris T.;
    • Conklin, Bruce R.;
    • Pico, Alexander R.;
    • Salomonis, Nathan
    Publication type:
    Article

  • Mosaic: making biological sense of complex networks.

    Published in:
    Bioinformatics, 2012, v. 28, n. 14, p. 1943, doi. 10.1093/bioinformatics/bts278
    By:
    • Zhang, Chao;
    • Hanspers, Kristina;
    • Kuchinsky, Allan;
    • Salomonis, Nathan;
    • Xu, Dong;
    • Pico, Alexander R.
    Publication type:
    Article