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Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Published in:
2020
By:
- Ostaszewski, Marek;
- Mazein, Alexander;
- Gillespie, Marc E.;
- Kuperstein, Inna;
- Niarakis, Anna;
- Hermjakob, Henning;
- Pico, Alexander R.;
- Willighagen, Egon L.;
- Evelo, Chris T.;
- Hasenauer, Jan;
- Schreiber, Falk;
- Dräger, Andreas;
- Demir, Emek;
- Wolkenhauer, Olaf;
- Furlong, Laura I.;
- Barillot, Emmanuel;
- Dopazo, Joaquin;
- Orta-Resendiz, Aurelio;
- Messina, Francesco;
- Valencia, Alfonso
Publication type:
Correction Notice
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Published in:
Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-0477-8
By:
- Ostaszewski, Marek;
- Mazein, Alexander;
- Gillespie, Marc E.;
- Kuperstein, Inna;
- Niarakis, Anna;
- Hermjakob, Henning;
- Pico, Alexander R.;
- Willighagen, Egon L.;
- Evelo, Chris T.;
- Hasenauer, Jan;
- Schreiber, Falk;
- Dräger, Andreas;
- Demir, Emek;
- Wolkenhauer, Olaf;
- Furlong, Laura I.;
- Barillot, Emmanuel;
- Dopazo, Joaquin;
- Orta-Resendiz, Aurelio;
- Messina, Francesco;
- Valencia, Alfonso
Publication type:
Article
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
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
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D803, doi. 10.1093/nar/gkn756
By:
- Pico, Alexander R.;
- Smirnov, Ivan V.;
- Chang, Jeffrey S.;
- Yeh, Ru-Fang;
- Wiemels, Joseph L.;
- Wiencke, John K.;
- Tihan, Tarik;
- Conklin, Bruce R.;
- Wrensch, Margaret
Publication type:
Article
Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk.
Published in:
Nature Genetics, 2014, v. 46, n. 7, p. 731, doi. 10.1038/ng.3004
By:
- Walsh, Kyle M;
- Codd, Veryan;
- Smirnov, Ivan V;
- Rice, Terri;
- Decker, Paul A;
- Hansen, Helen M;
- Kollmeyer, Thomas;
- Kosel, Matthew L;
- Molinaro, Annette M;
- McCoy, Lucie S;
- Bracci, Paige M;
- Cabriga, Belinda S;
- Pekmezci, Melike;
- Zheng, Shichun;
- Wiemels, Joseph L;
- Pico, Alexander R;
- Tihan, Tarik;
- Berger, Mitchell S;
- Chang, Susan M;
- Prados, Michael D
Publication type:
Article
A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation.
Published in:
Nature Genetics, 2012, v. 44, n. 10, p. 1122, doi. 10.1038/ng.2388
By:
- Jenkins, Robert B;
- Xiao, Yuanyuan;
- Sicotte, Hugues;
- Decker, Paul A;
- Kollmeyer, Thomas M;
- Hansen, Helen M;
- Kosel, Matthew L;
- Zheng, Shichun;
- Walsh, Kyle M;
- Rice, Terri;
- Bracci, Paige;
- McCoy, Lucie S;
- Smirnov, Ivan;
- Patoka, Joseph S;
- Hsuang, George;
- Wiemels, Joe L;
- Tihan, Tarik;
- Pico, Alexander R;
- Prados, Michael D;
- Chang, Susan M
Publication type:
Article
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility.
Published in:
Nature Genetics, 2009, v. 41, n. 8, p. 905, doi. 10.1038/ng.408
By:
- Wrensch, Margaret;
- Jenkins, Robert B.;
- Chang, Jeffrey S.;
- Ru-Fang Yeh;
- Yuanyuan Xiao;
- Decker, Paul A.;
- Ballman, Karla V.;
- Berger, Mitchel;
- Buckner, Jan C.;
- Chang, Susan;
- Giannini, Caterina;
- Halder, Chandralekha;
- Kollmeyer, Thomas M.;
- Kosel, Matthew L.;
- LaChance, Daniel H.;
- McCoy, Lucie;
- O'Neill, Brian P.;
- Patoka, Joe;
- Pico, Alexander R.;
- Prados, Michael
Publication type:
Article
A travel guide to Cytoscape plugins.
Published in:
Nature Methods, 2012, v. 9, n. 11, p. 1069, doi. 10.1038/nmeth.2212
By:
- Saito, Rintaro;
- Smoot, Michael E;
- Ono, Keiichiro;
- Ruscheinski, Johannes;
- Wang, Peng-Liang;
- Lotia, Samad;
- Pico, Alexander R;
- Bader, Gary D;
- Ideker, Trey
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
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
Published in:
Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad080
By:
- Morris, John H;
- Soman, Karthik;
- Akbas, Rabia E;
- Zhou, Xiaoyuan;
- Smith, Brett;
- Meng, Elaine C;
- Huang, Conrad C;
- Cerono, Gabriel;
- Schenk, Gundolf;
- Rizk-Jackson, Angela;
- Harroud, Adil;
- Sanders, Lauren;
- Costes, Sylvain V;
- Bharat, Krish;
- Chakraborty, Arjun;
- Pico, Alexander R;
- Mardirossian, Taline;
- Keiser, Michael;
- Tang, Alice;
- Hardi, Josef
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
Incident heart failure in chronic kidney disease: proteomics informs biology and risk stratification.
Published in:
European Heart Journal, 2024, v. 45, n. 30, p. 2752, doi. 10.1093/eurheartj/ehae288
By:
- Dubin, Ruth F;
- Deo, Rajat;
- Ren, Yue;
- Wang, Jianqiao;
- Pico, Alexander R;
- Mychaleckyj, Josyf C;
- Kozlitina, Julia;
- Arthur, Victoria;
- Lee, Hongzhe;
- Shah, Amil;
- Feldman, Harold;
- Bansal, Nisha;
- Zelnick, Leila;
- Rao, Panduranga;
- Sukul, Nidhi;
- Raj, Dominic S;
- Mehta, Rupal;
- Rosas, Sylvia E;
- Bhat, Zeenat;
- Weir, Matthew R
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
TELOMERE LENGTH VARIANTS ARE ASSOCIATED WITH HIGH-GRADE GLIOMA RISK: IDENTIFICATION OF A NOVEL GLIOMA RISK LOCUS BY GENOME-WIDE ASSOCIATION STUDY.
Published in:
Neuro-Oncology, 2014, v. 16, n. suppl_3, p. iii2
By:
- Walsh, Kyle M.;
- Codd, Veryan;
- Smirnov, Ivan V.;
- Rice, Terri;
- Decker, Paul A.;
- Hansen, Helen M.;
- Kollmeyer, Thomas;
- Kosel, Matthew L.;
- Molinaro, Annette M.;
- McCoy, Lucie S.;
- Bracci, Paige M.;
- Cabriga, Belinda S.;
- Pekmezci, Melike;
- Zheng, Shichun;
- Wiemels, Joseph L.;
- Pico, Alexander R.;
- Tihan, Tarik;
- Berger, Mitchell S.;
- Chang, Susan M.;
- Prados, Michael D.
Publication type:
Article
Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis.
Published in:
Neuro-Oncology, 2013, v. 15, n. 8, p. 1041, doi. 10.1093/neuonc/not051
By:
- Walsh, Kyle M.;
- Rice, Terri;
- Decker, Paul A.;
- Kosel, Matthew L.;
- Kollmeyer, Thomas;
- Hansen, Helen M.;
- Zheng, Shichun;
- McCoy, Lucie S.;
- Bracci, Paige M.;
- Anderson, Erik;
- Hsuang, George;
- Wiemels, Joe L.;
- Pico, Alexander R.;
- Smirnov, Ivan;
- Molinaro, Annette M.;
- Tihan, Tarik;
- Berger, Mitchell S.;
- Chang, Susan M.;
- Prados, Michael D.;
- Lachance, Daniel H.
Publication type:
Article
Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology.
Published in:
Neuro-Oncology, 2013, v. 15, n. 5, p. 535, doi. 10.1093/neuonc/nos324
By:
- Rice, Terri;
- Zheng, Shichun;
- Decker, Paul A.;
- Walsh, Kyle M.;
- Bracci, Paige;
- Xiao, Yuanyuan;
- McCoy, Lucie S.;
- Smirnov, Ivan;
- Patoka, Joseph S.;
- Hansen, Helen M.;
- Hsuang, George;
- Wiemels, Joe L.;
- Tihan, Tarik;
- Pico, Alexander R.;
- Prados, Michael D.;
- Chang, Susan M.;
- Berger, Mitchel S.;
- Caron, Alissa;
- Fink, Stephanie;
- Kollmeyer, Thomas
Publication type:
Article
Using published pathway figures in enrichment analysis and machine learning.
Published in:
BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09816-1
By:
- Shin, Min-Gyoung;
- Pico, Alexander R.
Publication type:
Article
PathVisio 3: An Extendable Pathway Analysis Toolbox.
Published in:
PLoS Computational Biology, 2015, v. 11, n. 2, p. 1, doi. 10.1371/journal.pcbi.1004085
By:
- Kutmon, Martina;
- van Iersel, Martijn P.;
- Bohler, Anwesha;
- Kelder, Thomas;
- Nunes, Nuno;
- Pico, Alexander R.;
- Evelo, Chris T.
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
PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi‐Omics Data.
Published in:
Proteomics, 2020, v. 20, n. 21/22, p. 1, doi. 10.1002/pmic.201900409
By:
- Odom, Gabriel J.;
- Ban, Yuguang;
- Colaprico, Antonio;
- Liu, Lizhong;
- Silva, Tiago Chedraoui;
- Sun, Xiaodian;
- Pico, Alexander R.;
- Zhang, Bing;
- Wang, Lily;
- Chen, Xi
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
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.
Published in:
PLoS Computational Biology, 2016, v. 12, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004989
By:
- Waagmeester, Andra;
- Kutmon, Martina;
- Riutta, Anders;
- Miller, Ryan;
- Willighagen, Egon L.;
- Evelo, Chris T.;
- Pico, Alexander R.
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
Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets.
Published in:
PLoS Biology, 2010, v. 8, n. 8, p. 1, doi. 10.1371/journal.pbio.1000472
By:
- Kelder, Thomas;
- Conklin, Bruce R.;
- Evelo, Chris T.;
- Pico, Alexander R.
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
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics.
Published in:
Nucleic Acids Research, 2024, v. 52, n. W1, p. W415, doi. 10.1093/nar/gkae456
By:
- Elizarraras, John M;
- Liao, Yuxing;
- Shi, Zhiao;
- Zhu, Qian;
- Pico, Alexander R;
- Zhang, Bing
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
Cytoscape Automation: empowering workflow-based network analysis.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1758-4
By:
- Otasek, David;
- Morris, John H.;
- Bouças, Jorge;
- Pico, Alexander R.;
- Demchak, Barry
Publication type:
Article
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.
Published in:
Nature Protocols, 2014, v. 9, n. 11, p. 2539, doi. 10.1038/nprot.2014.164
By:
- Morris, John H;
- Knudsen, Giselle M;
- Verschueren, Erik;
- Johnson, Jeffrey R;
- Cimermancic, Peter;
- Greninger, Alexander L;
- Pico, Alexander R
Publication type:
Article
Analysis of 60 Reported Glioma Risk SNPs Replicates Published GWAS Findings but Fails to Replicate Associations From Published Candidate-Gene Studies.
Published in:
Genetic Epidemiology, 2013, v. 37, n. 2, p. 222, doi. 10.1002/gepi.21707
By:
- Walsh, Kyle M.;
- Anderson, Erik;
- Hansen, Helen M.;
- Decker, Paul A.;
- Kosel, Matt L.;
- Kollmeyer, Thomas;
- Rice, Terri;
- Zheng, Shichun;
- Xiao, Yuanyuan;
- Chang, Jeffrey S.;
- McCoy, Lucie S.;
- Bracci, Paige M.;
- Wiemels, Joe L.;
- Pico, Alexander R.;
- Smirnov, Ivan;
- Lachance, Daniel H.;
- Sicotte, Hugues;
- Eckel‐Passow, Jeanette E.;
- Wiencke, John K.;
- Jenkins, Robert B.
Publication type:
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
Cytoscape App Store.
Published in:
Bioinformatics, 2013, v. 29, n. 10, p. 1350, doi. 10.1093/bioinformatics/btt138
By:
- Lotia, Samad;
- Montojo, Jason;
- Dong, Yue;
- Bader, Gary D.;
- 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

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