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pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species
Title pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species Author Rahmati Sara Jurišica Igor SAVNEIMU - Neuroimunologický ústav SAV ORCID Co-authors Abovsky Mark Pastrello Chiara Kotlyar Max Lu Richard Cumbaa Christian A. Rahman Proton Chandran Vinod Source document Nucleic acids research. Vol. 48, no. D1 (2020), p. D479-D488 Language eng - English Country GB - Great Britian Document kind rozpis článkov z periodík (rbx) Citations GHULAM, A. - LEI, X.J. - GUO, M. - BIAN, C. Comprehensive Analysis of Features and Annotations of Pathway Databases. In CURRENT BIOINFORMATICS. ISSN 1574-8936, 2020, vol. 15, no. 8, p. 803-820. AGAPITO, G. - CANNATARO, M. Using BioPAX-Parser (BiP) to Annotate Lists of Biological Entities with Pathway Data. In ADVANCES IN CONCEPTUAL MODELING, ER 2020. ISSN 0302-9743, 2020, vol. 12584, p. 92-101. CSICSATKOVA, N. - SZALAY, P. - MATYASOVA, K. - MATE, V. - CENTE, M. - SMOLEK, T. - BREZOVAKOVA, V. - KAWECKA, L. - ZILKA, N. - JADHAV, S. Transcriptomic signature of Alzheimer's disease tau seed-induced pathology. In GENERAL PHYSIOLOGY AND BIOPHYSICS. ISSN 0231-5882, 2021, vol. 40, no. 6, p. 541-549. BAINES, C. - LEREBOURS, A. - THOMAS, F. - FORT, J. - KREITSBERG, R. - GENTES, S. - MEITERN, R. - SAKS, L. - UJVARI, B. - GIRAUDEAU, M. - SEPP, T. Linking pollution and cancer in aquatic environments: A review. In ENVIRONMENT INTERNATIONAL. ISSN 0160-4120, APR 2021, vol. 149. MA, Z.L. - LI, S.Q. - WANG, Y.Q. - ZHANG, J.X. - ZENG, X.F. Upregulation of a novel LncRNA AC104958.2 stabilized by PCBP2 promotes proliferation and microvascular invasion in hepatocellular carcinoma. In EXPERIMENTAL CELL RESEARCH. ISSN 0014-4827, OCT 1 2021, vol. 407, no. 1. ZHAO, Y.F. - CAI, H.Y. - ZHANG, Z.B. - TANG, J. - LI, Y. Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data. In NATURE COMMUNICATIONS. SEP 6 2021, vol. 12, no. 1. ROK, J. - RZEPKA, Z. - MASZCZYK, M. - BEBEROK, A. - WRZESNIOK, D. Minocycline Impact on Redox Homeostasis of Normal Human Melanocytes HEMn-LP Exposed to UVA Radiation and Hydrogen Peroxide. In INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. FEB 2021, vol. 22, no. 4. Dostupné na: https://doi.org/10.3390/ijms22041642. ZHAO, P.P. - PENG, Y.Y. - XU, X. - WANG, Z.Y. - WU, Z.R. - LI, W.H. - TANG, Y. - LIU, G.X. In silico prediction of mitochondrial toxicity of chemicals using machine learning methods. In JOURNAL OF APPLIED TOXICOLOGY. ISSN 0260-437X, OCT 2021, vol. 41, no. 10, p. 1518-1526. Dostupné na: https://doi.org/10.1002/jat.4141. BEGUM, Sara - AIMAN, Sara - AHMAD, Shujaat - SAMAD, Abdus - ALMEHMADI, Mazen - ALLAHYANI, Mamdouh - ALJUAID, Abdulelah - AFRIDI, Sahib Gul - KHAN, Asifullah. Molecular Mimicry Analyses Unveiled the Human Herpes Simplex and Poxvirus Epitopes as Possible Candidates to Incite Autoimmunity. In PATHOGENS. NOV 2022, vol. 11, no. 11. Dostupné na: https://doi.org/10.3390/pathogens11111362. AGAPITO, Giuseppe - MILANO, Marianna - CANNATARO, Mario. A Python Clustering Analysis Protocol of Genes Expression Data Sets. In GENES. OCT 2022, vol. 13, no. 10. Dostupné na: https://doi.org/10.3390/genes13101839. TAHERI, Golnaz - HABIBI, Mahnaz. Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method. In APPLIED SOFT COMPUTING. ISSN 1568-4946, OCT 2022, vol. 128. Dostupné na: https://doi.org/10.1016/j.asoc.2022.109510. LAIAKIS, Evagelia C. - PINHEIRO, Maisa - NGUYEN, Tin - NGUYEN, Hung - BEHESHTI, Afshin - DUTTA, Sucharita M. - RUSSELL, William K. - EMMETT, Mark R. - BRITTEN, Richard A. Quantitative proteomic analytic approaches to identify metabolic changes in the medial prefrontal cortex of rats exposed to space radiation. In FRONTIERS IN PHYSIOLOGY. AUG 26 2022, vol. 13. Dostupné na: https://doi.org/10.3389/fphys.2022.971282. CHICCO, Davide - AGAPITO, Giuseppe. Nine quick tips for pathway enrichment analysis. In PLOS COMPUTATIONAL BIOLOGY. ISSN 1553-734X, AUG 2022, vol. 18, no. 8. Dostupné na: https://doi.org/10.1371/journal.pcbi.1010348. WU, Diana - TAIBI, Amel - LIN, Zhen - THOMPSON, Lilian U. - COMELLI, Elena M. Data on mammary gland microRNAs expression, their predicted gene targets and corresponding pathway analysis in female mice receiving flaxseed or its oil and secoisolariciresinol diglucoside components. In DATA IN BRIEF. ISSN 2352-3409, JUN 2022, vol. 42. Dostupné na: https://doi.org/10.1016/j.dib.2022.108328. RADU, Tudor Bogdan. Hijacking Cancer Signaling: First-In-Class JPRK-Targeting Ligands for Fibrolamellar Hepatocellular Carcinoma. Jan 01 2022. NAKAMURA, Akihiro. Macrophage Migration Inhibitory Factor as a Critical Disease Driver and Novel Therapeutic Target in Spondyloarthritis. Jan 01 2022. AGAPITO, Giuseppe - CANNATARO, Mario. A parallel software pipeline to select relevant genes for pathway enrichment. In 30TH EUROMICRO INTERNATIONAL CONFERENCE ON PARALLEL, DISTRIBUTED AND NETWORK-BASED PROCESSING (PDP 2022). ISSN 1066-6192, 2022, p. 219-225. Dostupné na: https://doi.org/10.1109/PDP55904.2022.00041. TSAMOU, Maria - CARPI, Donatella - PISTOLLATO, Francesca - ROGGEN, Erwin L. Sporadic Alzheimer's Disease- and Neurotoxicity-Related microRNAs Affecting Key Events of Tau-Driven Adverse Outcome Pathway Toward Memory Loss. In JOURNAL OF ALZHEIMERS DISEASE. ISSN 1387-2877, 2022, vol. 86, no. 3, p. 1427-+. Dostupné na: https://doi.org/10.3233/JAD-215434. HOLZINGER, Andreas - DEHMER, Matthias - EMMERT-STREIB, Frank - CUCCHIARA, Rita - AUGENSTEIN, Isabelle - DEL SER, Javier - SAMEK, Wojciech - JURISICA, Igor - DIAZ-RODRIGUEZ, Natalia. Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence. In INFORMATION FUSION. ISSN 1566-2535, MAR 2022, vol. 79, p. 263-278. Dostupné na: https://doi.org/10.1016/j.inffus.2021.10.007. HOWE, Caitlin G. - FOLEY, Helen B. - FARZAN, Shohreh F. - CHAVEZ, Thomas A. - JOHNSON, Mark - MEEKER, John D. - BASTAIN, Theresa M. - MARSIT, Carmen J. - BRETON, Carrie, V. Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort. In EPIGENETICS. ISSN 1559-2294, OCT 3 2022, vol. 17, no. 10, p. 1128-1142. Dostupné na: https://doi.org/10.1080/15592294.2021.1994189. HOLLANDER, Markus - DO, Trang - WILL, Thorsten - HELMS, Volkhard. Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. In FRONTIERS IN BIOINFORMATICS. SEP 8 2021, vol. 1. Dostupné na: https://doi.org/10.3389/fbinf.2021.724297. Category ADCA - Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted) Category of document (from 2022) V3 - Vedecký výstup publikačnej činnosti z časopisu Type of document článok Year 2020 Registered in WOS Registered in SCOPUS Registered in CCC DOI 10.1093/nar/gkz989 
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