• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4605772)   Today's Articles (4817)   Subscriber (49373)
For: Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ. The pathway ontology - updates and applications. J Biomed Semantics 2014;5:7. [PMID: 24499703 PMCID: PMC3922094 DOI: 10.1186/2041-1480-5-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 12/05/2013] [Indexed: 01/13/2023]  Open
Number Cited by Other Article(s)
1
Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data 2024;11:363. [PMID: 38605048 PMCID: PMC11009265 DOI: 10.1038/s41597-024-03171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]  Open
2
Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol 2024;15:1351678. [PMID: 38638909 PMCID: PMC11024261 DOI: 10.3389/fmicb.2024.1351678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/20/2024]  Open
3
Kilicoglu H, Ensan F, McInnes B, Wang LL. Semantics-enabled biomedical literature analytics. J Biomed Inform 2024;150:104588. [PMID: 38244957 DOI: 10.1016/j.jbi.2024.104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
4
Otero-Carrasco B, Ugarte Carro E, Prieto-Santamaría L, Diaz Uzquiano M, Caraça-Valente Hernández JP, Rodríguez-González A. Identifying patterns to uncover the importance of biological pathways on known drug repurposing scenarios. BMC Genomics 2024;25:43. [PMID: 38191292 PMCID: PMC10775474 DOI: 10.1186/s12864-023-09913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]  Open
5
Wishart DS, Kruger R, Sivakumaran A, Harford K, Sanford S, Doshi R, Khetarpal N, Fatokun O, Doucet D, Zubkowski A, Jackson H, Sykes G, Ramirez-Gaona M, Marcu A, Li C, Yee K, Garros C, Rayat D, Coleongco J, Nandyala T, Gautam V, Oler E. PathBank 2.0-the pathway database for model organism metabolomics. Nucleic Acids Res 2024;52:D654-D662. [PMID: 37962386 PMCID: PMC10767802 DOI: 10.1093/nar/gkad1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]  Open
6
Pastrello C, Kotlyar M, Abovsky M, Lu R, Jurisica I. PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. Nucleic Acids Res 2024;52:D663-D671. [PMID: 37994706 PMCID: PMC10767947 DOI: 10.1093/nar/gkad1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]  Open
7
Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023;224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]  Open
8
Laulederkind SJF, Hayman GT, Wang SJ, Kaldunski ML, Vedi M, Demos WM, Tutaj M, Smith JR, Lamers L, Gibson AC, Thorat K, Thota J, Tutaj MA, De Pons JL, Dwinell MR, Kwitek AE. The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species. Curr Protoc 2023;3:e804. [PMID: 37347557 PMCID: PMC10335880 DOI: 10.1002/cpz1.804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
9
Manicka S, Johnson K, Levin M, Murrugarra D. The nonlinearity of regulation in biological networks. NPJ Syst Biol Appl 2023;9:10. [PMID: 37015937 PMCID: PMC10073134 DOI: 10.1038/s41540-023-00273-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023]  Open
10
Taneja SB, Callahan TJ, Paine MF, Kane-Gill SL, Kilicoglu H, Joachimiak MP, Boyce RD. Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions. J Biomed Inform 2023;140:104341. [PMID: 36933632 PMCID: PMC10150409 DOI: 10.1016/j.jbi.2023.104341] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
11
DHULI KRISTJANA, BONETTI GABRIELE, ANPILOGOV KYRYLO, HERBST KARENL, CONNELLY STEPHENTHADDEUS, BELLINATO FRANCESCO, GISONDI PAOLO, BERTELLI MATTEO. Validating methods for testing natural molecules on molecular pathways of interest in silico and in vitro. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2022;63:E279-E288. [PMID: 36479497 PMCID: PMC9710400 DOI: 10.15167/2421-4248/jpmh2022.63.2s3.2770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
12
Giuseppe A, Chiara P, Yun N, Igor J. Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture. Brief Bioinform 2022;23:6691914. [PMID: 36063560 DOI: 10.1093/bib/bbac368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022]  Open
13
Martens M, Kreidl F, Ehrhart F, Jean D, Mei M, Mortensen HM, Nash A, Nymark P, Evelo CT, Cerciello F. A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. Front Oncol 2022;12:849640. [PMID: 35558518 PMCID: PMC9088009 DOI: 10.3389/fonc.2022.849640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 12/28/2022]  Open
14
Mubeen S, Tom Kodamullil A, Hofmann-Apitius M, Domingo-Fernández D. On the influence of several factors on pathway enrichment analysis. Brief Bioinform 2022;23:bbac143. [PMID: 35453140 PMCID: PMC9116215 DOI: 10.1093/bib/bbac143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 02/01/2023]  Open
15
Iatsiuk V, Malinka F, Pickova M, Tureckova J, Klema J, Spoutil F, Novosadova V, Prochazka J, Sedlacek R. Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns. BMC Gastroenterol 2022;22:186. [PMID: 35413796 PMCID: PMC9006408 DOI: 10.1186/s12876-022-02265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022]  Open
16
Mortensen HM, Martens M, Senn J, Levey T, Evelo CT, Willighagen EL, Exner T. The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. FRONTIERS IN TOXICOLOGY 2022;4:803983. [PMID: 35295213 PMCID: PMC8915825 DOI: 10.3389/ftox.2022.803983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/13/2022] [Indexed: 01/12/2023]  Open
17
Prashanth G, Vastrad B, Vastrad C, Kotrashetti S. Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. Bioinform Biol Insights 2022;15:11779322211067365. [PMID: 34992355 PMCID: PMC8725226 DOI: 10.1177/11779322211067365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]  Open
18
Muscolino A, Di Maria A, Rapicavoli RV, Alaimo S, Bellomo L, Billeci F, Borzì S, Ferragina P, Ferro A, Pulvirenti A. NETME: on-the-fly knowledge network construction from biomedical literature. APPLIED NETWORK SCIENCE 2022;7:1. [PMID: 35013714 PMCID: PMC8733431 DOI: 10.1007/s41109-021-00435-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/21/2021] [Indexed: 06/14/2023]
19
Pastrello C, Niu Y, Jurisica I. Pathway Enrichment Analysis of Microarray Data. Methods Mol Biol 2022;2401:147-159. [PMID: 34902127 DOI: 10.1007/978-1-0716-1839-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
20
Xiao Y, Zheng X, Song W, Tong F, Mao Y, Liu S, Zhao D. CIDO-COVID-19: An Ontology for COVID-19 Based on CIDO. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021;2021:2119-2122. [PMID: 34891707 DOI: 10.1109/embc46164.2021.9629555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
21
Mubeen S, Bharadhwaj VS, Gadiya Y, Hofmann-Apitius M, Kodamullil AT, Domingo-Fernández D. DecoPath: a web application for decoding pathway enrichment analysis. NAR Genom Bioinform 2021;3:lqab087. [PMID: 34568823 PMCID: PMC8459727 DOI: 10.1093/nargab/lqab087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/31/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022]  Open
22
Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, Hu F, Lopes EN, Martens M, Pham N, Shin W, Slenter DN, Waagmeester A, Willighagen EL, Winckers LA, Evelo CT, Pico AR. Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput Biol 2021;17:e1009226. [PMID: 34411100 PMCID: PMC8375987 DOI: 10.1371/journal.pcbi.1009226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
23
Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. Sci Rep 2021;11:16461. [PMID: 34385509 PMCID: PMC8361107 DOI: 10.1038/s41598-021-95637-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023]  Open
24
Roychowdhury D, Gupta S, Qin X, Arighi CN, Vijay-Shanker K. emiRIT: a text-mining-based resource for microRNA information. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2021:6287648. [PMID: 34048547 PMCID: PMC8163238 DOI: 10.1093/database/baab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/15/2021] [Accepted: 05/04/2021] [Indexed: 01/18/2023]
25
Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses. Sci Rep 2021;11:10136. [PMID: 33980888 PMCID: PMC8115341 DOI: 10.1038/s41598-021-89171-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022]  Open
26
Chen Y, Verbeek FJ, Wolstencroft K. Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations. BMC Bioinformatics 2021;22:178. [PMID: 33823788 PMCID: PMC8025515 DOI: 10.1186/s12859-021-04105-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/22/2021] [Indexed: 12/29/2022]  Open
27
Ghatnatti V, Vastrad B, Patil S, Vastrad C, Kotturshetti I. Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. AIMS Neurosci 2021;8:254-283. [PMID: 33709028 PMCID: PMC7940115 DOI: 10.3934/neuroscience.2021014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/29/2021] [Indexed: 02/05/2023]  Open
28
Kanza S, Graham Frey J. Semantic Technologies in Drug Discovery. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]  Open
29
Hanspers K, Riutta A, Summer-Kutmon M, Pico AR. Pathway information extracted from 25 years of pathway figures. Genome Biol 2020;21:273. [PMID: 33168034 PMCID: PMC7649569 DOI: 10.1186/s13059-020-02181-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022]  Open
30
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. GENE REPORTS 2020;21:100956. [PMID: 33553808 PMCID: PMC7854084 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
31
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020;10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022]  Open
32
Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
33
Balashanmugam MV, Shivanandappa TB, Nagarethinam S, Vastrad B, Vastrad C. Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. Biomolecules 2019;10:biom10010035. [PMID: 31881747 PMCID: PMC7022900 DOI: 10.3390/biom10010035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 12/31/2022]  Open
34
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. Med Oncol 2019;36:73. [DOI: 10.1007/s12032-019-1296-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
35
Alshabi AM, Shaikh IA, Vastrad C. Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. Biomolecules 2019;9:biom9070282. [PMID: 31311202 PMCID: PMC6681318 DOI: 10.3390/biom9070282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023]  Open
36
Kim S. Pathway Interactions Based on Drug-Induced Datasets. Cancer Inform 2019;18:1176935119851518. [PMID: 31205412 PMCID: PMC6535899 DOI: 10.1177/1176935119851518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 11/16/2022]  Open
37
Wang LL, Thomas Hayman G, Smith JR, Tutaj M, Shimoyama ME, Gennari JH. Predicting instances of pathway ontology classes for pathway integration. J Biomed Semantics 2019;10:11. [PMID: 31196182 PMCID: PMC6567466 DOI: 10.1186/s13326-019-0202-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/22/2019] [Indexed: 12/16/2022]  Open
38
Alshabi AM, Vastrad B, Shaikh IA, Vastrad C. Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. Biomolecules 2019;9:biom9050201. [PMID: 31137733 PMCID: PMC6571969 DOI: 10.3390/biom9050201] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]  Open
39
Joshi H, Vastrad B, Vastrad C. Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. J Mol Neurosci 2019;68:565-589. [PMID: 30982163 DOI: 10.1007/s12031-019-01318-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
40
Alur VC, Raju V, Vastrad B, Vastrad C. Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. Diagnostics (Basel) 2019;9:diagnostics9020039. [PMID: 30970615 PMCID: PMC6628368 DOI: 10.3390/diagnostics9020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/31/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022]  Open
41
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. Sci Rep 2019;9:523. [PMID: 30679503 PMCID: PMC6346040 DOI: 10.1038/s41598-018-36636-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/22/2018] [Indexed: 12/16/2022]  Open
42
Rat Genome Databases, Repositories, and Tools. Methods Mol Biol 2019;2018:71-96. [PMID: 31228152 DOI: 10.1007/978-1-4939-9581-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
43
Domingo-Fernández D, Hoyt CT, Bobis-Álvarez C, Marín-Llaó J, Hofmann-Apitius M. ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. NPJ Syst Biol Appl 2018;5:3. [PMID: 30564458 PMCID: PMC6292919 DOI: 10.1038/s41540-018-0078-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 11/09/2022]  Open
44
Lau E, Venkatraman V, Thomas CT, Wu JC, Van Eyk JE, Lam MPY. Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. J Proteome Res 2018;17:4267-4278. [PMID: 30256117 DOI: 10.1021/acs.jproteome.8b00393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
45
Vastrad C, Vastrad B. Bioinformatics analysis of gene expression profiles to diagnose crucial and novel genes in glioblastoma multiform. Pathol Res Pract 2018;214:1395-1461. [PMID: 30097214 DOI: 10.1016/j.prp.2018.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/27/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023]
46
Chowdhury S, Sinha N, Ganguli P, Bhowmick R, Singh V, Nandi S, Sarkar RR. BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. J Integr Bioinform 2018;15:/j/jib.ahead-of-print/jib-2017-0072/jib-2017-0072.xml. [PMID: 29547394 PMCID: PMC6340122 DOI: 10.1515/jib-2017-0072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/29/2018] [Indexed: 12/03/2022]  Open
47
Shimoyama M, Smith JR, Bryda E, Kuramoto T, Saba L, Dwinell M. Rat Genome and Model Resources. ILAR J 2017;58:42-58. [PMID: 28838068 PMCID: PMC6057551 DOI: 10.1093/ilar/ilw041] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 11/25/2022]  Open
48
Shimoyama M, Laulederkind SJF, De Pons J, Nigam R, Smith JR, Tutaj M, Petri V, Hayman GT, Wang SJ, Ghiasvand O, Thota J, Dwinell MR. Exploring human disease using the Rat Genome Database. Dis Model Mech 2017;9:1089-1095. [PMID: 27736745 PMCID: PMC5087824 DOI: 10.1242/dmm.026021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
49
Henry VJ, Goelzer A, Ferré A, Fischer S, Dinh M, Loux V, Froidevaux C, Fromion V. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. J Biomed Semantics 2017;8:53. [PMID: 29169408 PMCID: PMC5701433 DOI: 10.1186/s13326-017-0165-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 11/10/2017] [Indexed: 01/10/2023]  Open
50
Pengelly RJ, Alom T, Zhang Z, Hunt D, Ennis S, Collins A. Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. Sci Rep 2017;7:13509. [PMID: 29044180 PMCID: PMC5647373 DOI: 10.1038/s41598-017-13841-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/02/2017] [Indexed: 12/27/2022]  Open
PrevPage 1 of 2 12Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA