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For: Smith CL, Eppig JT. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 2012;23:653-68. [PMID: 22961259 PMCID: PMC3463787 DOI: 10.1007/s00335-012-9421-3] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023]
Number Cited by Other Article(s)
1
Berghöfer J, Khaveh N, Mundlos S, Metzger J. Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions. BMC Genomics 2025;26:285. [PMID: 40121435 PMCID: PMC11929999 DOI: 10.1186/s12864-025-11446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 03/05/2025] [Indexed: 03/25/2025]  Open
2
Duyzend MH, Cacheiro P, Jacobsen JO, Giordano J, Brand H, Wapner RJ, Talkowski ME, Robinson PN, Smedley D. Improving prenatal diagnosis through standards and aggregation. Prenat Diagn 2024;44:454-464. [PMID: 38242839 PMCID: PMC11006584 DOI: 10.1002/pd.6522] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024]
3
Abu-Toamih-Atamni HJ, Lone IM, Binenbaum I, Mott R, Pilalis E, Chatziioannou A, Iraqi FA. Mapping novel QTL and fine mapping of previously identified QTL associated with glucose tolerance using the collaborative cross mice. Mamm Genome 2024;35:31-55. [PMID: 37978084 DOI: 10.1007/s00335-023-10025-0] [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: 07/08/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
4
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos A, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon S, Castellanos F, Caufield JH, Chan LE, Chute C, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He Y(O, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus M, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, et alGargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos A, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon S, Castellanos F, Caufield JH, Chan LE, Chute C, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He Y(O, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus M, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts A, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res 2024;52:D1333-D1346. [PMID: 37953324 PMCID: PMC10767975 DOI: 10.1093/nar/gkad1005] [Show More Authors] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023]  Open
5
Wang Y, Lin Y, Wu S, Sun J, Meng Y, Jin E, Kong D, Duan G, Bei S, Fan Z, Wu G, Hao L, Song S, Tang B, Zhao W. BioKA: a curated and integrated biomarker knowledgebase for animals. Nucleic Acids Res 2024;52:D1121-D1130. [PMID: 37843156 PMCID: PMC10767812 DOI: 10.1093/nar/gkad873] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]  Open
6
Liu X, Bishir M, Hodgkinson C, Goldman D, Chang SL. The mechanisms underlying alcohol-induced decreased splenic size: A network meta-analysis study. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2024;48:72-87. [PMID: 38059389 PMCID: PMC11161039 DOI: 10.1111/acer.15234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023]
7
Bogue MA, Ball RL, Walton DO, Dunn MH, Kolishovski G, Berger A, Lamoureux A, Grubb SC, Gerring M, Kim M, Liang H, Emerson J, Stearns T, He H, Mukherjee G, Bluis J, Davis S, Desai S, Sundberg B, Kadakkuzha B, Kunde-Ramamoorthy G, Philip VM, Chesler EJ. Mouse phenome database: curated data repository with interactive multi-population and multi-trait analyses. Mamm Genome 2023;34:509-519. [PMID: 37581698 PMCID: PMC10627943 DOI: 10.1007/s00335-023-10014-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023]
8
Hill DP, Drabkin HJ, Smith CL, Van Auken KM, D’Eustachio P. Biochemical pathways represented by Gene Ontology-Causal Activity Models identify distinct phenotypes resulting from mutations in pathways. Genetics 2023;225:iyad152. [PMID: 37579192 PMCID: PMC10550311 DOI: 10.1093/genetics/iyad152] [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: 07/13/2023] [Revised: 07/13/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]  Open
9
Feng Q, Xia W, Feng Z, Tan Y, Zhang Y, Liu D, Zhang G. The accelerated organ senescence and proteotoxicity in thyrotoxicosis mice. J Cell Physiol 2023;238:2481-2498. [PMID: 37750538 DOI: 10.1002/jcp.31108] [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: 03/08/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023]
10
Powell G, Simon MM, Pulit S, Mallon AM, Lindgren CM. Genic constraint against nonsynonymous variation across the mouse genome. BMC Genomics 2023;24:562. [PMID: 37736706 PMCID: PMC10514939 DOI: 10.1186/s12864-023-09637-2] [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: 06/12/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023]  Open
11
Murray GC, Bubier JA, Zinder OJ, Harris B, Clark J, Christopher MC, Hanley C, Tjong H, Li M, Ngan CY, Reinholdt L, Burgess RW, Tadenev ALD. An allelic series of spontaneous Rorb mutant mice exhibit a gait phenotype, changes in retina morphology and behavior, and gene expression signatures associated with the unfolded protein response. G3 (BETHESDA, MD.) 2023;13:jkad131. [PMID: 37300435 PMCID: PMC10411600 DOI: 10.1093/g3journal/jkad131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
12
Hill DP, Drabkin HJ, Smith CL, Van Auken KM, D’Eustachio P. Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting from Mutations in Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541760. [PMID: 37293039 PMCID: PMC10245817 DOI: 10.1101/2023.05.22.541760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
13
Khaveh N, Schachler K, Berghöfer J, Jung K, Metzger J. Altered hair root gene expression profiles highlight calcium signaling and lipid metabolism pathways to be associated with curly hair initiation and maintenance in Mangalitza pigs. Front Genet 2023;14:1184015. [PMID: 37351343 PMCID: PMC10282778 DOI: 10.3389/fgene.2023.1184015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]  Open
14
Recanatini M, Menestrina L. Network modeling helps to tackle the complexity of drug-disease systems. WIREs Mech Dis 2023:e1607. [PMID: 36958762 DOI: 10.1002/wsbm.1607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 03/25/2023]
15
Beck T, Rowlands T, Shorter T, Brookes AJ. GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies. Nucleic Acids Res 2023;51:D986-D993. [PMID: 36350644 PMCID: PMC9825503 DOI: 10.1093/nar/gkac1017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022]  Open
16
Bogue MA, Ball RL, Philip VM, Walton DO, Dunn M, Kolishovski G, Lamoureux A, Gerring M, Liang H, Emerson J, Stearns T, He H, Mukherjee G, Bluis J, Desai S, Sundberg B, Kadakkuzha B, Kunde-Ramamoorthy G, Chesler E. Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes. Nucleic Acids Res 2023;51:D1067-D1074. [PMID: 36330959 PMCID: PMC9825561 DOI: 10.1093/nar/gkac1007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]  Open
17
Murray GC, Bais P, Hatton CL, Tadenev ALD, Hoffmann BR, Stodola TJ, Morelli KH, Pratt SL, Schroeder D, Doty R, Fiehn O, John SWM, Bult CJ, Cox GA, Burgess RW. Mouse models of NADK2 deficiency analyzed for metabolic and gene expression changes to elucidate pathophysiology. Hum Mol Genet 2022;31:4055-4074. [PMID: 35796562 PMCID: PMC9703942 DOI: 10.1093/hmg/ddac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022]  Open
18
Faubel RJ, Santos Canellas VS, Gaesser J, Beluk NH, Feinstein TN, Wang Y, Yankova M, Karunakaran KB, King SM, Ganapathiraju MK, Lo CW. Flow blockage disrupts cilia-driven fluid transport in the epileptic brain. Acta Neuropathol 2022;144:691-706. [PMID: 35980457 DOI: 10.1007/s00401-022-02463-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/28/2023]
19
Alghamdi SM, Schofield PN, Hoehndorf R. How much do model organism phenotypes contribute to the computational identification of human disease genes? Dis Model Mech 2022;15:275986. [PMID: 35758016 PMCID: PMC9366895 DOI: 10.1242/dmm.049441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/13/2022] [Indexed: 12/04/2022]  Open
20
Lindlöf A. The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies. Bioinform Biol Insights 2022;16:11779322211062722. [PMID: 35023907 PMCID: PMC8743926 DOI: 10.1177/11779322211062722] [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: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 12/06/2022]  Open
21
Quantitative phosphoproteomics reveals GSK3A substrate network is involved in the cryodamage of sperm motility. Biosci Rep 2021;41:229867. [PMID: 34596222 PMCID: PMC8521533 DOI: 10.1042/bsr20211326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 12/31/2022]  Open
22
Ringwald M, Richardson JE, Baldarelli RM, Blake JA, Kadin JA, Smith C, Bult CJ. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Mamm Genome 2021;33:4-18. [PMID: 34698891 PMCID: PMC8913530 DOI: 10.1007/s00335-021-09921-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022]
23
Konopka T, Ng S, Smedley D. Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. PLoS Comput Biol 2021;17:e1009283. [PMID: 34379637 PMCID: PMC8382188 DOI: 10.1371/journal.pcbi.1009283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/23/2021] [Accepted: 07/16/2021] [Indexed: 11/20/2022]  Open
24
Dorman A, Binenbaum I, Abu-Toamih Atamni HJ, Chatziioannou A, Tomlinson I, Mott R, Iraqi FA. Genetic mapping of novel modifiers for ApcMin induced intestinal polyps' development using the genetic architecture power of the collaborative cross mice. BMC Genomics 2021;22:566. [PMID: 34294033 PMCID: PMC8299641 DOI: 10.1186/s12864-021-07890-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/14/2021] [Indexed: 02/08/2023]  Open
25
Requena F, Abdallah HH, García A, Nitschké P, Romana S, Malan V, Rausell A. CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients. Nucleic Acids Res 2021;49:W93-W103. [PMID: 34019647 PMCID: PMC8262689 DOI: 10.1093/nar/gkab347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022]  Open
26
Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A. Prioritizing Pain-Associated Targets with Machine Learning. Biochemistry 2021;60:1430-1446. [PMID: 33606503 DOI: 10.1021/acs.biochem.0c00930] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
27
Lim N, Tesar S, Belmadani M, Poirier-Morency G, Mancarci BO, Sicherman J, Jacobson M, Leong J, Tan P, Pavlidis P. Curation of over 10 000 transcriptomic studies to enable data reuse. Database (Oxford) 2021;2021:6143045. [PMID: 33599246 PMCID: PMC7904053 DOI: 10.1093/database/baab006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 01/07/2023]
28
Baldarelli RM, Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Shaw DR, Beal JS, Blodgett O, Campbell J, Corbani LE, Frost PJ, Giannatto SC, Miers DB, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2021 update. Nucleic Acids Res 2021;49:D924-D931. [PMID: 33104772 PMCID: PMC7778941 DOI: 10.1093/nar/gkaa914] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 01/05/2023]  Open
29
Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett M, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres M, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg A, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res 2021;49:D1207-D1217. [PMID: 33264411 PMCID: PMC7778952 DOI: 10.1093/nar/gkaa1043] [Citation(s) in RCA: 674] [Impact Index Per Article: 168.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/11/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022]  Open
30
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
31
Binenbaum I, Atamni HAT, Fotakis G, Kontogianni G, Koutsandreas T, Pilalis E, Mott R, Himmelbauer H, Iraqi FA, Chatziioannou AA. Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity. BMC Genomics 2020;21:761. [PMID: 33143653 PMCID: PMC7640698 DOI: 10.1186/s12864-020-07173-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/21/2020] [Indexed: 12/28/2022]  Open
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Fernando PC, Mabee PM, Zeng E. Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. BMC Bioinformatics 2020;21:442. [PMID: 33028186 PMCID: PMC7542696 DOI: 10.1186/s12859-020-03773-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 09/22/2020] [Indexed: 01/04/2023]  Open
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Bogue MA, Philip VM, Walton DO, Grubb SC, Dunn MH, Kolishovski G, Emerson J, Mukherjee G, Stearns T, He H, Sinha V, Kadakkuzha B, Kunde-Ramamoorthy G, Chesler EJ. Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data. Nucleic Acids Res 2020;48:D716-D723. [PMID: 31696236 PMCID: PMC7145612 DOI: 10.1093/nar/gkz1032] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 01/27/2023]  Open
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Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res 2020;48:D704-D715. [PMID: 31701156 PMCID: PMC7056945 DOI: 10.1093/nar/gkz997] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022]  Open
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Sickle Cell Disease Ontology Working Group AdekileAdekunleAnieKofi AHamdaCherif BenBrownBiobeleBukiniDaimaCampbellAndrewChaouchMelekChimusaEmileChunda-LiyokaCatherineDennis-AntwiJemimaDerebailVimal KFlor-ParkMiriamGeardAmyGhediraKaisHaendelMelissaHanchardNeil AHotchkissJadeJonasMarioIbrahimMuntaserIngramClairInusaBabaJimohAdijat OzohuJuppSimonKamgaKarenKashimZainab AbimbolaKnight-MaddenJenniferLandouréGuidaLopez-SallPhilomeneMakaniJulieMalasaLeonardMasekoamengTshepisoMazanduGastonMnikaKhuthalaMulderNicolaMunungNchangwi SyntiaMunubeDeogratiasMwitaLiberataNembawareVictoriaNnoduObiageliOfori-AcquahSolomonOhene-FrempongKwakuOsei-AkotoAlexPaintsilVivianPanjiSumirRahimyMohamed CherifRoyalCharmaineSangedaRaphael ZTayoBamideleTiouiriInesTluwayFurahiniTreadwellMarshaTshiloloLeonVasilevskyNicoleWaiswaKasadhakawo MusaWonkamAmbroise. The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020;2019:5626537. [PMID: 31769834 PMCID: PMC6878945 DOI: 10.1093/database/baz118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/27/2022]
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Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res 2020;47:D1018-D1027. [PMID: 30476213 PMCID: PMC6324074 DOI: 10.1093/nar/gky1105] [Citation(s) in RCA: 438] [Impact Index Per Article: 87.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022]  Open
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Smith CM, Hayamizu TF, Finger JH, Bello SM, McCright IJ, Xu J, Baldarelli RM, Beal JS, Campbell J, Corbani LE, Frost PJ, Lewis JR, Giannatto SC, Miers D, Shaw DR, Kadin JA, Richardson JE, Smith CL, Ringwald M. The mouse Gene Expression Database (GXD): 2019 update. Nucleic Acids Res 2020;47:D774-D779. [PMID: 30335138 PMCID: PMC6324054 DOI: 10.1093/nar/gky922] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022]  Open
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Bioinformatic framework for analysis of transcription factor changes as the molecular link between replicative cellular senescence signaling pathways and carcinogenesis. Biogerontology 2020;21:357-366. [PMID: 32100207 DOI: 10.1007/s10522-020-09866-y] [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: 02/03/2020] [Accepted: 02/22/2020] [Indexed: 01/10/2023]
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Data-driven method to enhance craniofacial and oral phenotype vocabularies. J Am Dent Assoc 2019;150:933-939.e2. [PMID: 31668172 DOI: 10.1016/j.adaj.2019.05.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 01/29/2023]
40
Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. G3-GENES GENOMES GENETICS 2019;9:4223-4233. [PMID: 31645420 PMCID: PMC6893195 DOI: 10.1534/g3.119.400740] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kolishovski G, Lamoureux A, Hale P, Richardson JE, Recla JM, Adesanya O, Simons A, Kunde-Ramamoorthy G, Bult CJ. The JAX Synteny Browser for mouse-human comparative genomics. Mamm Genome 2019;30:353-361. [PMID: 31776723 PMCID: PMC6892358 DOI: 10.1007/s00335-019-09821-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/20/2019] [Indexed: 10/30/2022]
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Zhang W, Zhang H, Yang H, Li M, Xie Z, Li W. Computational resources associating diseases with genotypes, phenotypes and exposures. Brief Bioinform 2019;20:2098-2115. [PMID: 30102366 PMCID: PMC6954426 DOI: 10.1093/bib/bby071] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/01/2018] [Indexed: 12/16/2022]  Open
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Paquola C, Bethlehem RAI, Seidlitz J, Wagstyl K, Romero-Garcia R, Whitaker KJ, Vos de Wael R, Williams GB, NSPN Consortium, Vértes PE, Margulies DS, Bernhardt B, Bullmore ET. Shifts in myeloarchitecture characterise adolescent development of cortical gradients. eLife 2019;8:e50482. [PMID: 31724948 PMCID: PMC6855802 DOI: 10.7554/elife.50482] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022]  Open
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Karunakaran KB, Chaparala S, Ganapathiraju MK. Potentially repurposable drugs for schizophrenia identified from its interactome. Sci Rep 2019;9:12682. [PMID: 31481665 PMCID: PMC6722087 DOI: 10.1038/s41598-019-48307-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 07/11/2019] [Indexed: 12/13/2022]  Open
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Bogue MA, Grubb SC, Walton DO, Philip VM, Kolishovski G, Stearns T, Dunn MH, Skelly DA, Kadakkuzha B, TeHennepe G, Kunde-Ramamoorthy G, Chesler EJ. Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice. Nucleic Acids Res 2019;46:D843-D850. [PMID: 29136208 PMCID: PMC5753241 DOI: 10.1093/nar/gkx1082] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 12/25/2022]  Open
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Smith CL, Blake JA, Kadin JA, Richardson JE, Bult CJ. Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. Nucleic Acids Res 2019;46:D836-D842. [PMID: 29092072 PMCID: PMC5753350 DOI: 10.1093/nar/gkx1006] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/19/2017] [Indexed: 12/23/2022]  Open
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Jia J, An Z, Ming Y, Guo Y, Li W, Liang Y, Guo D, Li X, Tai J, Chen G, Jin Y, Liu Z, Ni X, Shi T. eRAM: encyclopedia of rare disease annotations for precision medicine. Nucleic Acids Res 2019;46:D937-D943. [PMID: 29106618 PMCID: PMC5753383 DOI: 10.1093/nar/gkx1062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/24/2017] [Indexed: 01/12/2023]  Open
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Recla JM, Bubier JA, Gatti DM, Ryan JL, Long KH, Robledo RF, Glidden NC, Hou G, Churchill GA, Maser RS, Zhang ZW, Young EE, Chesler EJ, Bult CJ. Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. Pain 2019;160:1740-1753. [PMID: 31335644 PMCID: PMC6668363 DOI: 10.1097/j.pain.0000000000001571] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bubier J, Hill D, Mukherjee G, Reynolds T, Baker EJ, Berger A, Emerson J, Blake JA, Chesler EJ. Curating gene sets: challenges and opportunities for integrative analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019;2019:5381578. [PMID: 30888410 PMCID: PMC6424415 DOI: 10.1093/database/baz036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/20/2022]
50
Zhao Y, Smith JR, Wang SJ, Dwinell MR, Shimoyama M. Quantitative phenotype analysis to identify, validate and compare rat disease models. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019;2019:5424140. [PMID: 30938777 PMCID: PMC6444380 DOI: 10.1093/database/baz037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/08/2019] [Accepted: 02/27/2019] [Indexed: 12/18/2022]
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