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A compendium of human gene functions derived from evolutionary modelling. Nature. 2025 Apr; 640(8057):146-154.
Feuermann M, Mi H, Gaudet P, Muruganujan A, Lewis SE, Ebert D, Mushayahama T, Gene Ontology Consortium, Thomas PD. PMID: 40011791; PMCID: PMC11964926.
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PubMed Mentions: Fields:
Translation:
Humans
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InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025 Jan 06; 53(D1):D444-D456.
Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, Bateman A. PMID: 39565202; PMCID: PMC11701551.
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PubMed Mentions:
18 Fields:
Translation:
Cells
-
Pathway Polygenic Risk Scores (pPRS) for the Analysis of Gene-environment Interaction. bioRxiv. 2024 Dec 19.
Gauderman WJ, Fu Y, Queme B, Kawaguchi E, Wang Y, Morrison J, Brenner H, Chan A, Gruber SB, Keku T, Li L, Moreno V, Pellatt AJ, Peters U, Samadder NJ, Schmit SL, Ulrich CM, Um C, Wu A, Lewinger JP, Drew DA, Mi H. PMID: 39763728; PMCID: PMC11702571.
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PubMed Mentions:
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The Gene Ontology knowledgebase in 2023. Genetics. 2023 05 04; 224(1).
Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. PMID: 36866529; PMCID: PMC10158837.
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PubMed Mentions:
727 Fields:
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PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships. NPJ Syst Biol Appl. 2023 04 03; 9(1):9.
Mills C, Marconett CN, Lewinger JP, Mi H. PMID: 37012250; PMCID: PMC10070356.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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InterPro in 2022. Nucleic Acids Res. 2023 01 06; 51(D1):D418-D427.
Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A. PMID: 36350672; PMCID: PMC9825450.
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PubMed Mentions:
848 Fields:
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Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. Nucleic Acids Res. 2022 07 05; 50(W1):W57-W65.
Liu Z, Mushayahama T, Queme B, Ebert D, Muruganujan A, Mills C, Thomas PD, Mi H. PMID: 35640593; PMCID: PMC9252745.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 2022 01; 31(1):8-22.
Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PMID: 34717010; PMCID: PMC8740835.
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PubMed Mentions:
623 Fields:
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Reactome and the Gene Ontology: digital convergence of data resources. Bioinformatics. 2021 Oct 11; 37(19):3343-3348.
Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou LP, Thomas PD, Mungall CJ, Blake JA, D'Eustachio P. PMID: 33964129; PMCID: PMC8504636.
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PubMed Mentions:
11 Fields:
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Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees. PLoS Comput Biol. 2021 02; 17(2):e1007948.
Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, Marjoram P. PMID: 33600408; PMCID: PMC7924801.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimals
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The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354.
Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. PMID: 33156333; PMCID: PMC7778928.
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PubMed Mentions:
955 Fields:
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PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2021 01 08; 49(D1):D394-D403.
Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, Thomas PD. PMID: 33290554; PMCID: PMC7778891.
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PubMed Mentions:
637 Fields:
Translation:
Cells
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The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021 01 08; 49(D1):D325-D334.
Gene Ontology Consortium. PMID: 33290552; PMCID: PMC7779012.
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PubMed Mentions:
1524 Fields:
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PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. Plant Direct. 2020 Dec; 4(12):e00293.
Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E. PMID: 33392435; PMCID: PMC7773024.
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PubMed Mentions:
19
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PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PLoS One. 2020; 15(12):e0243791.
Mills C, Muruganujan A, Ebert D, Marconett CN, Lewinger JP, Thomas PD, Mi H. PMID: 33320871; PMCID: PMC7737992.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet. 2019 10; 51(10):1429-1433.
Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. PMID: 31548717; PMCID: PMC7012280.
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PubMed Mentions:
52 Fields:
Translation:
HumansCells
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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 2019 Jun 13; 16(2).
Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A. PMID: 31199769; PMCID: PMC6798820.
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PubMed Mentions:
30 Fields:
Translation:
Cells
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SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 07 17; 103(2):217-234.e4.
Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M. PMID: 31171447; PMCID: PMC6764089.
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PubMed Mentions:
384 Fields:
Translation:
HumansAnimalsCells
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Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019 03; 14(3):703-721.
Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD. PMID: 30804569; PMCID: PMC6519457.
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PubMed Mentions:
704 Fields:
Translation:
HumansAnimals
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InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019 01 08; 47(D1):D351-D360.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. PMID: 30398656; PMCID: PMC6323941.
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PubMed Mentions:
729 Fields:
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PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 2019 01 08; 47(D1):D419-D426.
Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. PMID: 30407594; PMCID: PMC6323939.
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PubMed Mentions:
1455 Fields:
Translation:
Animals
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Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2018; 13:17.
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. PMID: 30117501; PMCID: PMC6083578.
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PubMed Mentions:
10
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Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. Database (Oxford). 2016; 2016.
Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD. PMID: 28025345; PMCID: PMC5199145.
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PubMed Mentions:
7 Fields:
Translation:
HumansAnimals
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InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. PMID: 27899635; PMCID: PMC5210578.
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PubMed Mentions:
711 Fields:
Translation:
HumansCells
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PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2017 01 04; 45(D1):D183-D189.
Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. PMID: 27899595; PMCID: PMC5210595.
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PubMed Mentions:
1039 Fields:
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PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42.
Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PMID: 26578592; PMCID: PMC4702852.
View in:
PubMed Mentions:
440 Fields:
Translation:
Humans
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Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. J Integr Bioinform. 2015 Sep 04; 12(2):265.
Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A. PMID: 26528563.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansAnimalsCells
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Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. J Integr Bioinform. 2015 Sep 04; 12(2):263.
Moodie S, Le Novère N, Demir E, Mi H, Villéger A. PMID: 26528561.
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PubMed Mentions:
18 Fields:
Translation:
HumansAnimalsCells
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Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J Integr Bioinform. 2015 Sep 04; 12(2):264.
Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A. PMID: 26528562.
View in:
PubMed Mentions:
19 Fields:
Translation:
HumansAnimalsCells
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The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. PMID: 25428371; PMCID: PMC4383996.
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PubMed Mentions:
649 Fields:
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PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84.
Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas PD, Altman T. PMID: 24285306; PMCID: PMC3965092.
View in:
PubMed Mentions:
15 Fields:
Translation:
Cells
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Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013 Aug; 8(8):1551-66.
Mi H, Muruganujan A, Casagrande JT, Thomas PD. PMID: 23868073; PMCID: PMC6519453.
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PubMed Mentions:
1269 Fields:
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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013 Jan; 41(Database issue):D377-86.
Mi H, Muruganujan A, Thomas PD. PMID: 23193289; PMCID: PMC3531194.
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PubMed Mentions:
901 Fields:
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Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. PMID: 23161678; PMCID: PMC3531070.
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PubMed Mentions:
286 Fields:
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Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012 Aug 01; 28(15):2016-21.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. PMID: 22581176; PMCID: PMC3400951.
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PubMed Mentions:
31 Fields:
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A mutation of OSOTP 51 leads to impairment of photosystem I complex assembly and serious photo-damage in rice. J Integr Plant Biol. 2012 Feb; 54(2):87-98.
Ye JW, Gong ZY, Chen CG, Mi HL, Chen GY. PMID: 22353560.
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PubMed Mentions:
9 Fields:
Translation:
AnimalsCells
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InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. PMID: 22096229; PMCID: PMC3245097.
View in:
PubMed Mentions:
550 Fields:
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BioPAX support in CellDesigner. Bioinformatics. 2011 Dec 15; 27(24):3437-8.
Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD. PMID: 22021903; PMCID: PMC3232372.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansAnimalsCells
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PharmGKB summary: dopamine receptor D2. Pharmacogenet Genomics. 2011 Jun; 21(6):350-6.
Mi H, Thomas PD, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB. PMID: 20736885; PMCID: PMC3091980.
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PubMed Mentions:
6 Fields:
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Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5.
Mi H, Thomas PD. PMID: 21519400; PMCID: PMC3081276.
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PubMed Mentions:
5
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The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. PMID: 20829833; PMCID: PMC3001121.
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PubMed Mentions:
311 Fields:
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PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10.
Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. PMID: 20015972; PMCID: PMC2808919.
View in:
PubMed Mentions:
302 Fields:
Translation:
HumansAnimalsCells
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The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug; 27(8):735-41.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. PMID: 19668183.
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PubMed Mentions:
348 Fields:
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[Construction of the dioxin bioassay method based on the clonal expressed aryl hydrocarbon receptor system]. Zhonghua Yu Fang Yi Xue Za Zhi. 2009 Aug; 43(8):705-9.
Wang Z, Zhao N, Shen J, Wang Y, Tang NJ, Wu YT, Zhang WQ, Mi HF. PMID: 20021851.
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PubMed Mentions: Fields:
Translation:
AnimalsCells
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A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet Genomics. 2009 Jul; 19(7):538-51.
Thomas PD, Mi H, Swan GE, Lerman C, Benowitz N, Tyndale RF, Bergen AW, Conti DV, Pharmacogenetics of Nicotine Addiction and Treatment Consortium. PMID: 19525886; PMCID: PMC6485245.
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PubMed Mentions:
8 Fields:
Translation:
Humans
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Dopamine genes and nicotine dependence in treatment-seeking and community smokers. Neuropsychopharmacology. 2009 Sep; 34(10):2252-64.
Bergen AW, Conti DV, Van Den Berg D, Lee W, Liu J, Li D, Guo N, Mi H, Thomas PD, Lessov-Schlaggar CN, Krasnow R, He Y, Nishita D, Jiang R, McClure JB, Tildesley E, Hops H, Tyndale RF, Benowitz NL, Lerman C, Swan GE. PMID: 19494806; PMCID: PMC3558036.
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PubMed Mentions:
16 Fields:
Translation:
Humans
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PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009; 563:123-40.
Mi H, Thomas P. PMID: 19597783; PMCID: PMC6608593.
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PubMed Mentions:
358 Fields:
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Effects of zebra leaf 1--a new variegation mutation--on chloroplast development in rice. Fen Zi Xi Bao Sheng Wu Xue Bao. 2008 Oct; 41(5):417-22.
Zhang DY, Gong ZY, Ye JW, Wu YX, Mi HL, Chen GY. PMID: 19127778.
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PubMed Mentions:
1 Fields:
Translation:
AnimalsCells
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Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11.
Thomas PD, Mi H, Lewis S. PMID: 17208035.
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PubMed Mentions:
32 Fields:
Translation:
HumansAnimals
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PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res. 2007 Jan; 35(Database issue):D247-52.
Mi H, Guo N, Kejariwal A, Thomas PD. PMID: 17130144; PMCID: PMC1716723.
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PubMed Mentions:
146 Fields:
Translation:
HumansAnimals
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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W645-50.
Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. PMID: 16912992; PMCID: PMC1538848.
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PubMed Mentions:
255 Fields:
Translation:
HumansAnimals
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The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8.
Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. PMID: 15608197; PMCID: PMC540032.
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PubMed Mentions:
362 Fields:
Translation:
HumansAnimalsCells
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PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003 Sep; 13(9):2129-41.
Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PMID: 12952881; PMCID: PMC403709.
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PubMed Mentions:
1395 Fields:
Translation:
HumansAnimalsCells
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Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep; 13(9):2118-28.
Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. PMID: 12952880; PMCID: PMC403707.
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PubMed Mentions:
16 Fields:
Translation:
Animals
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[Separation of hydrophobic NAD(P)H dehydrogenase subcomplexes from cyanobacterium Synechocystis PCC6803]. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003 Aug; 35(8):723-7.
Deng Y, Ye JY, Mi HL, Shen YG. PMID: 12897967.
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PubMed Mentions:
3 Fields:
Translation:
Cells
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PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003 Jan 01; 31(1):334-41.
Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O. PMID: 12520017; PMCID: PMC165562.
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PubMed Mentions:
287 Fields:
Translation:
HumansAnimalsCells
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Distribution of rSlo Ca2+-activated K+ channels in rat astrocyte perivascular endfeet. Brain Res. 2002 Nov 29; 956(2):183-93.
Price DL, Ludwig JW, Mi H, Schwarz TL, Ellisman MH. PMID: 12445685.
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PubMed Mentions:
48 Fields:
Translation:
AnimalsCells
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Induction of astrocyte differentiation by endothelial cells. J Neurosci. 2001 Mar 01; 21(5):1538-47.
Mi H, Haeberle H, Barres BA. PMID: 11222644; PMCID: PMC6762957.
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PubMed Mentions:
76 Fields:
Translation:
AnimalsCells
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The sequence of the human genome. Science. 2001 02 16; 291(5507):1304-51.
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. PMID: 11181995.
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PubMed Mentions:
2826 Fields:
Translation:
HumansAnimalsCells
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Identification and localization of Ca(2+)-activated K+ channels in rat sciatic nerve. Glia. 1999 Apr; 26(2):166-75.
Mi H, Harris-Warrick RM, Deerinck TJ, Inman I, Ellisman MH, Schwarz TL. PMID: 10384881.
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PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
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Purification and characterization of astrocyte precursor cells in the developing rat optic nerve. J Neurosci. 1999 Feb 01; 19(3):1049-61.
Mi H, Barres BA. PMID: 9920668; PMCID: PMC6782146.
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PubMed Mentions:
55 Fields:
Translation:
AnimalsCells
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The Involvement of Plastoquinone in the Pyocyanine-mediated Cyclic Electron Transport around Photosystem I. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 1997; 29(6):579-584.
Wang YJ, Ye JY, Mi HL, Li DY, Shen YG. PMID: 12215772.
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PubMed Mentions: Fields:
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Inwardly rectifying K+ channels that may participate in K+ buffering are localized in microvilli of Schwann cells. J Neurosci. 1996 Apr 15; 16(8):2421-9.
Mi H, Deerinck TJ, Jones M, Ellisman MH, Schwarz TL. PMID: 8786419; PMCID: PMC6578751.
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PubMed Mentions:
12 Fields:
Translation:
AnimalsCells
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Differential distribution of closely related potassium channels in rat Schwann cells. J Neurosci. 1995 May; 15(5 Pt 2):3761-74.
Mi H, Deerinck TJ, Ellisman MH, Schwarz TL. PMID: 7751944; PMCID: PMC6578200.
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PubMed Mentions:
32 Fields:
Translation:
AnimalsCells