Faculty

Back to Index
Huaiyu Mi, PhD
Assistant Professor of Research Preventive Medicine
Preventive Medicine
NRT 2509F 1450 Biggy Street Health Sciences Campus Los Angeles
+1 323 442 7994

Publications

Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016 Jan 4; 44(D1):D336-42. View in: PubMed

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. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015 Jan 28; 43(Database issue):D213-21. View in: PubMed

Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J Integr Bioinform. 2015; 12(2):264. View in: PubMed

Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1. 2. J Integr Bioinform. 2015; 12(2):265. View in: PubMed

Moodie S, Le Novère N, Demir E, Mi H, Villéger A. Systems Biology Graphical Notation: Process Description language Level 1 Version 1. 3. J Integr Bioinform. 2015; 12(2):263. View in: PubMed

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. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan 1; 42(1):D677-84. View in: PubMed

Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013 Aug; 8(8):1551-66. View in: PubMed

Mi H, Muruganujan A, Thomas PD. 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. View in: PubMed

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. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012 Aug 1; 28(15):2016-21. View in: PubMed

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. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. View in: PubMed

Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD. BioPAX support in CellDesigner. Bioinformatics. 2011 Dec 15; 27(24):3437-8. View in: PubMed

Mi H, Thomas PD, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB. PharmGKB summary: dopamine receptor D2. Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. View in: PubMed

Mi H, Thomas PD. Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5. View in: PubMed

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, 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. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. View in: PubMed

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. View in: PubMed

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. Dopamine genes and nicotine dependence in treatment-seeking and community smokers. Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. View in: PubMed

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. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug; 27(8):735-41. View in: PubMed

Thomas PD, Mi H, Swan GE, Lerman C, Benowitz N, Tyndale RF, Bergen AW, Conti DV. A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. View in: PubMed

Mi H, Thomas P. PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009; 563:123-40. View in: PubMed

Thomas PD, Mi H, Lewis S. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. View in: PubMed

Mi H, Guo N, Kejariwal A, Thomas PD. 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. View in: PubMed

Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006 Jul 1; 34(Web Server issue):W645-50. View in: PubMed

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. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D284-8. View in: PubMed

Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep; 13(9):2118-28. View in: PubMed

Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003 Sep; 13(9):2129-41. View in: PubMed

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. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003 Jan 1; 31(1):334-41. View in: PubMed

Powered bySC CTSI