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Huaiyu Mi, PhD

Title(s)Associate Professor Of Research Preventive Medicine
Phone+1 323 442 7994
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet. 2019 Sep 23. PMID: 31548717.
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    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. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 2019 Jun 13; 16(2). PMID: 31199769.
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    3. 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. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 07 17; 103(2):217-234.e4. PMID: 31171447.
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    4. Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD. 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. PMID: 30804569.
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    5. 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. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019 Jan 08; 47(D1):D351-D360. PMID: 30398656.
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    6. Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 2019 Jan 08; 47(D1):D419-D426. PMID: 30407594.
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    7. Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD. 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. PMID: 28025345.
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    8. 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. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. PMID: 27899635.
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    9. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. 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. PMID: 27899595.
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    10. 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 04; 44(D1):D336-42. PMID: 26578592.
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    11. 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 Sep 04; 12(2):265. PMID: 26528563.
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    12. 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 Sep 04; 12(2):263. PMID: 26528561.
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    13. 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 Sep 04; 12(2):264. PMID: 26528562.
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    14. 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; 43(Database issue):D213-21. PMID: 25428371.
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    15. Jia XH, Zhang PP, Shi DJ, Mi HL, Zhu JC, Huang XW, He PM. Regulation of pepc gene expression in Anabaena sp. PCC 7120 and its effects on cyclic electron flow around photosystem I and tolerances to environmental stresses. J Integr Plant Biol. 2015 May; 57(5):468-76. PMID: 25040477.
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    16. Tian QL, Shi DJ, Jia XH, Mi HL, Huang XW, He PM. Recombinant expression and functional analysis of a Chlamydomonas reinhardtii bacterial-type phosphoenolpyruvate carboxylase gene fragment. Biotechnol Lett. 2014 Apr; 36(4):821-7. PMID: 24375228.
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    17. 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. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. PMID: 24285306.
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    18. 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. PMID: 23868073.
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    19. 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. PMID: 23193289.
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    20. 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 01; 28(15):2016-21. PMID: 22581176.
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    21. 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. PMID: 22096229.
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    22. 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. PMID: 22021903.
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    23. 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. PMID: 20736885.
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    24. Mi H, Thomas PD. Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5. PMID: 21519400.
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    25. 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. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. PMID: 20829833.
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    26. 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. PMID: 20015972.
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    27. 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. PMID: 19668183.
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    28. 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. PMID: 19525886.
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    29. 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. PMID: 19494806.
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    30. Mi H, Thomas P. PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009; 563:123-40. PMID: 19597783.
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    31. Thomas PD, Mi H, Lewis S. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. PMID: 17208035.
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    32. 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. PMID: 17130144.
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    33. 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 01; 34(Web Server issue):W645-50. PMID: 16912992.
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    34. 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 01; 33(Database issue):D284-8. PMID: 15608197.
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    35. 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. PMID: 12952881.
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    36. 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. PMID: 12952880.
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    37. 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 01; 31(1):334-41. PMID: 12520017.
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