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Huaiyu Mi, PhD

Title(s)Associate Professor Of Research Preventive Medicine
Address2001 N Soto Street, #212
Health Sciences Campus
Los Angeles CA 90033
Phone+1 323 442 7994
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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.
      View in: PubMed   Mentions:
    2. 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.
      View in: PubMed   Mentions:    Fields:    
    3. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2020 Dec 08. Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, Thomas PD. PMID: 33290554.
      View in: PubMed   Mentions: 1     Fields:    
    4. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2020 Nov 06. 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.
      View in: PubMed   Mentions:    Fields:    
    5. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    6. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    7. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    8. 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.
      View in: PubMed   Mentions: 121     Fields:    Translation:HumansAnimals
    9. 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.
      View in: PubMed   Mentions: 227     Fields:    Translation:HumansAnimalsCells
    10. 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.
      View in: PubMed   Mentions: 297     Fields:    Translation:Animals
    11. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    12. 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.
      View in: PubMed   Mentions: 618     Fields:    
    13. 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.
      View in: PubMed   Mentions: 380     Fields:    Translation:HumansCells
    14. 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.
      View in: PubMed   Mentions: 338     Fields:    Translation:Humans
    15. 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: 8     Fields:    Translation:HumansAnimalsCells
    16. 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: 5     Fields:    Translation:HumansAnimalsCells
    17. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    18. 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.
      View in: PubMed   Mentions: 522     Fields:    Translation:Cells
    19. 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. Jia XH, Zhang PP, Shi DJ, Mi HL, Zhu JC, Huang XW, He PM. PMID: 25040477.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    20. Recombinant expression and functional analysis of a Chlamydomonas reinhardtii bacterial-type phosphoenolpyruvate carboxylase gene fragment. Biotechnol Lett. 2014 Apr; 36(4):821-7. Tian QL, Shi DJ, Jia XH, Mi HL, Huang XW, He PM. PMID: 24375228.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    21. 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.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    22. 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.
      View in: PubMed   Mentions: 817     Fields:    
    23. 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.
      View in: PubMed   Mentions: 635     Fields:    
    24. 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.
      View in: PubMed   Mentions: 27     Fields:    
    25. 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.
      View in: PubMed   Mentions: 512     Fields:    Translation:Cells
    26. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    27. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    28. Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5. Mi H, Thomas PD. PMID: 21519400.
      View in: PubMed   Mentions:
    29. 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.
      View in: PubMed   Mentions: 237     Fields:    Translation:Cells
    30. 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.
      View in: PubMed   Mentions: 249     Fields:    Translation:HumansAnimalsCells
    31. 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.
      View in: PubMed   Mentions: 269     Fields:    
    32. 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. PMID: 19525886.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    33. 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.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    34. 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.
      View in: PubMed   Mentions: 161     Fields:    
    35. 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.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
    36. 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.
      View in: PubMed   Mentions: 153     Fields:    Translation:HumansAnimals
    37. 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.
      View in: PubMed   Mentions: 211     Fields:    Translation:HumansAnimals
    38. 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.
      View in: PubMed   Mentions: 322     Fields:    Translation:HumansAnimalsCells
    39. 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.
      View in: PubMed   Mentions: 983     Fields:    Translation:HumansAnimalsCells
    40. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    41. 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.
      View in: PubMed   Mentions: 252     Fields:    Translation:HumansAnimalsCells
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