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Items: 15

1.

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).

Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD.

Nat Protoc. 2019 Mar;14(3):703-721. doi: 10.1038/s41596-019-0128-8. Epub 2019 Feb 25.

PMID:
30804569
2.

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.

Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D419-D426. doi: 10.1093/nar/gky1038.

3.

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.

Huang X, Albou LP, Mushayahama T, Muruganujan A, Tang H, Thomas PD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D271-D279. doi: 10.1093/nar/gky1009.

4.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD.

Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189. doi: 10.1093/nar/gkw1138. Epub 2016 Nov 29.

5.

PANTHER version 10: expanded protein families and functions, and analysis tools.

Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD.

Nucleic Acids Res. 2016 Jan 4;44(D1):D336-42. doi: 10.1093/nar/gkv1194. Epub 2015 Nov 17.

6.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26. Erratum in: Nucleic Acids Res. 2014 Oct 29;42(19):12330.

7.

Large-scale gene function analysis with the PANTHER classification system.

Mi H, Muruganujan A, Casagrande JT, Thomas PD.

Nat Protoc. 2013 Aug;8(8):1551-66. doi: 10.1038/nprot.2013.092. Epub 2013 Jul 18.

8.

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.

Mi H, Muruganujan A, Thomas PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D377-86. doi: 10.1093/nar/gks1118. Epub 2012 Nov 27.

9.

BioPAX support in CellDesigner.

Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD.

Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21.

10.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16.

11.

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W645-50.

12.

The PANTHER database of protein families, subfamilies, functions and pathways.

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.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8.

13.

PANTHER: a library of protein families and subfamilies indexed by function.

Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A.

Genome Res. 2003 Sep;13(9):2129-41.

14.

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

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.

Nucleic Acids Res. 2003 Jan 1;31(1):334-41. Erratum in: Nucleic Acids Res. 2003 Apr 1;31(7):2024.

15.

The sequence of the human genome.

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, 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.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995

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