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Items: 1 to 20 of 221

1.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND.

BMC Bioinformatics. 2017 Aug 10;18(1):367. doi: 10.1186/s12859-017-1777-7.

2.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.

3.

TabSQL: a MySQL tool to facilitate mapping user data to public databases.

Xia XQ, McClelland M, Wang Y.

BMC Bioinformatics. 2010 Jun 23;11:342. doi: 10.1186/1471-2105-11-342.

4.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

Zeng V, Extavour CG.

Database (Oxford). 2012 Nov 23;2012:bas048. doi: 10.1093/database/bas048. Print 2012.

5.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12. doi: 10.1186/1471-2105-11-S12-S12.

6.
7.

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.

Geib SM, Hall B, Derego T, Bremer FT, Cannoles K, Sim SB.

Gigascience. 2018 Apr 1;7(4):1-5. doi: 10.1093/gigascience/giy018.

8.

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong.

Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Review.

9.

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.

Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M.

BMC Bioinformatics. 2011 Jul 12;12:282. doi: 10.1186/1471-2105-12-282.

10.

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Huan T, Sivachenko AY, Harrison SH, Chen JY.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. doi: 10.1186/1471-2105-9-S9-S5.

11.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008. Print 2011.

12.

A data model and database for high-resolution pathology analytical image informatics.

Wang F, Kong J, Cooper L, Pan T, Kurc T, Chen W, Sharma A, Niedermayr C, Oh TW, Brat D, Farris AB, Foran DJ, Saltz J.

J Pathol Inform. 2011;2:32. doi: 10.4103/2153-3539.83192. Epub 2011 Jul 26.

13.

ESTIMA, a tool for EST management in a multi-project environment.

Kumar CG, LeDuc R, Gong G, Roinishivili L, Lewin HA, Liu L.

BMC Bioinformatics. 2004 Nov 4;5:176.

14.

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D466-70.

15.

FEATnotator: A tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments.

Podicheti R, Mockaitis K.

Methods. 2015 Jun;79-80:11-7. doi: 10.1016/j.ymeth.2015.04.028. Epub 2015 Apr 29.

PMID:
25934264
16.

CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.

Wang J, Qi M, Liu J, Zhang Y.

Plant J. 2015 Jul;83(2):359-74. doi: 10.1111/tpj.12894.

17.

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Médigue C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.

18.

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality.

Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, Nakachi M, Nomura M, Yaguchi J, Sasakura Y, Yamasaki C, Sera M, Yoshizawa AC, Imanishi T, Taniguchi H, Inaba K.

Nucleic Acids Res. 2011 Jan;39(Database issue):D807-14. doi: 10.1093/nar/gkq1144. Epub 2010 Nov 10.

19.

New resources for functional analysis of omics data for the genus Aspergillus.

Nitsche BM, Crabtree J, Cerqueira GC, Meyer V, Ram AF, Wortman JR.

BMC Genomics. 2011 Oct 5;12:486. doi: 10.1186/1471-2164-12-486.

20.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

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