Byers N, Parker C, Beecroft C, Reddy T, Salamon H, Garrity G
Sci Data. 2024; 11(1):1200.
PMID: 39505888
PMC: 11541499.
DOI: 10.1038/s41597-024-04049-7.
Macari G, Toti D, Polticelli F
J Comput Aided Mol Des. 2019; 33(10):887-903.
PMID: 31628659
DOI: 10.1007/s10822-019-00235-7.
Basalla J, Chatterjee P, Burgess E, Khan M, Verbrugge E, Wiegmann D
Appl Environ Microbiol. 2019; 85(23).
PMID: 31540982
PMC: 6856318.
DOI: 10.1128/AEM.01438-19.
Wagner A, Norris S, Chatterjee P, Morris P, Wildschutte H
Front Microbiol. 2018; 9:1007.
PMID: 29896163
PMC: 5986895.
DOI: 10.3389/fmicb.2018.01007.
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M
Nucleic Acids Res. 2016; 45(D1):D446-D456.
PMID: 27794040
PMC: 5210664.
DOI: 10.1093/nar/gkw992.
Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost.
Brumm P, Land M, Mead D
Stand Genomic Sci. 2016; 11:33.
PMID: 27123157
PMC: 4847372.
DOI: 10.1186/s40793-016-0153-y.
Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park.
Brumm P, Land M, Hauser L, Jeffries C, Chang Y, Mead D
Stand Genomic Sci. 2015; 10:81.
PMID: 26500717
PMC: 4617443.
DOI: 10.1186/s40793-015-0075-0.
Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park.
Brumm P, Land M, Mead D
Stand Genomic Sci. 2015; 10:73.
PMID: 26442136
PMC: 4593210.
DOI: 10.1186/s40793-015-0031-z.
Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.
Xu R, Zhou J, Wang H, He Y, Wang X, Liu B
BMC Syst Biol. 2015; 9 Suppl 1:S10.
PMID: 25708928
PMC: 4331676.
DOI: 10.1186/1752-0509-9-S1-S10.
The Pathogen-Host Interactions database (PHI-base): additions and future developments.
Urban M, Pant R, Raghunath A, Irvine A, Pedro H, Hammond-Kosack K
Nucleic Acids Res. 2014; 43(Database issue):D645-55.
PMID: 25414340
PMC: 4383963.
DOI: 10.1093/nar/gku1165.
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips.
Marcus S, Lee H, Schatz M
Bioinformatics. 2014; 30(24):3476-83.
PMID: 25398610
PMC: 4253837.
DOI: 10.1093/bioinformatics/btu756.
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.
Reddy T, Thomas A, Stamatis D, Bertsch J, Isbandi M, Jansson J
Nucleic Acids Res. 2014; 43(Database issue):D1099-106.
PMID: 25348402
PMC: 4384021.
DOI: 10.1093/nar/gku950.
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.
Simonyan V, Mazumder R
Genes (Basel). 2014; 5(4):957-81.
PMID: 25271953
PMC: 4276921.
DOI: 10.3390/genes5040957.
Prediction and redesign of protein-protein interactions.
Lua R, Marciano D, Katsonis P, Adikesavan A, Wilkins A, Lichtarge O
Prog Biophys Mol Biol. 2014; 116(2-3):194-202.
PMID: 24878423
PMC: 4246023.
DOI: 10.1016/j.pbiomolbio.2014.05.004.
Computational approaches for rational design of proteins with novel functionalities.
Tiwari M, Singh R, Singh R, Kim I, Lee J
Comput Struct Biotechnol J. 2014; 2:e201209002.
PMID: 24688643
PMC: 3962203.
DOI: 10.5936/csbj.201209002.
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Cipriano M, Novichkov P, Kazakov A, Rodionov D, Arkin A, Gelfand M
BMC Genomics. 2013; 14:213.
PMID: 23547897
PMC: 3639892.
DOI: 10.1186/1471-2164-14-213.
Bacterial genome mapper: A comparative bacterial genome mapping tool.
Lee K, Kim R, Yoon B, Kim D, Choi S, Kim D
Bioinformation. 2012; 8(11):532-4.
PMID: 22829725
PMC: 3398773.
DOI: 10.6026/97320630008532.
Defining sequence space and reaction products within the cyanuric acid hydrolase (AtzD)/barbiturase protein family.
Seffernick J, Erickson J, Cameron S, Cho S, Dodge A, Richman J
J Bacteriol. 2012; 194(17):4579-88.
PMID: 22730121
PMC: 3415516.
DOI: 10.1128/JB.00791-12.
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.
Kumar A, Suthers P, Maranas C
BMC Bioinformatics. 2012; 13:6.
PMID: 22233419
PMC: 3277463.
DOI: 10.1186/1471-2105-13-6.
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.
Pagani I, Liolios K, Jansson J, Chen I, Smirnova T, Nosrat B
Nucleic Acids Res. 2011; 40(Database issue):D571-9.
PMID: 22135293
PMC: 3245063.
DOI: 10.1093/nar/gkr1100.