Totals
Organisms: 48
Data Sets: 103
Accessions: 314

Available Data

Filter by      

Filter by First Author:   Search All Authors:

Published From:  To: 

Filter by Accession Number
(begin typing to see list)  

Clear Filter

click organism name to view available data


Acidothermus cellulolyticus

  • Protein structure of family 74 glycoside hydrolase from A. cellulolyticus
    Data Category: Proteomics
    Alahuhta, November 30, 2013. “Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 A resolution.”
    DOI: 10.1107/S1744309113030005
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Anaerocellum thermophilum

Data Sets: 1
Accessions: 3
Microbe


Arabidopsis

  • DNA sequence of UTP:N-acetylglucosamine-1-P uridylyltransferase-1 gene from Arabidopsis
    Data Category: Genomics
    Yang, June 17, 2010. “Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis.”
    DOI: 10.1042/BJ20100315
    View PDF
Data Sets: 1
Accessions: 1
Plant


Arabidopsis thaliana

  • Transcriptome data of Arabidopsis thaliana hy1, hy2, gun1-1, and gun4-1 mutants compared with control
    Data Category: Transcriptomics
    Czarnecki, October 29, 2012. “Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling.”
    DOI: 10.3389/fpls.2012.00236
    View PDF
  • DNA sequence of folylpolyglutamate synthetase plastidial isoform of Arabidopsis thaliana
    Data Category: Genomics
    Srivastava, January 13, 2011. “The Folylpolyglutamate Synthetase Plastidial Isoform is Required for Postembryonic Root Development in Arabidopsis.”
    DOI: 10.1104/pp.110.168278
    View PDF
Data Sets: 3
Accessions: 12
Plant


Azospirillum

Data Sets: 1
Accessions: 14
Microbe


Bacillus cereus

Data Sets: 2
Accessions: 4
Microbe


Bacteroides cellulosolvens

Data Sets: 1
Accessions: 1
Microbe


Bacteroides thetaiotamicron

Data Sets: 1
Accessions: 3
Metagenome


Brachypodium distachyon

Data Sets: 1
Accessions: 4
Plant


Burkholderia

Data Sets: 1
Accessions: 1
Microbe


Caldicellulosiruptor

  • Protein structure of xproteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor
    Data Category: Proteomics
    Blumer-Schuette, March 1, 2015. “Discrete and structurally unique proteins (tapirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose.”
    DOI: 10.1074/jbc.M115.641480
    View PDF
Data Sets: 4
Accessions: 17
Microbe


Caldicellulosiruptor bescii

  • Protein structure of family 3 pectate lyase with mode of action from C. Bescii
    Data Category: Proteomics
    Alahuhta, March 1, 2013. “The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction.”
    DOI: 10.1107/S0907444912050512
    View PDF
  • Protein structure of pectate lyase
    Data Category: Proteomics
    Alahuhta, November 1, 2011. “A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase.”
    DOI: 10.1107/S1744309111038449
    View PDF
  • The protein structure of Cbescii related cellulases
    Data Category: Proteomics
    Brunecky, December 20, 2013. “Revealing nature's cellulase diversity: the digestion mechanism of caldicellulosiruptor bescii celA.”
    DOI: 10.1126/science.1244273
    View PDF
Data Sets: 4
Accessions: 12
Microbe


Caldicellulosiruptor kristjanssonii

  • Methylation profiling in C. kristjanssonii
    Data Category: Transcriptomics
    Yu, July 15, 2015. “Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing.”
    DOI: 10.1093/nar/gkv738
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Caldicellulosiruptor obsidiansis

  • Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T
    Data Category: Genomics
    Elkins, October 1, 2010. “Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T.”
    DOI: 10.1128/JB.00950-10
    View PDF
  • Complete genomes sequences of Caldicellulosiruptor obsidiansis sp. Nov. isolated from the Obsidian Pool in Yellowstone National Park
    Data Category: Genomics
    Hamilton-Brehm, December 18, 2009. “Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park.”
    DOI: 10.1128/AEM.01903-09
    View PDF
Data Sets: 2
Accessions: 2
Microbe


Caldicellulosiruptor saccharolyticus

  • Transcriptome dataset of C. saccharolyticus grown under different mix sugar
    Data Category: Transcriptomics
    VanFossen, December 15, 2009. “Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences.”
    DOI: 10.1128/AEM.01959-09
    View PDF
  • Transcriptome dataset of C. saccharolyticus grown on different substates (glucose, xylose, xyloglucan, switchgrass, and poplar)
    Data Category: Transcriptomics
    VanFossen, March 11, 2011. “Glycoside Hydrolase Inventory Drives Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus.”
    DOI: 10.1002/bit.23093
    View PDF
Data Sets: 2
Accessions: 3
Microbe


Clostridia

Data Sets: 1
Accessions: 3
Microbe


Clostridium

  • Genome sequence of Clostridium sp. DL-VIII
    Data Category: Genomics
    Taghavi, August 8, 2013. “Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a novel solventogenic Clostridium species isolated from anaerobic sludge.”
    DOI: 10.1128/genomeA.00605-13
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Clostridium autoethanogenum

  • Complete genomic sequence of C. autoethanogenum
    Data Category: Genomics
    Brown, March 21, 2014. “Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.”
    DOI: 10.1186/1754-6834-7-40
    View PDF
Data Sets: 2
Accessions: 11
Microbe


Clostridium clariflavum

Data Sets: 1
Accessions: 1
Microbe


Clostridium pasteurianum

  • Genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525)
    Data Category: Genomics
    Pyne, August 1, 2014. “Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach.”
    DOI: 10.1128/genomeA.00790-14
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Clostridium sp. Strain BNL1100

  • Genome sequence of Clostridium sp. Strain BNL1100
    Data Category: Genomics
    Li, December 1, 2012. “Complete genome sequence of Clostridium sp. Strain BNL1100, a cellulolytic mesophile isolated from corn stover.”
    DOI: 10.1128/JB.01908-12
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Clostridium thermocellum

  • Protein structure of Cellulase K from C. thermocellum
    Data Category: Proteomics
    Alahuhta, January 1, 2011. “Structure of CBM4 from Clostridium thermocellum cellulase K.”
    ISSN 1744-3091
    View PDF
  • Protein structure of fibronectin type III-like module from C. thermocellum
    Data Category: Proteomics
    Alahuhta, July 1, 2010. “Structure of a fibronectin type III-like module from Clostridium thermocellum.”
    DOI: 10.1107/S1744309110022529
    View PDF
  • Crystal Structure of the Cellulosomal CBM4 from Clostridium thermocellum Cellulase CbhA show unique binding
    Data Category: Proteomics
    Alahuhta, July 1, 2010. “The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A.”
    DOI: 10.1016/j.jmb.2010.07.028
    View PDF
  • DNA sequence of a cloning vector pMU1647 for metbolic engineering
    Data Category: Genomics
    Argyros, September 30, 2011. “High Ethanol Titers from Cellulose using Metabolically Engineered Thermophilic, Anaerobic Microbes.”
    DOI: 10.1128/AEM.00646-11
    View PDF
  • Protein structure of CbhA complex from C. thermocellum
    Data Category: Proteomics
    Brunecky, March 1, 2012. “Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex.”
    DOI: 10.1107/S0907444912001680
    View PDF
  • RNAseq data set for transcriptional unit identification of C. thermocellum
    Data Category: Transcriptomics
    Chou, March 1, 2014. “Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.”
    DOI: 10.1093/nar/gkv177
    View PDF
  • Genome sequnce of C. thermocelleum after growth adaptationon on Populus hydrolysate
    Data Category: Genomics
    Linville, October 21, 2013. “Industrial robustness: understanding the mechanism of tolerance for the populus hydrolysate-tolerant mutant strain of clostridium thermocellum.”
    DOI: 10.1371/journal.pone.0078829
    View PDF
  • Transcriptome data set of Clostridium thermocellum Populus hydrolysate-tolerant compared with reference strain
    Data Category: Transcriptomics
    Linville, August 16, 2014. “Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain.”
    DOI: 10.1186/s12866-014-0215-5
    View PDF
  • DNA sequence of expression vector for metbolic engineering
    Data Category: Genomics
    Olson, December 1, 2012. “The role of the CipA scaffoldin protein in cellulose solubilization as determined by targeted gene deletion and complementation in Clostridium thermocellum.”
    DOI: 10.1128/JB.02014-12
    View PDF
  • Transcriprome profile of Clostridium thermocellum ATCC27405 under ethanol stress
    Data Category: Transcriptomics
    Wilson, September 12, 2013. “Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress.”
    DOI: 10.1186/1754-6834-6-131
    View PDF
  • Transciptome data during growth of C. thermocellum on dilute acid pretreated populus and switchgrass
    Data Category: Transcriptomics
    Wilson, December 2, 2013. “Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.”
    DOI: 10.1186/1754-6834-6-179
    View PDF
  • Time course transcriptome dataset of C. Thermocellum during ethanol stress compare with control
    Data Category: Transcriptomics
    Yang, July 23, 2012. “Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress.”
    DOI: 10.1186/1471-2164-13-336
    View PDF
Data Sets: 18
Accessions: 36
Microbe


Escherichia coli

  • Genome sequence and comparision of isobutatnal torrorance Ecoli isolate with the parental strain
    Data Category: Genomics
    Atsumi, December 21, 2010. “Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli.”
    DOI: 10.1038/msb.2010.98
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Eucalyptus

Data Sets: 1
Accessions: 1
Plant


Fungi

Data Sets: 1
Accessions: 4
Fungi


Hahella chejuensis

  • The X-ray structure of Hahella chejuensis family 48 glycosyl hydrolase
    Data Category: Proteomics
    Sukharnikov, October 10, 2012. “Sequence, Structure, and Evolution of cellulases in the glycoside Hydrolase Family 48.”
    DOI: 10.1074/jbc.M112.405720
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Halanaerobium hydrogenoformans

  • Genome sequence of Hydrogen Producing Halanaerobium hydrogenoformans
    Data Category: Genomics
    Brown, July 14, 2011. “Complete Genome Sequence of the Haloalkaliphilic, Hydrogen Producing Halanaerobium hydrogenoformans.”
    DOI: 10.1128/JB.05209-11
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Halomonas sp. Strain KO116/ a marine bacteria

Data Sets: 1
Accessions: 3
Microbe


Medicago truncatula

  • DNA sequence of LOB domain protein of M. turncatula
    Data Category: Genomics
    Zhou, August 14, 2012. “Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula.”
    DOI: 10.1111/j.1469-8137.2012.04268.x
    View PDF
Data Sets: 4
Accessions: 38
Plant


Metagenome

Data Sets: 5
Accessions: 16
Metagenome


Plant

  • Protein structure of Glycoside hydrolases of Humicola insolens
    Data Category: Proteomics
    McKee, April 24, 2012. “Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains.”
    DOI: 10.1073/pnas.1117686109
    View PDF
Data Sets: 1
Accessions: 3
Plant


Populus

  • DNA sequence of NBS-LRR-like protein gene partial cds of Poplus
    Data Category: Genomics
    Biswal, January 7, 2014. “Aspen pectate lyase PtxtPl1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield.”
    DOI: 10.1186/1754-6834-7-11
    View PDF
  • DNA sequence of glycosyltransferase family GT8 proteins (GATL1.1, and GATL1.2 ) mRNA of Populus
    Data Category: Genomics
    Kong, September 1, 2009. “Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis.”
    DOI: 10.1093/mp/ssp068
    View PDF
Data Sets: 5
Accessions: 13
Plant


Populus trichocarpa

Data Sets: 2
Accessions: 6
Plant


Pyrococcus furiosus

  • Genome sequence of Pyrococcus furiosus DSM 3638
    Data Category: Genomics
    Farkas, July 22, 2011. “Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon, Pyrococcus furiosus, needed for construction of a stable replicating shuttle vector.”
    DOI: 10.1128/AEM.05057-11
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Ralstonia solanacearum

  • DNA sequence of NAD-dependent dehydratase of R.solanacearum
    Data Category: Genomics
    Gu, March 19, 2010. “Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family.”
    DOI: 10.1074/jbc.M109.066803
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Rhodococcus rhodochrous

Data Sets: 1
Accessions: 1
Microbe


Saccharomyces cerevisiae

Data Sets: 1
Accessions: 5
Microbe


Serratia

  • Genome sequence of Serratia sp. Strain ATCC 39006
    Data Category: Genomics
    Fineran, December 12, 2013. “Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles.”
    DOI: 10.1128/genomeA.01039-13
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Setaria

Data Sets: 1
Accessions: 6
Plant


Sinorhizobium meliloti

Data Sets: 1
Accessions: 3
Microbe


Switchgrass Panicum virgatum L.

  • DNA sequence of cinnamyl alcohol dehydrogenase mRNA of Switchgrass
    Data Category: Genomics
    Fu, January 7, 2011. “Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass.”
    DOI: 10.1007/s12155-010-9109-z
    View PDF
  • DNA sequence of caffeic acid 3-O-methyltransferase (COMT) mRNA of switchgrass
    Data Category: Genomics
    Fu, March 1, 2011. “Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass.”
    DOI: 10.1073/pnas.1100310108
    View PDF
  • EST sequence of cells from the vascular tissues by LCM from switchgrass
    Data Category: Genomics
    Srivastava, May 1, 2011. “Collection and analysis of expressed sequence tags derived from laser capture microdissected switchgrass (Panicum virgatum L. Alamo) vascular tissues.”
    DOI: 10.1007/s12155-010-9080-8
    View PDF
Data Sets: 10
Accessions: 54
Plant


Thermoanaerobacter pseudothanolicus

  • Protein structure of furan aldehyde detoxification in T. pseudethanolicus
    Data Category: Proteomics
    Clarkson, December 3, 2014. “A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E.”
    DOI: 10.1186/s13068-014-0165-z
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Thermoanaerobacterium saccharolyticum

Data Sets: 2
Accessions: 8
Microbe


Thermobifida fusca

  • Protein structure of T. fusca GH48 D224N mutant
    Data Category: Proteomics
    Kostylev, April 1, 2014. “Cel48A From Thermobifida fusca: Structure and Site Directed Mutagenesis of Key Residues.”
    DOI: 10.1002/bit.25139
    View PDF
  • DNA sequence of polyphosphate-dependent glucokinase in T. fusca
    Data Category: Genomics
    Liao, July 16, 2011. “One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP.”
    DOI: 10.1007/s00253-011-3458-1
    View PDF
Data Sets: 2
Accessions: 2
Microbe


Thermodesulfobacterium geofontis

  • Genome sequencing of Thermodesulfobacterium geofontis OPF15
    Data Category: Genomics
    Elkins, April 11, 2013. “Complete genome sequence of the hyperthermophilic sulfate-reducing bacterium thermodesulfobacterium geofontis OPF15.”
    DOI: 10.1128/genomeA.00162-13
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Trypanosoma cruzi

Data Sets: 1
Accessions: 2
Microbe


Vibrio vulnificus

  • Protein struture of family 2 polysaccharide lyase from V. vulnificus
    Data Category: Proteomics
    McLean, July 9, 2015. “Functional analyses of resurrected and contemporary enzymes illuminate an evolutionary path for the emergence of exolysis in polysaccharide lyase family two.”
    DOI: 10.1074/jbs.M115.664847
    View PDF
Data Sets: 1
Accessions: 1
Microbe


Zymomonas mobilis

  • Transcriptome data of Z. mobilis subsp mobilis 8b (an xylose-utilizing recombinant) were carried out to investigate the effect of carbon source and acetate on Z. mobilis. One study compared the acetate effect in either glucose or xylose at exponential phase and another study investigated the acetate effect in mixed sugar of glucose and xylose at three growth phases of exponential, transition, and stationar
    Data Category: Transcriptomics
    Yang, September 11, 2014. “Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates.”
    DOI: 10.1186/s13068-014-0140-8
    View PDF
  • Transciptome profiles of exponential and stationary phase cells were analyzed for the wild-type Z. mobilis ZM4 and the acetate-tolerant mutant AcR under 12g/L sodium acetate and same molar concentration of sodium chloride (8.55g/L) control conditions
    Data Category: Genomics
    Yang, April 1, 2010. “Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae.”
    DOI: 10.1073/pnas.0914506107
    View PDF
  • Transcriptome data of wild-type cultures of Z. mobilis subsp mobilis ZM4 at different time points of 6, 10, 13.5, and 26h post-inoculation with 6% (v/v) treatment compared to that of control without ethanol supplementation
    Data Category: Genomics
    Yang, July 16, 2013. “Systems biology analysis of zymomonas mobilis ZM4 ethanol stress responses.”
    DOI: 10.1371/journal.pone.0068886
    View PDF
Data Sets: 4
Accessions: 7
Microbe

BioEnergy Science Center one of three DOE Bioenergy Research Centers established by the U.S. Department of Energy.