Genome-wide dynamic transcriptional profiling in clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq

[1]  H. Blaschek,et al.  Genome-wide dynamic transcriptional profiling in clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq , 2012, BMC Genomics.

[2]  H. Blaschek,et al.  Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq , 2011, BMC Genomics.

[3]  J. Hoch,et al.  Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum , 2011, Molecular microbiology.

[4]  P. Dürre,et al.  Genome-Wide Gene Expression Analysis of the Switch between Acidogenesis and Solventogenesis in Continuous Cultures of Clostridium acetobutylicum , 2011, Journal of Molecular Microbiology and Biotechnology.

[5]  Rex T. Nelson,et al.  RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome , 2010, BMC Plant Biology.

[6]  M. Hecker,et al.  A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture , 2010, Applied Microbiology and Biotechnology.

[7]  J. Poulain,et al.  mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. , 2010, Genome research.

[8]  E. Papoutsakis,et al.  Metabolite stress and tolerance in the production of biofuels and chemicals: Gene‐expression‐based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum , 2010, Biotechnology and bioengineering.

[9]  R. Bourret,et al.  Two-component signal transduction. , 2010, Current opinion in microbiology.

[10]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[11]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[12]  A. H. V. van Vliet.  Next generation sequencing of microbial transcriptomes: challenges and opportunities. , 2010, FEMS microbiology letters.

[13]  J. Heap,et al.  The ClosTron: Mutagenesis in Clostridium refined and streamlined. , 2010, Journal of microbiological methods.

[14]  Samuel A. Assefa,et al.  A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi , 2009, PLoS genetics.

[15]  Brian D. Ondov,et al.  Structure and Complexity of a Bacterial Transcriptome , 2009, Journal of bacteriology.

[16]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[17]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[18]  H. Blaschek,et al.  Transcriptional Analysis of Clostridium beijerinckii NCIMB 8052 and the Hyper-Butanol-Producing Mutant BA101 during the Shift from Acidogenesis to Solventogenesis , 2008, Applied and Environmental Microbiology.

[19]  T. Ezeji,et al.  Fermentation of dried distillers' grains and solubles (DDGS) hydrolysates to solvents and value-added products by solventogenic clostridia. , 2008, Bioresource technology.

[20]  G. Weiller,et al.  A gene expression atlas of the model legume Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[21]  E. Papoutsakis,et al.  The transcriptional program underlying the physiology of clostridial sporulation , 2008, Genome Biology.

[22]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[23]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[24]  P. Dürre.  Biobutanol: An attractive biofuel , 2007, Biotechnology journal.

[25]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[26]  Erin M. Conlon,et al.  The forespore line of gene expression in Bacillus subtilis. , 2006, Journal of molecular biology.

[27]  Eleftherios T. Papoutsakis,et al.  A comparative genomic view of clostridial sporulation and physiology , 2005, Nature Reviews Microbiology.

[28]  M. Saier,et al.  Comparative Genomic Analyses of the Bacterial Phosphotransferase System , 2005, Microbiology and Molecular Biology Reviews.

[29]  Eleftherios T. Papoutsakis,et al.  Transcriptional Program of Early Sporulation and Stationary-Phase Events in Clostridium acetobutylicum , 2005, Journal of bacteriology.

[30]  E. Papoutsakis,et al.  Design, optimization and validation of genomic DNA microarrays for examining theClostridium acetobutylicum transcriptome , 2005 .

[31]  M. Scotcher,et al.  Expression of abrB310 and sinR, and Effects of Decreased abrB310 Expression on the Transition from Acidogenesis to Solventogenesis, in Clostridium acetobutylicum ATCC 824 , 2005, Applied and Environmental Microbiology.

[32]  M. Tangney,et al.  Carbohydrate Uptake by the Phosphotransferase System and Other Mechanisms , 2005 .

[33]  Peter Dürre,et al.  Handbook on Clostridia , 2005 .

[34]  U. Völker,et al.  Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis. , 2005, Microbiology.

[35]  G. Wadhams,et al.  Making sense of it all: bacterial chemotaxis , 2004, Nature Reviews Molecular Cell Biology.

[36]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[37]  E. Papoutsakis,et al.  Transcriptional Analysis of spo0A Overexpression in Clostridium acetobutylicum and Its Effect on the Cell's Response to Butanol Stress , 2004, Journal of bacteriology.

[38]  C. Tomas,et al.  Transcriptional Analysis of Butanol Stress and Tolerance in Clostridium acetobutylicum , 2004, Journal of bacteriology.

[39]  P. Dürre,et al.  Initiation of endospore formation in Clostridium acetobutylicum. , 2004, Anaerobe.

[40]  E Terry Papoutsakis,et al.  Transcriptional organization of the Clostridium acetobutylicum genome. , 2004, Nucleic acids research.

[41]  P. Dürre,et al.  Characterization and Development of Two Reporter Gene Systems for Clostridium acetobutylicum , 2004, Applied and Environmental Microbiology.

[42]  M. Hill,et al.  Detrended correspondence analysis: An improved ordination technique , 2004, Vegetatio.

[43]  Shane T. Jensen,et al.  The Spo0A regulon of Bacillus subtilis , 2003, Molecular microbiology.

[44]  Eleftherios T. Papoutsakis,et al.  DNA Array-Based Transcriptional Analysis of Asporogenous, Nonsolventogenic Clostridium acetobutylicum Strains SKO1 and M5 , 2003, Journal of bacteriology.

[45]  J. Hoch,et al.  Evolution of signalling in the sporulation phosphorelay , 2002, Molecular microbiology.

[46]  Eleftherios T. Papoutsakis,et al.  Northern, Morphological, and Fermentation Analysis of spo0A Inactivation and Overexpression in Clostridium acetobutylicum ATCC 824 , 2002, Journal of bacteriology.

[47]  H. Hayashi,et al.  The luxS gene is involved in cell–cell signalling for toxin production in Clostridium perfringens , 2002, Molecular microbiology.

[48]  P. Setlow,et al.  The Products of the spoVA Operon Are Involved in Dipicolinic Acid Uptake into Developing Spores of Bacillus subtilis , 2002, Journal of bacteriology.

[49]  H. Blaschek,et al.  Erratum: Glucose uptake in Clostridium beijerinckii NCIMB 8052 and the solvent-hyperproducing mutant BA101 (Applied and Environmental Microbiology (2001) 67:11 (5025-5031)) , 2002 .

[50]  P. Stragier.  A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria , 2002 .

[51]  H. Blaschek,et al.  Glucose Uptake in Clostridium beijerinckii NCIMB 8052 and the Solvent-Hyperproducing Mutant BA101 , 2001, Applied and Environmental Microbiology.

[52]  George N. Bennett,et al.  Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum , 2001, Journal of bacteriology.

[53]  Ann M Stock,et al.  Histidine kinases and response regulator proteins in two-component signaling systems. , 2001, Trends in biochemical sciences.

[54]  N. Qureshi,et al.  Soy molasses as fermentation substrate for production of butanol using Clostridium beijerinckii BA101 , 2001, Journal of Industrial Microbiology and Biotechnology.

[55]  R. Losick,et al.  Bacillus Subtilis and Its Closest Relatives: From Genes to Cells , 2001 .

[56]  J. Hoch,et al.  Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis , 2000, Molecular microbiology.

[57]  P. Dürre,et al.  Differential regulation of two thiolase genes from Clostridium acetobutylicum DSM 792. , 2000, Journal of molecular microbiology and biotechnology.

[58]  P. Youngman,et al.  Spo0A directly controls the switch from acid to solvent production in solvent‐forming clostridia , 2000, Molecular microbiology.

[59]  D. Green,et al.  Membrane Topology of the Bacillus subtilis Pro-ςK Processing Complex , 2000, Journal of bacteriology.

[60]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[61]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[62]  A. Goffeau,et al.  The complete genome sequence of the Gram-positive bacterium Bacillus subtilis , 1997, Nature.

[63]  E. Papoutsakis,et al.  The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain , 1997, Journal of bacteriology.

[64]  R. Losick,et al.  SpoIIE governs the phosphorylation state of a protein regulating transcription factor sigma F during sporulation in Bacillus subtilis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[65]  H. Yang,et al.  Coordinate genetic regulation of glycogen catabolism and biosynthesis in Escherichia coli via the CsrA gene product , 1996, Journal of bacteriology.

[66]  Jiann-Shin Chen,et al.  Alcohol dehydrogenase: multiplicity and relatedness in the solvent-producing clostridia. , 1995, FEMS microbiology reviews.

[67]  U. Sauer,et al.  Differential induction of genes related to solvent formation during the shift from acidogenesis to solventogenesis in continuous culture of Clostridium acetobutylicum , 1995 .

[68]  M. Young,et al.  Molecular genetics and the initiation of solventogenesis in Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052. , 1995, FEMS microbiology reviews.

[69]  L. Kroos,et al.  Sporulation regulatory protein SpoIIID from Bacillus subtilis activates and represses transcription by both mother-cell-specific forms of RNA polymerase. , 1994, Journal of molecular biology.

[70]  G. Bennett,et al.  Sequence and arrangement of genes encoding enzymes of the acetone-production pathway of Clostridium acetobutylicum ATCC824. , 1993, Gene.

[71]  E. Papoutsakis,et al.  Molecular characterization of two Clostridium acetobutylicum ATCC 824 butanol dehydrogenase isozyme genes , 1992, Journal of bacteriology.

[72]  I. Smith,et al.  Bacillus subtilis early sporulation genes kinA, spo0F, and spo0A are transcribed by the RNA polymerase containing sigma H , 1992, Journal of bacteriology.

[73]  P Youngman,et al.  Spo0A controls the sigma A-dependent activation of Bacillus subtilis sporulation-specific transcription unit spoIIE , 1992, Journal of bacteriology.

[74]  R. Losick,et al.  Crisscross regulation of cell-type-specific gene expression during development in B. subtilis , 1992, Nature.

[75]  P. Dürre,et al.  mRNA analysis of the adc gene region of Clostridium acetobutylicum during the shift to solventogenesis , 1992, Journal of bacteriology.

[76]  R. Losick,et al.  Compartmentalized expression of a gene under the control of sporulation transcription factor sigma E in Bacillus subtilis. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[77]  H. Blaschek,et al.  Isolation and characterization of Clostridium acetobutylicum mutants with enhanced amylolytic activity , 1991, Applied and environmental microbiology.

[78]  J. Shaw,et al.  Properties of the glucose phosphotransferase system of Clostridium acetobutylicum NCIB 8052 , 1991, Applied and environmental microbiology.

[79]  D. Sun,et al.  Control of transcription of the Bacillus subtilis spoIIIG gene, which codes for the forespore-specific transcription factor sigma G , 1991, Journal of bacteriology.

[80]  R. Losick,et al.  Forespore-specific transcription of a gene in the signal transduction pathway that governs Pro-sigma K processing in Bacillus subtilis. , 1991, Genes & development.

[81]  I. Smith,et al.  Regulation of spo0H, a gene coding for the Bacillus subtilis sigma H factor , 1991, Journal of bacteriology.

[82]  L. Kroos,et al.  Processing of the mother-cell sigma factor, sigma K, may depend on events occurring in the forespore during Bacillus subtilis development. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[83]  P. Dürre,et al.  Cloning, sequencing, and molecular analysis of the acetoacetate decarboxylase gene region from Clostridium acetobutylicum , 1990, Journal of bacteriology.

[84]  R. Losick,et al.  Temporal and spatial control of the mother-cell regulatory gene spoIIID of Bacillus subtilis. , 1989, Genes & development.

[85]  E. Papoutsakis,et al.  Purification and characterization of the NADH-dependent butanol dehydrogenase from Clostridium acetobutylicum (ATCC 824). , 1989, Archives of biochemistry and biophysics.

[86]  R. Losick,et al.  Regulatory studies on the promoter for a gene governing synthesis and assembly of the spore coat in Bacillus subtilis. , 1989, Journal of molecular biology.

[87]  C. Moran,et al.  Organization and regulation of an operon that encodes a sporulation-essential sigma factor in Bacillus subtilis , 1987, Journal of bacteriology.

[88]  D. T. Jones,et al.  Characterization, Biosynthesis, and Regulation of Granulose in Clostridium acetobutylicum , 1986, Applied and environmental microbiology.

[89]  L. Kroos,et al.  Processing of the mother-cell ar factor, orK, may depend on events occurring in the forespore during Bacillus subtilis development , 2022 .