Search Results - "Uberbacher, Edward"

Gene and translation initiation site prediction in metagenomic sequences by HYATT, Doug, LOCASCIO, Philip F, HAULER, Loren J, UBERBACHER, Edward C

“…Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the…”
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CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database by Park, Byung H, Karpinets, Tatiana V, Syed, Mustafa H, Leuze, Michael R, Uberbacher, Edward C

“…The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich…”
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Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics by Zhang, Bing, VerBerkmoes, Nathan C, Langston, Michael A, Uberbacher, Edward, Hettich, Robert L, Samatova, Nagiza F

“…Recent studies have revealed a relationship between protein abundance and sampling statistics, such as sequence coverage, peptide count, and spectral count, in…”
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MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression by Paugh, Steven W, Coss, David R, Bao, Ju, Laudermilk, Lucas T, Grace, Christy R, Ferreira, Antonio M, Waddell, M Brett, Ridout, Granger, Naeve, Deanna, Leuze, Michael, LoCascio, Philip F, Panetta, John C, Wilkinson, Mark R, Pui, Ching-Hon, Naeve, Clayton W, Uberbacher, Edward C, Bonten, Erik J, Evans, William E

“…MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA)…”
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Ebolavirus comparative genomics by Jun, Se-Ran, Leuze, Michael R., Nookaew, Intawat, Uberbacher, Edward C., Land, Miriam, Zhang, Qian, Wanchai, Visanu, Chai, Juanjuan, Nielsen, Morten, Trolle, Thomas, Lund, Ole, Buzard, Gregory S., Pedersen, Thomas D., Wassenaar, Trudy M., Ussery, David W.

“…The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently…”
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Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity by GhattyVenkataKrishna, Pavan K., Alekozai, Emal M., Beckham, Gregg T., Schulz, Roland, Crowley, Michael F., Uberbacher, Edward C., Cheng, Xiaolin

“…Cellobiohydrolases processively hydrolyze glycosidic linkages in individual polymer chains of cellulose microfibrils, and typically exhibit specificity for…”
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Analyzing large biological datasets with association networks by Karpinets, Tatiana V, Park, Byung H, Uberbacher, Edward C

“…Due to advances in high-throughput biotechnologies biological information is being collected in databases at an amazing rate, requiring novel computational…”
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Effect of the amyloid β hairpin’s structure on the handedness of helices formed by its aggregates by GhattyVenkataKrishna, Pavan K., Uberbacher, Edward C., Cheng, Xiaolin

“…•We study the structure of amyloid β sheets.•Only negative staggers lead to left-handed helices.•These structural details are necessary for designing effective…”
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Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants by Karpinets, Tatiana V, Park, Byung H, Syed, Mustafa H, Klotz, Martin G, Uberbacher, Edward C

“…Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study…”
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Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ by Alekozai, Emal M, GhattyVenkataKrishna, Pavan K, Uberbacher, Edward C, Crowley, Michael F, Smith, Jeremy C, Cheng, Xiaolin

“…The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain…”
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Effect of temperature and glycerol on the hydrogen-bond dynamics of water by Ghattyvenkatakrishna, Pavan K, Uberbacher, Edward C

“…The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, a lot remains to…”
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BESC knowledgebase public portal by SYED, Mustafa H, KARPINETS, Tatiana V, PARANG, Morey, LEUZE, Michael R, PARK, Byung H, HYATT, Doug, BROWN, Steven D, MOULTON, Steve, GALLOWAY, Michael D, UBERBACHER, Edward C

“…The BioEnergy Science Center (BESC) is undertaking large experimental campaigns to understand the biosynthesis and biodegradation of biomass and to develop…”
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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes by Karpinets, Tatiana V., Obraztsova, Anna Y., Wang, Yanbing, Schmoyer, Denise D., Kora, Guruprasad H., Park, Byung H., Serres, Margrethe H., Romine, Margaret F., Land, Miriam L., Kothe, Terence B., Fredrickson, Jim K., Nealson, Kenneth H., Uberbacher, Edward C.

“…Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological…”
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MASPIC:  Intensity-Based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence by Narasimhan, Chandrasegaran, Tabb, David L, VerBerkmoes, Nathan C, Thompson, Melissa R, Hettich, Robert L, Uberbacher, Edward C

“…Algorithmic search engines bridge the gap between large tandem mass spectrometry data sets and the identification of proteins associated with biological…”
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Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA by Leuze, Michael R., Karpinets, Tatiana V., Syed, Mustafa H., Beliaev, Alexander S., Uberbacher, Edward C.

“…Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of…”
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Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris by Karpinets, Tatiana V, Pelletier, Dale A, Pan, Chongle, Uberbacher, Edward C, Melnichenko, Galina V, Hettich, Robert L, Samatova, Nagiza F

“…Anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for…”
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A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST by Razumovskaya, Jane, Olman, Victor, Xu, Dong, Uberbacher, Edward C., VerBerkmoes, Nathan C., Hettich, Robert L., Xu, Ying

“…High‐throughput protein identification in mass spectrometry is predominantly achieved by first identifying tryptic peptides by a database search and then by…”
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Computational tools for protein modeling by Xu, D, Xu, Y, Uberbacher, E C

“…Protein modeling is playing a more and more important role in protein and peptide sciences due to improvements in modeling methods, advances in computer…”
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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions by Karpinets, Tatiana V, Romine, Margaret F, Schmoyer, Denise D, Kora, Guruprasad H, Syed, Mustafa H, Leuze, Michael R, Serres, Margrethe H, Park, Byung H, Samatova, Nagiza F, Uberbacher, Edward C

“…Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy…”
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2D image segmentation using minimum spanning trees by Xu, Ying, Uberbacher, Edward C.

“…This paper presents a new algorithm for partitioning a gray-level image into connected homogeneous regions. The novelty of this algorithm lies in the fact…”
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