Search Results - "LAND, Miriam"

Prodigal: prokaryotic gene recognition and translation initiation site identification by Hyatt, Doug, Chen, Gwo-Liang, Locascio, Philip F, Land, Miriam L, Larimer, Frank W, Hauser, Loren J

“…The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing…”
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Insights from 20 years of bacterial genome sequencing by Land, Miriam, Hauser, Loren, Jun, Se-Ran, Nookaew, Intawat, Leuze, Michael R., Ahn, Tae-Hyuk, Karpinets, Tatiana, Lund, Ole, Kora, Guruprased, Wassenaar, Trudy, Poudel, Suresh, Ussery, David W.

“…Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA…”
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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation by Mavromatis, Konstantinos, Land, Miriam L, Brettin, Thomas S, Quest, Daniel J, Copeland, Alex, Clum, Alicia, Goodwin, Lynne, Woyke, Tanja, Lapidus, Alla, Klenk, Hans Peter, Cottingham, Robert W, Kyrpides, Nikos C

“…The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while…”
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The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens by Aklujkar, Muktak, Krushkal, Julia, DiBartolo, Genevieve, Lapidus, Alla, Land, Miriam L, Lovley, Derek R

“…The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that…”
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Enigmatic, ultrasmall, uncultivated Archaea by Baker, Brett J, Comolli, Luis R, Dick, Gregory J, Hauser, Loren J, Hyatt, Doug, Dill, Brian D, Land, Miriam L, VerBerkmoes, Nathan C, Hettich, Robert L, Banfield, Jillian F

“…Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge--particularly…”
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Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus by Tang, Kuo-Hsiang, Barry, Kerrie, Chertkov, Olga, Dalin, Eileen, Han, Cliff S, Hauser, Loren J, Honchak, Barbara M, Karbach, Lauren E, Land, Miriam L, Lapidus, Alla, Larimer, Frank W, Mikhailova, Natalia, Pitluck, Samuel, Pierson, Beverly K, Blankenship, Robert E

“…Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or…”
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Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production by Thammarongtham, Chinae, Nookaew, Intawat, Vorapreeda, Tayvich, Srisuk, Tanawut, Land, Miriam L., Jeennor, Sukanya, Laoteng, Kobkul

“…The selected robust fungus, Aspergillus oryzae strain BCC7051 is of interest for biotechnological production of lipid-derived products due to its capability to…”
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Use of simulated data sets to evaluate the fidelity of metagenomic processing methods by Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerrie, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C, Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip, Kyrpides, Nikos C

“…Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences,…”
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Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum by Brown, Steven D., Guss, Adam M., Karpinets, Tatiana V., Parks, Jerry M., Smolin, Nikolai, Yang, Shihui, Land, Miriam L., Klingeman, Dawn M., Bhandiwad, Ashwini, Rodriguez, Miguel, Raman, Babu, Shao, Xiongjun, Mielenz, Jonathan R., Smith, Jeremy C., Keller, Martin, Lynd, Lee R.

“…Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass…”
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase by Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W., Henry, Chris S., Arkin, Adam P.

“…Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun…”
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Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides by BROWN, Steven D, UTTURKAR, Sagar M, KLINGEMAN, Dawn M, JOHNSON, Courtney M, MARTIN, Stanton L, LAND, Miriam L, LU, Tse-Yuan S, SCHADT, Christopher W, DOKTYCZ, Mitchel J, PELLETIER, Dale A

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences by Utturkar, Sagar M, Klingeman, Dawn M, Land, Miriam L, Schadt, Christopher W, Doktycz, Mitchel J, Pelletier, Dale A, Brown, Steven D

“…To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences…”
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Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis by Utturkar, Sagar M, Cude, W Nathan, Robeson, Jr, Michael S, Yang, Zamin K, Klingeman, Dawn M, Land, Miriam L, Allman, Steve L, Lu, Tse-Yuan S, Brown, Steven D, Schadt, Christopher W, Podar, Mircea, Doktycz, Mitchel J, Pelletier, Dale A

“…Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above-…”
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Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth by Ayala-del-Río, Héctor L, Chain, Patrick S, Grzymski, Joseph J, Ponder, Monica A, Ivanova, Natalia, Bergholz, Peter W, Di Bartolo, Genevive, Hauser, Loren, Land, Miriam, Bakermans, Corien, Rodrigues, Debora, Klappenbach, Joel, Zarka, Dan, Larimer, Frank, Richardson, Paul, Murray, Alison, Thomashow, Michael, Tiedje, James M

“…Psychrobacter arcticus strain 273-4, which grows at temperatures as low as -10°C, is the first cold-adapted bacterium from a terrestrial environment whose…”
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Genomics of an extreme psychrophile, Psychromonas ingrahamii by Riley, Monica, Staley, James T, Danchin, Antoine, Wang, Ting Zhang, Brettin, Thomas S, Hauser, Loren J, Land, Miriam L, Thompson, Linda S

“…The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this…”
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The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments by Aklujkar, Muktak, Young, Nelson D, Holmes, Dawn, Chavan, Milind, Risso, Carla, Kiss, Hajnalka E, Han, Cliff S, Land, Miriam L, Lovley, Derek R

“…Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III)…”
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Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX by LYKIDIS, Athanasios, MAVROMATIS, Konstantinos, RICHARDSON, Paul, WILSON, David B, KYRPIDES, Nikos, IVANOVA, Natalia, ANDERSON, Iain, LAND, Miriam, DIBARTOLO, Genevieve, MARTINEZ, Michele, LAPIDUS, Alla, LUCAS, Susan, COPELAND, Alex

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms by ALIAGA GOLTSMAN, Daniela S, DENEF, Vincent J, BAKER, Brett J, HAUSER, Loren, LAND, Miriam, SHAH, Manesh B, THELEN, Michael P, HETTICH, Robert L, BANFIELD, Jillian F, SINGER, Steven W, VERBERKMOES, Nathan C, LEFSRUD, Mark, MUELLER, Ryan S, DICK, Gregory J, SUN, Christine L, WHEELER, Korin E, ZEMLA, Adam

“…Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit…”
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Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis by Jun, Se-Ran, Wassenaar, Trudy M, Nookaew, Intawat, Hauser, Loren, Wanchai, Visanu, Land, Miriam, Timm, Collin M, Lu, Tse-Yuan S, Schadt, Christopher W, Doktycz, Mitchel J, Pelletier, Dale A, Ussery, David W

“…The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and…”
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