Search Results - "PATI, Amrita"

Plasmonic Slot Waveguide Propagation Analysis by Pati, Amrita, Gordon, Reuven

“…Plasmonic slot waveguides provide extreme light confinement with the benefits of having naturally present electrodes for switching and high thermal…”
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IMG 4 version of the integrated microbial genomes comparative analysis system by Markowitz, Victor M, Chen, I-Min A, Palaniappan, Krishna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Woyke, Tanja, Huntemann, Marcel, Anderson, Iain, Billis, Konstantinos, Varghese, Neha, Mavromatis, Konstantinos, Pati, Amrita, Ivanova, Natalia N, Kyrpides, Nikos C

“…The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG…”
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1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life by Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C

“…Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea. We…”
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations by Bendall, Matthew L, Stevens, Sarah LR, Chan, Leong-Keat, Malfatti, Stephanie, Schwientek, Patrick, Tremblay, Julien, Schackwitz, Wendy, Martin, Joel, Pati, Amrita, Bushnell, Brian, Froula, Jeff, Kang, Dongwan, Tringe, Susannah G, Bertilsson, Stefan, Moran, Mary A, Shade, Ashley, Newton, Ryan J, McMahon, Katherine D, Malmstrom, Rex R

“…Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding…”
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Stop codon reassignments in the wild by Ivanova, Natalia N., Schwientek, Patrick, Tripp, H. James, Rinke, Christian, Pati, Amrita, Huntemann, Marcel, Visel, Axel, Woyke, Tanja, Kyrpides, Nikos C., Rubin, Edward M.

“…The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of…”
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Microbial species delineation using whole genome sequences by Varghese, Neha J., Mukherjee, Supratim, Ivanova, Natalia, Konstantinidis, Konstantinos T., Mavrommatis, Kostas, Kyrpides, Nikos C., Pati, Amrita

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Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs by Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., Ivanova, Natalia N.

“…Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here…”
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Computing Genomic Signatures Using de Bruijn Chains by Heath, Lenwood S., Pati, Amrita

“…Genomic DNA sequences have both deterministic and random aspects and exhibit features at numerous scales, from codons to regions of conserved or divergent gene…”
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ProDeGe: a computational protocol for fully automated decontamination of genomes by Tennessen, Kristin, Andersen, Evan, Clingenpeel, Scott, Rinke, Christian, Lundberg, Derek S, Han, James, Dangl, Jeff L, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos, Pati, Amrita

“…Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However,…”
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Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions by He, Shaomei, Malfatti, Stephanie A, McFarland, Jack W, Anderson, Frank E, Pati, Amrita, Huntemann, Marcel, Tremblay, Julien, Glavina del Rio, Tijana, Waldrop, Mark P, Windham-Myers, Lisamarie, Tringe, Susannah G

“…Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as…”
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Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph” by SINGER, Esther, WEBB, Eric A, NELSON, William C, HEIDELBERG, John F, IVANOVA, Natalia, PATI, Amrita, EDWARDS, Katrina J

“…Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit…”
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IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites by Hadjithomas, Michalis, Chen, I-Min Amy, Chu, Ken, Ratner, Anna, Palaniappan, Krishna, Szeto, Ernest, Huang, Jinghua, Reddy, T B K, Cimermančič, Peter, Fischbach, Michael A, Ivanova, Natalia N, Markowitz, Victor M, Kyrpides, Nikos C, Pati, Amrita

“…In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of…”
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The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) by Huntemann, Marcel, Ivanova, Natalia N, Mavromatis, Konstantinos, Tripp, H James, Paez-Espino, David, Tennessen, Kristin, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A, Pati, Amrita, Nielsen, Torben, Markowitz, Victor M, Kyrpides, Nikos C

“…The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the…”
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Genome Sequence of “Candidatus Frankia datiscae” Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca glomerata by PERSSON, Tomas, BENSON, David R, SHUNSHENG HAN, HAN, James, WOYKE, Tanja, PITLUCK, Sam, PENNACCHIO, Len, NOLAN, Matt, IVANOVA, Natalia, PATI, Amrita, LAND, Miriam L, PAWLOWSKI, Katharina, NORMAND, Philippe, BERRY, Alison M, VANDEN HEUVEL, Brian, PUJIC, Petar, CHERTKOV, Olga, TESHIMA, Hazuki, BRUCE, David C, DETTER, Chris, TAPIA, Roxanne

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host by Eardly, Bertrand, Meor Osman, Wan Adnawani, Ardley, Julie, Zandberg, Jaco, Gollagher, Margaret, van Berkum, Peter, Elia, Patrick, Marinova, Dora, Seshadri, Rekha, Reddy, T B K, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Kyrpides, Nikos, Loedolff, Matthys, Laird, Damian W, Reeve, Wayne

“…Although forms highly effective symbioses with the comparatively acid-sensitive genus , its introduction into acid soils appears to have selected for symbiotic…”
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Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus by BLUMER-SCHUETTE, Sara E, OZDEMIR, Inci, WOYKE, Tanja, MIKHAILOVA, Natalia, PATI, Amrita, KYRPIDES, Nikos C, IVANOVA, Natalia, DETTER, John C, WALSTON-DAVENPORT, Karen, SHUNSHENG HAN, ADAMS, Michael W. W, KELLY, Robert M, MISTRY, Dhaval, LUCAS, Susan, LAPIDUS, Alla, CHENG, Jan-Fang, GOODWIN, Lynne A, PITLUCK, Samuel, LAND, Miriam L, HAUSER, Loren J

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Large-scale contamination of microbial isolate genomes by Illumina PhiX control by Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia, Kyrpides, Nikos C, Pati, Amrita

“…With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world's biggest…”
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Estimating DNA coverage and abundance in metagenomes using a gamma approximation by Hooper, Sean D., Dalevi, Daniel, Pati, Amrita, Mavromatis, Konstantinos, Ivanova, Natalia N., Kyrpides, Nikos C.

“…Motivation: Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the…”
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The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) by Huntemann, Marcel, Ivanova, Natalia N, Mavromatis, Konstantinos, Tripp, H James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A, Pati, Amrita, Nielsen, Torben, Markowitz, Victor M, Kyrpides, Nikos C

“…The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the…”
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High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes by Isanapong, Jantiya, Goodwin, Lynne, Bruce, David, Chen, Amy, Detter, Chris, Han, James, Han, Cliff S, Held, Brittany, Huntemann, Marcel, Ivanova, Natalia, Land, Miriam L, Mavromatis, Konstantinos, Nolan, Matt, Pati, Amrita, Pennacchio, Len, Pitluck, Sam, Szeto, Ernest, Tapia, Roxanne, Woyke, Tanja, Rodrigues, Jorge L. M

“…Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae…”
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