Search Results - "Pavlovikj, Natasha"

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses by Pavlovikj, Natasha, Gomes-Neto, Joao Carlos, Deogun, Jitender S., Benson, Andrew K.

“…Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and…”
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Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping by Pavlovikj, Natasha, Gomes-Neto, Joao Carlos, Deogun, Jitender S, Benson, Andrew K

“…Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1)…”
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Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs by Gomes-Neto, Joao Carlos, Pavlovikj, Natasha, Korth, Nate, Naberhaus, Samantha A, Arruda, Bailey, Benson, Andrew K, Kreuder, Amanda J

“…Swine are a major reservoir of an array of zoonotic subsp. lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium)…”
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Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions by Gonçalves, Joseane Penteado Rosa, Melo, Antonio Diego Brandão, Yang, Qinnan, de Oliveira, Marllon José Karpeggiane, Marçal, Danilo Alves, Ortiz, Manoela Trevisan, Righetti Arnaut, Pedro, França, Ismael, Alves da Cunha Valini, Graziela, Silva, Cleslei Alisson, Korth, Nate, Pavlovikj, Natasha, Campos, Paulo Henrique Reis Furtado, Brand, Henrique Gastmann, Htoo, John Kyaw, Gomes-Neto, João Carlos, Benson, Andrew K, Hauschild, Luciano

“…A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned…”
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Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety by Gomes-Neto, Joao Carlos, Pavlovikj, Natasha, Cano, Carmen, Abdalhamid, Baha, Al-Ghalith, Gabriel Asad, Loy, John Dustin, Knights, Dan, Iwen, Peter C., Chaves, Byron D., Benson, Andrew K.

“…The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source…”
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Addressing Bioinformatics Bottlenecks for Scalable Microbial Population Genomics Analyses by Pavlovikj, Natasha

“…With population genomics analyses, researchers can understand genetic relationships in populations and their environments, find genomic patterns, and for…”
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations by Pavlovikj, Natasha, Gomes-Neto, Joao Carlos, Benson, Andrew K

“…Routine and systematic use of bacterial whole-genome sequencing (WGS) is enhancing the accuracy and resolution of epidemiological investigations carried out by…”
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PSVI-7 A traceable signature for a recovery microbiome composition after a dysbiosis caused by a sanitary challenge in pigs by Brandao Melo, Antonio Diego Brandão, da Valini, Graziela Alves Cunha, Gomes-Neto, João Carlos, de Oliveira, Marllon José Karpeggiane, Marçal, Danilo Alves, Arnaut, Pedro Righetti, França, Ismael, Korth, Nate, Pavlovikj, Natasha, Htoo, John K, Brand, Henrique Gastmann, Benson, Andrew K, Hauschild, Luciano

“…Recent insights continue to point to a causal role of the gastrointestinal (GI) microbiome in digestion, nutrient absorption, and host metabolism. The GI…”
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PSII-19 Fecal microbiota composition of weaned piglets under mixed management and poor housing conditions fed diets increased in threonine, methionine and tryptophan by Marçal, Danilo Alves, Brandao Melo, Antonio Diego Brandão, Rosa Gonçalves, Joseane Penteado, Yang, Qinnan, de Oliveira, Marllon José Karpeggiane, Arnaut, Pedro Righetti, Ortiz, Manoela Trevizan, França, Ismael, da Cunha Valini, Graziela Alves, Korth, Nate, Pavlovikj, Natasha, Furtado Campo, Paulo Henrique Reis, Brand, Henrique Gastmann, Htoo, John K, Gomes-Neto, João Carlos, Benson, Andrew, Hauschild, Luciano

“…This study evaluated the effects of increased dietary Thr, Met and Trp supplementation on fecal microbiota composition of weaned piglets raised under…”
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Captive Common Marmosets (Callithrix jacchus) Are Colonized throughout Their Lives by a Community of Bifidobacterium Species with Species-Specific Genomic Content That Can Support Adaptation to Distinct Metabolic Niches by Zhu, Lifeng, Yang, Qinnan, Suhr Van Haute, Mallory J, Kok, Car Reen, Gomes-Neto, Joao Carlos, Pavlovikj, Natasha, Pillai, Resmi, Sinha, Rohita, Hassenstab, Haley, Mustoe, Aaryn, Moriyama, Etsuko N, Hutkins, Robert, French, Jeffrey, Benson, Andrew K

“…The common marmoset (Callithrix jacchus) is an omnivorous New World primate whose diet in the wild includes large amounts of fruit, seeds, flowers, and a…”
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Captive Common Marmosets ( Callithrix jacchus ) Are Colonized throughout Their Lives by a Community of italic toggle="yes">Bifidobacterium /italic> Species with Species-Specific Genomic Content That Can Support Adaptation to Distinct Metabolic Niches by Lifeng Zhu, Qinnan Yang, Mallory J. Suhr Van Haute, Car Reen Kok, Joao Carlos Gomes-Neto, Natasha Pavlovikj, Resmi Pillai, Rohita Sinha, Haley Hassenstab, Aaryn Mustoe, Etsuko N. Moriyama, Robert Hutkins, Jeffrey French, Andrew K. Benson

“…ABSTRACT The common marmoset (Callithrix jacchus) is an omnivorous New World primate whose diet in the wild includes large amounts of fruit, seeds, flowers,…”
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Comparative analysis of alignment tools for nanopore reads by Pavlovikj, Natasha, Moriyama, Etsuko N., Deogun, Jitender S.

“…Alignment of sequence reads is an important step of many bioinformatics workflows. While the alignment of short reads is well investigated, the alignment of…”
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Analysis of transcriptome assembly pipelines for wheat by Pavlovikj, Natasha, Begcy, Kevin, Behera, Sairam, Campbell, Malachy, Walia, Harkamal, Deogun, Jitender S.

“…With advances in next-generation sequencing technologies, transcriptome sequencing has emerged as a powerful tool for performing transcriptome analysis for…”
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A Comparison of a Campus Cluster and Open Science Grid Platforms for Protein-Guided Assembly Using Pegasus Workflow Management System by Pavlovikj, Natasha, Begcy, Kevin, Behera, Sairam, Campbell, Malachy, Walia, Harkamal, Deogun, Jitender S.

“…Scientific workflows are a useful tool for managing large and complex computational tasks. Due to its intensive resource requirements, the scientific workflows…”
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