Search Results - "Knight, Rob"

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges by Hamady, Micah, Knight, Rob

“…High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental and computational…”
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Role of the microbiome in human development by Dominguez-Bello, Maria Gloria, Godoy-Vitorino, Filipa, Knight, Rob, Blaser, Martin J

“…The host-microbiome supraorganism appears to have coevolved and the unperturbed microbial component of the dyad renders host health sustainable. This…”
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The gut microbiota in human energy homeostasis and obesity by Rosenbaum, Michael, Knight, Rob, Leibel, Rudolph L.

“…•This manuscript provides an overview of what is known about the role of the gut microbiota in rodent and human energy homeostasis.•This manuscript reviews the…”
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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations by Eisenhofer, Raphael, Minich, Jeremiah J., Marotz, Clarisse, Cooper, Alan, Knight, Rob, Weyrich, Laura S.

“…Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher…”
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The microbiome and human cancer by Sepich-Poore, Gregory D, Zitvogel, Laurence, Straussman, Ravid, Hasty, Jeff, Wargo, Jennifer A, Knight, Rob

“…Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies have provocatively claimed that…”
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Microbiota succession throughout life from the cradle to the grave by Martino, Cameron, Dilmore, Amanda Hazel, Burcham, Zachary M, Metcalf, Jessica L, Jeste, Dilip, Knight, Rob

“…Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological…”
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Microbial endocrinology: the interplay between the microbiota and the endocrine system by Neuman, Hadar, Debelius, Justine W., Knight, Rob, Koren, Omry

“…The new field of microbiome research studies the microbes within multicellular hosts and the many effects of these microbes on the host's health and…”
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UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context by Lozupone, Catherine, Hamady, Micah, Knight, Rob

“…Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial…”
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Global patterns in bacterial diversity by Lozupone, Catherine A, Knight, Rob

“…Microbes are difficult to culture. Consequently, the primary source of information about a fundamental evolutionary topic, life's diversity, is the…”
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The Earth Microbiome project: successes and aspirations by Gilbert, Jack A, Jansson, Janet K, Knight, Rob

“…Doc number: 69 Abstract: No abstract…”
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Gut microbes and the brain: paradigm shift in neuroscience by Mayer, Emeran A, Knight, Rob, Mazmanian, Sarkis K, Cryan, John F, Tillisch, Kirsten

“…The discovery of the size and complexity of the human microbiome has resulted in an ongoing reevaluation of many concepts of health and disease, including…”
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Establishing microbial composition measurement standards with reference frames by Morton, James T., Marotz, Clarisse, Washburne, Alex, Silverman, Justin, Zaramela, Livia S., Edlund, Anna, Zengler, Karsten, Knight, Rob

“…Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial…”
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UniFrac: a new phylogenetic method for comparing microbial communities by Lozupone, Catherine, Knight, Rob

“…We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the…”
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Structure-based protein function prediction using graph convolutional networks by Gligorijević, Vladimir, Renfrew, P. Douglas, Kosciolek, Tomasz, Leman, Julia Koehler, Berenberg, Daniel, Vatanen, Tommi, Chandler, Chris, Taylor, Bryn C., Fisk, Ian M., Vlamakis, Hera, Xavier, Ramnik J., Knight, Rob, Cho, Kyunghyun, Bonneau, Richard

“…The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated…”
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UniFrac: an effective distance metric for microbial community comparison by Lozupone, Catherine, Lladser, Manuel E, Knights, Dan, Stombaugh, Jesse, Knight, Rob

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Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism by Zarrinpar, Amir, Chaix, Amandine, Xu, Zhenjiang Z., Chang, Max W., Marotz, Clarisse A., Saghatelian, Alan, Knight, Rob, Panda, Satchidananda

“…Antibiotic-induced microbiome depletion (AIMD) has been used frequently to study the role of the gut microbiome in pathological conditions. However, unlike…”
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UCHIME improves sensitivity and speed of chimera detection by Edgar, Robert C., Haas, Brian J., Clemente, Jose C., Quince, Christopher, Knight, Rob

“…Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or…”
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Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale by Lauber, Christian L, Hamady, Micah, Knight, Rob, Fierer, Noah

“…Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding…”
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Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort by Qin, Youwen, Havulinna, Aki S., Liu, Yang, Jousilahti, Pekka, Ritchie, Scott C., Tokolyi, Alex, Sanders, Jon G., Valsta, Liisa, Brożyńska, Marta, Zhu, Qiyun, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Loomba, Rohit, Cheng, Susan, Jain, Mohit, Niiranen, Teemu, Lahti, Leo, Knight, Rob, Salomaa, Veikko, Inouye, Michael, Méric, Guillaume

“…Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations…”
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Evolving approaches to profiling the microbiome in skin disease by Chen, Yang, Knight, Rob, Gallo, Richard L.

“…Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, and microscopic mites. These microbes form…”
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