Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Marcus W. Fedarko"'
Autor:
Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
Publikováno v:
mSystems, Vol 6, Iss 2 (2021)
ABSTRACT Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community
Externí odkaz:
https://doaj.org/article/e2521341b8c54c5ba66aaaecd17f94ff
Autor:
Samantha L. Huey, Lingjing Jiang, Marcus W. Fedarko, Daniel McDonald, Cameron Martino, Farhana Ali, David G. Russell, Shobha A. Udipi, Aparna Thorat, Varsha Thakker, Padmini Ghugre, R. D. Potdar, Harsha Chopra, Kripa Rajagopalan, Jere D. Haas, Julia L. Finkelstein, Rob Knight, Saurabh Mehta
Publikováno v:
mSphere, Vol 5, Iss 5 (2020)
ABSTRACT In this cross-sectional study, we describe the composition and diversity of the gut microbiota among undernourished children living in urban slums of Mumbai, India, and determine how nutritional status, including anthropometric measurements,
Externí odkaz:
https://doaj.org/article/043ca626a00c444fabd5dd50be30bac8
Publikováno v:
Genome research, vol 32, iss 11-12
The advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In parti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::533b206bbed8ae221ec38e690fdcd6f8
https://escholarship.org/uc/item/12c620kh
https://escholarship.org/uc/item/12c620kh
Autor:
Jason Dang, Timothy D. Arthur, Zhenjiang Zech Xu, Rodolfo A. Salido, Cameron Martino, Rob Knight, James Gaffney, Jon G. Sanders, Mahdieh Khosroheidari, Greg Humphrey, Jeremiah J. Minich, Brigid S. Boland, Kristen Jepsen, Qiyun Zhu, John T. Chang, Marlon Liyanage, Pieter C. Dorrestein, Robert A. Quinn, Douglas Conrad, Karenina Sanders, Caitriona Brennan, Feng Chen, William J. Sandborn, Marcus W. Fedarko, Cliff Green, Larry Smarr, Pavel A. Pevzner, Anton Bankevich, Tariq M. Rana, Sergey Nurk, Vanessa V. Phelan
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019)
Genome biology, vol 20, iss 1
Genome Biology
Genome biology, vol 20, iss 1
Genome Biology
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderbo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::deb3b955c172d0cbd4d56dcb79affbfe
http://link.springer.com/article/10.1186/s13059-019-1834-9
http://link.springer.com/article/10.1186/s13059-019-1834-9
Autor:
Anupriya Tripathi, Kristian G. Andersen, Kalen Cantrell, Daniel McDonald, Clarisse Marotz, Anna Paola Carrieri, James T. Morton, Pieter C. Dorrestein, Ho-Cheol Kim, Niina Haiminen, Stefan Janssen, Yimeng Yang, Marcus W. Fedarko, Se Jin Song, George Armstrong, Jon G. Sanders, Laxmi Parida, Austin D. Swafford, Cameron Martino, Kristen L. Beck, Antonio Gonzalez, Mehrbod Estaki, Thant Zaw, Erfan Sayyari, Nathaniel L. Matteson, Gibraan Rahman, Rob Knight, Qiyun Zhu, Julia M. Gauglitz, Yoshiki Vázquez-Baeza
Publikováno v:
mSystems, vol 6, iss 2
mSystems, Vol 6, Iss 2 (2021)
mSystems
mSystems, Vol 6, Iss 2 (2021)
mSystems
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cfe0b0b3da6011816b23d04499dd931e
https://escholarship.org/uc/item/8fw922f0
https://escholarship.org/uc/item/8fw922f0
Autor:
Jamie Morton, Yoshiki Vázquez-Baeza, Marcus W. Fedarko, Mehrbod Estaki, Se Jin Song, Cameron Martino, Nathaniel L. Matteson, Daniel McDonald, Antonio Gonzalez, Gibraan Rahman, Erfan Sayyari, Niina Haiminen, Rob Knight, Laxmi Parida, Kristian G. Andersen, Kristen L. Beck, Pieter C. Dorrestein, Austin D. Swafford, Kalen Cantrell, Qiyun Zhu, Thant Zaw, Clarisse Marotz, Anupriya Tripathi, Ho-Cheol Kim, Jon G. Sanders, Stefan Janssen, Yimeng Yang, Julia M. Gauglitz, Anna Paola Carrieri
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive tool for visualizing trees in the context of microbiome, metabolome, etc. community data scalable beyo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b5a69defc0fd215a4661c537b6af7943
https://doi.org/10.1101/2020.10.06.327080
https://doi.org/10.1101/2020.10.06.327080
Autor:
David G. Russell, Lingjing Jiang, Aparna Thorat, Harsha Chopra, Padmini Ghugre, Jere D. Haas, Marcus W. Fedarko, Samantha L Huey, Kripa Rajagopalan, Farhana Ali, Julia L. Finkelstein, Ramesh D. Potdar, Varsha Thakker, Saurabh Mehta, Cameron Martino, Shobha Udipi, Daniel McDonald, Rob Knight
Publikováno v:
mSphere, vol 5, iss 5
mSphere, Vol 5, Iss 5 (2020)
mSphere
mSphere, Vol 5, Iss 5 (2020)
mSphere
The impact of comprehensive nutritional status, defined as growth, nutritional blood biomarkers, dietary intakes, and feeding practices, on the gut microbiome in children living in low-resource settings has remained underreported in microbiome resear
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::589241cfb8a0644fe33b7a614b2bdc1b
https://escholarship.org/uc/item/6zm3278q
https://escholarship.org/uc/item/6zm3278q
Autor:
Clarisse Marotz, Rob Knight, Eric E. Allen, Antonio Gonzalez, Cameron Martino, Gibraan Rahman, James T. Morton, Jeremiah J. Minich, Marcus W. Fedarko
Publikováno v:
Nar Genomics and Bioinformatics
Many tools for dealing with compositional ‘ ’omics’ data produce feature-wise values that can be ranked in order to describe features’ associations with some sort of variation. These values include differentials (which describe features’ as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::944bf6175b568948a3b143d9488b16b3
https://doi.org/10.1093/nargab/lqaa023
https://doi.org/10.1093/nargab/lqaa023
Autor:
Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Jeremiah J. Minich, Eric E. Allen, Marcus W. Fedarko, James T. Morton, Clarisse Marotz, Rob Knight
Many tools for dealing with compositional “’omics” data produce feature-wise values that can be ranked in order to describe features’ associations with some sort of variation. These values include differentials (which describe features’ ass
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76e24177161b1c9df6a5d0121c54b10d
https://doi.org/10.1101/2019.12.17.880047
https://doi.org/10.1101/2019.12.17.880047
Publikováno v:
Genome Biology
Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019)
Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019)
Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a commun
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7cc30a14e33b3845c6cbb94de232b405
https://pubmed.ncbi.nlm.nih.gov/31451112
https://pubmed.ncbi.nlm.nih.gov/31451112