Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Erfan Sayyari"'
Autor:
Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B. Yin, Shi Huang, Nimaichand Salam, Jian-Yu Jiao, Zijun Wu, Zhenjiang Z. Xu, Kalen Cantrell, Yimeng Yang, Erfan Sayyari, Maryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
The authors build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on 381 markers. The results indicate a remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that used fewe
Externí odkaz:
https://doaj.org/article/963471f628f44741a9d932ae0fd75f6b
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
Publikováno v:
BMC Bioinformatics, Vol 19, Iss S6, Pp 15-30 (2018)
Abstract Background Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees whil
Externí odkaz:
https://doaj.org/article/3b80498fe94c49e78a1a07fc30cd90e3
Autor:
Erfan Sayyari, Siavash Mirarab
Publikováno v:
BMC Genomics, Vol 17, Iss S10, Pp 101-113 (2016)
Abstract Background Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. Results We introduce DISTIQUE, a new statistically consis
Externí odkaz:
https://doaj.org/article/6aa835a8e50d468dbd476da3fbcec16d
Publikováno v:
PLoS ONE, Vol 12, Iss 8, p e0182238 (2017)
Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for disc
Externí odkaz:
https://doaj.org/article/4cb8ce6ded624f6fb85e946092aa1f9c
Publikováno v:
Bioinformatics
Motivation Learning associations of traits with the microbial composition of a set of samples is a fundamental goal in microbiome studies. Recently, machine learning methods have been explored for this goal, with some promise. However, in comparison
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:
Dominic S. Nguyen, Wout Bittremieux, Rodrigo Moreira da Silva, Juliano Geraldo Amaral, Jae H. Kim, Lucas Miranda Marques, Rob Knight, Christine M. Aceves, Monica Guma, Gregory Humphrey, Morgan Panitchpakdi, Pieter C. Dorrestein, Julia Beauchamp-Walters, Daniel McDonald, Douglas Galasko, Thiago M. Cunha, Nicole Sikora, Qiyun Zhu, Candace L. Williams, Mark J. Manary, Austin D. Swafford, Pedro Belda-Ferre, Robert H. Mills, Alan K. Jarmusch, Lourdes Herrera, Flávio Protaso Veras, Parambir S. Dulai, Francesca Di Ottavio, Fernando Vargas, Abigail J. Johnson, Michelli F. Oliveira, Kelly C. Weldon, Justin P. Shaffer, Paulo Louzada-Junior, Renê Donizeti Ribeiro de Oliveira, Erfan Sayyari, MacKenzie Bryant, Julia M. Gauglitz, Anupriya Tripathi, David Gonzalez, Maria Gloria Dominguez-Bello, Kyung E. Rhee, Daniela Vargas Robles, Katharina Spengler, Norberto Peporine Lopes, Kenneth P. Wright, Robert Terkeltaub, Emmanuel O. Elijah, Rachel J. Dutton, Megan M. Doty, Clarisse Marotz, Dana Withrow, Brigid S. Boland, Curt Wittenberg, Tara Schwartz, Edgar Diaz, Cameron Martino, Lindsay DeRight Goldasich, Kate E. Sprecher, Roxana Coras, Elizabeth Brown, Barry J. Bradford, Gail Ackermann, Mingxun Wang
SummaryThe human metabolome has remained largely unknown, with most studies annotating ∼10% of features. In nucleic acid sequencing, annotating transcripts by source has proven essential for understanding gene function. Here we generalize this conc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8d75498d82cefe93b03c3a2591989835
https://doi.org/10.1101/2020.07.08.194159
https://doi.org/10.1101/2020.07.08.194159
Publikováno v:
Molecular phylogenetics and evolution. 151
Sabellida is a well-known clade containing tube-dwelling annelid worms with a radiolar crown. Iterative phylogenetic analyses over three decades have resulted in three main clades being recognized; Fabriciidae, Serpulidae and Sabellidae, with Fabrici