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1.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Lloyd-Price, Jason; Arze, Cesar; Ananthakrishnan, Ashwin N; Schirmer, Melanie; Avila-Pacheco, Julian; Poon, Tiffany W; Andrews, Elizabeth; Ajami, Nadim J; Bonham, Kevin S; Brislawn, Colin J; Casero, David; Courtney, Holly; Gonzalez, Antonio; Graeber, Thomas G; Hall, A Brantley; Lake, Kathleen; Landers, Carol J; Mallick, Himel; Plichta, Damian R; Prasad, Mahadev; Rahnavard, Gholamali; Sauk, Jenny; Shungin, Dmitry; Vázquez-Baeza, Yoshiki; White, Richard A; Braun, Jonathan; Denson, Lee A; Jansson, Janet K; Knight, Rob; Kugathasan, Subra; McGovern, Dermot P B; Petrosino, Joseph F; Stappenbeck, Thaddeus S; Winter, Harland S; Clish, Clary B; Franzosa, Eric A; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis.

Nature ; 569(7758): 655-662, 2019 05.

Artículo en Inglés | MEDLINE | ID: mdl-31142855

2.

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.

Armstrong, George; Cantrell, Kalen; Huang, Shi; McDonald, Daniel; Haiminen, Niina; Carrieri, Anna Paola; Zhu, Qiyun; Gonzalez, Antonio; McGrath, Imran; Beck, Kristen L; Hakim, Daniel; Havulinna, Aki S; Méric, Guillaume; Niiranen, Teemu; Lahti, Leo; Salomaa, Veikko; Jain, Mohit; Inouye, Michael; Swafford, Austin D; Kim, Ho-Cheol; Parida, Laxmi; Vázquez-Baeza, Yoshiki; Knight, Rob.

Genome Res ; 31(11): 2131-2137, 2021 11.

Artículo en Inglés | MEDLINE | ID: mdl-34479875

3.

Challenges in benchmarking metagenomic profilers.

Sun, Zheng; Huang, Shi; Zhang, Meng; Zhu, Qiyun; Haiminen, Niina; Carrieri, Anna Paola; Vázquez-Baeza, Yoshiki; Parida, Laxmi; Kim, Ho-Cheol; Knight, Rob; Liu, Yang-Yu.

Nat Methods ; 18(6): 618-626, 2021 06.

Artículo en Inglés | MEDLINE | ID: mdl-33986544

4.

SnapShot: the human microbiome.

González, Antonio; Vázquez-Baeza, Yoshiki; Knight, Rob.

Cell ; 158(3): 690-690.e1, 2014 Jul 31.

Artículo en Inglés | MEDLINE | ID: mdl-25083877

5.

The gut microbiome is a significant risk factor for future chronic lung disease.

Liu, Yang; Teo, Shu Mei; Méric, Guillaume; Tang, Howard H F; Zhu, Qiyun; Sanders, Jon G; Vázquez-Baeza, Yoshiki; Verspoor, Karin; Vartiainen, Ville A; Jousilahti, Pekka; Lahti, Leo; Niiranen, Teemu; Havulinna, Aki S; Knight, Rob; Salomaa, Veikko; Inouye, Michael.

J Allergy Clin Immunol ; 151(4): 943-952, 2023 04.

Artículo en Inglés | MEDLINE | ID: mdl-36587850

6.

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.

Tripathi, Anupriya; Vázquez-Baeza, Yoshiki; Gauglitz, Julia M; Wang, Mingxun; Dührkop, Kai; Nothias-Esposito, Mélissa; Acharya, Deepa D; Ernst, Madeleine; van der Hooft, Justin J J; Zhu, Qiyun; McDonald, Daniel; Brejnrod, Asker D; Gonzalez, Antonio; Handelsman, Jo; Fleischauer, Markus; Ludwig, Marcus; Böcker, Sebastian; Nothias, Louis-Félix; Knight, Rob; Dorrestein, Pieter C.

Nat Chem Biol ; 17(2): 146-151, 2021 02.

Artículo en Inglés | MEDLINE | ID: mdl-33199911

7.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob.

Nature ; 551(7681): 457-463, 2017 11 23.

Artículo en Inglés | MEDLINE | ID: mdl-29088705

8.

Learning representations of microbe-metabolite interactions.

Morton, James T; Aksenov, Alexander A; Nothias, Louis Felix; Foulds, James R; Quinn, Robert A; Badri, Michelle H; Swenson, Tami L; Van Goethem, Marc W; Northen, Trent R; Vazquez-Baeza, Yoshiki; Wang, Mingxun; Bokulich, Nicholas A; Watters, Aaron; Song, Se Jin; Bonneau, Richard; Dorrestein, Pieter C; Knight, Rob.

Nat Methods ; 16(12): 1306-1314, 2019 12.

Artículo en Inglés | MEDLINE | ID: mdl-31686038

9.

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Dillon, Matthew R; Bolyen, Evan; Adamov, Anja; Belk, Aeriel; Borsom, Emily; Burcham, Zachary; Debelius, Justine W; Deel, Heather; Emmons, Alex; Estaki, Mehrbod; Herman, Chloe; Keefe, Christopher R; Morton, Jamie T; Oliveira, Renato R M; Sanchez, Andrew; Simard, Anthony; Vázquez-Baeza, Yoshiki; Ziemski, Michal; Miwa, Hazuki E; Kerere, Terry A; Coote, Carline; Bonneau, Richard; Knight, Rob; Oliveira, Guilherme; Gopalasingam, Piraveen; Kaehler, Benjamin D; Cope, Emily K; Metcalf, Jessica L; Robeson Ii, Michael S; Bokulich, Nicholas A; Caporaso, J Gregory.

PLoS Comput Biol ; 17(6): e1009056, 2021 06.

Artículo en Inglés | MEDLINE | ID: mdl-34166363

10.

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data.

Jiang, Lingjing; Haiminen, Niina; Carrieri, Anna-Paola; Huang, Shi; Vázquez-Baeza, Yoshiki; Parida, Laxmi; Kim, Ho-Cheol; Swafford, Austin D; Knight, Rob; Natarajan, Loki.

Biometrics ; 78(3): 1155-1167, 2022 09.

Artículo en Inglés | MEDLINE | ID: mdl-33914902

11.

Impacts of the Human Gut Microbiome on Therapeutics.

Vázquez-Baeza, Yoshiki; Callewaert, Chris; Debelius, Justine; Hyde, Embriette; Marotz, Clarisse; Morton, James T; Swafford, Austin; Vrbanac, Alison; Dorrestein, Pieter C; Knight, Rob.

Annu Rev Pharmacol Toxicol ; 58: 253-270, 2018 01 06.

Artículo en Inglés | MEDLINE | ID: mdl-28968189

12.

Qiita: rapid, web-enabled microbiome meta-analysis.

Gonzalez, Antonio; Navas-Molina, Jose A; Kosciolek, Tomasz; McDonald, Daniel; Vázquez-Baeza, Yoshiki; Ackermann, Gail; DeReus, Jeff; Janssen, Stefan; Swafford, Austin D; Orchanian, Stephanie B; Sanders, Jon G; Shorenstein, Joshua; Holste, Hannes; Petrus, Semar; Robbins-Pianka, Adam; Brislawn, Colin J; Wang, Mingxun; Rideout, Jai Ram; Bolyen, Evan; Dillon, Matthew; Caporaso, J Gregory; Dorrestein, Pieter C; Knight, Rob.

Nat Methods ; 15(10): 796-798, 2018 10.

Artículo en Inglés | MEDLINE | ID: mdl-30275573

13.

Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk.

Nguyen, Tanya T; Kosciolek, Tomasz; Daly, Rebecca E; Vázquez-Baeza, Yoshiki; Swafford, Austin; Knight, Rob; Jeste, Dilip V.

Brain Behav Immun ; 91: 245-256, 2021 01.

Artículo en Inglés | MEDLINE | ID: mdl-33098964

14.

Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice.

Brunt, Vienna E; Gioscia-Ryan, Rachel A; Richey, James J; Zigler, Melanie C; Cuevas, Lauren M; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Battson, Micah L; Smithson, Andrew T; Gilley, Andrew D; Ackermann, Gail; Neilson, Andrew P; Weir, Tiffany; Davy, Kevin P; Knight, Rob; Seals, Douglas R.

J Physiol ; 597(9): 2361-2378, 2019 05.

Artículo en Inglés | MEDLINE | ID: mdl-30714619

15.

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.

Allaband, Celeste; McDonald, Daniel; Vázquez-Baeza, Yoshiki; Minich, Jeremiah J; Tripathi, Anupriya; Brenner, David A; Loomba, Rohit; Smarr, Larry; Sandborn, William J; Schnabl, Bernd; Dorrestein, Pieter; Zarrinpar, Amir; Knight, Rob.

Clin Gastroenterol Hepatol ; 17(2): 218-230, 2019 01.

Artículo en Inglés | MEDLINE | ID: mdl-30240894

16.

Reply to: Examining microbe-metabolite correlations by linear methods.

Morton, James T; McDonald, Daniel; Aksenov, Alexander A; Nothias, Louis Felix; Foulds, James R; Quinn, Robert A; Badri, Michelle H; Swenson, Tami L; Van Goethem, Marc W; Northen, Trent R; Vazquez-Baeza, Yoshiki; Wang, Mingxun; Bokulich, Nicholas A; Watters, Aaron; Song, Se Jin; Bonneau, Richard; Dorrestein, Pieter C; Knight, Rob.

Nat Methods ; 18(1): 40-41, 2021 01.

Artículo en Inglés | MEDLINE | ID: mdl-33398188

17.

Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations.

Casals-Pascual, Climent; González, Antonio; Vázquez-Baeza, Yoshiki; Song, Se Jin; Jiang, Lingjing; Knight, Rob.

Gastroenterology ; 158(6): 1524-1528, 2020 05.

Artículo en Inglés | MEDLINE | ID: mdl-31930986

18.

Meta-analyses of studies of the human microbiota.

Lozupone, Catherine A; Stombaugh, Jesse; Gonzalez, Antonio; Ackermann, Gail; Wendel, Doug; Vázquez-Baeza, Yoshiki; Jansson, Janet K; Gordon, Jeffrey I; Knight, Rob.

Genome Res ; 23(10): 1704-14, 2013 Oct.

Artículo en Inglés | MEDLINE | ID: mdl-23861384

19.

Striped UniFrac: enabling microbiome analysis at unprecedented scale.

McDonald, Daniel; Vázquez-Baeza, Yoshiki; Koslicki, David; McClelland, Jason; Reeve, Nicolai; Xu, Zhenjiang; Gonzalez, Antonio; Knight, Rob.

Nat Methods ; 15(11): 847-848, 2018 11.

Artículo en Inglés | MEDLINE | ID: mdl-30377368

20.

Guiding longitudinal sampling in IBD cohorts.

Vázquez-Baeza, Yoshiki; Gonzalez, Antonio; Xu, Zhenjiang Zech; Washburne, Alex; Herfarth, Hans H; Sartor, R Balfour; Knight, Rob.

Gut ; 67(9): 1743-1745, 2018 09.

Artículo en Inglés | MEDLINE | ID: mdl-29055911

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