11 research outputs found
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
- Author
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2013
- Field of study
American Gut: an Open Platform for Citizen Science Microbiome Research
- Author
- Abramson Max
- Ackermann Gail
- Ajami Nadim
- Aksenov Alexander A.
- Amir Amnon
- Ball Madeleine
- Behsaz Bahar
- Berg-Lyons Donna
- Bittinger Kyle
- Blaser Martin
- Bloss Cinnamon
- Bobe Jason
- Bolyen Evan
- Brennan Caitriona
- Bushman Frederic D.
- Butyaev Alexander
- Callewaert Chris
- Cani Patrice D.
- Caporaso J. Gregory
- Chase John H.
- Chen Yingfeng
- Chia Nicholas
- Chopra Deepak
- Church George M.
- Clemente Jose C.
- Debelius Justine W.
- DeRight Goldasich Lindsay
- Dillon Lindsay
- Dominguez-Bello Maria G.
- Dorrestein Pieter C.
- Drogaris Chris
- Dunn Robert R.
- Dutton Rachel
- Eisen Jonathan A.
- Eshoo-Anton Tifani W.
- Fahimipour Ashkaan K.
- Fang Xin
- Fierer Noah
- Frazier Angel
- Gaffney James
- Gajer Pawel
- Galzerani Daniela Domingos
- Gauglitz Julia
- Geier Justin
- German J. Bruce
- Gevers Dirk
- Gilbert Jack A.
- Gogul Grant
- Gonzalez Antonio
- Gonzalez David J.
- Goodrich Julia
- Gottel Neil R.
- Green Jessica L.
- Gunderson Beau
- Hampton-Marcell Jarrad T.
- Heale Arthur Cole
- Holmes Susan
- Holscher Hanna D.
- Hugenholtz Philip
- Humphrey Greg
- Huttenhower Curtis
- Hyde Embriette
- Jackson Matthew A.
- Jacobs Julian
- Jankowska Marta M.
- Janssen Stefan
- Jansson Janet K.
- Jarmusch Alan
- Jeste Dilip V.
- Jiang Lingjing
- Kashyap Purna
- Kelley Scott T.
- Kerr Jacqueline
- Klemmer Scott
- Knight Rob
- Knights Dan
- Kopylova Evguenia
- Kosciolek Tomasz
- Krajmalnik-Brown Rosa
- Kurisu Mike
- Ladau Joshua
- Lauber Christian L.
- Leach Jeff
- Lebrilla Carlito
- Lewis Cecil M.
- Lewis James D.
- Lewis Kim
- Ley Ruth
- Lovelace Elijah
- Lowry Christopher A.
- Lozupone Catherine
- Mann Allison E.
- Marotz Clarisse
- Martino Cameron
- Matamoros SĂ©bastien
- Mayer Kris
- McDonald Daniel
- Meleshko Dmitry
- Melnik Alexey V.
- Metcalf Jessica L.
- Mills David A.
- Mills Robert H.
- Minson Michael
- Mirarab Siavash
- Mohimani Hosein
- Monk Jonathan
- Montassier Emmanuel
- Moorman Stephanie
- Morton James T.
- Navas-Molina Jose
- Nazarova Elena
- Nguyen Dominic
- Nguyen Tanya T.
- Owens Sarah M.
- Pandey Vineet
- Park Rachel S.
- Peddada Shyamal
- Petrosino Joseph
- Pevzner Pavel
- Pierce Emily
- Pirrung Meg
- Pollard Katherine S.
- Raes Jeroen
- Rahnavard Gholamali
- Raison Charles
- Ravel Jacques
- Reeve Nicolai
- Robbins-Pianka Adam
- Salido Benitez Rodolfo Antonio
- Sanders Karenina
- Sangwan Naseer
- Saxe Gordon
- Schriml Lynn M.
- Schwartz Tara
- Sears Dorothy D.
- Shorenstein Joshua
- Silva Ricardo
- Smarr Larry
- Song Se Jin
- Spector Timothy
- Strandwitz Philip
- Suchodolski Jan S.
- Swafford Austin D.
- Swanson Kelly S.
- TerAvest Emily
- Thackray Varykina G.
- Thompson Luke R.
- Treuren Will Van
- Tripathi Anupriya
- Ugrina Ivo
- Vigers Tim
- Vrbanac Alison
- Vázquez-Baeza Yoshiki
- WaldispĂĽhl JĂ©rĂ´me
- Warinner Christina
- Wendel Doug
- White Owen
- Willner Dana
- Wischmeyer Paul
- Wolfe Elaine
- Wozniak Jacob M.
- Wu Gary D.
- Xavier Ramnik J.
- Zaramela Livia S.
- Zech Xu Zhenjiang
- Zengler Karsten
- Zhang Chi
- Zhu Qiyun
- Publication venue
- 'American Society for Microbiology'
- Publication date
- 01/01/2018
- Field of study
McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18
movie_s2.mp4
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
Placing changes in the microbiome in the context of the American Gut. We accumulated samples over sequencing runs to demonstrate the structural consistency in the data. We demonstrate that while the ICU dataset (https://www.ncbi.nlm.nih.gov/pubmed/27602409) falls within the American Gut samples, they do not fall close to most samples at any of the body sites. We then highlight samples from the United Kingdom, Australia, the United States and other countries to show that nationality does not overcome the variation in body site. We then highlight the utility of the American Gut in meta-analysis by reproducing results from (https://www.ncbi.nlm.nih.gov/pubmed/20668239) and (https://www.ncbi.nlm.nih.gov/pubmed/23861384), using the AGP dataset as the context for dynamic microbiome changes instead of the HMP dataset. We show rapid, complete recovery of C. diff patients following fecal material transplantation and also contextualized the change in an infant gut over time until it settles into an adult state. This demonstrates the power of the American Gut dataset, both as a cohesive study and as a context for other investigations
ag_tree.tre
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The SEPP (Mirarab et al Pac Symp Biocomput 2012) fragment insertion tree used for phylogenetic analyses
American Gut Project fecal sOTU counts table
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The Deblur sOTU counts table for the fecal samples used in the American Gut Project manuscript. The samples were trimmed to a common read length of 125nt, and processed by Deblur (Amir et al mSystems 2017). Blooms were removed (Amir et al mSystems 2017) and any sample with fewer than 1250 sequences was omitted. This table is not rarefied,
American Gut Project fecal sOTU relative abundance table
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The Deblur sOTU relative abundance table for the fecal samples used in the American Gut Project manuscript. The samples were trimmed to a common read length of 125nt, and processed by Deblur (Amir et al mSystems 2017). Blooms were removed (Amir et al mSystems 2017) and any sample with fewer than 1250 sequences was omitted. This table is not rarefied, and is normalized to 1
American Gut collated alpha diversities
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
Collated alpha diversity values for the 9511 fecal samples used in the American Gut Project manuscript
Unweighted UniFrac distances
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The unweighted UniFrac distance (Lozupone and Knight AEM 2005) matrix of the 9511 fecal samples used in the American Gut paper. UniFrac was computed using Striped UniFrac (https://github.com/biocore/unifrac). Prior to execution of UniFrac, Deblur (Amir et al mSystems 2017) was run on the samples, all bloom sOTUs were removed (Amir et al mSystems 2017), and samples were rarefied to a depth of 1250 reads (Weiss et al Microbiome 2017). For the phylogeny, fragments were inserted using SEPP (Mirarab et al Pac Symp Biocomput 2012) into the Greengenes 13_5 99% OTU tree (McDonald et al ISME 2012)
Full American Gut Project mapping file
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The full American Gut Project mapping file, includes non-fecal samples
Weighted normalized UniFrac distances
- Author
- Adam Robbins-Pianka (2016013)
- Alan Jarmusch (4900324)
- Alexander A. Aksenov (584220)
- Alexey V. Melnik (3341477)
- Alison Vrbanac (4900219)
- Allison E. Mann (4900213)
- Amnon Amir (45764)
- Angel Frazier (4900234)
- Antonio Gonzalez (2150521)
- Anupriya Tripathi (4228504)
- Arthur Cole Heale (4900390)
- Ashkaan K. Fahimipour (4900240)
- Austin Swafford (4900381)
- Bahar Behsaz (762520)
- Brennan Caitriona (4900387)
- Caitriona Brennen (4900216)
- Cameron Martino (4900222)
- Carlito Lebrilla (2083105)
- Catherine Lozupone (21305)
- Cecil M. Lewis Jr. (269417)
- Charles Raison (4900237)
- Chi Zhang (9857)
- Chris Callewaert (444348)
- Christian L. Lauber (191243)
- Christina Warinner (513402)
- Christopher A. Lowry (592172)
- Cinnamon Bloss (619703)
- Clarisse Marotz (4890046)
- Curtis Huttenhower (21159)
- Dan Knights (103804)
- Dana Willner (171081)
- Daniel McDonald (47302)
- Daniel McDonald (4899922)
- Daniela Domingos Galzerani (4900225)
- David A. Mills (128485)
- David J. Gonzalez (4449451)
- Deepak Chopra (328612)
- Dilip V. Jeste (811193)
- Dirk Gevers (50883)
- Dmitry Meleshko (4900336)
- Dominic Nguyen (4900330)
- Donna Berg-Lyons (191238)
- Dorothy D. Sears (359780)
- Doug Wendel (4900231)
- Elaine Wolfe (4900243)
- Elijah Lovelace (4900228)
- Embriette R. Hyde (478209)
- Emily Pierce (4900255)
- Emily TerAvest (4900252)
- Emmanuel Montassier (2181862)
- Evan Bolyen (3571697)
- Evguenia Kopylova (4900294)
- Frederic D. Bushman (22634)
- Gail Ackermann (618902)
- Gary D. Wu (142852)
- George M. Church (102039)
- Gholamali Rahnavard (4805520)
- Gordon Saxe (4900258)
- Grant Gogul (4900270)
- Gregory Humphrey (4900273)
- Hannah D. Holscher (786621)
- Hosein Mohimani (1327503)
- Ivo Ugrina (4384318)
- J. Bruce German (223525)
- J. Gregory Caporaso (229094)
- Jack Gilbert (139767)
- Jacob M. Wozniak (4900267)
- Jacqueline Kerr (785884)
- Jacques Ravel (5502)
- James D. Lewis (142856)
- James Gaffney (4900264)
- James T. Morton (4455616)
- Jan S. Suchodolski (107343)
- Janet K. Jansson (117759)
- Jarrad T. Hampton-Marcell (4045862)
- Jason Bobe (4900261)
- Jeff Leach (4900249)
- Jeroen Raes (6041)
- Jessica L. Green (109204)
- Jessica L. Metcalf (3253854)
- John H. Chase (276379)
- Jonathan A. Eisen (93505)
- Jonathan Monk (3548066)
- Jose A. Navas-Molina (4900303)
- Jose C. Clemente (280826)
- Joseph Petrosino (39790)
- Joshua Ladau (232530)
- Joshua Shorenstein (4900300)
- Julia Gauglitz (4900288)
- Julia Goodrich (3454907)
- Julian Jacobs (4900366)
- Justin Geier (4900327)
- Justine W. Debelius (618901)
- Karenina Sanders (4900369)
- Karsten Zengler (247723)
- Katherine S. Pollard (14217)
- Kelly S. Swanson (210272)
- Kim Lewis (20864)
- Kris Mayer (4900312)
- Kyle Bittinger (137003)
- Larry Smarr (379158)
- Lindsay DeRight Goldasich (4900375)
- Lindsay Dillon (4634245)
- Lingjing Jiang (4900372)
- Livia S. Zaramela (631780)
- Luke R. Thompson (265546)
- Lynn M. Schriml (579376)
- Maria G. Dominguez-Bello (4900348)
- Marta M. Jankowska (4900393)
- Martin Blaser (2167843)
- Matthew A. Jackson (4900291)
- Max Abramson (4900342)
- Meg Pirrung (4900318)
- Michael Minson (2140813)
- Mike Kurisu (4900345)
- Nadim Ajami (3526169)
- Naseer Sangwan (130913)
- Neil R. Gottel (3266802)
- Nicholas Chia (233775)
- Nicolai Reeve (4900354)
- Noah Fierer (121024)
- Owen White (189)
- Patrice D. Cani (152762)
- Paul Wischmeyer (4900285)
- Pavel Pevzner (29423)
- Pawel Gajer (178443)
- Philip Strandwitz (4708879)
- Phillip Hugenholtz (222811)
- Pieter C Dorrestein (4900363)
- Purna Kashyap (3460319)
- Qiyun Zhu (694450)
- Rachel Dutton (4900378)
- Rachel S. Park (4900339)
- Ramnik J. Xavier (153776)
- Ricardo Silva (4739820)
- Rob Knight (11635)
- Robert H. Mills (4900333)
- Robert R. Dunn (121034)
- Rodolfo Antonio Salido Benitez (4900321)
- Rosa Krajmalnik-Brown (430268)
- Ruth Ley (3454904)
- Sarah M. Owens (512539)
- Scott Klemmer (4900357)
- Scott T. Kelley (158464)
- Se Jin Song (3243147)
- Shyamal Peddada (3457745)
- Siavash Mirarab (3259020)
- Stefan Janssen (44445)
- Stephanie Moorman (4900306)
- Susan Holmes (243177)
- SĂ©bastien Matamoros (4900315)
- Tanya Nguyen (4900309)
- Tanya T. Nguyen (4900351)
- Tara Schwartz (508198)
- Tifani W. Eshoo-Anton (4900297)
- Tim Vigers (4900360)
- Timothy Spector (348486)
- Tomasz Kosciolek (538142)
- Varykina G. Thackray (665721)
- Vineet Pandey (4900384)
- Will Van Treuren (745942)
- Xin Fang (134979)
- Yingfeng Chen (2457415)
- Yoshiki Vázquez-Baeza (542947)
- Zhenjiang Zech Xu (754869)
- Publication venue
- Publication date
- Field of study
The weighted normalized UniFrac distance (Lozupone et al AEM 2007) matrix of the 9511 fecal samples used in the American Gut paper. UniFrac was computed using Striped UniFrac (https://github.com/biocore/unifrac). Prior to execution of UniFrac, Deblur (Amir et al mSystems 2017) was run on the samples, all bloom sOTUs were removed (Amir et al mSystems 2017), and samples were rarefied to a depth of 1250 reads (Weiss et al Microbiome 2017). For the phylogeny, fragments were inserted using SEPP (Mirarab et al Pac Symp Biocomput 2012) into the Greengenes 13_5 99% OTU tree (McDonald et al ISME 2012)