|
🐜
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
112 auth.
Evan Bolyen,
J. Rideout,
Matthew R. Dillon,
N. Bokulich,
C. Abnet,
Gabriel A. Al-Ghalith,
Harriet Alexander,
E. Alm,
Manimozhiyan Arumugam,
F. Asnicar,
Yang Bai,
J. Bisanz,
K. Bittinger,
A. Brejnrod,
Colin J. Brislawn,
...
C. T. Brown,
B. Callahan,
A. Caraballo-Rodríguez,
John H. Chase,
Emily K. Cope,
R. D. da Silva,
C. Diener,
P. Dorrestein,
G. Douglas,
D. Durall,
C. Duvallet,
C. Edwardson,
Madeleine Ernst,
M. Estaki,
Jennifer T. Fouquier,
J. Gauglitz,
S. Gibbons,
D. Gibson,
Antonio Gonzalez,
Kestrel Gorlick,
Jiarong Guo,
Benjamin M Hillmann,
S. Holmes,
H. Holste,
C. Huttenhower,
G. Huttley,
Stefan Janssen,
A. Jarmusch,
Lingjing Jiang,
Benjamin D. Kaehler,
K. Kang,
Christopher R. Keefe,
P. Keim,
S. Kelley,
D. Knights,
I. Koester,
T. Kosciólek,
Jorden Kreps,
M. Langille,
Joslynn S. Lee,
R. Ley,
Yong-xin Liu,
E. Loftfield,
C. Lozupone,
Massoud Maher,
C. Marotz,
Bryan D. Martin,
Daniel McDonald,
L. McIver,
A. Melnik,
J. Metcalf,
S. C. Morgan,
James T. Morton,
Ahmad Turan Naimey,
Jose A Navas-Molina,
Louis-Félix Nothias,
Stephanie B. Orchanian,
Talima R. Pearson,
Samuel L. Peoples,
D. Petráš,
M. Preuss,
E. Pruesse,
Lasse Buur Rasmussen,
A. Rivers,
M. Robeson,
P. Rosenthal,
N. Segata,
Michael Shaffer,
A. Shiffer,
R. Sinha,
Se Jin Song,
J. Spear,
Austin D. Swafford,
Luke R. Thompson,
P. Torres,
Pauline Trinh,
A. Tripathi,
P. Turnbaugh,
Sabah Ul-Hasan,
J. V. D. van der Hooft,
Fernando Vargas,
Y. Vázquez-Baeza,
E. Vogtmann,
Max von Hippel,
William Walters,
Yunhu Wan,
Mingxun Wang,
Jonathan Warren,
Kyle C. Weber,
C. H. Williamson,
A. Willis,
Z. Xu,
Jesse R. Zaneveld,
Yilong Zhang,
Qiyun Zhu,
R. Knight,
J. Caporaso
|
13 |
2019 |
13
🐜
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|
🐜
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QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
120 auth.
Evan Bolyen,
J. Rideout,
Matthew R. Dillon,
N. Bokulich,
C. Abnet,
Gabriel A. Al-Ghalith,
Harriet Alexander,
Harriet Alexander,
E. Alm,
Manimozhiyan Arumugam,
F. Asnicar,
Yang Bai,
J. Bisanz,
K. Bittinger,
A. Brejnrod,
...
Colin J. Brislawn,
C. T. Brown,
B. Callahan,
A. Caraballo-Rodríguez,
John H. Chase,
Emily K. Cope,
R. R. Silva,
P. Dorrestein,
G. Douglas,
D. Durall,
C. Duvallet,
C. Edwardson,
Madeleine Ernst,
M. Estaki,
Jennifer T. Fouquier,
J. Gauglitz,
D. Gibson,
Antonio Gonzalez,
Kestrel Gorlick,
Jiarong Guo,
Benjamin M Hillmann,
S. Holmes,
H. Holste,
C. Huttenhower,
C. Huttenhower,
G. Huttley,
Stefan Janssen,
A. Jarmusch,
Lingjing Jiang,
Benjamin D. Kaehler,
K. Kang,
K. Kang,
Christopher R. Keefe,
P. Keim,
S. Kelley,
D. Knights,
I. Koester,
I. Koester,
T. Kosciólek,
Jorden Kreps,
M. Langille,
Joslynn S. Lee,
R. Ley,
R. Ley,
Yong-xin Liu,
E. Loftfield,
C. Lozupone,
Massoud Maher,
C. Marotz,
Bryan D. Martin,
Daniel McDonald,
L. McIver,
L. McIver,
A. Melnik,
J. Metcalf,
S. C. Morgan,
James T. Morton,
Ahmad Turan Naimey,
Jose A Navas-Molina,
Jose A Navas-Molina,
Louis-Félix Nothias,
Stephanie B. Orchanian,
Talima R. Pearson,
Samuel L. Peoples,
Samuel L. Peoples,
D. Petráš,
M. Preuss,
E. Pruesse,
Lasse Buur Rasmussen,
A. Rivers,
Ii Michael S Robeson,
P. Rosenthal,
N. Segata,
Michael Shaffer,
A. Shiffer,
R. Sinha,
Se Jin Song,
J. Spear,
Austin D. Swafford,
Luke R. Thompson,
Luke R. Thompson,
P. Torres,
Pauline Trinh,
A. Tripathi,
A. Tripathi,
P. Turnbaugh,
Sabah Ul-Hasan,
J. J. Hooft,
Fernando Vargas,
Y. Vázquez-Baeza,
E. Vogtmann,
Max von Hippel,
William Walters,
Yunhu Wan,
Mingxun Wang,
Jonathan Warren,
Kyle C. Weber,
Kyle C. Weber,
Chase Williamson,
A. Willis,
Z. Xu,
Jesse R. Zaneveld,
Yilong Zhang,
R. Knight,
J. Caporaso
|
10 |
2018 |
10
🐜
|
|
🦁
|
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
11 auth.
Jiarong Guo,
B. Bolduc,
A. Zayed,
A. Varsani,
Guillermo Domínguez-Huerta,
Tom O. Delmont,
...
Akbar Adjie Pratama,
M. C. Gazitúa,
D. Vik,
M. Sullivan,
S. Roux
|
9 |
2021 |
9
🦁
|
|
🐜
|
A genomic catalog of Earth’s microbiomes
267 auth.
Stephen Nayfach,
S. Roux,
Rekha Seshadri,
Daniel W. Udwary,
N. Varghese,
Frederik Schulz,
Dongying Wu,
David Páez-Espino,
I. Chen,
Marcel Huntemann,
Krishna Palaniappan,
J. Ladau,
Supratim Mukherjee,
T. Reddy,
T. Nielsen,
...
Edward Kirton,
José P. Faria,
Janaka N. Edirisinghe,
C. Henry,
S. Jungbluth,
D. Chivian,
Paramvir S. Dehal,
E. Wood-Charlson,
A. Arkin,
S. Tringe,
A. Visel,
H. Abreu,
S. Acinas,
E. Allen,
M. Allen,
L. Alteio,
G. Andersen,
A. Anesio,
G. Attwood,
Viridiana Avila-Magaña,
Yacine Badis,
J. Bailey,
B. Baker,
P. Baldrian,
H. Barton,
D. Beck,
Eric D. Becraft,
H. Beller,
J. Beman,
R. Bernier-Latmani,
T. Berry,
Anthony D. Bertagnolli,
S. Bertilsson,
Jennifer M. Bhatnagar,
J. Bird,
Jeffrey L. Blanchard,
Sara E. Blumer-Schuette,
B. Bohannan,
M. Borton,
Allyson Brady,
S. Brawley,
J. Brodie,
Steven Brown,
Jennifer R. Brum,
A. Brune,
D. Bryant,
A. Buchan,
D. Buckley,
J. Buongiorno,
H. Cadillo-Quiroz,
S. Caffrey,
A. Campbell,
Barbara Campbell,
S. Carr,
J. Carroll,
S. Cary,
Anna M. Cates,
R. Cattolico,
R. Cavicchioli,
L. Chistoserdova,
Maureen L. Coleman,
P. Constant,
Jonathan M. Conway,
W. M. Mac Cormack,
S. Crowe,
B. Crump,
C. Currie,
R. Daly,
Kristen M. DeAngelis,
Vincent J. Denef,
S. Denman,
A. Desta,
H. Dionisi,
J. Dodsworth,
Nina Dombrowski,
Timothy Donohue,
Mark Dopson,
Timothy P. Driscoll,
P. Dunfield,
C. Dupont,
Katherine A. Dynarski,
V. Edgcomb,
E. Edwards,
M. Elshahed,
Israel Figueroa,
Beverly E. Flood,
Nathaniel W. Fortney,
Caroline S. Fortunato,
C. Francis,
C. Gachon,
S. Garcia,
M. C. Gazitúa,
T. Gentry,
L. Gerwick,
Javad Gharechahi,
P. Girguis,
J. Gladden,
M. Gradoville,
S. Grasby,
Kelly Gravuer,
C. Grettenberger,
R. Gruninger,
Jiarong Guo,
M. Habteselassie,
S. Hallam,
R. Hatzenpichler,
B. Hausmann,
T. Hazen,
B. Hedlund,
C. Henny,
L. Herfort,
Maria Hernandez,
Olivia S. Hershey,
M. Hess,
E. Hollister,
L. Hug,
D. Hunt,
J. Jansson,
J. Jarett,
V. Kadnikov,
C. Kelly,
R. Kelly,
W. Kelly,
C. Kerfeld,
Jefferey A Kimbrel,
J. Klassen,
K. Konstantinidis,
Laura L. Lee,
Wenjun Li,
Andrew J. Loder,
A. Loy,
M. Lozada,
B. MacGregor,
C. Magnabosco,
Aline Maria da Silva,
R. McKay,
K. McMahon,
C. McSweeney,
Mónica Medina,
Laura K. Meredith,
Jessica E. Mizzi,
T. Mock,
L. Momper,
M. Moran,
C. Morgan-Lang,
D. Moser,
G. Muyzer,
D. Myrold,
Maisie Nash,
C. Nesbø,
A. Neumann,
R. Neumann,
D. Noguera,
T. Northen,
J. Norton,
Brent Nowinski,
K. Nüsslein,
M. O’Malley,
R. Oliveira,
Valéria Maia de Oliveira,
T. Onstott,
J. Osvatic,
Ouyang Yang,
M. Pachiadaki,
J. Parnell,
L. Partida-Martínez,
K. Peay,
D. Pelletier,
Xuefeng Peng,
Michael Pester,
J. Pett‐Ridge,
Sari Peura,
P. Pjevac,
Alvaro M. Plominsky,
Anja Poehlein,
P. Pope,
N. Ravin,
M. Redmond,
Rebecca A. Reiss,
V. Rich,
Christian Rinke,
J. L. M. Rodrigues,
W. Rodríguez-Reillo,
K. Rossmassler,
Joshua D. Sackett,
G. Salekdeh,
Scott Saleska,
M. Scarborough,
D. Schachtman,
C. Schadt,
M. Schrenk,
A. Sczyrba,
A. Sengupta,
J. Setubal,
A. Shade,
Christine Sharp,
D. Sherman,
O. Shubenkova,
I. N. Sierra-Garcia,
R. Simister,
H. Simon,
S. Sjöling,
J. Slonczewski,
Rafael Soares Correa de Souza,
J. Spear,
J. Stegen,
R. Stepanauskas,
F. Stewart,
G. Suen,
Matthew B. Sullivan,
D. Sumner,
B. Swan,
W. Swingley,
J. Tarn,
G. Taylor,
H. Teeling,
M. Tekere,
A. Teske,
T. Thomas,
C. Thrash,
J. Tiedje,
C. Ting,
B. Tully,
G. Tyson,
Osvlado Ulloa,
D. Valentine,
Marc Warwick Van Goethem,
J. VanderGheynst,
T. Verbeke,
John Vollmers,
A. Vuillemin,
N. Waldo,
D. Walsh,
B. Weimer,
T. Whitman,
P. van der Wielen,
Michael Wilkins,
Timothy J. Williams,
B. Woodcroft,
Jamie Woolet,
K. Wrighton,
Jun Ye,
E. Young,
N. Youssef,
F. Yu,
T. Zemskaya,
Ryan M. Ziels,
T. Woyke,
N. Mouncey,
Natalia N. Ivanova,
N. Kyrpides,
E. Eloe-Fadrosh
|
9 |
2020 |
9
🐜
|
|
🐜
|
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
112 auth.
Evan Bolyen,
J. Rideout,
Matthew R. Dillon,
N. Bokulich,
C. Abnet,
Gabriel A. Al-Ghalith,
Harriet Alexander,
E. Alm,
Manimozhiyan Arumugam,
F. Asnicar,
Yang Bai,
J. Bisanz,
K. Bittinger,
A. Brejnrod,
Colin J. Brislawn,
...
C. T. Brown,
B. Callahan,
A. Caraballo-Rodríguez,
John H. Chase,
Emily K. Cope,
R. D. da Silva,
C. Diener,
P. Dorrestein,
G. Douglas,
D. Durall,
C. Duvallet,
C. Edwardson,
Madeleine Ernst,
M. Estaki,
Jennifer T. Fouquier,
J. Gauglitz,
S. Gibbons,
D. Gibson,
Antonio Gonzalez,
Kestrel Gorlick,
Jiarong Guo,
Benjamin M Hillmann,
S. Holmes,
H. Holste,
C. Huttenhower,
G. Huttley,
Stefan Janssen,
A. Jarmusch,
Lingjing Jiang,
Benjamin D. Kaehler,
K. Kang,
Christopher R. Keefe,
P. Keim,
S. Kelley,
D. Knights,
I. Koester,
T. Kosciólek,
Jorden Kreps,
M. Langille,
Joslynn S. Lee,
R. Ley,
Yong-xin Liu,
E. Loftfield,
C. Lozupone,
Massoud Maher,
C. Marotz,
Bryan D. Martin,
Daniel McDonald,
L. McIver,
A. Melnik,
J. Metcalf,
S. C. Morgan,
James T. Morton,
Ahmad Turan Naimey,
Jose A Navas-Molina,
Louis-Félix Nothias,
Stephanie B. Orchanian,
Talima R. Pearson,
Samuel L. Peoples,
D. Petráš,
M. Preuss,
E. Pruesse,
Lasse Buur Rasmussen,
A. Rivers,
M. Robeson,
P. Rosenthal,
N. Segata,
Michael Shaffer,
A. Shiffer,
R. Sinha,
Se Jin Song,
J. Spear,
Austin D. Swafford,
Luke R. Thompson,
P. Torres,
Pauline Trinh,
A. Tripathi,
P. Turnbaugh,
Sabah Ul-Hasan,
J. V. D. van der Hooft,
Fernando Vargas,
Y. Vázquez-Baeza,
E. Vogtmann,
Max von Hippel,
William Walters,
Yunhu Wan,
Mingxun Wang,
Jonathan Warren,
Kyle C. Weber,
C. H. Williamson,
A. Willis,
Z. Xu,
Jesse R. Zaneveld,
Yilong Zhang,
Qiyun Zhu,
R. Knight,
J. Caporaso
|
8 |
2019 |
8
🐜
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|
🐜
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The khmer software package: enabling efficient nucleotide sequence analysis
61 auth.
M. Crusoe,
Hussien F Alameldin,
Sherine Awad,
Elmar Boucher,
A. Caldwell,
Reed Cartwright,
Amanda L Charbonneau,
B. Constantinides,
Greg Edvenson,
S. Fay,
Jacob Fenton,
T. Fenzl,
Jordan A. Fish,
Leonor García-Gutiérrez,
P. Garland,
...
J. Gluck,
Iván González,
Sarah M. Guermond,
Jiarong Guo,
Aditi Gupta,
J. Herr,
A. Howe,
Alex J. Hyer,
Andreas Härpfer,
L. Irber,
R. Kidd,
David Lin,
J. Lippi,
T. Mansour,
Pamela McA'Nulty,
Eric McDonald,
Jessica E. Mizzi,
Kevin D. Murray,
Joshua R. Nahum,
Kaben G. Nanlohy,
A. Nederbragt,
H. Ortiz-Zuazaga,
J. Ory,
J. Pell,
C. Pepe-Ranney,
Zachary N. Russ,
E. Schwarz,
Camille Scott,
Josiah D. Seaman,
Scott Sievert,
J. Simpson,
Connor T. Skennerton,
J. Spencer,
R. Srinivasan,
Daniel S. Standage,
J. Stapleton,
S. Steinman,
Joe Stein,
Benjamin Taylor,
W. Trimble,
H. Wiencko,
Michael Wright,
B. Wyss,
Qingpeng Zhang,
en zyme,
C. T. Brown
|
8 |
2015 |
8
🐜
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|
🐜
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Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
57 auth.
A. Zayed,
J. Wainaina,
Guillermo Domínguez-Huerta,
É. Pelletier,
Jiarong Guo,
Mohamed Mohssen,
F. Tian,
Akbar Adjie Pratama,
B. Bolduc,
Olivier Zablocki,
Dylan Cronin,
L. Solden,
E. Delage,
A. Alberti,
J. Aury,
...
Q. Carradec,
C. da Silva,
K. Labadie,
J. Poulain,
Hans-Joachim Ruscheweyh,
Guillem Salazar,
E. Shatoff,
R. Bundschuh,
K. Fredrick,
L. Kubatko,
Samuel Chaffron,
Alexander I. Culley,
S. Sunagawa,
J. Kuhn,
P. Wincker,
M. Sullivan,
S. Acinas,
M. Babin,
P. Bork,
E. Boss,
C. Bowler,
G. Cochrane,
C. de Vargas,
G. Gorsky,
L. Guidi,
N. Grimsley,
P. Hingamp,
D. Iudicone,
O. Jaillon,
S. Kandels,
L. Karp‐Boss,
E. Karsenti,
F. Not,
H. Ogata,
N. Poulton,
S. Pesant,
C. Sardet,
S. Speich,
L. Stemmann,
M. Sullivan,
Shinichi Sungawa,
P. Wincker
|
7 |
2022 |
7
🐜
|
|
🐜
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Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses
7 auth.
Bing-Bing Li,
Sarah S. Roley,
David S. Duncan,
Jiarong Guo,
J. Quensen,
Hanqing Yu,
...
J. Tiedje
|
7 |
2021 |
7
🐜
|
|
🐜
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Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems
7 auth.
Xun Qian,
Santosh Gunturu,
Jiarong Guo,
Benli Chai,
J. Cole,
Jie Gu,
...
J. Tiedje
|
6 |
2020 |
6
🐜
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|
🐜
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Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation
10 auth.
Akbar Adjie Pratama,
B. Bolduc,
A. Zayed,
Zhi-Ping Zhong,
Jiarong Guo,
D. Vik,
...
M. C. Gazitúa,
J. Wainaina,
S. Roux,
M. Sullivan
|
6 |
2021 |
6
🐜
|
|
🐜
|
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
13 auth.
Marie E. Kroeger,
Tom O. Delmont,
A. M. Eren,
Kyle M. Meyer,
Jiarong Guo,
K. Khan,
J. Rodrigues,
B. Bohannan,
S. Tringe,
C. D. Borges,
...
J. Tiedje,
S. Tsai,
K. Nüsslein
|
6 |
2018 |
6
🐜
|
|
🦁
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Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes
Jiarong Guo,
J. Cole,
Qingpeng Zhang,
C. T. Brown,
J. Tiedje
|
5 |
2015 |
5
🦁
|
|
🐜
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Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems
12 auth.
Bangzhou Zhang,
Bangzhou Zhang,
C. Penton,
C. Penton,
Chao Xue,
Chao Xue,
...
J. Quensen,
Sarah S. Roley,
Jiarong Guo,
A. Garoutte,
T. Zheng,
J. Tiedje
|
5 |
2017 |
5
🐜
|
|
🐜
|
Root-associated microbiome of maize genotypes with contrasting phosphorus use efficiency.
8 auth.
E. Gomes,
U. Lana,
J. Quensen,
S. Sousa,
C. Oliveira,
Jiarong Guo,
...
L. J. M. Guimarães,
J. Tiedje
|
5 |
2018 |
5
🐜
|
