|
🐜
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
8 auth.
Christian Quast,
E. Pruesse,
Pelin Yilmaz,
Jan Gerken,
Timmy Schweer,
P. Yarza,
...
J. Peplies,
F. Glöckner
|
14 |
2012 |
14
🐜
|
|
🐜
|
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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|
🐜
|
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
7 auth.
A. Klindworth,
E. Pruesse,
Timmy Schweer,
J. Peplies,
Christian Quast,
M. Horn,
...
F. Glöckner
|
12 |
2012 |
12
🐜
|
|
🦁
|
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
7 auth.
E. Pruesse,
Christian Quast,
K. Knittel,
B. Fuchs,
W. Ludwig,
J. Peplies,
...
F. Glöckner
|
12 |
2007 |
12
🦁
|
|
🐜
|
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
10 auth.
Pelin Yilmaz,
L. Parfrey,
P. Yarza,
Jan Gerken,
E. Pruesse,
Christian Quast,
...
Timmy Schweer,
J. Peplies,
W. Ludwig,
F. Glöckner
|
11 |
2013 |
11
🐜
|
|
🦁
|
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
E. Pruesse,
J. Peplies,
F. Glöckner
|
11 |
2012 |
11
🦁
|
|
🐜
|
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
10 auth.
P. Yarza,
Pelin Yilmaz,
E. Pruesse,
F. Glöckner,
W. Ludwig,
K. Schleifer,
...
W. Whitman,
J. Euzéby,
R. Amann,
R. Rosselló-Móra
|
10 |
2014 |
10
🐜
|
|
🐜
|
Bioconda: sustainable and comprehensive software distribution for the life sciences
152 auth.
Ryan K. Dale,
B. Grüning,
A. Sjödin,
Jillian Rowe,
Brad A. Chapman,
C. Tomkins-Tinch,
Renan Valieris,
Bérénice Batut,
A. Caprez,
T. Cokelaer,
Dilmurat Yusuf,
Kyle A. Beauchamp,
K. Břinda,
Thomas Wollmann,
Gildas Le Corguillé,
...
D. Ryan,
A. Bretaudeau,
Y. Hoogstrate,
Brent S. Pedersen,
S. V. Heeringen,
Martin Raden,
Sebastian Luna-Valero,
N. Soranzo,
Matthias De Smet,
Greg Von Kuster,
Rory D. Kirchner,
L. Pantano,
Z. Charlop-Powers,
Kevin R. Thornton,
Marcel Martin,
Marius van den Beek,
Daniel Maticzka,
Milad Miladi,
S. Will,
Kévin Gravouil,
P. Unneberg,
C. Brueffer,
Clemens Blank,
V. Piro,
Joachim Wolff,
T. Antão,
Simon L. Gladman,
I. Shlyakhter,
M. de Hollander,
P. Mabon,
Wei Shen,
J. Boekel,
M. Holtgrewe,
Dave Bouvier,
J. D. de Ruiter,
Jennifer Cabral,
S. Choudhary,
N. Harding,
Robert Kleinkauf,
E. Enns,
Florian Eggenhofer,
Joseph M Brown,
P. Cock,
H. Timm,
Cristel G. Thomas,
Xiao-ou Zhang,
Matt Chambers,
Nitesh Turaga,
E. Seiler,
Colin J. Brislawn,
E. Pruesse,
Jörg Fallmann,
Jerome Kelleher,
Hai Nguyen,
Lance L. Parsons,
Zhuoqing Fang,
E. B. Stovner,
Nicholas Stoler,
Simon H. Ye,
Inken Wohlers,
Rick Farouni,
M. Freeberg,
James E. Johnson,
Marcel Bargull,
P. Kensche,
T. Webster,
J. Eppley,
C. Stahl,
Alexander S. Rose,
Alex P. Reynolds,
Liang Wang,
Xavier Garnier,
Simon Dirmeier,
Michael Knudsen,
James Taylor,
Avi Srivastava,
Vivek Rai,
Rasmus Agren,
Alexander Junge,
R. Guimera,
Aziz Khan,
S. Schmeier,
Guowei He,
Luca Pinello,
E. Hägglund,
Alexander S. Mikheyev,
J. Preussner,
Nicholas R. Waters,
Wei Li,
Jordi Capellades,
A. Chande,
Yuri Pirola,
Saskia D. Hiltemann,
M. Bendall,
Sourav Singh,
W. Dunn,
Alexandre Drouin,
Tomás Di Domenico,
Ino de Bruijn,
D. Larson,
D. Chicco,
Elena Grassi,
Giorgio Gonnella,
B. Jaivarsan,
Liya Wang,
F. Giacomoni,
Erik L. Clarke,
Daniel J. Blankenberg,
Camy Tran,
Robert Patro,
S. Laurent,
Matthew Gopez,
B. Sennblad,
J. Baaijens,
Philip A. Ewels,
Patrick R. Wright,
Oana M. Enache,
Pierrick Roger,
W. Dampier,
David Koppstein,
Upendra Kumar Devisetty,
T. Rausch,
MacIntosh G. Cornwell,
A. Salatino,
Julien Seiler,
Matthieu Jung,
E. Kornobis,
Fabio Cumbo,
David Lähnemann,
Bianca K. Stöcker,
O. Moskalenko,
D. Bogema,
M. Workentine,
S. Newhouse,
Felipe da Veiga Leprevost,
Kevin J. Arvai,
Johannes Köster
|
10 |
2018 |
10
🐜
|
|
🐜
|
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
🐜
|
|
🐜
|
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
98 auth.
Pelin Yilmaz,
R. Kottmann,
D. Field,
R. Knight,
J. Cole,
L. Amaral-Zettler,
J. Gilbert,
I. Karsch-Mizrachi,
Anjanette Johnston,
G. Cochrane,
Robert Vaughan,
Chris I. Hunter,
Joonhong Park,
N. Morrison,
P. Rocca-Serra,
...
P. Sterk,
Manimozhiyan Arumugam,
M. Bailey,
L. Baumgartner,
B. Birren,
M. Blaser,
Vivien R. Bonazzi,
Tim Booth,
P. Bork,
F. Bushman,
P. Buttigieg,
P. Chain,
Emily S. Charlson,
E. Costello,
Heather Huot-Creasy,
P. Dawyndt,
T. DeSantis,
N. Fierer,
J. Fuhrman,
R. Gallery,
D. Gevers,
R. Gibbs,
I. S. Gil,
A. González,
J. Gordon,
R. Guralnick,
Wolfgang Hankeln,
S. Highlander,
P. Hugenholtz,
J. Jansson,
A. Kau,
S. Kelley,
Jerry Kennedy,
D. Knights,
O. Koren,
Justin Kuczynski,
N. Kyrpides,
R. Larsen,
C. Lauber,
T. Legg,
R. Ley,
C. Lozupone,
W. Ludwig,
Donna Lyons,
E. Maguire,
B. Methé,
Folker Meyer,
B. Muegge,
S. Nakielny,
K. Nelson,
D. Nemergut,
J. Neufeld,
L. Newbold,
Anna E. Oliver,
N. Pace,
G. Palanisamy,
J. Peplies,
J. Petrosino,
L. Proctor,
E. Pruesse,
Christian Quast,
J. Raes,
S. Ratnasingham,
J. Ravel,
D. Relman,
Susanna Assunta-Sansone,
P. Schloss,
L. Schriml,
R. Sinha,
M. Smith,
E. Sodergren,
A. Spor,
Jesse Stombaugh,
J. Tiedje,
D. Ward,
G. Weinstock,
Doug Wendel,
Owen White,
A. Whiteley,
Andreas Wilke,
J. Wortman,
Tanya Yatsunenko,
F. Glöckner
|
9 |
2011 |
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
🐜
|
|
🐢
|
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Harald R. Gruber-Vodicka,
B. Seah,
E. Pruesse
|
7 |
2020 |
7
🐢
|
|
🐜
|
Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium
28 auth.
S. Sajuthi,
P. DeFord,
Yingchun Li,
Nathan D. Jackson,
M. Montgomery,
J. Everman,
C. Rios,
E. Pruesse,
J. Nolin,
E. Plender,
M. Wechsler,
Angel C. Y. Mak,
C. Eng,
S. Salazar,
V. Medina,
...
E. M. Wohlford,
S. Huntsman,
D. Nickerson,
S. Germer,
M. Zody,
G. Abecasis,
H. Kang,
K. Rice,
R. Kumar,
Sam S. Oh,
J. Rodriguez-Santana,
E. Burchard,
M. Seibold
|
6 |
2020 |
6
🐜
|
|
🐜
|
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium
27 auth.
S. Sajuthi,
P. DeFord,
Nathan D. Jackson,
M. Montgomery,
J. Everman,
C. Rios,
E. Pruesse,
J. Nolin,
E. Plender,
M. Wechsler,
Angel C. Y. Mak,
C. Eng,
S. Salazar,
V. Medina,
E. M. Wohlford,
...
S. Huntsman,
D. Nickerson,
S. Germer,
M. Zody,
G. Abecasis,
H. Kang,
K. Rice,
R. Kumar,
Sam S. Oh,
J. Rodriguez-Santana,
E. Burchard,
M. Seibold
|
6 |
2020 |
6
🐜
|
|
🐢
|
phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
Harald R. Gruber-Vodicka,
B. Seah,
E. Pruesse
|
5 |
2019 |
5
🐢
|
