A citation-based method for searching scientific literature

Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes. Nat Methods 2016
Times Cited: 4212







List of co-cited articles
301 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
36


Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar,[...]. Nat Biotechnol 2019
28

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20

QIIME allows analysis of high-throughput community sequencing data.
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon,[...]. Nat Methods 2010
17

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.
Nicholas A Bokulich, Benjamin D Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A Huttley, J Gregory Caporaso. Microbiome 2018
649
16

Metagenomic biomarker discovery and explanation.
Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower. Genome Biol 2011
11

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.
Benjamin J Callahan, Paul J McMurdie, Susan P Holmes. ISME J 2017
680
11

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
J Gregory Caporaso, Christian L Lauber, William A Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M Owens, Jason Betley, Louise Fraser, Markus Bauer,[...]. ISME J 2012
10

UniFrac: a new phylogenetic method for comparing microbial communities.
Catherine Lozupone, Rob Knight. Appl Environ Microbiol 2005
10

Waste not, want not: why rarefying microbiome data is inadmissible.
Paul J McMurdie, Susan Holmes. PLoS Comput Biol 2014
9


FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
9

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Qiong Wang, George M Garrity, James M Tiedje, James R Cole. Appl Environ Microbiol 2007
8

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.
Anna Klindworth, Elmar Pruesse, Timmy Schweer, Jörg Peplies, Christian Quast, Matthias Horn, Frank Oliver Glöckner. Nucleic Acids Res 2013
8

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
T Z DeSantis, P Hugenholtz, N Larsen, M Rojas, E L Brodie, K Keller, T Huber, D Dalevi, P Hu, G L Andersen. Appl Environ Microbiol 2006
7


VSEARCH: a versatile open source tool for metagenomics.
Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé. PeerJ 2016
7

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z DeSantis, Alexander Probst, Gary L Andersen, Rob Knight, Philip Hugenholtz. ISME J 2012
6


Analysis of composition of microbiomes: a novel method for studying microbial composition.
Siddhartha Mandal, Will Van Treuren, Richard A White, Merete Eggesbø, Rob Knight, Shyamal D Peddada. Microb Ecol Health Dis 2015
573
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6

Diet rapidly and reproducibly alters the human gut microbiome.
Lawrence A David, Corinne F Maurice, Rachel N Carmody, David B Gootenberg, Julie E Button, Benjamin E Wolfe, Alisha V Ling, A Sloan Devlin, Yug Varma, Michael A Fischbach,[...]. Nature 2014
6

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.
James J Kozich, Sarah L Westcott, Nielson T Baxter, Sarah K Highlander, Patrick D Schloss. Appl Environ Microbiol 2013
6

Ribosomal Database Project: data and tools for high throughput rRNA analysis.
James R Cole, Qiong Wang, Jordan A Fish, Benli Chai, Donna M McGarrell, Yanni Sun, C Titus Brown, Andrea Porras-Alfaro, Cheryl R Kuske, James M Tiedje. Nucleic Acids Res 2014
6

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.
Nicole M Davis, Diana M Proctor, Susan P Holmes, David A Relman, Benjamin J Callahan. Microbiome 2018
386
6

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.
Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner. Nucleic Acids Res 2014
846
5

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.
Morgan G I Langille, Jesse Zaneveld, J Gregory Caporaso, Daniel McDonald, Dan Knights, Joshua A Reyes, Jose C Clemente, Deron E Burkepile, Rebecca L Vega Thurber, Rob Knight,[...]. Nat Biotechnol 2013
5

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
J Gregory Caporaso, Christian L Lauber, William A Walters, Donna Berg-Lyons, Catherine A Lozupone, Peter J Turnbaugh, Noah Fierer, Rob Knight. Proc Natl Acad Sci U S A 2011
5

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.
Adithya Murali, Aniruddha Bhargava, Erik S Wright. Microbiome 2018
81
6

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.
Catherine A Lozupone, Micah Hamady, Scott T Kelley, Rob Knight. Appl Environ Microbiol 2007
5


A metagenome-wide association study of gut microbiota in type 2 diabetes.
Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu, Fan Zhang, Suisha Liang, Wenwei Zhang, Yuanlin Guan, Dongqian Shen,[...]. Nature 2012
5

Differential abundance analysis for microbial marker-gene surveys.
Joseph N Paulson, O Colin Stine, Héctor Corrada Bravo, Mihai Pop. Nat Methods 2013
832
4

Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
4

UniFrac: an effective distance metric for microbial community comparison.
Catherine Lozupone, Manuel E Lladser, Dan Knights, Jesse Stombaugh, Rob Knight. ISME J 2011
4

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata. Nucleic Acids Res 2002
4

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.
Jethro S Johnson, Daniel J Spakowicz, Bo-Young Hong, Lauren M Petersen, Patrick Demkowicz, Lei Chen, Shana R Leopold, Blake M Hanson, Hanako O Agresta, Mark Gerstein,[...]. Nat Commun 2019
188
4

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.
Patrick D Schloss, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson,[...]. Appl Environ Microbiol 2009
4

Human gut microbiome viewed across age and geography.
Tanya Yatsunenko, Federico E Rey, Mark J Manary, Indi Trehan, Maria Gloria Dominguez-Bello, Monica Contreras, Magda Magris, Glida Hidalgo, Robert N Baldassano, Andrey P Anokhin,[...]. Nature 2012
4

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.
Claire Duvallet, Sean M Gibbons, Thomas Gurry, Rafael A Irizarry, Eric J Alm. Nat Commun 2017
298
4

Gut metagenome in European women with normal, impaired and diabetic glucose control.
Fredrik H Karlsson, Valentina Tremaroli, Intawat Nookaew, Göran Bergström, Carl Johan Behre, Björn Fagerberg, Jens Nielsen, Fredrik Bäckhed. Nature 2013
4


Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea.
Daniel Pr Herlemann, Matthias Labrenz, Klaus Jürgens, Stefan Bertilsson, Joanna J Waniek, Anders F Andersson. ISME J 2011
887
3

Proteobacteria: microbial signature of dysbiosis in gut microbiota.
Na-Ri Shin, Tae Woong Whon, Jin-Woo Bae. Trends Biotechnol 2015
846
3


Bacterial strategies along nutrient and time gradients, revealed by metagenomic analysis of laboratory microcosms.
Ho-Kyung Song, Woojin Song, Mincheol Kim, Binu M Tripathi, Hyoki Kim, Piotr Jablonski, Jonathan M Adams. FEMS Microbiol Ecol 2017
7
42

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. Mol Biol Evol 2009
3

Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults.
Nadja Larsen, Finn K Vogensen, Frans W J van den Berg, Dennis Sandris Nielsen, Anne Sofie Andreasen, Bente K Pedersen, Waleed Abu Al-Soud, Søren J Sørensen, Lars H Hansen, Mogens Jakobsen. PLoS One 2010
3

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
Daniel H Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu. PLoS Comput Biol 2016
575
3


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.