A citation-based method for searching scientific literature

Benjamin S Beresford-Jones, Samuel C Forster, Mark D Stares, George Notley, Elisa Viciani, Hilary P Browne, Daniel J Boehmler, Amelia T Soderholm, Nitin Kumar, Kevin Vervier, Justin R Cross, Alexandre Almeida, Trevor D Lawley, Virginia A Pedicord. Cell Host Microbe 2022
Times Cited: 11







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



Times Cited
  Times     Co-cited
Similarity


A human gut bacterial genome and culture collection for improved metagenomic analyses.
Samuel C Forster, Nitin Kumar, Blessing O Anonye, Alexandre Almeida, Elisa Viciani, Mark D Stares, Matthew Dunn, Tapoka T Mkandawire, Ana Zhu, Yan Shao,[...]. Nat Biotechnol 2019
219
36

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.
Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U Foesel, Jan P Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler,[...]. Nat Microbiol 2016
211
36

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
27

A new genomic blueprint of the human gut microbiota.
Alexandre Almeida, Alex L Mitchell, Miguel Boland, Samuel C Forster, Gregory B Gloor, Aleksandra Tarkowska, Trevor D Lawley, Robert D Finn. Nature 2019
497
27

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Chirag Jain, Luis M Rodriguez-R, Adam M Phillippy, Konstantinos T Konstantinidis, Srinivas Aluru. Nat Commun 2018
27

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
Yuanqiang Zou, Wenbin Xue, Guangwen Luo, Ziqing Deng, Panpan Qin, Ruijin Guo, Haipeng Sun, Yan Xia, Suisha Liang, Ying Dai,[...]. Nat Biotechnol 2019
215
27

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. Bioinformatics 2014
27

Duodenal infusion of donor feces for recurrent Clostridium difficile.
Els van Nood, Anne Vrieze, Max Nieuwdorp, Susana Fuentes, Erwin G Zoetendal, Willem M de Vos, Caroline E Visser, Ed J Kuijper, Joep F W M Bartelsman, Jan G P Tijssen,[...]. N Engl J Med 2013
27

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
27

A complete domain-to-species taxonomy for Bacteria and Archaea.
Donovan H Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J Mussig, Philip Hugenholtz. Nat Biotechnol 2020
381
27

The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria.
Chang Liu, Nan Zhou, Meng-Xuan Du, Yu-Tong Sun, Kai Wang, Yu-Jing Wang, Dan-Hua Li, Hai-Ying Yu, Yuqin Song, Bing-Bing Bai,[...]. Nat Commun 2020
30
27

FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
27

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.
Charlie G Buffie, Vanni Bucci, Richard R Stein, Peter T McKenney, Lilan Ling, Asia Gobourne, Daniel No, Hui Liu, Melissa Kinnebrew, Agnes Viale,[...]. Nature 2015
27

Bile acid metabolites control TH17 and Treg cell differentiation.
Saiyu Hang, Donggi Paik, Lina Yao, Eunha Kim, Jamma Trinath, Jingping Lu, Soyoung Ha, Brandon N Nelson, Samantha P Kelly, Lin Wu,[...]. Nature 2019
358
27

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians.
Yuko Sato, Koji Atarashi, Damian R Plichta, Yasumichi Arai, Satoshi Sasajima, Sean M Kearney, Wataru Suda, Kozue Takeshita, Takahiro Sasaki, Shoki Okamoto,[...]. Nature 2021
90
27

The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis.
Patrick M Smith, Michael R Howitt, Nicolai Panikov, Monia Michaud, Carey Ann Gallini, Mohammad Bohlooly-Y, Jonathan N Glickman, Wendy S Garrett. Science 2013
27

Multiple levels of the unknown in microbiome research.
Andrew Maltez Thomas, Nicola Segata. BMC Biol 2019
49
18

Diversity of the human intestinal microbial flora.
Paul B Eckburg, Elisabeth M Bik, Charles N Bernstein, Elizabeth Purdom, Les Dethlefsen, Michael Sargent, Steven R Gill, Karen E Nelson, David A Relman. Science 2005
18

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice.
Andrew L Goodman, George Kallstrom, Jeremiah J Faith, Alejandro Reyes, Aimee Moore, Gautam Dantas, Jeffrey I Gordon. Proc Natl Acad Sci U S A 2011
453
18

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.
Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra. Nat Rev Microbiol 2014
18

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
18


A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.
Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz. Nat Biotechnol 2018
18

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun. Int J Syst Evol Microbiol 2017
18

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.
Ilias Lagkouvardos, Divya Joseph, Martin Kapfhammer, Sabahattin Giritli, Matthias Horn, Dirk Haller, Thomas Clavel. Sci Rep 2016
180
18


A large-scale evaluation of algorithms to calculate average nucleotide identity.
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun. Antonie Van Leeuwenhoek 2017
18

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.
Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner. Bioinformatics 2012
18

probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.
Daniel Greuter, Alexander Loy, Matthias Horn, Thomas Rattei. Nucleic Acids Res 2016
92
18

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank.
Chang Liu, Meng-Xuan Du, Rexiding Abuduaini, Hai-Ying Yu, Dan-Hua Li, Yu-Jing Wang, Nan Zhou, Min-Zhi Jiang, Peng-Xia Niu, Shan-Shan Han,[...]. Microbiome 2021
20
18

Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.
Hilary P Browne, Samuel C Forster, Blessing O Anonye, Nitin Kumar, B Anne Neville, Mark D Stares, David Goulding, Trevor D Lawley. Nature 2016
599
18

Elevated rates of horizontal gene transfer in the industrialized human microbiome.
Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M Gibbons, Laure Segurel, Alain Froment,[...]. Cell 2021
60
18


A proposed genus boundary for the prokaryotes based on genomic insights.
Qi-Long Qin, Bin-Bin Xie, Xi-Ying Zhang, Xiu-Lan Chen, Bai-Cheng Zhou, Jizhong Zhou, Aharon Oren, Yu-Zhong Zhang. J Bacteriol 2014
446
18

Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age.
Jan P Meier-Kolthoff, Hans-Peter Klenk, Markus Göker. Int J Syst Evol Microbiol 2014
347
18

Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis.
J J Godon, E Zumstein, P Dabert, F Habouzit, R Moletta. Appl Environ Microbiol 1997
576
18

Recent advances in culture-based gut microbiome research.
Thomas C A Hitch, Afrizal Afrizal, Thomas Riedel, Antonios Kioukis, Dirk Haller, Ilias Lagkouvardos, Jörg Overmann, Thomas Clavel. Int J Med Microbiol 2021
5
40

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
18

A unified catalog of 204,938 reference genomes from the human gut microbiome.
Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martin Beracochea, Zhou Jason Shi, Katherine S Pollard, Ekaterina Sakharova, Donovan H Parks, Philip Hugenholtz,[...]. Nat Biotechnol 2021
210
18

metaSPAdes: a new versatile metagenomic assembler.
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Res 2017
18

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.
Till R Lesker, Abilash C Durairaj, Eric J C Gálvez, Ilias Lagkouvardos, John F Baines, Thomas Clavel, Alexander Sczyrba, Alice C McHardy, Till Strowig. Cell Rep 2020
43
18


The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri.
Steven A Frese, Andrew K Benson, Gerald W Tannock, Diane M Loach, Jaehyoung Kim, Min Zhang, Phaik Lyn Oh, Nicholas C K Heng, Prabhu B Patil, Nathalie Juge,[...]. PLoS Genet 2011
195
18

How informative is the mouse for human gut microbiota research?
Thi Loan Anh Nguyen, Sara Vieira-Silva, Adrian Liston, Jeroen Raes. Dis Model Mech 2015
687
18

Altered Microbiota Contributes to Reduced Diet-Induced Obesity upon Cold Exposure.
Marika Ziętak, Petia Kovatcheva-Datchary, Lidia H Markiewicz, Marcus Ståhlman, Leslie P Kozak, Fredrik Bäckhed. Cell Metab 2016
178
18

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis.
Jun Chen, Kerry Wright, John M Davis, Patricio Jeraldo, Eric V Marietta, Joseph Murray, Heidi Nelson, Eric L Matteson, Veena Taneja. Genome Med 2016
364
18

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota.
Guolin Li, Cen Xie, Siyu Lu, Robert G Nichols, Yuan Tian, Licen Li, Daxeshkumar Patel, Yinyan Ma, Chad N Brocker, Tingting Yan,[...]. Cell Metab 2017
257
18

Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
18


Short- and long-term effects of oral vancomycin on the human intestinal microbiota.
Sandrine Isaac, Jose U Scher, Ana Djukovic, Nuria Jiménez, Dan R Littman, Steven B Abramson, Eric G Pamer, Carles Ubeda. J Antimicrob Chemother 2017
161
18


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.