pypi: MetaPhlAn | Projects | Ecosyste.ms: Papers

10.3390/ijms150712364

Exploring Neighborhoods in the Metagenome Universe
Cited by: 1
Author(s): Kathrin Petra Aßhauer, Heiner Klingenberg, Thomas Lingner, Peter Meinicke
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0117711

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS
Cited by: 23
Author(s): Martin Lindner, Bernhard Y. Renard
Software Mentions: 1
Published: almost 10 years ago

10.1186/gb-2014-15-3-r46

Kraken: ultrafast metagenomic sequence classification using exact alignments
Cited by: 3,166
Author(s): Derrick E. Wood, Steven L. Salzberg
Software Mentions: 1
Published: over 10 years ago

Biogeography of the ecosystems of the healthy human body
Cited by: 472
Author(s): Yanjiao Zhou, Hongyu Gao, Kathie A. Mihindukulasuriya, Patricio S. La Rosa, Kristine M. Wylie, Tatiana A. Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I. Tarr, David E. Nelson, J D Fortenberry, Martin J. Holland, Sarah E. Burr, William D. Shannon, Erica Sodergren, George M. Weinstock
Software Mentions: 1
Published: almost 12 years ago

10.1186/gb-2012-13-12-r122

Ray Meta: scalable de novo metagenome assembly and profiling
Cited by: 517
Author(s): Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0068919

Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans
Cited by: 39
Author(s): Bridget A. Neville, Paul O. Sheridan, Hugh M. B. Harris, Simone Coughlan, Harry J. Flint, Sylvia H. Duncan, Ian B. Jeffery, Marcus J. Claesson, R. Paul Ross, Karen P. Scott, Paul W. O’Toole
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-015-0821-z

Identification of low abundance microbiome in clinical samples using whole genome sequencing
Cited by: 79
Author(s): Chao Zhang, Kyle Cleveland, Felice Schnoll‐Sussman, Bridget McClure, Michelle Bigg, Prashant V. Thakkar, Nikolaus Schultz, Manish A. Shah, Doron Betel
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0162442

MetaStorm: A Public Resource for Customizable Metagenomics Annotation
Cited by: 57
Author(s): Gustavo Arango-Argoty, Gargi Singh, Lenwood S. Heath, Amy Pruden, Weidong Xiao, Liqing Zhang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0167870

Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing
Cited by: 56
Author(s): Susan R. Leonard, Mark K. Mammel, David W. Lacher, Christopher A. Elkins
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0228899

Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
Cited by: 90
Author(s): Kyle D. Brumfield, Anwar Huq, Rita R. Colwell, James L. Olds, Menu B. Leddy
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-019-5883-y

HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples
Cited by: 20
Author(s): Matteo Soverini, Silvia Turroni, Elena Biagi, Patrizia Brigidi, Marco Candela, Simone Rampelli
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0084689

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Cited by: 272
Author(s): Mariel M. Finucane, Thomas J. Sharpton, Timothy Laurent, Katherine S. Pollard
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1002863

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets
Cited by: 428
Author(s): Omry Koren, Daniel Knights, Antonio González, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1006277

Removing contaminants from databases of draft genomes
Cited by: 73
Author(s): Jennifer Lu, Steven L. Salzberg
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1004957

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
Cited by: 1,199
Author(s): Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans‐Joachim Ruscheweyh, Rewati Tappu
Software Mentions: 1
Published: over 8 years ago

10.1128/mSystems.00198-19

Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics
Cited by: 9
Author(s): Xing Shi, Changjun Shao, Chunxiong Luo, Yanan Chu, Jian Wang, Qingren Meng, Jun Yu, Zhancheng Gao, Yu Kang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1004557

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
Cited by: 216
Author(s): James J. Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam Dantas, Curtis Huttenhower
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1005107

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
Cited by: 35
Author(s): Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-020-03555-w

MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis
Cited by: 1
Author(s): Yuanyuan Ma, Junliang Zhao, Yingjun Ma
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj.425

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
Cited by: 77
Author(s): Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Bas E. Dutilh, Robert A. Edwards
Software Mentions: 1
Published: over 10 years ago

10.1186/s13073-016-0271-6

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes
Cited by: 194
Author(s): Moran Yassour, Mi Young Lim, Hyun Sun Yun, Timothy L. Tickle, Joohon Sung, Yun Mi Song, Kayoung Lee, Eric A. Franzosa, Xochitl C. Morgan, Dirk Gevers, Eric S. Lander, Ramnik J. Xavier, Bruce W. Birren, Gwang Pyo Ko, Curtis Huttenhower
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13073-018-0515-8

Host genetic variation and its microbiome interactions within the Human Microbiome Project
Cited by: 116
Author(s): Raivo Kolde, Eric A. Franzosa, Ali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J. Daly, Ramnik J. Xavier, Curtis Huttenhower
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.2928

Antibiotic resistance potential of the healthy preterm infant gut microbiome
Cited by: 34
Author(s): Graham Rose, Alexander Shaw, Kathleen Sim, David Wooldridge, Mingshi Li, Saheer E. Gharbia, Raju Misra, J. Simon Kroll
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.6554

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
Cited by: 4
Author(s): Ksenia M. Klimina, Artem S. Kasianov, Е. У. Полуэктова, Kirill V. Emelyanov, Viktoriya Voroshilova, Natalia V. Zakharevich, Anna V. Kudryavtseva, Vsevolod J. Makeev, В. Н. Даниленко
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3837

Evaluation of ddRADseq for reduced representation metagenome sequencing
Cited by: 11
Author(s): Michael Y. Liu, Paul Worden, Leigh G. Monahan, Matthew Z. DeMaere, Catherine Burke, Steven P. Djordjevic, Ian G. Charles, Aaron E. Darling
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-14-S8-S4

MetaID: A novel method for identification and quantification of metagenomic samples
Cited by: 12
Author(s): Satish Srinivasan, Chittibabu Guda
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12859-018-2431-8

What we can see from very small size sample of metagenomic sequences
Cited by: 6
Author(s): Jaesik Kwak, Joonhong Park
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.6594

Assessing alignment-based taxonomic classification of ancient microbial DNA
Cited by: 21
Author(s): Raphael Eisenhofer, Laura S. Weyrich
Software Mentions: 1
Published: over 5 years ago

10.1038/ismej.2017.105

Methanethiol-dependent dimethylsulfide production in soil environments
Cited by: 44
Author(s): Ornella Carrión, Jennifer Pratscher, Andrew R. J. Curson, Beth T. Williams, Wayne G. Rostant, J. Colin Murrell, Jonathan D. Todd
Software Mentions: 1
Published: over 7 years ago

10.3390/v10050256

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting
Cited by: 6
Author(s): Bashar Ibrahim, Ksenia Arkhipova, Arno C. Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene V. Koonin, Anne Kupczok, Philippe Lemey, Alice C. McHardy, Dino P. McMahon, Brett E. Pickett, David L. Robertson, Richard H. Scheuermann, Alexandra Zhernakova, Mark P. Zwart, Alexander Schönhuth, Bas E. Dutilh, Manja Marz
Software Mentions: 1
Published: over 6 years ago

10.1099/acmi.0.000104

Sensitivity of shotgun metagenomics to host DNA: abundance estimates depend on bioinformatic tools and contamination is the main issue
Cited by: 13
Author(s): Andrew McArdle, Myrsini Kaforou
Software Mentions: 1
Published: over 4 years ago

10.1093/gigascience/giy057

ASaiM: a Galaxy-based framework to analyze microbiota data
Cited by: 23
Author(s): Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Éric Peyretaillade, Pierre Peyret
Software Mentions: 1
Published: over 6 years ago

10.1186/s10020-021-00371-7

A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents
Cited by: 8
Author(s): Sofía Morán-Ramos, Luis Macías-Kauffer, Blanca E. López-Contreras, Hugo Villamil‐Ramírez, Elvira Ocampo-Medina, Paola León-Mimila, Blanca Estela Del Río-Navarro, Omar Granados‐Portillo, Isabel Ibarra-González, Marcela Vela-Amieva, Armando R. Tovar, Nimbe Torres, Francisco J. Gómez-Pérez, Carlos A. Aguilar-Salinas, Samuel Cañizales-Quinteros
Software Mentions: 1
Published: about 3 years ago

10.3390/microorganisms8050684

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data
Cited by: 6
Author(s): Nathanael J. Bangayan, Baochen Shi, Jerry Trinh, Emma Barnard, Gabriela Kasimatis, Emily Curd, Huiying Li
Software Mentions: 1
Published: over 4 years ago

10.1136/gutjnl-2019-320204

Interaction between drugs and the gut microbiome
Cited by: 354
Author(s): Rinse K. Weersma, Alexandra Zhernakova, Jingyuan Fu
Software Mentions: 1
Published: over 4 years ago

10.1186/s40168-018-0571-8

Competitive lottery-based assembly of selected clades in the human gut microbiome
Cited by: 42
Author(s): Adrian J. Verster, Elhanan Borenstein
Software Mentions: 1
Published: about 6 years ago

10.1186/s40168-015-0086-5

Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries
Cited by: 16
Author(s): Kathy N. Lam, Trevor C. Charles
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-015-0503-6

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets
Cited by: 69
Author(s): Matthias Scheuch, Dirk W. Höper, Martin Beer
Software Mentions: 1
Published: over 9 years ago

10.1186/s13099-018-0272-7

Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing
Cited by: 17
Author(s): Yvonne Qvarnström, Yuping Wei-Pridgeon, Erik Van Roey, Subin Park, Ganesh Srinivasamoorthy, Fernanda S. Nascimento, Delynn M. Moss, Eldin Talundzic, Michael J. Arrowood
Software Mentions: 1
Published: about 6 years ago

10.1093/jac/dkx017

Overexpression of antibiotic resistance genes in hospital effluents over time
Cited by: 84
Author(s): Will Rowe, Craig Baker‐Austin, David W. Verner–Jeffreys, Jim J. Ryan, Christianne Micallef, Duncan J. Maskell, G.P. Pearce
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-5699-9

MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
Cited by: 24
Author(s): Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin
Software Mentions: 1
Published: over 5 years ago

10.1007/s13238-018-0596-6

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade
Cited by: 62
Author(s): Jiaxing Cui, Henggang Cui, Minmin Yang, Shiyu Du, Junfeng Li, Yingxue Li, Liyang Liu, Xuegong Zhang, Shao Li
Software Mentions: 1
Published: almost 6 years ago

10.3390/ani10122350

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli
Cited by: 14
Author(s): Ome Kalsoom Afridi, Johar Ali, Jeong Ho Chang
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41597-020-0516-5

Large-scale metabolic interaction network of the mouse and human gut microbiota
Cited by: 11
Author(s): Roktaek Lim, Josephine Jill Cabatbat, Thomas L.P. Martin, Haneul Kim, Seunghyeon Kim, Jaeyun Sung, Cheol-Min Ghim, Pan-Jun Kim
Software Mentions: 1
Published: over 4 years ago

10.1186/s40425-019-0650-9

Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma
Cited by: 269
Author(s): Yi Zheng, Tingting Wang, Xintao Tu, Yun Huang, Hangyu Zhang, Di Tan, Weiqin Jiang, Shunfeng Cai, Peng Zhao, Ruixue Song, Peilu Li, Nan Qin, Weijia Fang
Software Mentions: 1
Published: over 5 years ago

10.1186/s40168-017-0318-y

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling
Cited by: 35
Author(s): Vitor C. Piro, Marcel Matschkowski, Bernhard Y. Renard
Software Mentions: 1
Published: over 7 years ago

10.1186/s40168-019-0629-2

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome
Cited by: 118
Author(s): Wencong Shi, Mingcong Li, Guangshan Wei, Renmao Tian, Cuiping Li, Bing Wang, Runmao Lin, Chunyu Shi, Chi Xiu-li, Bo Zhou, Zheng Gao
Software Mentions: 1
Published: almost 6 years ago

10.1038/srep24207

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers
Cited by: 74
Author(s): Nicola Segata, Francesco Baldini, Julien Pompon, Wendy S. Garrett, Duy Tin Truong, Roch K. Dabiré, Abdoulaye Diabaté, Elena A. Levashina, Flaminia Catteruccia
Software Mentions: 1
Published: over 8 years ago

10.1186/s40168-018-0410-y

A human gut phage catalog correlates the gut phageome with type 2 diabetes
Cited by: 128
Author(s): Yingfei Ma, Xiao-Yan You, Guoqin Mai, Taku A. Tokuyasu, Chenli Liu
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep40826

Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration
Cited by: 133
Author(s): Martin S. Zinkernagel, Denise C. Zysset-Burri, Irene Keller, Lieselotte Erika Berger, Alexander Benedikt Leichtle, Carlo R. Largiadèr, Georg Martin Fiedler, Sebastian Wolf
Software Mentions: 1
Published: almost 8 years ago

10.1186/s40168-018-0426-3

Improving saliva shotgun metagenomics by chemical host DNA depletion
Cited by: 193
Author(s): Clarisse Marotz, Jon G. Sanders, Cristal Zuñiga, Livia S. Zaramela, Rob Knight, Karsten Zengler
Software Mentions: 1
Published: over 6 years ago

10.1155/2015/246203

Excretion of Host DNA in Feces Is Associated with Risk ofClostridium difficileInfection
Cited by: 17
Author(s): Caroline Vincent, Sudeep Mehrotra, Vivian G. Loo, Ken Dewar, Amee R. Manges
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-017-11385-9

Pan-genome analysis of Bacillus for microbiome profiling
Cited by: 28
Author(s): Yihwan Kim, Insong Koh, Mi Young Lim, Won‐Hyong Chung, Mina Rho
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-15079-0

Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications
Cited by: 25
Author(s): Shuai Zheng, Shulin Shao, Zhiyu Qiao, Xue Chen, Chunmei Piao, Ying Yu, Feng Gao, Jie Zhang, Jie Du
Software Mentions: 1
Published: about 7 years ago

10.1186/s40168-021-01067-0

Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA
Cited by: 28
Author(s): Yacine Amar, Ilias Lagkouvardos, Rafaela L. Silva, Oluwaseun Ayodeji Ishola, Bärbel U. Foesel, Susanne Kublik, Anne Schöler, Sebastian Niedermeier, Rachela Bleuel, Alexander Zink, Klaus Neuhaus, Michael Schloter, Tilo Biedermann, Martin Köberle
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-016-3097-0

HIPPI: highly accurate protein family classification with ensembles of HMMs
Cited by: 14
Author(s): Nam Nguyen, Michael Nute, Siavash Mirarab, Tandy Warnow
Software Mentions: 1
Published: about 8 years ago

10.1099/mgen.0.000377

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
Cited by: 31
Author(s): Yuhao Chen, Thomas C. Brook, Cho Zin Soe, Ian O’Neill, Cristina Alcon-Giner, Onnicha Leelastwattanagul, Sarah Phillips, Shabhonam Caim, Paul Clarke, Lindsay J. Hall, Lesley Hoyles
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-018-31873-w

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens
Cited by: 47
Author(s): Natacha Couto, Leonard Schuele, Erwin Raangs, Miguel P. Machado, Catarina Mendes, Tiago S. Jesus, Monika A. Chlebowicz, Sigrid Rosema, Mário Ramirez, João André Carriço, Ingo B. Autenrieth, Alex Friedrich, Silke Peter, John W. A. Rossen
Software Mentions: 1
Published: about 6 years ago

10.1080/20002297.2018.1495976

Functional profiles of coronal and dentin caries in children
Cited by: 28
Author(s): Christine A. Kressirer, Tsute Chen, Kristie Lake Harriman, Jorge Frias-Lopez, Floyd E. Dewhirst, Mary Tavares, A. C. R. Tanner
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-4273-6

Higher recall in metagenomic sequence classification exploiting overlapping reads
Cited by: 13
Author(s): Samuele Girotto, Matteo Comin, Cinzia Pizzi
Software Mentions: 1
Published: almost 7 years ago

10.1264/jsme2.ME16024

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond
Cited by: 70
Author(s): Satoshi Hiraoka, Ching-chia Yang, Wataru Iwasaki
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13062-019-0242-0

Massive metagenomic data analysis using abundance-based machine learning
Cited by: 27
Author(s): Zachary N. Harris, Eliza Dhungel, Matthew Mosior, Tae-Hyuk Ahn
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-60992-6

High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection
Cited by: 22
Author(s): Ci-Xiu Li, Wei Li, Jun Zhou, Bing Zhang, Feng Yan, Chang-ping Xu, Yi‐Yu Lu, Edward C. Holmes, Mǎng Shī
Software Mentions: 1
Published: over 4 years ago

10.1093/bioinformatics/btu340

Exploration and retrieval of whole-metagenome sequencing samples
Cited by: 27
Author(s): Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela
Software Mentions: 1
Published: over 10 years ago

10.3389/fimmu.2016.00029

The Challenge and Potential of Metagenomics in the Clinic
Cited by: 28
Author(s): Heidi Mulcahy-O’Grady, Matthew L. Workentine
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-020-74090-0

Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors
Cited by: 17
Author(s): Jieun Kim, Youna Cho, Minah Seo, Moo-Ho Bae, Bongyoung Kim, Mina Rho, Hyunjoo Pai
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2019.00972

Microbiome Big-Data Mining and Applications Using Single-Cell Technologies and Metagenomics Approaches Toward Precision Medicine
Cited by: 26
Author(s): Mingyue Cheng, Le Cao, Kang Ning
Software Mentions: 1
Published: about 5 years ago

10.1186/1944-3277-9-13

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012
Cited by: 0
Author(s): Jack A. Gilbert, Mad Price Ball, Paul C. Blainey, Martin J. Blaser, Brendan J. M. Bohannan, Ashley Bateman, John Bunge, María Gloria Domínguez-Bello, Slava S. Epstein, Noah Fierer, Dirk Gevers, Tracy C. Grikscheit, Leila J. Hamdan, James Harvey, Curtis Huttenhower, Benjamin C. Kirkup, Heidi H. Kong, Christian L. Lauber, Katherine P. Lemon, Susan V. Lynch, Lance Martin, Charlene M. Mello, Joseph Palma, Roy Parker, Joseph F. Petrosino, Julia A. Segre, Leslie B. Vosshall, Rui Yi, Rob Knight
Software Mentions: 1
Published: almost 10 years ago

10.7554/eLife.20145

A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development
Cited by: 92
Author(s): Jennifer Hampton Hill, Eric A. Franzosa, Curtis Huttenhower, Karen Guillemin
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2019.00276

UltraStrain: An NGS-Based Ultra Sensitive Strain Typing Method for Salmonella enterica
Cited by: 4
Author(s): Wenxian Yang, Lihong Huang, Chong Shi, Liansheng Wang, Rongshan Yu
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.00213

Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data
Cited by: 10
Author(s): Man Guo, Xu Er, Dongmei Ai
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.02910

Quantification of Human Oral and Fecal Streptococcus parasanguinis by Use of Quantitative Real-Time PCR Targeting the groEL Gene
Cited by: 12
Author(s): Qiurong Chen, Guojun Wu, Hui Chen, Hui Li, Shuo Li, Chenhong Zhang, Xiaoyan Pang, Linghua Wang, Liping Zhao, Jian Shen
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41398-018-0107-9

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia
Cited by: 71
Author(s): Loes Olde Loohuis, Serghei Mangul, Anil P.S. Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P. Boks, Catherine Lomen‐Hoerth, Martina Wiedau‐Pazos, Rita M. Cantor, Willem M. de Vos, René S. Kahn, Eleazar Eskin, Roel A. Ophoff
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2018.03249

A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease?
Cited by: 66
Author(s): Jessica D. Forbes, Çharles N. Bernstein, Helen Tremlett, Gary Van Domselaar, Natalie Knox
Software Mentions: 1
Published: almost 6 years ago

10.3389/fcimb.2021.532989

Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species
Cited by: 5
Author(s): Ingrid Hänel, Eva Müller, Belén González-Santamarina, Herbert Tomaso, Helmut Hotzel, Anne Busch
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.701414

Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake
Cited by: 9
Author(s): Bishav Bhattarai, Ananda S. Bhattacharjee, Felipe H. Coutinho, Ramesh Goel
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2017.02181

Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes
Cited by: 29
Author(s): Ryan Joynson, Leighton Pritchard, Ekenakema Osemwekha, Nicolas Ferry
Software Mentions: 1
Published: about 7 years ago

10.3389/fcimb.2017.00051

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research
Cited by: 12
Author(s): Shaocun Zhang, Xiaocang Cao, He Huang
Software Mentions: 1
Published: over 7 years ago

10.3389/fcimb.2021.752664

Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status
Cited by: 6
Author(s): Daniel Belstrøm, Florentin Constancias, Merete Markvart, Martin Sikora, Christiane Elisabeth Sørensen, Michael Givskov
Software Mentions: 1
Published: about 3 years ago

10.12688/f1000research.12867.2

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi
Cited by: 7
Author(s): Amy L. Longmuir, Peter L. Beech, Mark F. Richardson
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2016.00965

Current Technological Improvements in Enzymes toward Their Biotechnological Applications
Cited by: 52
Author(s): Mehak Baweja, Lata Nain, Yutaka Kawarabayasi, Pratyoosh Shukla
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-020-3429-6

A big data approach to metagenomics for all-food-sequencing
Cited by: 19
Author(s): Robin Kobus, José Manuel Abuín, André C. Müller, Sören Lukas Hellmann, Juan C. Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
Software Mentions: 1
Published: over 4 years ago

10.1093/emph/eoaa051

Too much of a good thing
Cited by: 11
Author(s): Misty D. Thomas, Akamu J. Ewunkem, Sada Boyd, Danielle K. Williams, Adiya Moore, Kristen L. Rhinehardt, Emma Van Beveren, Bobi Yang, Anna Tapia, Jian Han, Scott H. Harrison, Joseph L. Graves
Software Mentions: 1
Published: almost 4 years ago

10.1093/bioinformatics/btt389

Scalable metagenomic taxonomy classification using a reference genome database
Cited by: 173
Author(s): Sasha Ames, David Hysom, Shea N. Gardner, Greg Lloyd, Maya Gokhale, Jonathan Allen
Software Mentions: 1
Published: over 11 years ago

10.1155/2017/8358151

Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula
Cited by: 11
Author(s): Cui Liu, Chao Zhang, Weijie Lv, Limin Chao, Zengquan Li, Dayou Shi, Shining Guo
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2020.01474

Metagenomics Study Reveals Changes in Gut Microbiota in Centenarians: A Cohort Study of Hainan Centenarians
Cited by: 30
Author(s): Zhe Luan, Gang Sun, Yun Huang, Yunsheng Yang, Ruifu Yang, Congyong Li, Tingting Wang, Di Tan, Shirui Qi, Jun Chen, Cong Wang, Shufang Wang, Yiming Zhao, Yujia Jing
Software Mentions: 1
Published: over 4 years ago

10.1016/j.csbj.2015.04.002

Under-detection of endospore-forming Firmicutes in metagenomic data
Cited by: 79
Author(s): Sevasti Filippidou, Thomas Junier, Tina Wunderlin, Chien-Chi Lo, Po E Li, Patrick Chain, Pilar Junier
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2016.00996

Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea
Cited by: 28
Author(s): Mario López‐Pérez, Nikole E. Kimes, Jose M. Haro‐Moreno, Francisco Rodríguez‐Valera
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2017.02165

Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing
Cited by: 37
Author(s): Yanfen Cheng, Ying Wang, Yuanfei Li, Yipeng Zhang, Tianyi Liu, Yu Wang, Thomas J. Sharpton, Weiyun Zhu
Software Mentions: 1
Published: about 7 years ago

10.1093/bioinformatics/btt077

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Cited by: 35
Author(s): Heiner Klingenberg, Kathrin Petra Aßhauer, Thomas Lingner, Peter Meinicke
Software Mentions: 1
Published: almost 12 years ago

10.3389/fmicb.2019.00806

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
Cited by: 32
Author(s): Alise J. Ponsero, Bonnie Hurwitz
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-015-0788-5

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
Cited by: 125
Author(s): Michael A. Peabody, Thea Van Rossum, Raymond Lo, Fiona S. L. Brinkman
Software Mentions: 1
Published: about 9 years ago

10.1093/cid/civ850

Assessing the Intestinal Microbiota in the SHINE Trial
Cited by: 12
Author(s): Ethan Gough, Andrew J. Prendergast, Kuda Mutasa, Rebecca J. Stoltzfus, Amee R. Manges
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0196482

Oral health status in historic population: Macroscopic and metagenomic evidence
Cited by: 18
Author(s): Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Élodie Cabot, Pierre Chevet, Éric Crubézy, Ludovic Orlando, Rémi Esclassan, Catherine Thèves
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2017.02105

MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage
Cited by: 37
Author(s): Yu Xia, An Dong Li, Yu Deng, Xiao Tao Jiang, Li Guan Li, Tong Zhang
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2020.01687

Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study
Cited by: 9
Author(s): Adriana Maria Sanabria, Erik Hjerde, Mona Johannessen, Johanna U. Ericson Sollid, Gunnar Skov Simonsen, Anne-Merethe Hanssen
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0091784

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification
Cited by: 38
Author(s): David Koslicki, Simon Foucart, Gail Rosen
Software Mentions: 1
Published: over 10 years ago

10.1186/s13040-015-0045-5

Bacterial rose garden for metagenomic SNP-based phylogeny visualization
Cited by: 1
Author(s): Dmitry Alexeev, Tanya Bibikova, Boris A. Kovarsky, Damir Melnikov, Alexander Tyakht, Vadim M. Govorun
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0076096

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
Cited by: 151
Author(s): George R. Feehery, Erbay Yigit, Samuel O. Oyola, Bradley W. Langhorst, Victor T. Schmidt, Fiona Stewart, Eileen T. Dimalanta, Linda Amaral‐Zettler, Theodore B. Davis, Michael A. Quail, Sriharsa Pradhan
Software Mentions: 1
Published: about 11 years ago

10.1186/s12887-021-02835-5

The Pregnancy and EARly Life study (PEARL) - a longitudinal study to understand how gut microbes contribute to maintaining health during pregnancy and early life
Cited by: 2
Author(s): Sarah Phillips, Rachel Watt, Thomas G. Atkinson, George M. Savva, Antonietta Hayhoe, Lindsay J. Hall, Pearl study team
Software Mentions: 1
Published: about 3 years ago

Projects: pypi: MetaPhlAn

Papers Mentioning MetaPhlAn 306