Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: MUSiCC

https://packages.ecosyste.ms/registries/pypi.org/packages/MUSiCC

MUSICC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome.
5 versions
Latest release: almost 5 years ago

Papers Mentioning MUSiCC 19

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines
Cited by: 9
Author(s): Josephine Z. Rapp, Matthew B. Sullivan, Jody W. Deming
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-44338-5

In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner
Cited by: 25
Author(s): Timothy A. Johnson, Matthew J. Sylte, Torey Looft
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.595910

A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data
Cited by: 17
Author(s): Xiaochen Yin, Tomer Altman, Erica Rutherford, Kiana West, Yonggan Wu, Jinlyung Choi, Paul L. Beck, Gilaad G. Kaplan, Karim Dabbagh, Todd Z. DeSantis, Shoko Iwai
Software Mentions: 4
Published: almost 4 years ago

10.3389/fphys.2016.00606

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Cited by: 30
Author(s): Alejandra Contreras, Benjamin Cocom-Chan, Georgina Hernández-Montes, Tobías Portillo-Bobadilla, Osbaldo Resendis‐Antonio
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12866-021-02305-z

Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences
Cited by: 5
Author(s): Alexander Eng, Hillary S. Hayden, Charles E. Pope, M. Brittnacher, Anh T. Vo, Eli Weiss, Kyle R. Hager, Daniel H. Leung, Sonya L. Heltshe, Daniel Raftery, Samuel I. Miller, Lucas R. Hoffman, Elhanan Borenstein
Software Mentions: 3
Published: about 3 years ago

10.1186/s13059-015-0610-8

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
Cited by: 76
Author(s): Ohad Manor, Elhanan Borenstein
Software Mentions: 3
Published: over 9 years ago

10.1186/s40168-017-0244-z

Proteobacteria explain significant functional variability in the human gut microbiome
Cited by: 127
Author(s): Patrick H. Bradley, Katherine S. Pollard
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-018-0398-3

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease
Cited by: 81
Author(s): Gavin M. Douglas, Richard Hansen, C. M. Jones, Katherine A. Dunn, A. Comeau, Joseph P. Bielawski, Rachel Tayler, Emad El-Omar, Richard K. Russell, Georgina L. Hold, Morgan G. I. Langille, Johan Van Limbergen
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2015.01405

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality
Cited by: 45
Author(s): Thea Van Rossum, Michael A. Peabody, Miguel Uyaguari, Kirby Cronin, Michael W.Y. Chan, Jared R. Slobodan, Matthew J. Nesbitt, Curtis A. Suttle, William W. L. Hsiao, Patrick Tang, Natalie Prystajecky, Fiona S. L. Brinkman
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-020-03815-9

MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
Cited by: 12
Author(s): Alexander Eng, Adrian J. Verster, Elhanan Borenstein
Software Mentions: 1
Published: about 4 years ago

10.1186/s40560-020-00523-7

Music Use for Sedation in Critically ill Children (MUSiCC trial): a pilot randomized controlled trial
Cited by: 11
Author(s): Gonzalo Garcia Guerra, Ari R. Joffe, Cathy Sheppard, Krista Hewson, Irina Dinu, Morteza Hajihosseini, Allan deCaen, Hsing Jou, Lisa Hartling, Sunita Vohra
Software Mentions: 1
Published: almost 4 years ago

10.1186/s40168-017-0231-4

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome
Cited by: 20
Author(s): Ohad Manor, Elhanan Borenstein
Software Mentions: 1
Published: over 7 years ago

10.1186/s40168-018-0425-4

Taxa-function robustness in microbial communities
Cited by: 50
Author(s): Alexander Eng, Elhanan Borenstein
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms9020356

Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure
Cited by: 7
Author(s): Adrien Vigneron, Perrine Cruaud, Frederic Ducellier, Ian M. Head, Nicolas Tsesmetzis
Software Mentions: 1
Published: over 3 years ago

10.1186/s40814-020-0563-x

Music Use for Sedation in Critically ill Children (MUSiCC trial): study protocol for a pilot randomized controlled trial
Cited by: 3
Author(s): Gonzalo Garcia Guerra, Ari R. Joffe, Cathy Sheppard, Krista Hewson, Irina Dinu, Allan de Caen, Hsing Jou, Lisa Hartling, Sunita Vohra
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers12092705

Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients
Cited by: 5
Author(s): Boram Kim, Eun Ju Cho, Jung‐Hwan Yoon, Soon Sun Kim, Jae Youn Cheong, Sung Won Cho, Taesung Park
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2018.00466

The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data
Cited by: 30
Author(s): Eria A. Rebollar, Ana Gutiérrez-Preciado, Cecilia Noecker, Alexander Eng, Myra C. Hughey, Daniel Medina, Jenifer B. Walke, Elhanan Borenstein, Roderick V. Jensen, Lisa K. Belden, Reid N. Harris
Software Mentions: 1
Published: over 6 years ago

10.1038/srep22493

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis
Cited by: 84
Author(s): Ohad Manor, Roie Levy, Charles E. Pope, Hillary S. Hayden, M. Brittnacher, Robert D. Carr, Matthew C. Radey, Kyle R. Hager, Sonya L. Heltshe, Bonnie W. Ramsey, Samuel I. Miller, Lucas R. Hoffman, Elhanan Borenstein
Software Mentions: 1
Published: over 8 years ago

10.1128/mSystems.00013-15

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation
Cited by: 146
Author(s): Cecilia Noecker, Alexander Eng, Sujatha Srinivasan, Casey M. Theriot, Vincent B. Young, Janet Jansson, David N. Fredricks, Elhanan Borenstein
Software Mentions: 1
Published: over 8 years ago