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: cran: HMP

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/HMP

Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
11 versions
Latest release: about 5 years ago
1 dependent package
352 downloads last month

Papers Mentioning HMP 25

Environmental vulnerability of the global ocean epipelagic plankton community interactome
Cited by: 47
Author(s): Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Patrick Wincker, Lee Karp‐Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0100570

LADES: A Software for Constructing and Analyzing Longitudinal Designs in Biomedical Research
Cited by: 0
Author(s): Alan Vázquez-Alcocer, Daniel Ladislao Garzón-Cortes, Rosa Sánchez‐Casas
Software Mentions: 8
Published: over 10 years ago

10.7717/peerj.1029

Compact graphical representation of phylogenetic data and metadata with GraPhlAn
Cited by: 584
Author(s): Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: over 9 years ago

10.12688/f1000research.24345.2

Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
Cited by: 0
Author(s): Justin Wagner, Jayaram Kancherla, Domenick J. Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-017-0237-y

Normalization and microbial differential abundance strategies depend upon data characteristics
Cited by: 1,253
Author(s): Sophie Weiss, Zhenjiang Zech Xu, Shyamal D. Peddada, Amir Almasi‐Hashiani, Kyle Bittinger, Antonio González, Catherine Lozupone, Jesse Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight
Software Mentions: 5
Published: over 7 years ago

10.1186/s12986-020-00505-4

Oatmeal induced gut microbiota alteration and its relationship with improved lipid profiles: a secondary analysis of a randomized clinical trial
Cited by: 9
Author(s): Mengyao Ye, Jianqin Sun, Yanqiu Chen, Qian Ren, Zhen Li, Ying Zhao, Yue Pan, Huijun Xue
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-03591-6

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
Cited by: 1
Author(s): Yulia Kondratenko, Anton Korobeynikov, Alla Lapidus
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225796

The diversity and abundance of fungi and bacteria on the healthy and dandruff affected human scalp
Cited by: 38
Author(s): Sally Grimshaw, Adrian Smith, David H. Arnold, Elaine Xu, Michael Hoptroff, Barry Murphy
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0048996

Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data
Cited by: 17
Author(s): Patricio S. La Rosa, Berkley Shands, Elena Deych, Yanjiao Zhou, Erica Sodergren, George M. Weinstock, William D. Shannon
Software Mentions: 4
Published: about 12 years ago

10.1128/mSystems.00319-21

Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual
Cited by: 7
Author(s): Lu Wang, Yining Xu, Chung-Ching Chu, Zehua Jing, Yabin Chen, Jingsong Zhang, Mingming Pu, Tingyan Mi, Yaping Du, Zong-Qi Liang, Chandraprabha Doraiswamy, Tao Zeng, Jiarui Wu, Luonan Chen
Software Mentions: 4
Published: about 3 years ago

10.1186/1471-2164-15-257

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities
Cited by: 69
Author(s): Jun Ma, Cristian Coarfa, Xiang Qin, Penelope E. Bonnen, Aleksandar Milosavljevic, James Versalovic, Kjersti M. Aagaard
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-020-02200-2

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Cited by: 36
Author(s): Daniel R. Utter, Gary G. Borisy, A. Murat Eren, Colleen M. Cavanaugh, Jessica L. Mark Welch
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0162302

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study
Cited by: 12
Author(s): Nicholas J. Ollberding, Eszter Völgyi, Maurizio Macaluso, Ranjit Kumar, Casey D. Morrow, Frances A. Tylavsky, Chandrika J. Piyathilake
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-60130-2

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
Cited by: 45
Author(s): Robert Marsland, Wenping Cui, Pankaj Mehta
Software Mentions: 2
Published: over 4 years ago

10.1051/parasite/2020074

Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection
Cited by: 12
Author(s): Yanyan Jiang, Zhongying Yuan, Yujuan Shen, Bruce A. Rosa, John Martin, Shengkui Cao, Yanjiao Zhou, Makedonka Mitreva, Jianping Cao
Software Mentions: 2
Published: almost 4 years ago

10.1038/srep38993

Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis
Cited by: 83
Author(s): Shareef M Dabdoub, Sukirth M. Ganesan, Purnima Kumar
Software Mentions: 2
Published: almost 8 years ago

10.1080/19490976.2021.1957536

A double-blind, 377-subject randomized study identifies Ruminococcus, Coprococcus, Christensenella, and Collinsella as long-term potential key players in the modulation of the gut microbiome of lactose intolerant individuals by galacto-oligosaccharides
Cited by: 11
Author(s): M. Andrea Azcárate-Peril, Jeffrey Roach, Alan J. Marsh, William D. Chey, William J. Sandborn, Andrew J. Ritter, Dennis Savaiano, Todd R. Klaenhammer
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40168-019-0620-y

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016
Cited by: 135
Author(s):
Software Mentions: 1
Published: over 5 years ago

10.1155/2018/4095789

The Gut Microbiome Profile in Obesity: A Systematic Review
Cited by: 296
Author(s): Olga Castañer, Albert Goday, Young Jun Park, Seung‐Hwan Lee, Faidon Magkos, Sue-Anne Toh Ee Shiow, Helmut Schröder
Software Mentions: 1
Published: almost 7 years ago

10.2196/24043

Increasing HIV Testing and Viral Suppression via Stigma Reduction in a Social Networking Mobile Health Intervention Among Black and Latinx Young Men and Transgender Women Who Have Sex With Men (HealthMpowerment): Protocol for a Randomized Controlled Trial
Cited by: 22
Author(s): Kathryn E. Muessig, Jesse Golinkoff, Lisa Hightow-Weidman, Aimee E Rochelle, Marta Mulawa, Sabina Hirshfield, A. Lina Rosengren, Subhash Aryal, Nickie Buckner, M Skye Wilson, Dovie L Watson, Steven T. Houang, José A. Bauermeister
Software Mentions: 1
Published: almost 4 years ago

10.3390/metabo10050181

Metabolome–Microbiome Crosstalk and Human Disease
Cited by: 46
Author(s): Kathleen Lee-Sarwar, Jessica Lasky‐Su, Rachel S. Kelly, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.01619

Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity
Cited by: 8
Author(s): Zhanshan Ma, Lianwei Li, Wendy Li
Software Mentions: 1
Published: over 6 years ago

10.3390/s130303530

Deployment of a Fully-Automated Green Fluorescent Protein Imaging System in a High Arctic Autonomous Greenhouse
Cited by: 6
Author(s): Talal Abboud, Matthew Bamsey, Anna‐Lisa Paul, Thomas Graham, Stephen Braham, Rita Noumeir, Alain Berinstain, Robert J. Ferl
Software Mentions: 1
Published: over 11 years ago

10.3390/s19030529

RGB-D Object Recognition Using Multi-Modal Deep Neural Network and DS Evidence Theory
Cited by: 10
Author(s): Hui Zeng, Bin Yang, Xiuqing Wang, Jiwei Liu, Dongmei Fu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-015-0499-y

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe
Cited by: 6
Author(s): Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin‐Hui Xing, Takuji Yamada
Software Mentions: 1
Published: over 9 years ago