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: MicrobeCensus

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

A command-line tool for estimating average genome size from shotgun sequence data
8 versions
Latest release: over 1 year ago
39 downloads last month

Papers Mentioning MicrobeCensus 25

10.1186/s40168-020-00813-0

Disinfection exhibits systematic impacts on the drinking water microbiome
Cited by: 37
Author(s): Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Quyen Melina Bautista-de los Santos, A. Murat Eren, P.W.J.J. van der Wielen, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 7
Published: almost 5 years ago

10.1128/mBio.02634-20

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
Cited by: 22
Author(s): Nastassia V. Patin, Angela Peña-Gonzalez, Janet K. Hatt, Christine L. Moe, Amy Kirby, Konstantinos T. Konstantinidis
Software Mentions: 6
Published: about 4 years ago

10.1038/s41396-021-00931-z

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Cited by: 8
Author(s): Grégoire Michoud, David Kamanda Ngugi, Alan Barozzi, Giuseppe Merlino, María Ll. Calleja, António Delgado Huertas, Xosé Anxelu G. Morán, Daniele Daffonchio
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13068-018-1036-9

Genome-resolved metagenomics of sugarcane vinasse bacteria
Cited by: 16
Author(s): Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2021.623799

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management
Cited by: 11
Author(s): Ahmad Nuruddin Khoiri, Supapon Cheevadhanarak, Jiraporn Jirakkakul, Sudarat Dulsawat, Peerada Prommeenate, Anuwat Tachaleat, Kanthida Kusonmano, Songsak Wattanachaisaereekul, Sawannee Sutheeworapong
Software Mentions: 6
Published: almost 4 years ago

10.1186/s40168-017-0304-4

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome
Cited by: 145
Author(s): Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giaa046

Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples
Cited by: 49
Author(s): Rafael R. C. Cuadrat, Maria Sorokina, Bruno de Bezerril Andrade, Tobias Goris, Alberto M. R. Dávila
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-3031-y

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data
Cited by: 14
Author(s): Emiliano Pereira-Flores, Frank Oliver Glöckner, Antonio Fernández-Guerra
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.4075

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.
Cited by: 17
Author(s): Miriam E. Shiffman, Rochelle M. Soo, Paul G. Dennis, Mark Morrison, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2015.01087

Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog
Cited by: 81
Author(s): Stuart E. Denman, Gonzalo Martínez Fernández, Takumi Shinkai, Makoto Mitsumori, Christopher S. McSweeney
Software Mentions: 4
Published: about 9 years ago

10.3389/fpls.2018.00902

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Cited by: 74
Author(s): Gloria Torres-Cortés, Sophie Bonneau, Olivier Bouchez, Clémence Genthon, Martial Briand, Marie‐Agnès Jacques, Matthieu Barret
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-015-0611-7

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
Cited by: 206
Author(s): Stephen Nayfach, Katherine S. Pollard
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-019-46106-x

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome
Cited by: 32
Author(s): Caroline De Tender, Bart Mesuere, Felix Van der Jeugt, Annelies Haegeman, Tom Ruttink, Bart Vandecasteele, Peter Dawyndt, Jane Debode, Eiko E. Kuramae
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1005706

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
Cited by: 62
Author(s): Julia Fukuyama, Laurie Rumker, Kris Sankaran, P. Jeganathan, Les Dethlefsen, David A. Relman, Susan Holmes
Software Mentions: 3
Published: over 7 years ago

10.1186/s12866-017-1111-6

Temporal dynamics in microbial soil communities at anthrax carcass sites
Cited by: 11
Author(s): Karoline Valseth, Camilla Nesbø, W. Ryan Easterday, Wendy C. Turner, Jaran Strand Olsen, Nils Chr. Stenseth, Thomas Haverkamp
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1004573

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes
Cited by: 45
Author(s): Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy Laurent, Ann B. Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton
Software Mentions: 2
Published: about 9 years ago

10.1128/mSystems.00374-19

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes
Cited by: 12
Author(s): Ximei Zhang, Eric R. Johnston, Yaosheng Wang, Qiang Yu, Dashuan Tian, Zhiping Wang, Yanqing Zhang, Daozhi Gong, Chun Luo, Wei Liu, Junjie Yang, Xingguo Han
Software Mentions: 2
Published: about 5 years ago

10.1038/s41396-020-00889-4

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Cited by: 60
Author(s): Heyu Lin, David B. Ascher, Yoochan Myung, Carl H. Lamborg, Steven J. Hallam, Caitlin M. Gionfriddo, Kathryn E. Holt, John W. Moreau
Software Mentions: 2
Published: almost 4 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: about 9 years ago

10.3389/fmicb.2016.01751

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes
Cited by: 68
Author(s): Hannes Horn, Beate M. Slaby, Martin T. Jahn, Kristina Bayer, Lucas Moitinho‐Silva, Frank Förster, Usama Ramadan Abdelmohsen, Ute Hentschel
Software Mentions: 1
Published: about 8 years ago

10.1038/s41396-019-0365-4

Co-culture and biogeography of Prochlorococcus and SAR11
Cited by: 71
Author(s): Jamie W. Becker, Shane L. Hogle, Kali Rosendo, Sallie W. Chisholm
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2016.00363

Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge
Cited by: 20
Author(s): Xinxu Zhang, Xiaoyuan Feng, Fengping Wang
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41396-020-00852-3

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones
Cited by: 22
Author(s): Xin Sun, Claudia Frey, Emilio García‐Robledo, Amal Jayakumar, Bess B. Ward
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.59726

Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes
Cited by: 39
Author(s): Daniel Dar, Linda S. Thomashow, David M. Weller, Dianne K. Newman
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8050725

Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics
Cited by: 31
Author(s): Eiko E. Kuramae, Stan Derksen, Thiago R. Schlemper, Maurício R. Dimitrov, Ohana Y.A. Costa, Adriana Parada Dias da Silveira
Software Mentions: 1
Published: over 4 years ago