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: EukRep

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

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
8 versions
Latest release: over 4 years ago
37 downloads last month

Papers Mentioning EukRep 14

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0244616

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia
Cited by: 11
Author(s): Jan Niklas Macher, Martina Prazeres, Sarah Taudien, Jamaluddin Jompa, Aleksey Sadekov, Willem Renema
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-021-01031-y

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Cited by: 25
Author(s): Tina Keller‐Costa, Asunción Lago‐Lestón, J. Saraiva, Rodolfo Brizola Toscan, Sandra Godinho Silva, Jorge M. S. Gonçalves, Cymon J. Cox, Nikos C. Kyrpides, Ulisses Nunes da Rocha, Rodrigo Costa
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.701186

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: about 3 years ago

10.1038/s41396-020-00885-8

Comparative genomics reveals new functional insights in uncultured MAST species
Cited by: 17
Author(s): Aurélie Labarre, Lior David, Francisco Latorre, Guy Leonard, François Bucchini, Aleix Obiol, Corinne Cruaud, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Klaas Vandepoele, Ramiro Logares, Ramón Massana
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2020.603692

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench
Cited by: 3
Author(s): Xiaoyu Zhu, Jiwen Liu, Chun-Xu Xue, Jiwei Tian, Xiao‐Hua Zhang
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms8091350

Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake
Cited by: 14
Author(s): Diana E. Ayala, William D. Burgos, Javier Sánchez España, Estelle Couradeau, Carmen Falagán, Jennifer L. Macalady
Software Mentions: 4
Published: about 4 years ago

10.1186/s40168-021-01085-y

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics
Cited by: 14
Author(s): Patrick T. West, Samantha L. Peters, Matthew R. Olm, Feiqiao Brian Yu, Haley Gause, Yue Clare Lou, Brian Firek, Robyn Baker, Alexander D. Johnson, Michael J. Morowitz, Robert L. Hettich, Jillian F. Banfield
Software Mentions: 3
Published: about 3 years ago

10.1186/s40168-019-0638-1

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
Cited by: 52
Author(s): Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian Firek, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 3
Published: over 5 years ago

10.1128/AEM.01171-18

Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML
Cited by: 7
Author(s): Blake W. Stamps, Heather S. Nunn, Victoria A. Petryshyn, Ronald S. Oremland, Laurence G. Miller, Michael R. Rosen, Kohen W. Bauer, Katherine Jenny Thompson, Elise M. Tookmanian, Anna R. Waldeck, S. J. Loyd, Hope A. Johnson, Bradley S. Stevenson, William M. Berelson, Frank A. Corsetti, John R. Spear
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-021-04212-6

Expanding the taxonomic range in the fecal metagenome
Cited by: 1
Author(s): Theo R. Allnutt, Alexandra J. Roth‐Schulze, Leonard C. Harrison
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.561194

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake
Cited by: 11
Author(s): Graham A. Colby, Matti O. Ruuskanen, Kyra A. St. Pierre, Vincent L. St. Louis, Alexandre J. Poulain, Stéphane Aris‐Brosou
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00127-20

Metagenome-Assembled Genome Sequences of Three Uncultured <i>Planktomarina</i> sp. Strains from the Northeast Atlantic Ocean
Cited by: 5
Author(s): Matilde Marques, Nuno Borges, Sandra Godinho Silva, Ulisses Nunes da Rocha, Asunción Lago‐Lestón, Tina Keller‐Costa, Rodrigo Costa
Software Mentions: 1
Published: over 4 years ago

10.1186/s40168-020-00808-x

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
Cited by: 90
Author(s): Eli Levy Karin, Milot Mirdita, Johannes Söding
Software Mentions: 1
Published: over 4 years ago