pypi: kraken | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.1038/s41598-021-88698-3

In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
Cited by: 23
Author(s): Kolja Becker, H. Klein, Eric J. Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor Chong, Markus H. Kuehn, Francesc Fernández-Albert, Remko A. Bakker
Software Mentions: 11
Published: over 3 years ago

10.3389/fmicb.2019.01805

Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing
Cited by: 44
Author(s): Josephine Grützke, Burkhard Malorny, Jens A. Hammerl, Anne Busch, Simon H. Tausch, Herbert Tomaso, Carlus Deneke
Software Mentions: 8
Published: over 5 years ago

10.1186/s12862-018-1251-9

Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity
Cited by: 12
Author(s): Sarah E. Lower, Kathrin F. Stanger‐Hall, David W. Hall
Software Mentions: 8
Published: about 6 years ago

10.3389/fmicb.2021.607289

The Relationship Between Microbiomes and Selective Regimes in the Sponge Genus Ircinia
Cited by: 5
Author(s): J. B. Kelly, David E. Carlson, Jun Siong Low, Tyler Rice, Robert Thacker
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0227639

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Cited by: 15
Author(s): Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri
Software Mentions: 6
Published: almost 5 years ago

10.1111/1751-7915.12757

Relative abundance of ‘ <i>Candidatus</i> Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community
Cited by: 25
Author(s): Anthony P. Malanoski, Baochuan Lin, Brian J. Eddie, Zheng Wang, W. Judson Hervey, Sarah M. Glaven
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.13195

Resistome diversity in cattle and the environment decreases during beef production
Cited by: 88
Author(s): Noelle Noyes, Xiang Yang, Lyndsey Linke, Roberta J. Magnuson, Adam Dettenwanger, Shaun R. Cook, Ifigenia Geornaras, D. Woerner, Sheryl Gow, Tim A. McAllister, Hua Yang, Jaime Ruiz, Kenneth L. Jones, Christina Boucher, Paul S. Morley, K. E. Belk
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-021-07531-3

A tail of two pandas— whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca)
Cited by: 0
Author(s): Mátyás Cserháti
Software Mentions: 4
Published: over 3 years ago

10.1186/s12920-016-0193-6

Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values
Cited by: 6
Author(s): Matteo Comin, Michele Schimd
Software Mentions: 4
Published: over 8 years ago

10.3390/microorganisms7100393

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?
Cited by: 15
Author(s): Léa Siegwald, Ségolène Caboche, Gaël Even, Éric Viscogliosi, Christophe Audebert, Magali Chabé
Software Mentions: 4
Published: about 5 years ago

10.3390/v11111041

Viruses in the Invasive Hornet Vespa velutina
Cited by: 36
Author(s): Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, Maxime Thomasson, Elisabeth A. Herniou, Cédric Alaux, Yves Le Conte
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2019.00826

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing
Cited by: 27
Author(s): Stephen R. Doyle, Geetha Sankaranarayanan, Fiona Allan, Duncan Berger, Pablo David Jimenez Castro, James B. Collins, Thomas Crellen, María A. Duque-Correa, Peter Ellis, Tegegn G. Jaleta, Roz Laing, Kirsty Maitland, Catherine McCarthy, Tchonfienet Moundai, Ben Softley, Elizabeth A. Thiele, Philippe Tchindebet Ouakou, John Vianney Tushabe, Joanne P. Webster, Adam Weiss, James B. Lok, Eileen Devaney, Ray M. Kaplan, James A. Cotton, Matthew Berriman, Nancy Holroyd
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-95054-y

Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
Cited by: 4
Author(s): Sergio Alan Cervantes-Pérez, Lenin Yong-Villalobos, Nathalia Flórez-Zapata, Araceli Oropeza-Aburto, Félix Rico-Reséndiz, Itzel Amasende-Morales, Tianying Lan, Octavio Martínez, Jean‐Philippe Vielle‐Calzada, Victor A. Albert, Luis Herrera‐Estrella
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0176469

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads
Cited by: 59
Author(s): Thomas Nordahl Petersen, Oksana Lukjancenko, Martin Christen Frølund Thomsen, Maria Maddalena Sperotto, Ole Lund, Frank Møller Aarestrup, Thomas Sicheritz-Pontén
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-47145-0

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition
Cited by: 48
Author(s): Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Heather D. Bracken‐Grissom, Tin‐Yam Chan, Adam D. Miller, Christopher M. Austin
Software Mentions: 3
Published: over 5 years ago

10.12688/f1000research.16804.4

Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
Cited by: 10
Author(s): Federica Cattonaro, Alessandro Spadotto, Slobodanka Radović, Fabio Marroni
Software Mentions: 3
Published: almost 5 years ago

10.1099/mgen.0.000325

Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events
Cited by: 8
Author(s): Mariana G. López, John B. Dogba, Manuela Torres-Puente, Galo A. Goig, Miguel Moreno-Molina, Luis M Villamayor, Simeon Cadmus, Iñaki Comas
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/giaa028

Binning unassembled short reads based on k-mer abundance covariance using sparse coding
Cited by: 6
Author(s): Olexiy Kyrgyzov, Vincent Prost, Stéphane Gazut, Bruno Farcy, Thomas Brüls
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0163527

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences
Cited by: 24
Author(s): Ahmed A. Metwally, Yang Dai, Patricia W. Finn, David L. Perkins
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2019.02499

A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification
Cited by: 13
Author(s): Enrique Doster, Pablo Rovira, Noelle Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Lyndsey Linke, Roberta J. Magnuson, Christina Boucher, K. E. Belk, Paul S. Morley
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-018-29334-5

Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
Cited by: 183
Author(s): Andrea D. Tyler, Laura Mataseje, Chantel Urfano, Lisa Schmidt, Kym Antonation, Michael R. Mulvey, Cindi R. Corbett
Software Mentions: 2
Published: over 6 years ago

10.1016/j.micinf.2017.12.011

Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis
Cited by: 6
Author(s): Nira R. Pollock, Rebika Dhiman, Nada Daifalla, Farhat Mustafa, Antonio Campos‐Neto
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.11942

Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (<i>Romerolagus diazi)</i>
Cited by: 4
Author(s): Leslie M. Montes-Carreto, José Luis Aguirre-Noyola, Itzel A. Solís-García, Jorge Ortega, Esperanza Martı́nez-Romero, José Antonio Chamizo Guerrero
Software Mentions: 1
Published: over 3 years ago

Ecosyste.ms: Papers

Projects: pypi: kraken

Papers Mentioning kraken 24