pypi: guppy | Projects | Ecosyste.ms: Papers

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the Drosophila intestine
Cited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-021-02473-1

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Cited by: 20
Author(s): Rachel Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.pone.0217050

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
Cited by: 61
Author(s): Lucas Czech, Alexandros Stamatakis
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.ppat.1009304

Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Cited by: 39
Author(s): Anna Both, Jia-Bin Huang, Minyue Qi, Christian Lausmann, Samira Weißelberg, Henning Büttner, Susanne Lezius, Antonio Virgilio Failla, Coralie Martin, Marc Stegger, Thorsten Gehrke, Sharmin Baig, Mustafa Citak, Malik Alawi, Martin Aepfelbacher, Holger Rohde
Software Mentions: 6
Published: almost 4 years ago

10.3389/fgene.2020.00211

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets
Cited by: 35
Author(s): Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva María Novoa
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-021-02296-0

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Cited by: 12
Author(s): Matthew T Parker, Katarzyna Knop, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evab148

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains
Cited by: 2
Author(s): Kun Wu, Zhou‐Hua Cheng, Emily Williams, Nathan T Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dongfeng Liu, Michael Lynch, Hongan Long
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0037818

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
Cited by: 511
Author(s): Sujatha Srinivasan, Noah G. Hoffman, Martin Morgan, F. A. Matsen, Tina L. Fiedler, Richard Hall, Frederick J. Ross, Connor O. McCoy, Roger E. Bumgarner, Jeanne M. Marrazzo, David N. Fredricks
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-020-07183-9

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Cited by: 7
Author(s): Sophie Dhorne–Pollet, Éric Barrey, Nicolas Pollet
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-021-02283-5

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
Cited by: 24
Author(s): Vahid Akbari, Jean-Michel Garant, Kieran O’Neill, Pawan Pandoh, Richard A. Moore, Marco A. Marra, Martin Hirst, Steven J.M. Jones
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms9071427

How Do Polymer Coatings Affect the Growth and Bacterial Population of a Biofilm Formed by Total Human Salivary Bacteria?—A Study by 16S-RNA Sequencing
Cited by: 3
Author(s): Ali Al‐Ahmad, Kira Wollensak, Sibylle J. Rau, Diana Lorena Guevara Solarte, Stefan Paschke, Karen Lienkamp, Ori Staszewski
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-49134-9

Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach
Cited by: 13
Author(s): Sohini Claverie, Alassane Ouattara, Murielle Hoareau, Denis Filloux, Arvind Varsani, Philippe Roumagnac, Darren P. Martin, Jean‐Michel Lett, Pierre Lefeuvre
Software Mentions: 4
Published: about 5 years ago

10.3390/genes11091097

Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae)
Cited by: 11
Author(s): Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Amy Litt, Elizabeth W. McCarthy
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-021-02411-1

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Cited by: 15
Author(s): Laura Schulz, Manuel Torres-Diz, Mariela Cortés-López, Katharina E. Hayer, Mukta Asnani, Sarah K. Tasian, Yoseph Barash, Elena Sotillo, Kathi Zarnack, Julian König, Andrei Thomas-Tikhonenko
Software Mentions: 4
Published: over 3 years ago

10.3390/v13081424

Application of Oxford Nanopore Technology to Plant Virus Detection
Cited by: 32
Author(s): L. W. Liefting, David W. Waite, Jeremy R. Thompson
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.120.401059

A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly
Cited by: 8
Author(s): Graham B. Wiley, Matthew J. Miller
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giaa027

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C
Cited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 4 years ago

10.1186/s12876-021-01885-4

Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis—a prospective multicentre translational study
Cited by: 2
Author(s): Christoph Ammer‐Herrmenau, Thomas Asendorf, Georg Beyer, S Buchholz, Silke Cameron, Marko Damm, Fabian Frost, Robert Henker, Robert Jaster, Veit Phillip, Marius Placzek, C. Ratei, Simon Sirtl, T. van den Berg, Molly Weingarten, Julia Woitalla, Julia Mayerle, Volker Ellenrieder, Albrecht Neeße
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-020-00840-x

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
Cited by: 31
Author(s): Michael P. Doane, Megan M. Morris, Bhavya Papudeshi, Lauren B. Allen, Dnyanada Pande, John M. Haggerty, Shaili Johri, Abigail C. Turnlund, Meredith Peterson, Dovi Kacev, Andy Nosal, Deni Ramirez, Kevin A. Hovel, Julia Ledbetter, Amanda T. Alker, Jackeline Avalos, Kristi Baker, Shruti Bhide, E Billings, Steven Byrum, Molly Clemens, Amelia Juliette Demery, Laís Farias Oliveira Lima, Oscar Gómez, O. Gutiérrez, Selena Hinton, Donald Kieu, Angie Kim, Rebeca Loaiza, Alexander S. Martinez, Jordan McGhee, Kristine Nguyen, Sabrina Parlan, Amanda Pham, Rosalyn Price-Waldman, Robert A. Edwards, Elizabeth A. Dinsdale
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.658256

De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides)
Cited by: 8
Author(s): Luis J. Chueca, Judith Kochmann, Tilman Schell, Carola Greve, Axel Janke, Markus Pfenninger, Sven Klimpel
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.120.401149

The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions
Cited by: 2
Author(s): Anna Fijarczyk, Mathieu Hénault, Souhir Marsit, Guillaume Charron, Tobias Fischborn, Luc Nicole-Labrie, Christian R. Landry
Software Mentions: 3
Published: about 4 years ago

10.1093/gigascience/giab001

metaXplor: an interactive viral and microbial metagenomic data manager
Cited by: 2
Author(s): Guilhem Sempéré, Adrien Pétel, Magsen Abbé, Pierre Lefeuvre, Philippe Roumagnac, Frédéric Mahé, Gaël Baurens
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.soilbio.2019.107613

Calcium exerts a strong influence upon phosphohydrolase gene abundance and phylogenetic diversity in soil
Cited by: 13
Author(s): Andrew L. Neal, M. J. Glendining
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-021-07500-w

Consistent ultra-long DNA sequencing with automated slow pipetting
Cited by: 7
Author(s): Trent M. Prall, Emma K Neumann, Julie A. Karl, Cecilia G. Shortreed, David Baker, Hailey E. Bussan, Roger W. Wiseman, David H. O’Connor
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.157

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
Cited by: 63
Author(s): Connor O. McCoy, F. A. Matsen
Software Mentions: 2
Published: about 11 years ago

10.1186/s12934-021-01517-2

Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions
Cited by: 15
Author(s): Theresa Zwiener, Marina Dziuba, Frank Mickoleit, Christian Rückert, Tobias Busche, Jörn Kalinowski, René Uebe, Dirk Schüler
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2021.671371

Chromosome-Scale Genome for a Red-Fruited, Perpetual Flowering and Runnerless Woodland Strawberry (Fragaria vesca)
Cited by: 6
Author(s): Elizabeth I. Alger, Adrian E. Platts, Sontosh K Deb, Xi Luo, Shujun Ou, Yao Cao, Kim E. Hummer, Xiong Zhang, Steven J. Knapp, Zhongchi Liu, Michael R. McKain, Patrick P. Edger
Software Mentions: 2
Published: over 3 years ago

10.1093/gbe/evz137

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase
Cited by: 32
Author(s): Jessica Nelson, Duncan Hauser, José A. Gudiño, Yessenia A Guadalupe, John C. Meeks, Noris Salazar Allen, Juan Carlos Villarreal, Fay‐Wei Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00959

High-Quality Genome Assembly of Fusarium oxysporum f. sp. lini
Cited by: 16
Author(s): George S. Krasnov, Elena N. Pushkova, Roman O. Novakovskiy, Ludmila P. Kudryavtseva, Tatiana A. Rozhmina, Ekaterina M. Dvorianinova, Liubov V. Povkhova, Anna V. Kudryavtseva, Alexey A. Dmitriev, Nataliya V. Melnikova
Software Mentions: 2
Published: about 4 years ago

10.1186/s12866-021-02124-2

Identification and elimination of genomic regions irrelevant for magnetosome biosynthesis by large-scale deletion in Magnetospirillum gryphiswaldense
Cited by: 7
Author(s): Theresa Zwiener, Frank Mickoleit, Marina Dziuba, Christian Rückert, Tobias Busche, Jörn Kalinowski, Damien Faivre, René Uebe, Dirk Schüler
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.00199

Exploring Rain as Source of Biological Control Agents for Fire Blight on Apple
Cited by: 15
Author(s): Marco E. Mechan Llontop, Kelly Hurley, Long Tian, Vivian Bernal-Galeano, Hans Wildschutte, Sasha C. Marine, Keith S. Yoder, Boris A. Vinatzer
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-5094-y

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
Cited by: 98
Author(s): Nicholas D. Sanderson, Teresa Street, Dona Foster, Jeremy Swann, Bridget L. Atkins, Andrew Brent, Martin McNally, Sarah Oakley, Adrian Taylor, Tim E. A. Peto, Derrick W. Crook, David W Eyre
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0184146

Molecular prediction of lytic vs lysogenic states for Microcystis phage: Metatranscriptomic evidence of lysogeny during large bloom events
Cited by: 29
Author(s): Joshua M. A. Stough, Xiangming Tang, Lauren E. Krausfeldt, Morgan M. Steffen, Guang Gao, Gregory L. Boyer, Steven W. Wilhelm
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0243412

Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka
Cited by: 25
Author(s): Chitra Pattabiraman, Farhat Habib, Pulleri Kandi Harsha, Risha Rasheed, Pramada Prasad, Vijayalakshmi Reddy, Prameela Dinesh, Tina Damodar, Kiran Hosallimath, Anson K. George, Nakka Vijay Kiran Reddy, Banerjee John, Amrita Pattanaik, Narendra Kumar, Reeta Subramaniam Mani, Manjunatha M. Venkataswamy, Shafeeq K Shahul Hameed, Brind Kumar, Anita Desai, Vasanthapuram Ravi
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.594524

The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria
Cited by: 26
Author(s): Sofia Esquivel-Elizondo, Caner Bağcı, Monika Temovska, Byoung Seung Jeon, Irina Bessarab, Rohan B. H. Williams, Daniel H. Huson, Largus T. Angenent
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0047075

Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project
Cited by: 147
Author(s): Sean Conlan, Heidi H. Kong, Julia A. Segre
Software Mentions: 2
Published: about 12 years ago

10.1186/s12866-021-02251-w

Isolation and characterization of lytic phage TUN1 specific for Klebsiella pneumoniae K64 clinical isolates from Tunisia
Cited by: 14
Author(s): Simone Eckstein, Jana Stender, Sonia Mzoughi, Kilian Vogele, Jana Kühn, Daniela Friese, Christina Bugert, Susann Handrick, Mustapha Ferjani, Roman Wölfel, Andrew Millard, Mohamed Ben Moussa, Joachim Jakob Bugert
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.01470-17

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii
Cited by: 22
Author(s): Emanuel Schmid‐Siegert, Sophie Richard, Amanda Luraschi, Konrad Mühlethaler, Marco Pagni, Philippe M. Hauser
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13148-019-0629-x

Novel familial distal imprinting centre 1 (11p15.5) deletion provides further insights in imprinting regulation
Cited by: 13
Author(s): Florian Kraft, Katharina Wesseler, Matthias Begemann, Ingo Kurth, Miriam Elbracht, Thomas Eggermann
Software Mentions: 1
Published: almost 6 years ago

10.1093/database/bav080

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
Cited by: 41
Author(s): Dominique Le Bœuf, Stéphane Audic, Loraine Brillet-Guéguen, Christophe Caron, Christian Jeanthon
Software Mentions: 1
Published: almost 10 years ago

10.3390/plants9101274

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales
Cited by: 9
Author(s): Malte Mäder, Hilke Schroeder, Thomas Schott, Katrin Schöning-Stierand, Ana Paula Leite Montalvão, Heike Liesebach, Mirko Liesebach, Barbara Fussi, Birgit Kersten
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.571472

Genomic Analysis of SXT/R391 Integrative Conjugative Elements From Proteus mirabilis Isolated in Brazil
Cited by: 6
Author(s): Juliana Lumi Sato, Marina Rocha Borges da Fonseca, Louise Cerdeira, Maria Cristina Bronharo Tognim, Thaís Cristine Marques Sincero, Mario Cesar Noronha do Amaral, Nilton Lincopán, Rodrigo S. Galhardo
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2015.00694

Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities
Cited by: 30
Author(s): Łukasz Dziewit, Adam Pyzik, Krzysztof Romaniuk, Adam Sobczak, Paweł Szczęsny, Leszek Lipiński, Dariusz Bartosik, Łukasz Drewniak
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2020.545591

Co-infection With Chromosomally-Located blaCTX-M-14 and Plasmid-Encoding blaCTX-M-15 in Pathogenic Escherichia coli in the Republic of Korea
Cited by: 1
Author(s): Jungsun Park, Eunkyung Shin, Ae Kyung Park, Soojin Kim, Hyun Ju Jeong, Jin Seok Kim, Young‐Hee Jin, Nan Joo Park, Jeong-Hoon Chun, Kyu-Jam Hwang, Kwang Jun Lee, Junyoung Kim
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.00951

Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy
Cited by: 15
Author(s): Carmen Hogendoorn, Arjan Pol, Nunzia Picone, Geert Cremers, Theo A. van Alen, Antonina Lisa Gagliano, Mike S. M. Jetten, Walter D’Alessandro, Paola Quatrini, Huub J. M. Op den Camp
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms21249433

Many Different LINE-1 Retroelements Are Activated in Bladder Cancer
Cited by: 7
Author(s): Patcharawalai Whongsiri, Wolfgang Goering, Tobias Lautwein, Christiane Hader, Günter Niegisch, Karl Köhrer, Michèle J. Hoffmann, Wolfgang A. Schulz
Software Mentions: 1
Published: almost 4 years ago

10.3390/v12080841

Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing
Cited by: 11
Author(s): Carole Grädel, Miguel Angel Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L. Leib, Franziska Suter‐Riniker, Alban Ramette
Software Mentions: 1
Published: over 4 years ago

10.1534/genetics.120.303774

Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans
Cited by: 16
Author(s): Georgina Gómez-Saldívar, Jaime Osuna-Luque, Jennifer I. Semple, Dominique A. Glauser, Sophie Jarriault, Peter Meister
Software Mentions: 1
Published: almost 4 years ago

10.1186/s40168-021-01010-3

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
Cited by: 136
Author(s): Ryan Cook, Steve Hooton, Urmi Trivedi, Liz King, Christine E. R. Dodd, Jon L. Hobman, Dov J. Stekel, Michael A. Jones, Andrew Millard
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00020-21

Complete Genome Sequence of Mycobacterium heckeshornense JCM 15655 T , Closely Related to a Pathogenic Nontuberculous Mycobacterial Species, Mycobacterium xenopi
Cited by: 0
Author(s): Mitsunori Yoshida, Hanako Fukano, Takanori Asakura, Masato Suzuki, Yoshihiko Hoshino
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.01287-20

Complete Genome Sequence of the Bacterial Component of Mysorin Biopreparation
Cited by: 1
Author(s): Alexey М. Afonin, Emma S. Gribchenko, Gulnar A. Akhtemova, Yu.V. Laktionov, A. P. Kozhemyakov, В. А. Жуков
Software Mentions: 1
Published: over 3 years ago

10.1093/biomethods/bpaa026

Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples
Cited by: 21
Author(s): Sara D’Andreano, Anna Cuscó, Olga Francino
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: guppy

Papers Mentioning guppy 53