Ecosyste.ms: Papers

10.1371/journal.pgen.1009291

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci
Cited by: 30
Author(s): Marisa E. Miller, Eric S. Nazareno, Susan M. Rottschaefer, Jakob Riddle, Daniel A. Pereira, Feng Li, Hoa Nguyen-Phuc, Eva C Henningsen, Antoine Persoons, Diane G. O. Saunders, Eva H. Stukenbrock, Peter N. Dodds, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 13
Published: almost 4 years ago

10.3389/fmicb.2017.00682

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: over 7 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: almost 8 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 6 years ago

10.3389/fmicb.2020.587972

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil
Cited by: 11
Author(s): Julian Yu, Michael J. Pavia, Lauren M. Deem, Susan E. Crow, Jonathan Deenik, C. Ryan Penton
Software Mentions: 9
Published: about 4 years ago

10.12688/f1000research.19675.1

Large-scale sequence comparisons with sourmash
Cited by: 103
Author(s): Pierce Nt, Luiz Irber, Taylor Reiter, Phillip T. Brooks, Brown Ct
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: over 7 years ago

10.1186/s40168-021-01087-w

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches
Cited by: 5
Author(s): Sharon Huws, Joan E. Edwards, Wen Lin, Francesco Rubino, Mark Alston, David Swarbreck, Shabhonam Caim, Pauline Rees Stevens, Justin A. Pachebat, Mi Young Won, Linda Oyama, Christopher J. Creevey, Alison H. Kingston‐Smith
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07526-0

Transcriptional profiling of identified neurons in leech
Cited by: 6
Author(s): Elizabeth A. C. Heath‐Heckman, Shinja Yoo, Christopher J. Winchell, Maurizio Pellegrino, James D. Angstadt, Veronica B. Lammardo, Diana M. Bautista, Francisco F. De‐Miguel, David A. Weisblat
Software Mentions: 6
Published: over 3 years ago

10.1128/AEM.01285-16

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: over 8 years ago

10.1093/gigascience/giy158

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes
Cited by: 51
Author(s): Lisa K. Johnson, Harriet Alexander, C. Titus Brown
Software Mentions: 6
Published: about 6 years ago

10.3389/fvets.2020.00255

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces
Cited by: 24
Author(s): Nicole Ricker, Julian Trachsel, Phillip Colgan, Jennifer Jones, Jinlyung Choi, Jaejin Lee, Johann F. Coetzee, Adina Howe, Susan L. Brockmeier, Crystal L. Loving, Heather K. Allen
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.3817

Benchmarking viromics: an <i>in silico</i> evaluation of metagenome-enabled estimates of viral community composition and diversity
Cited by: 208
Author(s): Simon Roux, Joanne B. Emerson, Emiley A. Eloe‐Fadrosh, Matthew B. Sullivan
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-014-0555-3

Determining the quality and complexity of next-generation sequencing data without a reference genome
Cited by: 27
Author(s): Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, M.A. van Galen, Irina Pulyakhina, Yavuz Ariyürek, Ken Kraaijeveld, Johan T. den Dunnen, Peter de Knijff, Peter A C ‘t Hoen, Jeroen F. J. Laros
Software Mentions: 4
Published: about 10 years ago

10.1186/s12915-019-0626-8

Transcriptome, proteome and draft genome of Euglena gracilis
Cited by: 88
Author(s): ThankGod Echezona Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis C. O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson O. Obado, Sara Silva Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimı́r Hampl, Mark Carrington, Michael L. Ginger, Joel B. Dacks, Steven L. Kelly, Mark C. Field
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: over 3 years ago

10.1093/bioinformatics/btw116

Goldilocks: a tool for identifying genomic regions that are ‘just right’
Cited by: 2
Author(s): Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
Software Mentions: 4
Published: almost 9 years ago

10.3390/microorganisms9010030

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments
Cited by: 17
Author(s): Marc Cozannet, Guillaume Borrel, Erwan G. Roussel, Yann Moalic, Maxime Allioux, Sanvoisin Amandine, Laurent Toffin, Karine Alain
Software Mentions: 4
Published: almost 4 years ago

10.12688/f1000research.6924.1

The khmer software package: enabling efficient nucleotide sequence analysis
Cited by: 325
Author(s): Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, R.A. Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan A. Fish, Leonor García-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David M. Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, McDonald Eric, Jessica E. Mizzi, Kevin Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander J. Nederbragt, Humberto Ortíz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich M. Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared T. Simpson, Connor T. Skennerton, James Spencer, S. Ramakrishnan, Daniel Standage, James A. Stapleton, Susan R. Steinman, J.J. Stein, Benjamin A. Taylor, W. Trimble, Heather L. Wiencko, Michael J. Wright, Brian Wyss, Zhang Qingpeng, en zyme, C. Titus Brown
Software Mentions: 4
Published: about 9 years ago

10.3389/fgene.2013.00237

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
Cited by: 238
Author(s): Sujai Kumar, Martin O. Jones, Georgios Koutsovoulos, Michael J. Clarke, Mark Blaxter
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13059-020-02066-4

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
Cited by: 34
Author(s): C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan
Software Mentions: 4
Published: over 4 years ago

10.1038/srep42110

Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal
Cited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-017-19128-6

Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence
Cited by: 9
Author(s): Teri Evans, Andrew D. Johnson, Matthew Loose
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-75270-8

Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists
Cited by: 8
Author(s): D. N. U. Naranpanawa, C. H. W. M. R. B. Chandrasekara, P. C. G. Bandaranayake, Asitha U. Bandaranayake
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-79436-2

Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima
Cited by: 12
Author(s): David J. Quispe-Parra, Joshua G. Medina-Feliciano, Sebastián Cruz-González, Humberto Ortíz-Zuazaga, José E. García‐Arrarás
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0101271

These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure
Cited by: 88
Author(s): Zhang Qingpeng, Jason Pell, Rosangela Canino-Koning, Adina Howe, C. Titus Brown
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.00737

Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum
Cited by: 19
Author(s): Vincent Perkins, Stéphanie Vignola, Marie-Hélène Lessard, Pier-Luc Plante, Jacques Corbeil, Éric Dugat-Bony, Michel Frenette, Steve Labrie
Software Mentions: 3
Published: over 4 years ago

10.1111/pbi.12742

Assembly and comparison of two closely related <i>Brassica napus</i> genomes
Cited by: 129
Author(s): Philipp E. Bayer, Bhavna Hurgobin, Agnieszka A. Golicz, Chon‐Kit Kenneth Chan, Yuxuan Yuan, HueyTyng Lee, Michael Renton, Jianghong Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J. King, Jacqueline Batley, David Edwards
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1254-5

Global transcriptomic profiling demonstrates induction of oxidative stress and of compensatory cellular stress responses in brown trout exposed to glyphosate and Roundup
Cited by: 85
Author(s): Tamsyn M. Uren Webster, Eduarda M. Santos
Software Mentions: 3
Published: almost 10 years ago

10.3389/fmicb.2016.00783

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data
Cited by: 23
Author(s): Patricio Jeraldo, Alvaro G. Hernandez, Henrik Bjørn Nielsen, Xianfeng Chen, Bryan A. White, Nigel Goldenfeld, Heidi Nelson, David Alhquist, Lisa A. Boardman, Nicholas Chia
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-446

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea
Cited by: 14
Author(s): Facundo Giorello, Matías Feijoo, Guillermo D’Elı́a, Lourdes Valdez, Juan C. Opazo, Valeria Varas, Daniel E. Naya, Enrique P. Lessa
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-017-17484-x

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals
Cited by: 109
Author(s): Christian Cr Voolstra, Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean‐François Flot, Sylvie Tambutté, Denis Allemand, Manuel Aranda
Software Mentions: 3
Published: about 7 years ago

10.1093/gbe/evx242

Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia
Cited by: 18
Author(s): Taruna Schuelke, Guangxi Wu, Anthony Westbrook, Keith Woeste, David C. Plachetzki, Kirk Broders, Matthew D. MacManes
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2017.02384

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone
Cited by: 48
Author(s): Clara A. Fuchsman, Allan H. Devol, Jaclyn K. Saunders, Cedar McKay, Gabrielle Rocap
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1006561

Ten simple rules for documenting scientific software
Cited by: 41
Author(s): Benjamin D. Lee
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-015-0729-7

Exploiting single-molecule transcript sequencing for eukaryotic gene prediction
Cited by: 115
Author(s): André E. Minoche, Juliane C. Dohm, Jessica Schneider, Daniela Holtgräwe, Prisca Viehöver, Magda Montfort, Thomas Rosleff Sörensen, Bernd Weißhaar, Heinz Himmelbauer
Software Mentions: 3
Published: over 9 years ago

10.1186/gb-2013-14-8-r89

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Cited by: 191
Author(s): Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing‐Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Software Mentions: 3
Published: almost 12 years ago

10.1093/molbev/msw083

A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian
Cited by: 13
Author(s): Tom A. Williams, Sirintra Nakjang, Scott E. Campbell, Mark Freeman, Matthías Eydal, Karen Moore, Robert P. Hirt, T. Martin Embley, Bryony A. P. Williams
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pntd.0004406

Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host
Cited by: 18
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Patrick Tan, Libor Mikeš, Martin Kašný, Petr Horák, Robin B. Gasser
Software Mentions: 3
Published: almost 9 years ago

10.1186/2049-2618-2-25

The dynamics of a family’s gut microbiota reveal variations on a theme
Cited by: 86
Author(s): Patrick D. Schloss, Kathryn Iverson, Joseph F. Petrosino, Sarah J Schloss
Software Mentions: 3
Published: over 10 years ago

10.3390/genes12030426

Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide
Cited by: 10
Author(s): Jessica Lumian, Anne D. Jungblut, Megan L Dillion, Ian Hawes, Peter T. Doran, Tyler J. Mackey, Gregory J. Dick, Christen L. Grettenberger, D. Y. Sumner
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-37669-2

Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds
Cited by: 10
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Jana Bulantová, Veronika Jeřábková, Martin Kašný, Robin B. Gasser, Petr Horák
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpls.2014.00209

An introduction to the analysis of shotgun metagenomic data
Cited by: 402
Author(s): Thomas J. Sharpton
Software Mentions: 3
Published: over 10 years ago

10.1152/physiolgenomics.00123.2014

Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout
Cited by: 14
Author(s): Tamsyn M. Uren Webster, Janice A. Shears, Karen Moore, Eduarda M. Santos
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2018.02254

To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies
Cited by: 44
Author(s): Diego Santos-García, Ksenia Juravel, Shiri Freilich, Einat Zchori-Fein, Amparo Latorre, Andrés Moya, Shai Morin, Francisco J. Silva
Software Mentions: 3
Published: about 6 years ago

10.1093/ve/veaa099

GRACy: A tool for analysing human cytomegalovirus sequence data
Cited by: 4
Author(s): Salvatore Camiolo, Nicolás M. Suárez, Antonia Chalka, Cristina Venturini, Judith Breuer, Andrew J. Davison
Software Mentions: 2
Published: almost 4 years ago

10.1186/1756-3305-7-151

Identification and characterization of alternative splicing in parasitic nematode transcriptomes
Cited by: 6
Author(s): Sahar Abubucker, Samantha N. McNulty, Bruce A. Rosa, Makedonka Mitreva
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pntd.0005216

Yersinia enterocolitica, a Neglected Cause of Human Enteric Infections in Côte d’Ivoire
Cited by: 28
Author(s): Saraka Daniel, Cyril Savin, Stéphane Kan Kouassi, Bakary Cissé, Eugène Koffi, Nicolas Cabanel, Sylvie Brémont, H. Faye-Ketté, Mireille Dosso, Élisabeth Carniel
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pntd.0005752

Different but overlapping populations of Strongyloides stercoralis in dogs and humans—Dogs as a possible source for zoonotic strongyloidiasis
Cited by: 96
Author(s): Tegegn G. Jaleta, Siyu Zhou, Felix Bemm, Fabian Schär, Virak Khieu, Sinuon Muth, Peter Odermatt, James B. Lok, Adrian Streit
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0171908

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)
Cited by: 19
Author(s): Gabriele Sales, Bruce E. Deagle, Enrica Calura, Paolo Martini, Alberto Biscontin, Cristiano De Pittà, So Kawaguchi, Chiara Romualdi, Bettina Meyer, Rodolfo Costa, Simon Jarman
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0167216

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures
Cited by: 10
Author(s): Senta Heiss-Blanquet, Françoise Fayolle-Guichard, Vincent Lombard, Agnès Hébert, Pedro M. Coutinho, Alexis Groppi, Annick Barre, Bernard Henrissat
Software Mentions: 2
Published: about 8 years ago

10.1038/s42003-021-02105-1

Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts
Cited by: 42
Author(s): Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, David A. Duchêne, Lara Puetz, Tom O. Delmont, Harald Sveier, Louise von Gersdorff Jørgensen, Kim Præbel, Michael D. Martin, Anders Miki Bojesen, M. Thomas P. Gilbert, Karsten Kristiansen, Morten T. Limborg
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-015-2007-1

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation
Cited by: 77
Author(s): Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kanazawa, Shigehiro Kuraku
Software Mentions: 2
Published: about 9 years ago

10.12688/f1000research.16415.1

Large-scale protein function prediction using heterogeneous ensembles
Cited by: 11
Author(s): Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2018.01152

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface
Cited by: 16
Author(s): Zachary C. Landry, Kevin L. Vergin, Christopher Mannenbach, Stephen Block, Yingjie Qiao, Paul C. Blainey, Craig A. Carlson, Stephen J. Giovannoni
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2015.01074

Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River
Cited by: 10
Author(s): Maria W. Smith, R. E. Davis, Nicholas D. Youngblut, Tuomas Kärnä, Lydie Herfort, Rachel J. Whitaker, William W. Metcalf, Bradley M. Tebo, António M. Baptista, Holly M. Simon
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-015-1553-x

Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
Cited by: 60
Author(s): Joann Diray‐Arce, Mark J. Clement, Bilquees Gul, M. Ajmal Khan, Brent L. Nielsen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12862-017-0973-4

Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms
Cited by: 26
Author(s): Frank E. Anderson, Bronwyn W. Williams, Kevin M. Horn, Christer Erséus, Kenneth M. Halanych, Scott R. Santos, Samuel W. James
Software Mentions: 2
Published: over 7 years ago

10.1128/genomeA.00802-14

Whole-Genome Sequences of Three Symbiotic <i>Endozoicomonas</i> Strains
Cited by: 52
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-14-160

Disk-based k-mer counting on a PC
Cited by: 61
Author(s): Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Szymon Grabowski
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-021-92174-3

Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology
Cited by: 5
Author(s): Petr Soukal, Štěpánka Hrdá, Anna Karnkowska, Rafał Milanowski, Jana Szabová, Miluše Hradilová, Hynek Strnad, Čestmı́r Vlček, Ivan Čepička, Vladimı́r Hampl
Software Mentions: 2
Published: over 3 years ago

10.1186/s13073-019-0707-x

Epigenetic therapy of myelodysplastic syndromes connects to cellular differentiation independently of endogenous retroelement derepression
Cited by: 17
Author(s): Anastasiya Kazachenka, George R. Young, Jan Attig, Chryssoula Kordella, Eleftheria Lamprianidou, Emmanuela Zoulia, George Vrachiolias, Menelaos Papoutselis, Elsa Bernard, Elli Papaemmanuil, Ιoannis Kotsianidis, George Kassiotis
Software Mentions: 2
Published: about 5 years ago

10.1093/gigascience/gix003

drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes
Cited by: 16
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-021-03996-x

MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata
Cited by: 3
Author(s): Moustafa Shokrof, C. Titus Brown, Tamer Mansour
Software Mentions: 2
Published: almost 4 years ago

10.3390/insects11110736

Gene Sequences of Potential Targets of Insecticidal PF2 Lectin Identified from the Larval De Novo Transcriptome of the Mexican Bean Weevil (Zabrotes Subfasciatus; Boheman 1833)
Cited by: 3
Author(s): Irlanda Lagarda-Díaz, Miguel Ángel Hernández‐Oñate, José Ángel Huerta‐Ocampo, Ana María Guzmán-Partida, Joy J. Winzerling, Dawn L. Geiser, Luz Vázquez–Moreno
Software Mentions: 2
Published: about 4 years ago

10.1038/sdata.2016.30

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors
Cited by: 87
Author(s): Luisa Orsini, Donald G. Gilbert, Ram Podicheti, Mieke Jansen, James Brown, Omid Shams Solari, Katina I. Spanier, John K. Colbourne, Douglas B Rush, Ellen Decaestecker, Jana Asselman, Karel A.C. De Schamphelaere, Dieter Ebert, Christoph R. Haag, Jouni Kvist, Christian Laforsch, Adam Petrusek, Andrew P. Beckerman, Tom J. Little, Anurag Chaturvedi, Michael E. Pfrender, Luc De Meester, Mikko J. Frilander
Software Mentions: 2
Published: over 8 years ago

10.1038/s41597-020-00581-4

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Cited by: 23
Author(s): Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Špela Tomaž, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-39860-5

New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation
Cited by: 45
Author(s): Chiara Lauritano, Danièle De Luca, Mariano M. Amoroso, Salvatore Benfatto, Simone Maestri, Claudia Racioppi, Francesco Esposito, Adrianna Ianora
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-40830-0

Metatranscriptomic evidence for classical and RuBisCO-mediated CO2 reduction to methane facilitated by direct interspecies electron transfer in a methanogenic system
Cited by: 28
Author(s): Peixian Yang, Giin-Yu Amy Tan, Muhammad Aslam, Jeong‐Hwan Kim, Po‐Heng Lee
Software Mentions: 2
Published: almost 6 years ago

10.1038/msb.2013.22

Computational meta'omics for microbial community studies
Cited by: 252
Author(s): Nicola Segata, Daniela Boernigen, Timothy L. Tickle, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pbio.2006062

Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries
Cited by: 81
Author(s): Jacob A. Tennessen, Na Wei, Shannon C. K. Straub, Rajanikanth Govindarajulu, Aaron Liston, Tia‐Lynn Ashman
Software Mentions: 1
Published: over 6 years ago

10.1534/g3.113.008516

Inducible Defenses Stay Up Late: Temporal Patterns of Immune Gene Expression in <i>Tenebrio molitor</i>
Cited by: 68
Author(s): Paul R. Johnston, Olga Makarova, Jens Rolff
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0146851

Proteinaceous Pheromone Homologs Identified from the Cloacal Gland Transcriptome of a Male Axolotl, Ambystoma mexicanum
Cited by: 6
Author(s): Kevin W. Hall, Heather L. Eisthen, Barry L. Williams
Software Mentions: 1
Published: almost 9 years ago

10.5334/jors.35

Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab
Cited by: 6
Author(s): Michael R. Crusoe, C. Titus Brown
Software Mentions: 1
Published: about 8 years ago

10.1128/genomeA.00420-15

Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador
Cited by: 8
Author(s): Ondrej Reznicek, Francisca A. Luesken, Sandra J. Facey, Bernhard Hauer
Software Mentions: 1
Published: over 9 years ago

10.1128/genomeA.00422-15

Draft Genome Sequence of a Papaverine-Degrading, Gram-positive <i>Arthrobacter</i> sp., Isolated from Soil Near Hohenheim, Germany
Cited by: 3
Author(s): Ondrej Reznicek, Sandra J. Facey, Bernhard Hauer
Software Mentions: 1
Published: over 9 years ago

10.1128/genomeA.00279-16

Genome Sequence of the Endophytic Bacterium <i>Bacillus thuringiensis</i> Strain KB1, a Potential Biocontrol Agent against Phytopathogens
Cited by: 16
Author(s): Heisawn Jeong, Sung Hee Jo, Chi Eun Hong, Jeong Mee Park
Software Mentions: 1
Published: over 8 years ago

10.1128/genomeA.00544-16

Genome Sequence of <i>Fusarium</i> Isolate MYA-4552 from the Midgut of <i>Anoplophora glabripennis</i> , an Invasive, Wood-Boring Beetle
Cited by: 11
Author(s): Joshua R. Herr, Erin D. Scully, Scott M. Geib, Kelli Hoover, John E. Carlson, David M. Geiser
Software Mentions: 1
Published: over 8 years ago

10.1128/genomeA.00779-16

Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete
Cited by: 5
Author(s): Hideo Dohra, Tomohiro Suzuki, Yuto Inoue, Shinya Kodani
Software Mentions: 1
Published: over 8 years ago

10.1128/genomeA.00262-17

Draft Genome Sequence of Brevundimonas sp. Strain SH203, Producing Cellouronate (β-1,4-Linked Polyglucuronate) Lyase
Cited by: 1
Author(s): Tomohiro Suzuki, Masako Kikuchi, Naotake Konno, Naoto Habu
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00697-17

Whole-Genome Sequence of the Soil Bacterium <i>Micrococcus</i> sp. KBS0714
Cited by: 6
Author(s): Venus Kuo, William R. Shoemaker, Mario E. Muscarella, Jay T Lennon
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.01048-17

Draft Genome Sequence of Streptomyces olivochromogenes NBRC 3561, a Bioactive Peptide-Producing Actinobacterium
Cited by: 5
Author(s): Hideo Dohra, Yuto Miyake, Shinya Kodani
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1004397

Palaeosymbiosis Revealed by Genomic Fossils of Wolbachia in a Strongyloidean Nematode
Cited by: 50
Author(s): Georgios Koutsovoulos, Benjamin L. Makepeace, Vincent N. Tanya, Mark Blaxter
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.11652

The characteristics of host lipid body biogenesis during coral-dinoflagellate endosymbiosis
Cited by: 1
Author(s): Hung-Kai Chen, Sabrina L. Rosset, Li-Hsueh Wang, Chii-Shiarng Chen
Software Mentions: 1
Published: over 3 years ago

10.1186/1745-6150-8-9

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
Cited by: 91
Author(s): Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, Anna‐Louise Reysenbach
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-016-1108-8

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Cited by: 404
Author(s): Ola Brønstad Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-41502-9

Improving in-silico normalization using read weights
Cited by: 8
Author(s): Dilip Ariyur Durai, Marcel H. Schulz
Software Mentions: 1
Published: over 5 years ago

10.1016/j.btre.2018.e00281

Isolation by Miniaturized Culture Chip of an Antarctic bacterium Aequorivita sp. with antimicrobial and anthelmintic activity
Cited by: 10
Author(s): Fortunato Palma Esposito, Colin J. Ingham, Raquel Hurtado-Ortiz, Chantal Bizet, Deniz Taşdemir, Donatella de Pascale
Software Mentions: 1
Published: about 6 years ago

10.1186/s13071-016-1785-x

Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini
Cited by: 10
Author(s): Ben-wen Li, Samantha N. McNulty, Bruce A. Rosa, Rahul Tyagi, Qing Ren Zeng, Kongzhen Gu, Gary J. Weil, Makedonka Mitreva
Software Mentions: 1
Published: over 8 years ago

10.1186/s13073-020-00805-7

Population genomics and antimicrobial resistance in Corynebacterium diphtheriae
Cited by: 36
Author(s): Mélanie Hennart, Leonardo G. Panunzi, Carla Rodrigues, Quentin Gaday, Sarah L. Baines, Marina Barros-Pinkelnig, Annick Carmi–Leroy, Mélody Dazas, Annemarie Wehenkel, Xavier Didelot, Julie Toubiana, Edgar Badell, Sylvain Brisse
Software Mentions: 1
Published: about 4 years ago

10.1128/MRA.01000-18

Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423
Cited by: 3
Author(s): Haeyoung Jeong, Jung-Ae Kim, Soo Keun Choi, Jae-Gu Pan
Software Mentions: 1
Published: over 6 years ago

10.1128/MRA.00876-18

Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria
Cited by: 5
Author(s): Angelo Joshua A. Victoria, Ernelea P. Cao, Nico Salmaso, Nicola Segata, Claudio Donati
Software Mentions: 1
Published: over 6 years ago

10.1186/s40168-019-0631-8

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes
Cited by: 46
Author(s): J. Alfredo Blakeley-Ruiz, Alison R. Erickson, Brandi L. Cantarel, Weili Xiong, Rachel M Adams, Janet K. Jansson, Claire M. Fraser, Robert L. Hettich
Software Mentions: 1
Published: almost 6 years ago

10.1093/jxb/erw488

Shared characteristics underpinning C₄leaf maturation derived from analysis of multiple C₃and C₄species of<i>Flaveria</i>
Cited by: 19
Author(s): Britta M. C. Kümpers, Steven J. Burgess, Ivan Reyna-Llorens, Richard Smith-Unna, Chris Boursnell, Julian M. Hibberd
Software Mentions: 1
Published: almost 8 years ago

10.12688/f1000research.12636.2

Draft genome of tule elk Cervus canadensis nannodes
Cited by: 4
Author(s): Jessica E. Mizzi, Zachary T. Lounsberry, C. Titus Brown, Benjamin N. Sacks
Software Mentions: 1
Published: about 7 years ago

10.1098/rsob.170184

Comparative genomic analysis of the ‘pseudofungus’<i>Hyphochytrium catenoides</i>
Cited by: 29
Author(s): Guy Leonard, Aurélie Labarre, David S. Milner, Adam Monier, Darren M. Soanes, Jeremy G. Wideman, Finlay Maguire, Sam Stevens, Divya Sain, Xavier Grau‐Bové, Arnau Sebé-Pedrós, Jason E. Stajich, Konrad Paszkiewicz, Matthew W. Brown, Neil Hall, Bill Wickstead, Thomas A. Richards
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2021.613791

Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms
Cited by: 54
Author(s): Alla Lapidus, Anton Korobeynikov
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2016.00387

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus
Cited by: 16
Author(s): Stefano Romano, Antonio Fernández-Guerra, F. Jerry Reen, Frank Oliver Glöckner, Susan P. Crowley, Órla O'Sullivan, Paul D. Cotter, Claire Adams, Alan D. W. Dobson, Fergal O’Gara
Software Mentions: 1
Published: over 8 years ago

10.1111/1751-7915.12420

Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea
Cited by: 65
Author(s): Yizhi Song, Anne‐Kristin Kaster, John Vollmers, Yanqing Song, Paul A. Davison, Martinique Frentrup, Gail M. Preston, Ian P. Thompson, J. Colin Murrell, Huabing Yin, C. Neil Hunter, Wei E. Huang
Software Mentions: 1
Published: about 8 years ago

10.1186/s12936-016-1296-4

Differences in PfEMP1s recognized by antibodies from patients with uncomplicated or severe malaria
Cited by: 20
Author(s): Michael Duffy, Rintis Noviyanti, Takafumi Tsuboi, Zhiping Feng, Leily Trianty, Boni F. Sebayang, Eizo Takashima, Fransisca Sumardy, Daniel A. Lampah, Louise Turner, Thomas Lavstsen, Freya J. I. Fowkes, Peter Siba, Stephen J. Rogerson, Thor G. Theander, Jutta Marfurt, Ric N. Price, Nicholas M. Anstey, Graham V. Brown, Anthony T. Papenfuss
Software Mentions: 1
Published: over 8 years ago