pypi: velvet | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000499

A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Cited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: almost 4 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

10.1111/1755-0998.12443

The de novo genome assembly and annotation of a female domestic dromedary of North African origin
Cited by: 56
Author(s): Robert R. Fitak, Elmira Mohandesan, Jukka Corander, Pamela A. Burger
Software Mentions: 9
Published: over 9 years ago

10.1111/mec.15648

Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
Cited by: 11
Author(s): Christian Rellstab, Stefan Zoller, Christian Sailer, Andrew Tedder, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer, Martin C. Fischer
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pcbi.1003706

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Cited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2164-12-227

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Cited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: over 13 years ago

10.1186/s13742-015-0060-y

VirAmp: a galaxy-based viral genome assembly pipeline
Cited by: 31
Author(s): Yinan Wan, Daniel W. Renner, István Albert, Moriah L. Szpara
Software Mentions: 6
Published: over 9 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

10.7554/eLife.24133

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Cited by: 103
Author(s): Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, C. D. Holland, Gil G. Rosenthal, Molly Przeworski
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0029685

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Cited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: almost 13 years ago

10.7717/peerj.484

The mitochondrial genome ofParagonimus westermani(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-018-26484-4

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Cited by: 11
Author(s): David W. Waite, Melissa Dsouza, Yuji Sekiguchi, Philip Hugenholtz, Michael W. Taylor
Software Mentions: 5
Published: over 6 years ago

10.1111/1755-0998.12465

Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes
Cited by: 24
Author(s): Nina F. Ockendon, Lauren A. O’Connell, Stephen J. Bush, Jimena Monzón‐Sandoval, Holly Barnes, Tamás Székely, Hans A. Hofmann, Steve Dorus, Araxi O. Urrutia
Software Mentions: 5
Published: about 9 years ago

10.3389/fpls.2012.00220

RNA-Seq Assembly – Are We There Yet?
Cited by: 79
Author(s): Simon Schliesky, Udo Gowik, Andreas P.M. Weber, Andrea Bräutigam
Software Mentions: 5
Published: almost 13 years ago

10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: over 10 years ago

10.12688/wellcomeopenres.14265.2

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Cited by: 37
Author(s): John A. Lees, Michaela Kendall, Julian Parkhill, Caroline Colijn, SD Bentley, Rachel Harris
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0208054

Agnostic detection of genomic alterations by holistic DNA structural interrogation
Cited by: 1
Author(s): Ryan K. Shultzaberger, Rachel E. Abrams, Challise J. Sullivan, Anthony Schmitt, T. W. Thompson, John Dresios
Software Mentions: 4
Published: about 6 years ago

10.1111/j.1574-6968.2011.02339.x

Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors
Cited by: 78
Author(s): Simon Heilbronner, Matthew T. G. Holden, Andries J. van Tonder, Joan A. Geoghegan, Timothy J. Foster, Julian Parkhill, Stephen D. Bentley
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0132450

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)
Cited by: 11
Author(s): Dinesh Kumar Sahu, Soumya Prasad Panda, Prem Kumar Meher, Paramananda Das, P. Routray, Jitendra Kumar Sundaray, P. Jayasankar, Samiran Nandi
Software Mentions: 4
Published: over 9 years ago

10.1038/srep18630

De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty
Cited by: 17
Author(s): Debasis Chakrabarty, Puneet Singh Chauhan, Abhishek Chauhan, Yuvraj Indoliya, U. C. Lavania, Puneet Singh Chauhan
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1007915

Functional lability of RNA-dependent RNA polymerases in animals
Cited by: 27
Author(s): Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Héctor Escrivà, Hervé Seitz
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2011-12-8-r76

The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: almost 14 years ago

10.1534/g3.117.300245

Genome-Wide Screen forSaccharomyces cerevisiaeGenes Contributing to Opportunistic Pathogenicity in an Invertebrate Model Host
Cited by: 7
Author(s): Sujal Phadke, Calum J. Maclean, Serena Zhao, Emmi A. Mueller, Lucas A. Michelotti, Kaitlyn L. Norman, Anuj Kumar, Timothy Y. James
Software Mentions: 4
Published: almost 7 years ago

10.1099/mgen.0.000059

Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK
Cited by: 23
Author(s): Ali Al‐Shahib, Anthony Underwood, Baharak Afshar, Claire E. Turner, Theresa Lamagni, Shiranee Sriskandan, Androulla Efstratiou
Software Mentions: 4
Published: over 8 years ago

10.1186/s12862-020-01689-2

Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity
Cited by: 2
Author(s): Britta Bueker, Marco Alexandre Guerreiro, Michael E. Hood, Andreas Brachmann, Sven Rahmann, Dominik Begerow
Software Mentions: 4
Published: over 4 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

10.1186/1471-2164-13-261

The immune gene repertoire of an important viral reservoir, the Australian black flying fox
Cited by: 98
Author(s): Anthony T. Papenfuss, Michelle L. Baker, Zhiping Feng, Mary Tachedjian, Gary Crameri, Christopher Cowled, Justin H. J. Ng, Vijaya Janardhana, Hume Field, Lin‐Fa Wang
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0046219

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels
Cited by: 93
Author(s): Naseer Sangwan, Pushp Lata, Vatsala Dwivedi, Amit Kumar Singh, Neha Niharika, Jasvinder Kaur, Shailly Anand, Jaya Malhotra, Swati Jindal, Aeshna Nigam, Devi Lal, Ankita Dua, Anupam Saxena, Nidhi Garg, Mansi Verma, Jaspreet Kaur, Udita Mukherjee, Jack A. Gilbert, Scot E. Dowd, Raman Rajagopal, Paramjit Khurana, Jitendra P. Khurana, Rup Lal
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2105-11-S12-S5

Community-driven computational biology with Debian Linux
Cited by: 42
Author(s): Steffen Möller, Hajo N. Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi, Charles Plessy
Software Mentions: 3
Published: about 14 years ago

10.1007/s11626-017-0140-7

Relevant principal factors affecting the reproducibility of insect primary culture
Cited by: 2
Author(s): Naoya Ogata, Kikuo Iwabuchi
Software Mentions: 3
Published: almost 8 years ago

10.1186/gb-2012-13-2-r14

Chromatin structure changes around satellite repeats on the Schistosoma mansoni female sex chromosome suggest a possible mechanism for sex chromosome emergence
Cited by: 30
Author(s): Julie M. J. Lepesant, Céline Cosseau, Jérôme Boissier, Michael Freitag, Julien Portela, Déborah Climent, Cécile Perrin, Adhemar Zerlotini, Christoph Grunau
Software Mentions: 3
Published: almost 13 years ago

10.4056/sigs.4258318

Genome sequence of the Litoreibacter arenae type strain (DSM 19593T), a member of the Roseobacter clade isolated from sea sand
Cited by: 8
Author(s): Thomas Riedel, Anne Fiebig, Jörn Petersen, Sabine Gronow, Nikos C. Kyrpides, Markus Göker, Hans‐Peter Klenk
Software Mentions: 3
Published: about 11 years ago

10.1002/2211-5463.12033

Reconstruction and applications of consensus yeast metabolic network based on <scp>RNA</scp> sequencing
Cited by: 4
Author(s): Yuqi Zhao, Yanjie Wang, Lei Zou, Jing‐Fei Huang
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-49467-5

The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone
Cited by: 18
Author(s): Swaine L. Chen, Ying Ding, Anucha Apisarnthanarak, Shirin Kalimuddin, Sophia Archuleta, Sharifah Faridah Syed Omar, Partha Pratim De, Tse Hsien Koh, Kean Lee Chew, Nadia Atiya, Nuntra Suwantarat, Rukumani Devi Velayuthan, Joshua Wong, David C. Lye
Software Mentions: 3
Published: over 5 years ago

10.1186/s13062-017-0195-0

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
Cited by: 12
Author(s): Adam M. Dinan, John F. Atkins, Andrew E. Firth
Software Mentions: 3
Published: about 7 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

10.1186/s40793-015-0069-y

Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata
Cited by: 9
Author(s): Julie Meyer, Brian A. Dillard, J. Michael Rodgers, Kim B. Ritchie, Valerie J. Paul, Max Teplitski
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-017-3679-5

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
Cited by: 21
Author(s): William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson, Weizhong Li
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0053779

Mining of Novel Thermo-Stable Cellulolytic Genes from a Thermophilic Cellulose-Degrading Consortium by Metagenomics
Cited by: 44
Author(s): Yu Xia, Feng Ju, Hhp Fang, Tong Zhang
Software Mentions: 3
Published: almost 12 years ago

10.1186/s40168-015-0101-x

Structure and function of the healthy pre-adolescent pediatric gut microbiome
Cited by: 271
Author(s): Emily B. Hollister, Kevin Riehle, Ruth Ann Luna, Erica M. Weidler, Michelle Rubio-Gonzales, Toni Ann Mistretta, Sabeen Raza, Harshavardhan Doddapaneni, Ginger Metcalf, Donna M. Muzny, Richard A. Gibbs, Joseph F. Petrosino, Robert J. Shulman, James Versalovic
Software Mentions: 3
Published: over 9 years ago

10.1093/database/bax009

HopBase: a unified resource for Humulus genomics
Cited by: 27
Author(s): Steven T. Hill, Ramcharan Sudarsanam, Jimmy C. Henning, David A. Hendrix
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.06974

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites
Cited by: 175
Author(s): Yong Woo, Hifzur Rahman Ansari, Thomas D. Otto, Christen M. Klinger, Martin Kolísko, Jan Michálek, Alka Saxena, Dhanasekaran Shanmugam, Annageldi Tayyrov, Alaguraj Veluchamy, Shahjahan Ali, Axel Bernal, Javier del Campo, Jaromír Cihlář, Pavel Flegontov, Sebastian G. Gornik, Eva Hajdušková, Aleš Horák, Jan Janouškovec, Nicholas J. Katris, Fred D. Mast, Diego Miranda‐Saavedra, Tobias Mourier, Raeece Naeem, Mridul Nair, Aswini K. Panigrahi, Neil D. Rawlings, Eriko Padron-Regalado, Abhinay Ramaprasad, Nadira Samad, Aleš Tomčala, Jonathan M. Wilkes, Daniel E. Neafsey, Christian Doerig, Chris Bowler, Patrick J. Keeling, David S. Roos, Joel B. Dacks, Thomas J. Templeton, Ross F. Waller, Julius Lukeš, Miroslav Oborník, Arnab Pain
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-015-0840-5

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Cited by: 17
Author(s): Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce A. Roth, Josh Schulte, Greg B. Donarum, Ed Fochler, Jessica M. Hill, Alvin T. Liem, Michael R. Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard, Melanie C. Melendrez, Evan W. Skowronski, Phenix‐Lan Quan, W. Ian Lipkin, Henry S. Gibbons, David L. Hirschberg, Gustavo Palacios, C. Nicole Rosenzweig
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0237087

Sequencing and assembly of the Egyptian buffalo genome
Cited by: 10
Author(s): Dina A. El-Khishin, Amr Ageez, Mohamed E. Saad, Amr Ibrahim, Moustafa Shokrof, L. Hassan, Mohamed Abouelhoda
Software Mentions: 3
Published: over 4 years ago

10.1038/srep34315

Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis
Cited by: 21
Author(s): Rachapudi Venkata Sreeharsha, Shalini Mudalkar, Kambam Tamna Singha, A. Ramachandra Reddy
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-017-3789-0

Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad
Cited by: 13
Author(s): Kanny Diallo, Kadija Gamougam, Doumagoum Moto Daugla, Odile B. Harrison, James E. Bray, Dominique A. Caugant, Jay Lucidarme, Caroline Trotter, Musa Hassan-King, James M. Stuart, Olivier Manigart, Brian Greenwood, Martin C. J. Maiden
Software Mentions: 3
Published: over 7 years ago

10.1080/21505594.2017.1384895

Galleria mellonella as an infection model to investigate virulence of Vibrio parahaemolyticus
Cited by: 38
Author(s): Sariqa Wagley, Richard Borne, Jamie Harrison, Craig Baker‐Austin, Donatella Ottaviani, Francesca Leoni, Varaporn Vuddhakul, Richard W. Titball
Software Mentions: 2
Published: about 7 years ago

10.1186/s12862-018-1130-4

Phylogenomics of a rapid radiation: the Australian rainbow skinks
Cited by: 25
Author(s): Jason G. Bragg, Sally Potter, Ana C. Afonso Silva, Conrad J. Hoskin, Benjamin Y H Bai, Craig Moritz
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-017-4282-5

Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes
Cited by: 15
Author(s): Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-015-2011-5

The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer
Cited by: 30
Author(s): Ryan A. Melnyk, John D. Coates
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-15-96

Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood
Cited by: 144
Author(s): K. G. Frey, J. Enrique Herrera-Galeano, C. L. Redden, Truong Luu, Stephanie L. Servetas, Alfred Mateczun, Vishwesh Mokashi, Kimberly A. Bishop‐Lilly
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-016-2515-7

HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads
Cited by: 16
Author(s): Anas Al-okaily
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1467-7

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii
Cited by: 25
Author(s): Valentin Loux, Mahendra Mariadassou, Síntia Almeida, Hélène Chiapello, Amal Plaudet Hammani, Julien Buratti, Annie Gendrault, Valérie Barbe, Jean‐Marc Aury, Stéphanie-Marie Deutsch, Sandrine Parayre, Marie‐Noëlle Madec, Victoria Chuat, Gwenaël Jan, Pierre Peterlongo, Vasco Azevedo, Yves Le Loir, Hélène Falentin
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-696

The genome of Eimeria falciformis - reduction and specialization in a single host apicomplexan parasite
Cited by: 44
Author(s): Emanuel Heitlinger, Simone Spork, Richard Lucius, Christoph Dieterich
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-13-382

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution
Cited by: 44
Author(s): Sheng Zhu, You Zhi Cao, Cong Jiang, Bi Yue Tan, Zhong Wang, Sisi Feng, Liang Zhang, Xiao Hua Su, Broňa Brejová, Tomáš Vinař, Meng Xu, Ming Xiu Wang, Shou Gong Zhang, Min Huang, Rongling Wu, Yan Zhou
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-13-354

Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms
Cited by: 37
Author(s): Frank M. You, Karin R. Deal, Jirui Wang, Monica Britton, Joseph Fass, Dazhen Lin, Abhaya M. Dandekar, Charles A. Leslie, Mallikarjuna K. Aradhya, Ming Luo, Jan Dvořák
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-12-590

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq
Cited by: 28
Author(s): Geng Chen, Ruiyuan Li, Leming Shi, Ji Qi, Pengzhan Hu, Jian Luo, Mingyao Liu, Tieliu Shi
Software Mentions: 2
Published: about 13 years ago

10.1186/s12864-017-3895-z

Interpreting whole genome and exome sequencing data of individual gastric cancer samples
Cited by: 10
Author(s): Daniela Esser, Niklas Holze, Jill D. Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel, Christoph Röcken
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-14-703

Large-scale polymorphism discovery in macaque G-protein coupled receptors
Cited by: 6
Author(s): Dharmendra B. Goswami, Lisa M. Ogawa, Joshua Ward, Gregory M. Miller, Eric J. Vallender
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2180-13-302

Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing
Cited by: 43
Author(s): Anthony Underwood, Garan Jones, M. Mentasti, Norman K. Fry, Timothy G. Harrison
Software Mentions: 2
Published: almost 12 years ago

10.1093/bioinformatics/btu170

Trimmomatic: a flexible trimmer for Illumina sequence data
Cited by: 39,409
Author(s): Anthony Bolger, Marc Lohse, Björn Usadel
Software Mentions: 2
Published: over 10 years ago

10.1099/mgen.0.000120

Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt
Cited by: 6
Author(s): Araceli Lamelas, Julia Hauser, Jean-Pierre Dangy, Abdul-Wahab Mawuko Hamid, Katharina Röltgen, Mohamad Sater, Abraham Hodgson, Ali Sié, Thomas Junghanss, Simon R. Harris, Julian Parkhill, Stephen D. Bentley, Gerd Pluschke
Software Mentions: 2
Published: over 7 years ago

10.1099/mic.0.055459-0

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
Cited by: 431
Author(s): Keith A. Jolley, Carly M. Bliss, Julia S. Bennett, Holly B. Bratcher, Carina Brehony, Frances M. Colles, Helen Wimalarathna, Odile B. Harrison, Samuel K. Sheppard, Alison J. Cody, Martin C. J. Maiden
Software Mentions: 2
Published: over 12 years ago

10.1099/mic.0.068874-0

Distribution and diversity of the haemoglobin–haptoglobin iron-acquisition systems in pathogenic and non-pathogenic Neisseria
Cited by: 21
Author(s): Odile B. Harrison, Julia S. Bennett, Jeremy P. Derrick, Martin C. J. Maiden, Christopher D. Bayliss
Software Mentions: 2
Published: over 11 years ago

10.1080/23802359.2018.1464412

The complete chloroplast genome of Sisymbrium irio
Cited by: 2
Author(s): Takahiro Kawanabe, Hiroaki Nukii, Hazuka Y. Furihata, Takanori Yoshida, Akira Kawabe
Software Mentions: 2
Published: over 6 years ago

10.1186/1743-422X-10-169

Comparative analysis of the genome sequences and replication profiles of chikungunya virus isolates within the East, Central and South African (ECSA) lineage
Cited by: 38
Author(s): Karen Caiyun Chen, Yiu‐Wing Kam, Raymond Pin Tzer Lin, Mary Mah-Lee Ng, Lisa F. P. Ng, Justin Jang Hann Chu
Software Mentions: 2
Published: over 11 years ago

10.1186/s12985-015-0332-2

Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach
Cited by: 12
Author(s): Xiu Su, Shuai Fu, Yajuan Qian, Yi Xu, Xueping Zhou
Software Mentions: 2
Published: over 9 years ago

10.1186/s12985-020-01438-3

First report of Plum bark necrosis stem pitting-associated virus infecting grapevine in China
Cited by: 2
Author(s): Yang Yang, Yifan Sun, Qingliang Li, Yufeng Wu, Deya Wang
Software Mentions: 2
Published: about 4 years ago

10.3390/v12080879

Tomato Brown Rugose Fruit Virus Contributes to Enhanced Pepino Mosaic Virus Titers in Tomato Plants
Cited by: 20
Author(s): Chen Klap, Neta Luria, Elisheva Smith, Lior Hadad, Elena Bakelman, Noa Sela, Eduard Belausov, Oded Lachman, Diana Leibman, Aviv Dombrovsky
Software Mentions: 2
Published: over 4 years ago

10.3390/v13020235

The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3
Cited by: 7
Author(s): Paula Lagan, Ryan Devaney, Victoria Smyth
Software Mentions: 2
Published: almost 4 years ago

10.12688/wellcomeopenres.9876.1

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
Cited by: 101
Author(s): Sarah Auburn, Ulrike Böhme, Sascha Steinbiss, Hidayat Trimarsanto, Jessica B. Hostetler, Mandy Sanders, Qi Gao, François Nosten, Chris Newbold, Matthew Berriman, Ric N. Price, Thomas D. Otto
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.3275

Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fishXiphophorus multilineatus
Cited by: 4
Author(s): Yuan Lu, Charlotte Marie Klimovich, Kalen Z Robeson, William Boswell, Oscar Ríos-Cardenas, Ronald B. Walter, Molly R. Morris
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0004384

Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections
Cited by: 27
Author(s): Ehtesham Mofiz, Torsten Seemann, Melanie Bahlo, Deborah C. Holt, Bart J. Currie, Katja Fischer, Anthony T. Papenfuss
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0104405

An Improved Method for Including Upper Size Range Plasmids in Metamobilomes
Cited by: 31
Author(s): Anders Norman, Leise Riber, Wenting Luo, L i Li Li, Lars Hestbjerg Hansen, Søren J. Sørensen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0196032

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment
Cited by: 11
Author(s): Heath W. Garris, Susan A. Baldwin, John Taylor, David B. Gurr, Daniel R. Denesiuk, Jonathan D. Van Hamme, Lauchlan H. Fraser
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0205582

De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation
Cited by: 5
Author(s): Ghana S. Challa, Wanlong Li
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0061011

Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System
Cited by: 58
Author(s): Yaohui Bai, Ruiping Liu, Jinsong Liang, Jiuhui Qu
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0031410

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach
Cited by: 76
Author(s): Marvin Mundry, Erich Bornberg‐Bauer, Michael Sammeth, Philine G. D. Feulner
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0049533

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant
Cited by: 21
Author(s): Reeta Sharma, Benoît Goossens, Célia Kun‐Rodrigues, Tatiana Teixeira, Nurzhafarina Othman, Jason Q. Boone, Nathaniel K. Jue, Craig Obergfell, Rachel J. O’Neill, Lounès Chikhi
Software Mentions: 2
Published: about 12 years ago

10.1093/database/bax032

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
Cited by: 59
Author(s): Surya Saha, Prashant S. Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa D. Shippy, Mirella Flores, Andrew J. Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan E. Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E. Dixon, Andrew G. Cridge, Liliana Cano, Xiaolong Cao, Haobo Jiang, Nan Li, Shannon L. Johnson, Brandi L. Cantarel, Stephen Richards, Adam C. English, Robert G. Shatters, Christopher P. Childers, Mei-Ju Chen, Wayne B. Hunter, Michelle Cilia, Lukas A. Mueller, Monica Munoz‐Torres, David R. Nelson, Monica Poelchau, Joshua B. Benoit, Helen Wiersma-Koch, Tom D’Elia, Susan J. Brown
Software Mentions: 2
Published: almost 8 years ago

10.1080/22221751.2018.1563455

Detection of human parvovirus 4 DNA in the patients with acute encephalitis syndrome during seasonal outbreaks of the disease in Gorakhpur, India
Cited by: 6
Author(s): Vidya A. Arankalle, Navin Srivastava, K. P. Kushwaha, Agnibha Sen, Ashwini Y. Ramdasi, Priyanka Patel, Sumeet Kuthe, Bangari Haldipur, Gajanan N. Sakpal, Kavita S. Lole, Nilesh Ingle
Software Mentions: 2
Published: almost 6 years ago

10.1111/j.1462-2920.2012.02836.x

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
Cited by: 146
Author(s): Bonnie Hurwitz, Li Deng, Bonnie T. Poulos, Matthew B. Sullivan
Software Mentions: 2
Published: over 12 years ago

10.3389/fcimb.2020.575084

Enteric Phageome Alterations in Patients With Type 2 Diabetes
Cited by: 11
Author(s): Qian Chen, Xiaojing Ma, Chong Li, Yun Shen, Wei Zhu, Yan Zhang, Xin Guo, Jian Zhou, Chang Liu
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2017.00442

Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea
Cited by: 10
Author(s): Lars Wöhlbrand, Bernd Wemheuer, Christoph Feenders, Hanna S. Ruppersberg, Christina Hinrichs, Bernd Blasius, Rolf Daniel, Ralf Rabus
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2016.00238

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
Cited by: 46
Author(s): Annika C. Mosier, Christopher S. Miller, Kyle R. Frischkorn, Robin A. Ohm, Li Zhou, Kurt LaButti, Alla Lapidus, Anna Lipzen, Cindy Chen, Jenifer Johnson, Erika Lindquist, Chongle Pan, Robert L. Hettich, Igor V. Grigoriev, Steven W. Singer, Jillian F. Banfield
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2018.01827

The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus
Cited by: 12
Author(s): Brian Couger, Tyler Weirick, André R.L. Damásio, Fernando Segato, Maria de Lourdes Teixeira de Moraes Polizeli, Ricardo Sérgio Almeida, Gustavo H. Goldman, Rolf A. Prade
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2014.00750

Current strategies for mobilome research
Cited by: 26
Author(s): Tue Sparholt Jørgensen, Anne S. Kiil, Mette Sif Hansen, Søren J. Sørensen, Lars Hansen
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2020.612474

Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs
Cited by: 10
Author(s): Huimin Liu, Zhibin Shi, Chunguo Liu, Pengfei Wang, Ming Wang, Shida Wang, Zaisi Liu, Lili Wei, Zhenzhao Sun, Xijun He, Jingfei Wang
Software Mentions: 2
Published: about 4 years ago

10.1534/g3.112.002881

Genomes of Ashbya Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications
Cited by: 31
Author(s): Fred S. Dietrich, Sylvia Voegeli, Sidney Kuo, Peter Philippsen
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-015-0756-4

De novo ChIP-seq analysis
Cited by: 8
Author(s): Xin He, A. Ercüment Çiçek, Yuhao Wang, Marcel H. Schulz, Hai-Son Le, Ziv Bar‐Joseph
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-01181-w

White spot syndrome virus VP28 specific double-stranded RNA provides protection through a highly focused siRNA population
Cited by: 28
Author(s): Pål Nilsen, Marius Karlsen, Kallaya Sritunyalucksana, Siripong Thitamadee
Software Mentions: 2
Published: over 7 years ago

10.1186/1751-0473-9-8

Software for pre-processing Illumina next-generation sequencing short read sequences
Cited by: 169
Author(s): Chuming Chen, Sari Khaleel, Hongzhan Huang, Cathy H. Wu
Software Mentions: 2
Published: over 10 years ago

10.1186/s40793-015-0050-9

Genome sequence of the pink–pigmented marine bacterium Loktanella hongkongensis type strain (UST950701–009PT), a representative of the Roseobacter group
Cited by: 1
Author(s): S. S. Lau, Thomas Riedel, Anne Fiebig, James Han, Marcel Huntemann, Jörn Petersen, Natalia Ivanova, Victor Markowitz, Tanja Woyke, Markus Göker, Nikos C. Kyrpides, Hans Peter Klenk, Pei‐Yuan Qian
Software Mentions: 2
Published: over 9 years ago

10.1155/2015/528395

Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease inLagerstroemia indica
Cited by: 7
Author(s): Xinwang Wang, Weibing Shi, Timothy A. Rinehart
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-018-29986-3

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates
Cited by: 42
Author(s): Prasit Palittapongarnpim, Pravech Ajawatanawong, Wasna Viratyosin, Nat Smittipat, Areeya Disratthakit, Surakameth Mahasirimongkol, Hideki Yanai, Norio Yamada, Supalert Nedsuwan, Worarat Imasanguan, Pacharee Kantipong, Boonchai Chaiyasirinroje, Jiraporn Wongyai, Licht Toyo-Oka, Jody Phelan, Julian Parkhill, Taane G. Clark, Martin L. Hibberd, Wuthiwat Ruengchai, P Palittapongarnpim, Tada Juthayothin, Sissades Tongsima, Katsushi Tokunaga
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0101021

Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens
Cited by: 45
Author(s): Oliver Deusch, Ciaran O’Flynn, Alison Colyer, Penelope J. Morris, David Allaway, Paul Jones, Kelly S. Swanson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0087346

Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China
Cited by: 10
Author(s): Dongliang Yu, Borui Pi, Yan Chen, Yanfei Wang, Zhi Ruan, Michael Otto, Yunsong Yu
Software Mentions: 1
Published: almost 11 years ago

10.1093/dnares/dst055

Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803
Cited by: 40
Author(s): Matthias Kopf, Stephan Klähn, Nadin Pade, Christian Weingärtner, Martin Hagemann, Björn Voß, Wolfgang R. Hess
Software Mentions: 1
Published: almost 11 years ago

10.1080/23802359.2021.1967803

The complete chloroplast genome sequence of Casuarina equisetifolia
Cited by: 6
Author(s): Jiaji Zhang, Yuhao Weng, Daiquan Ye, Yunfei You, Jisen Shi, Jinhui Chen
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-018-33767-3

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development
Cited by: 35
Author(s): Ernest Diez Benavente, Damilola R. Oresegun, Paola Flórez de Sessions, E. A. Walker, Cally Roper, Jamille Gregório Dombrowski, Rodrigo Medeiros de Souza, Cláudio R. F. Marinho, Colin J. Sutherland, Martin L. Hibberd, Fady Mohareb, David A. Baker, Taane G. Clark, Susana Campino
Software Mentions: 1
Published: about 6 years ago

Projects: pypi: velvet

Papers Mentioning velvet 156