pypi: velvet | Projects | Ecosyste.ms: Papers

10.1002/ece3.7381

Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris
Cited by: 15
Author(s): Jingyao Ping, Peipei Feng, Jinye Li, Rongjing Zhang, Yingjuan Su, Ting Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-019-6259-z

Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation
Cited by: 5
Author(s): Xiaoyu Wang, Songling Zhu, Jinyan Zhao, Hongchu Bao, Huidi Liu, Tie-Min Ding, Guirong Liu, Yongguo Li, Randal N. Johnston, Fenglin Cao, Le Tang, Shulin Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2105-11-560

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Cited by: 32
Author(s): Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn, Vishal Thapar
Software Mentions: 1
Published: almost 14 years ago

10.1080/23802359.2021.1886886

The complete chloroplast genome of Abutilon theophrasti medic (Malvaceae)
Cited by: 1
Author(s): Yanping Lv, Yuqi Yi, Richou Han, Xiaohui Tong, Hiroki Takahashi
Software Mentions: 1
Published: over 3 years ago

10.1080/23802359.2021.1885316

The complete chloroplast genome of Clerodendrum japonicum (Thunb.) Sweet, a traditional Chinese medicinal plant
Cited by: 1
Author(s): Xiaofei Long, Yan Pan, Yuhao Weng, Zhaodong Hao, Daiquan Ye, Yunfei You, Jinhui Chen, Jisen Shi
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-14-485

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
Cited by: 86
Author(s): Alexis P Yelton, Luis R. Comolli, Nicholas B. Justice, Cindy J. Castelle, Vincent J. Denef, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 1
Published: about 11 years ago

10.3389/fcimb.2017.00383

The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides
Cited by: 42
Author(s): Alfonso Benı́tez-Páez, Eva M. Gómez del Pulgar, Yolanda Sanz
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2018.01321

Identification of Novel Biomarkers for Priority Serotypes of Shiga Toxin-Producing Escherichia coli and the Development of Multiplex PCR for Their Detection
Cited by: 7
Author(s): Matthias Kiel, Pierre Sagory-Zalkind, Céline Miganeh, Christoph Stork, Andreas Leimbach, Camilla Sekse, Alexander Mellmann, François Rechenmann, Ulrich Dobrindt
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms17081355

Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation
Cited by: 24
Author(s): Xian Zhang, Xue Feng, Jiemeng Tao, Liyuan Ma, Yunhua Xiao, Yili Liang, Xueduan Liu, Huaqun Yin
Software Mentions: 1
Published: about 8 years ago

10.1080/23802359.2017.1419088

The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki × Broussonetia papyifera)
Cited by: 10
Author(s): Zhenggang Xu, Guiyan Yang, Dong Meng, Liang Wu, Wan Zhang, Yunlin Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/s40793-015-0037-6

High quality draft genomic sequence of Flavihumibacter solisilvae 3-3T
Cited by: 3
Author(s): Gang Zhou, Chong Chen, Che Ok Jeon, Gejiao Wang, Mingshun Li
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2148-13-88

Phylogenomics of strongylocentrotid sea urchins
Cited by: 44
Author(s): Kord M. Kober, Giacomo Bernardi
Software Mentions: 1
Published: over 11 years ago

10.1080/23802359.2021.1872453

The complete chloroplast genome sequence of Sloanea sinensis
Cited by: 3
Author(s): Yuhao Weng, Daiquan Ye, Yunfei You, Yitang Chen, Fujin Fan, Jisen Shi, Jinhui Chen
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00356-19

Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire
Cited by: 27
Author(s): Mark D. Adams, Meredith S. Wright, James Karichu, Pratap Venepally, Derrick E. Fouts, Agnes P. Chan, Sandra Richter, Michael Jacobs, Robert A. Bonomo
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2148-13-8

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes
Cited by: 90
Author(s): Felix Grewe, Wenhu Guo, Emily A Gubbels, Anne Hansen, Jeffrey P. Mower
Software Mentions: 1
Published: over 11 years ago

10.3389/fphys.2014.00173

DNA methylation and temperature stress in an Antarctic polychaete, Spiophanes tcherniai
Cited by: 64
Author(s): Adam G. Marsh, Annamarie A. Pasqualone
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2020.00943

The Genome of Microthlaspi erraticum (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils
Cited by: 4
Author(s): Bagdevi Mishra, Sebastián Ploch, Fabian Runge, Angelika Schmuker, Xiaojuan Xia, Deepak Kumar Gupta, Rahul Sharma, Marco Thines
Software Mentions: 1
Published: about 4 years ago

10.1186/s12936-016-1254-1

Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines
Cited by: 18
Author(s): Susana Campino, Ernest Diez Benavente, Samuel Assefa, Eloise Thompson, Laura Drought, Catherine Taylor, Zaria Gorvett, Céline Carret, Christian Flueck, Al Ivens, Dominic P. Kwiatkowski, Pietro Alano, David A. Baker, Taane G. Clark
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2020.00313

Badnaviruses of Sweet Potato: Symptomless Coinhabitants on a Global Scale
Cited by: 15
Author(s): Jan Kreuze, Antonio Martín Pérez, Marco Galvez Gargurevich, Wilmer J. Cuellar
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms19020602

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing
Cited by: 26
Author(s): Akira Kawabe, Hiroaki Nukii, Hazuka Y. Furihata
Software Mentions: 1
Published: over 6 years ago

10.1186/s13068-018-1092-1

Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5
Cited by: 67
Author(s): Yujia Jiang, Dong Guo, Jiasheng Lu, Peter Dürre, Weiliang Dong, Wei Yan, Wenming Zhang, Jiangfeng Ma, Min Jiang, Fengxue Xin
Software Mentions: 1
Published: over 6 years ago

10.1534/g3.120.401200

Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]
Cited by: 11
Author(s): Xiaozhu Wang, Yogeshwar D. Kelkar, Xiong Xiao, Ellen O. Martinson, Jeremy A. Lynch, Chao Zhang, John H. Werren
Software Mentions: 1
Published: about 4 years ago

10.1128/genomeA.01294-14

Draft Genome Sequence of New Bacillus cereus Strain tsu1
Cited by: 8
Author(s): Hui Li, Suping Zhou, Terrance L. Johnson, Koen Vercruysse, Alexander J. Ropelewski, Theodore W. Thannhauser
Software Mentions: 1
Published: over 9 years ago

10.1186/s13104-017-2878-0

Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium?
Cited by: 16
Author(s): Manal Mohammed
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12866-014-0213-7

Comparative analysis of hapalindole, ambiguine and welwitindolinone gene clusters and reconstitution of indole-isonitrile biosynthesis from cyanobacteria
Cited by: 67
Author(s): Melinda L. Micallef, Deepti Sharma, Brittney M Bunn, Lena Gerwick, Rajesh Viswanathan, Michelle C. Moffitt
Software Mentions: 1
Published: about 10 years ago

10.1093/infdis/jiw420

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000–2013
Cited by: 181
Author(s): Yonatan H. Grad, Simon R. Harris, Robert D. Kirkcaldy, Anna G. Green, Debora S. Marks, Stephen D. Bentley, David L. Trees, Marc Lipsitch
Software Mentions: 1
Published: about 8 years ago

10.1186/s13073-016-0279-y

Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment
Cited by: 58
Author(s): Meredith S. Wright, Alina Iovleva, Michael Jacobs, Robert A. Bonomo, Mark D. Adams
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-10-479

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey
Cited by: 78
Author(s): Hindrik H. D. Kerstens, R.P.M.A. Crooijmans, A. Veenendaal, Bert Dibbits, Thomas F. C. Chin-A-Woeng, Johan T. den Dunnen, Martien A. M. Groenen
Software Mentions: 1
Published: almost 15 years ago

10.1093/gigascience/gix114

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader
Cited by: 19
Author(s): Mark F. Richardson, Fernando Sequeira, D. Selechnik, Miguel Carneiro, Marcelo Vallinoto, Jack G. Reid, Andrea J. West, Michael R. Crossland, Richard Shine, Lee A. Rollins
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.ppat.1003745

Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining
Cited by: 76
Author(s): Etienne G. J. Danchin, Marie-Jeanne Arguel, Amandine Campan-Fournier, Laetitia Perfus‐Barbeoch, Marc Magliano, Marie‐Noëlle Rosso, Martine Da Rocha, Corinne Da Silva, Nicolas Nottet, Karine Labadie, Julie Guy, François Artiguenave, Pierre Abad
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.ppat.1009535

Borrelia peptidoglycan interacting Protein (BpiP) contributes to the fitness of Borrelia burgdorferi against host-derived factors and influences virulence in mouse models of Lyme disease
Cited by: 2
Author(s): Yue Chen, Sean M. Vargas, Trever C. Smith, Sai Lakshmi Rajasekhar Karna, Taylor MacMackin Ingle, Karen L. Wozniak, Floyd L. Wormley, J. Seshu
Software Mentions: 1
Published: over 3 years ago

10.1038/s41597-019-0190-7

Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill
Cited by: 5
Author(s): Hua Yang, Chengran Zhou, Guolin Li, Jing Wang, Ping Gao, Maolin Wang, Rui Wang, Yun Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1038/srep17653

Re-engineering cellular physiology by rewiring high-level global regulatory genes
Cited by: 21
Author(s): Stephen Fitzgerald, Shane C. Dillon, Tzu-Chiao Chao, Heather L. Wiencko, Karsten Hokamp, Andrew D. S. Cameron, Charles J. Dorman
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-3865-5

Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis
Cited by: 31
Author(s): Gajendra Singh Jeena, Shahnoor Fatima, Pankaj Tripathi, Swati Upadhyay, Rakesh Shukla
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1003771

Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii
Cited by: 45
Author(s): Kerstin Voelz, Hansong Ma, Sujal Phadke, Edmond J. Byrnes, Pinkuan Zhu, Olaf Mueller, Rhys A. Farrer, Daniel A. Henk, Yonathan Lewit, Yu-Ting Hsueh, Matthew C. Fisher, Alexander Idnurm, Joseph Heitman, Robin C. May
Software Mentions: 1
Published: about 11 years ago

10.1038/srep20934

Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae
Cited by: 21
Author(s): Jia Li, Lei Gao, Shanshan Chen, Ke Tao, Yingjuan Su, Ting Wang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0055738

SOLiD™ Sequencing of Genomes of Clinical Isolates of Leishmania donovani from India Confirm Leptomonas Co-Infection and Raise Some Key Questions
Cited by: 36
Author(s): Neeloo Singh, Surendra K. Chikara, Shyam Sundar
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0153248

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics
Cited by: 12
Author(s): Nicola Harrison, Richard J. Harrison, Catherine Kidner
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-14-711

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology
Cited by: 12
Author(s): Jue Ruan, Lan Jiang, Zechen Chong, Qiang Gong, Heng Li, Chunyan Li, Yong Tao, Caihong Zheng, Weiwei Zhai, David A. Turissini, Charles H. Cannon, Xuemei Lu, Chung I. Wu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pbio.3000069

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation
Cited by: 65
Author(s): Stephanie Lauer, Grace Avecilla, Pieter Spealman, Gunjan Sethia, Nathan Brandt, Sasha F. Levy, David Gresham
Software Mentions: 1
Published: almost 6 years ago

10.1038/srep34464

Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera
Cited by: 40
Author(s): Akansha Pandey, Vishakha Swarnkar, Tushar Pandey, Piush Srivastava, Sanjeev Kanojiya, D. K. Mishra, Vineeta Tripathi
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.6374

Genes of the pig, Sus scrofa, reconstructed with EvidentialGene
Cited by: 37
Author(s): Donald G Gilbert
Software Mentions: 1
Published: over 5 years ago

10.1186/s12862-015-0349-6

Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
Cited by: 29
Author(s): Inoka K Hettiarachchige, Piyumi N Ekanayake, Ross Mann, Kathryn M. Guthridge, Tim Sawbridge, Germán Spangenberg, John W. Forster
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0057355

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology
Cited by: 295
Author(s): Bonnie Hurwitz, Matthew B. Sullivan
Software Mentions: 1
Published: over 11 years ago

10.3390/v11111080

Characterization of Klebsiella pneumoniae ST11 Isolates and Their Interactions with Lytic Phages
Cited by: 39
Author(s): Demeng Tan, Yiyuan Zhang, Mengjun Cheng, Shuai Le, Jingmin Gu, Juan Francisco Gibaja Bao, Jinhong Qin, Xin Guo, Tongyu Zhu
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0187089

Seasonal recurrence of cowpox virus outbreaks in captive cheetahs (Acinonyx jubatus)
Cited by: 13
Author(s): Julia Stagegaard, Andreas Kurth, Daniel Stern, Piotr Wojtek Dabrowski, Ann Pocknell, Andreas Nitsche, Livia Schrick
Software Mentions: 1
Published: almost 7 years ago

10.3390/v11090802

Lettuce Chlorosis Virus Disease: A New Threat to Cannabis Production
Cited by: 16
Author(s): Lior Hadad, Neta Luria, Elisheva Smith, Noa Sela, Oded Lachman, Aviv Dombrovsky
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0108185

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil
Cited by: 73
Author(s): Jinming Luo, Yaohui Bai, Jinsong Liang, Jiuhui Qu
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12985-016-0539-x

Next-generation sequencing for virus detection: covering all the bases
Cited by: 64
Author(s): Marike Visser, Rachelle Bester, Johan T. Burger, Hans J. Maree
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-3838-8

The pepper virome: natural co-infection of diverse viruses and their quasispecies
Cited by: 58
Author(s): Yeonhwa Jo, Hoseong Choi, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0089398

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia
Cited by: 28
Author(s): Clifford J. Beall, Alisha G. Campbell, Daniel M. Dayeh, Ann L. Griffen, Mircea Podar, Eugene J. Leys
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0108581

Whole Plastome Sequences from Five Ginger Species Facilitate Marker Development and Define Limits to Barcode Methodology
Cited by: 16
Author(s): Justin N. Vaughn, Srinivasa R. Chaluvadi, Tushar, Latha Rangan, Jeffrey L. Bennetzen
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0129207

Whole Genome Sequencing Investigation of a Tuberculosis Outbreak in Port-au-Prince, Haiti Caused by a Strain with a “Low-Level” rpoB Mutation L511P – Insights into a Mechanism of Resistance Escalation
Cited by: 14
Author(s): Oksana Ocheretina, Lishuang Shen, Vincent Escuyer, Marie-Marcelle Mabou, Gertrude Royal-Mardi, Sean E Collins, Jean William Pape, Daniel W. Fitzgerald
Software Mentions: 1
Published: over 9 years ago

10.1111/mec.14546

Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group
Cited by: 39
Author(s): Guillaume Méric, Leonardos Mageiros, Ben Pascoe, Dan J. Woodcock, Evangelos Mourkas, Sarah Lamble, Rory Bowden, Keith A. Jolley, Ben Raymond, Samuel K. Sheppard
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-27164-z

Investigating the viral ecology of global bee communities with high-throughput metagenomics
Cited by: 52
Author(s): David A. Galbraith, Zachary L. Fuller, Allyson M. Ray, Axel Brockmann, Maryann Frazier, Mary Gikungu, J. Francisco Iturralde Martinez, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Cristina Rosa, Joyce M. Sakamoto, Scott E. Stanley, Anthony D. Vaudo, Christina M. Grozinger
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0011370

Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines
Cited by: 80
Author(s): Xiaodong Bai, Wei Zhang, Lucia C. Orantes, Tae Hwan Jun, Omprakash Mittapalli, M. A. Rouf Mian, Andrew P. Michel
Software Mentions: 1
Published: about 14 years ago

Projects: pypi: velvet

Papers Mentioning velvet 156