Ecosyste.ms: Papers

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 years ago

10.1099/mgen.0.000492

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: over 3 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: almost 7 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

10.1186/s12859-020-03667-3

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
Cited by: 49
Author(s): Yi Yue, Hao Huang, Qi Zhao, Huimin Dou, Xinyi Liu, Tian-Fei Han, Yue Chen, Xiangjun Song, Youhua Zhang, Jing Tu
Software Mentions: 9
Published: about 4 years ago

10.26508/lsa.202000897

Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: over 3 years ago

10.3390/cancers13051136

Nanopore Sequencing Reveals Global Transcriptome Signatures of Mitochondrial and Ribosomal Gene Expressions in Various Human Cancer Stem-like Cell Populations
Cited by: 13
Author(s): Kaya E. Witte, Oliver Hertel, Beatrice A. Windmöller, Laureen P. Helweg, Anna L. Höving, Cornelius Knabbe, Tobias Busche, Johannes F. W. Greiner, Jörn Kalinowski, Thomas Noll, F. Mertzlufft, Morris Beshay, Jesco Pfitzenmaier, Barbara Kaltschmidt, Christian Kaltschmidt, Constanze Banz‐Jansen, Matthias Simon
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giy164

Genome sequence of<i>Malania oleifera</i>, a tree with great value for nervonic acid production
Cited by: 34
Author(s): Chaoqun Xu, Hui Liu, Shanshan Zhou, Dongxu Zhang, Zhao Wang, Wang Si-hai, Chen Fu, Yuze Sun, Shuai Nie, Kai‐Hua Jia, Si-Qian Jiao, Rengang Zhang, Quanzheng Yun, Wei Guan, Xuewen Wang, Qiong Gao, Jeffrey L. Bennetzen, Fatemeh Maghuly, Ilga Porth, Yves Van de Peer, Xiaoru Wang, Yongpeng Ma, Jian‐Feng Mao
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3001017

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing
Cited by: 38
Author(s): Xiaoying Fan, Dong Tang, Yuhan Liao, Pidong Li, Yu Zhang, Minxia Wang, Fan Liang, Xiao Wang, Yun Gao, Lu Wen, Depeng Wang, Yan Wang, Fuchou Tang
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02426-8

Haploflow: strain-resolved de novo assembly of viral genomes
Cited by: 15
Author(s): Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmueller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn, Alice C. McHardy
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-020-02157-2

GraphAligner: rapid and versatile sequence-to-graph alignment
Cited by: 76
Author(s): Mikko Rautiainen, Tobias Marschall
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1007819

The complex architecture and epigenomic impact of plant T-DNA insertions
Cited by: 98
Author(s): Florian Jupe, Angeline Rivkin, Todd P. Michael, Mark Zander, S. Timothy Motley, Justin P. Sandoval, R. Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R. Nery, Joseph R. Ecker
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.11146.2

De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
Cited by: 5
Author(s): Michael Liem, Hans J. Jansen, Ron P. Dirks, Christiaan V. Henkel, G. Paul H. van Heusden, Richard J.L.F. Lemmers, Trifa Omer, Shuai Shao, Peter J. Punt, Herman P. Spaink
Software Mentions: 4
Published: about 6 years ago

10.3390/v11121132

Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools
Cited by: 22
Author(s): Shaoyuan Tan, Cheryl M.T. Dvorak, Michael P. Murtaugh
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.120.401550

Solyntus, the New Highly Contiguous Reference Genome for Potato (<i>Solanum tuberosum</i>)
Cited by: 34
Author(s): Natascha van Lieshout, Ate van der Burgt, Michiel E. de Vries, Menno ter Maat, David Eickholt, Danny Esselink, Martijn van Kaauwen, Linda Kodde, Richard G. F. Visser, P. Lindhout, Richard Finkers
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pntd.0007612

An improved genome assembly of the fluke Schistosoma japonicum
Cited by: 44
Author(s): Fang Luo, Mingbo Yin, Xiaojin Mo, Chengsong Sun, Qunfeng Wu, Bingkuan Zhu, Manyu Xiang, Jipeng Wang, Yi Wang, Jian Li, Ting Zhang, Bin Xu, Huajun Zheng, Zijian Feng, Wei Hu
Software Mentions: 4
Published: about 5 years ago

10.1101/2021.01.25.428049

Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomes
Cited by: 3
Author(s): Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmüller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn, Alice C. McHardy
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giaa021

De novo assembly of the cattle reference genome with single-molecule sequencing
Cited by: 343
Author(s): Benjamin D. Rosen, Derek M. Bickhart, Robert D. Schnabel, Sergey Koren, Christine G. Elsik, Elizabeth Tseng, Troy N. Rowan, Wai Yee Low, Aleksey V. Zimin, Christine Couldrey, Richard J. Hall, Wenli Li, Arang Rhie, Jay Ghurye, Stephanie McKay, Françoise Thibaud‐Nissen, Jinna Hoffman, Brenda M. Murdoch, W. M. Snelling, T. G. McDaneld, John A. Hammond, John C. Schwartz, Wilson Nandolo, Darren E. Hagen, Christian Dreischer, Sebastian J. Schultheiß, Steven G. Schroeder, Adam M. Phillippy, John B. Cole, Curtis P. Van Tassell, George E. Liu, Timothy P. L. Smith, Juan F. Medrano
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-6337-2

LRScaf: improving draft genomes using long noisy reads
Cited by: 47
Author(s): Xingran Liao, Shigang Wu, Alun Li, Fengli Zhao, Feng Hu, Lulu Ding, Jue Ruan
Software Mentions: 3
Published: almost 5 years ago

10.1099/mgen.0.000132

Completing bacterial genome assemblies with multiplex MinION sequencing
Cited by: 460
Author(s): Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt
Software Mentions: 3
Published: almost 7 years ago

10.1128/MRA.00891-20

Complete Genome Sequences of Methicillin-Resistant Staphylococcus aureus Strains 110900 and 128254, Two Representatives of the CRISPR-Cas-Carrying Sequence Type 630/ <i>spa</i> Type t4549 Lineage
Cited by: 5
Author(s): Raphael N. Sieber, Søren Overballe‐Petersen, Hülya Kaya, Anders Rhod Larsen, Andreas Petersen
Software Mentions: 3
Published: almost 4 years ago

10.1534/g3.118.200162

Rapid Low-Cost Assembly of the <i>Drosophila melanogaster</i> Reference Genome Using Low-Coverage, Long-Read Sequencing
Cited by: 73
Author(s): Edwin Solares, Mahul Chakraborty, Danny E. Miller, Shannon Kalsow, Kate Hall, Anoja Perera, J. J. Emerson, R. Scott Hawley
Software Mentions: 3
Published: almost 6 years ago

10.1093/g3journal/jkab083

Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes
Cited by: 21
Author(s): Eric S. Tvedte, Mark Gasser, Benjamin C. Sparklin, Jane Michalski, Carl E. Hjelmen, J. Spencer Johnston, Xüna Zhao, Robin E. Bromley, Luke J. Tallon, Lisa Sadzewicz, David A. Rasko, Julie C. Dunning Hotopp
Software Mentions: 3
Published: over 3 years ago

10.1534/genetics.118.301765

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the<i>Drosophila melanogaster</i>Y Chromosome
Cited by: 88
Author(s): Ching-Ho Chang, Amanda M. Larracuente
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1008623

The endosymbiont Wolbachia rebounds following antibiotic treatment
Cited by: 14
Author(s): Emma L. Gunderson, Ian Vogel, Laura Chappell, Christina Bulman, K. C. Lim, Mona Luo, Jeffrey D. Whitman, Chris Franklin, Young Jun Choi, Emilie Lefoulon, Travis A. Clark, Brenda T. Beerntsen, Barton E. Slatko, Makedonka Mitreva, William Sullivan, Judy Sakanari
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms22094326

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
Cited by: 10
Author(s): Parwinder Kaur, Christopher Lui, Olga Dudchenko, Raja Sekhar Nandety, Bhavna Hurgobin, Melanie Pham, E Aiden, Jiangqi Wen, Kirankumar S. Mysore
Software Mentions: 3
Published: over 3 years ago

10.1128/MRA.00688-19

Complete Genome Sequence of GD1696, a Low-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
Cited by: 0
Author(s): Jo-Ann McClure, Steven M. Shideler, Kunyan Zhang
Software Mentions: 2
Published: about 5 years ago

10.1128/mSphere.00314-18

Complete Genome Sequence of a <i>bla</i> _KPC-2 -Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan
Cited by: 41
Author(s): Tsuyoshi Sekizuka, Koji Yatsu, Yuba Inamine, Takaya Segawa, Masayuki Nishio, Norimi Kishi, Makoto Kuroda
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.67130

FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip
Cited by: 49
Author(s): Manoj Kumar, Sneha Gulati, Asgar Hussain Ansari, Rhythm Phutela, Sundaram Acharya, Mohd Azhar, Jayaram Murthy, Poorti Kathpalia, Akshay Kanakan, Ranjeet Maurya, Janani Srinivasa Vasudevan, S Aparna, Rajesh Pandey, Souvik Maiti, Debojyoti Chakraborty
Software Mentions: 2
Published: over 3 years ago

10.1128/genomeA.00258-18

Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada
Cited by: 7
Author(s): Olga Andrievskaia, Marc‐Olivier Duceppe, Dara Lloyd
Software Mentions: 2
Published: over 6 years ago

10.1128/MRA.00687-19

Complete Genome Sequence of GD1108, a Moderate-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
Cited by: 1
Author(s): Jo-Ann McClure, Steven M. Shideler, Kunyan Zhang
Software Mentions: 2
Published: about 5 years ago

10.1128/MRA.00327-19

Complete Genome Sequence of Halomonas sulfidaeris Strain Esulfide1 Isolated from a Metal Sulfide Rock at a Depth of 2,200 Meters, Obtained Using Nanopore Sequencing
Cited by: 1
Author(s): Midori Saito, Akane Nishigata, Josephine Galipon, Kazuharu Arakawa
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-021-02447-3

Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Cited by: 15
Author(s): Readman Chiu, Indhu‐Shree Rajan‐Babu, Jan M. Friedman, İnanç Birol
Software Mentions: 2
Published: about 3 years ago

10.1128/MRA.00686-19

Complete Genome Sequence of GD487, a High-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
Cited by: 0
Author(s): Jo-Ann McClure, Steven M. Shideler, Kunyan Zhang
Software Mentions: 2
Published: about 5 years ago

10.1016/j.gpb.2016.05.004

Oxford Nanopore MinION Sequencing and Genome Assembly
Cited by: 591
Author(s): Hengyun Lu, Francesca Giordano, Zemin Ning
Software Mentions: 2
Published: almost 8 years ago

10.1128/MRA.01064-19

Complete Genome and Plasmid Sequences of Salmonella enterica subsp. <i>enterica</i> Serovar Enteritidis PT1, Obtained from the <i>Salmonella</i> Reference Laboratory at Public Health England, Colindale, United Kingdom
Cited by: 4
Author(s): Muhammad Zohaib Anwar, Athanasios Zervas, Lars Hestbjerg Hansen, Gary Barker, Alexandre M. Anesio, Carsten Suhr Jacobsen
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.00244-20

Complete Genome Sequence of Community-Acquired Methicillin-Resistant Staphylococcus aureus Strain RJ1267, Isolated in Shanghai, China
Cited by: 1
Author(s): Xianchun Zong, Dehua Liu, Min Li, Baolin Sun
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btaa1054

Minimally overlapping words for sequence similarity search
Cited by: 22
Author(s): Martin C. Frith, Laurent Noé, Grégory Kucherov
Software Mentions: 2
Published: almost 4 years ago

10.1073/pnas.1905179116

Unexpected host dependency of Antarctic Nanohaloarchaeota
Cited by: 105
Author(s): Joshua N Hamm, Susanne Erdmann, Emiley A. Eloe‐Fadrosh, Allegra Angeloni, Ling Zhong, Christopher Brownlee, Timothy J. Williams, Kirston Barton, Shaun Carswell, Martin A. Smith, Sarah Brazendale, Alyce M. Hancock, Michelle A. Allen, Mark J. Raftery, Ricardo Cavicchioli
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-60659-2

A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid
Cited by: 21
Author(s): Takashi Yamagishi, Mari Matsui, Tsuyoshi Sekizuka, Hiroaki Ito, Munehisa Fukusumi, Tomoko Uehira, Miyuki Tsubokura, Yoshihiko Ogawa, Atsushi Miyamoto, Shoji Nakamori, Akio Tawa, Takahisa Yoshimura, Hideki Yoshida, Hidetetsu Hirokawa, Satowa Suzuki, Takeshi Matsui, Keigo Shibayama, Makoto Kuroda, Kazunori Oishi
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-70491-3

Assembly methods for nanopore-based metagenomic sequencing: a comparative study
Cited by: 50
Author(s): Adriel Latorre‐Pérez, Pascual Villalba-Bermell, Javier Pascual, Cristina Vilanova
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-72900-z

Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies
Cited by: 9
Author(s): Ru Zhang, Jinwu He, Zhiwei Dong, Guichun Liu, Yuan Yin, Xinying Zhang, Qi Li, Yandong Ren, Yongzhi Yang, Wei Liu, Xianqing Chen, Wenhao Xia, Di Kang, Fei Hao, Qisheng Wang, Jie Yang, Zhou Chang, Ruoping Zhao, Wenting Wan, Sihan Lu, Yan‐Qiong Peng, Siqin Ge, Wen Wang, Xueyan Li
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12985-021-01583-3

Genome sequences of human cytomegalovirus strain TB40/E variants propagated in fibroblasts and epithelial cells
Cited by: 7
Author(s): Ahmed Al Qaffas, Salvatore Camiolo, Mai-Tram Vo, Alexis Aguiar, Amine Ourahmane, Myrna Sorono, Andrew J. Davison, Michael A. McVoy, Laura Hertel
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.02068

Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
Cited by: 22
Author(s): Yu-Chieh Liao, Hung‐Wei Cheng, Han Chieh Wu, Shu‐Chen Kuo, Tsai‐Ling Lauderdale, Feng-Jui Chen
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2019.00781

Agglutinin-Like Sequence (ALS) Genes in the Candida parapsilosis Species Complex: Blurring the Boundaries Between Gene Families That Encode Cell-Wall Proteins
Cited by: 20
Author(s): Se H. Oh, Brooke Smith, Andrew N. Miller, Bart L. Staker, Christopher J. Fields, Alvaro G. Hernandez, Lois L. Hoyer
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2019.00507

A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems
Cited by: 16
Author(s): Jillian M. Lang, Álvaro L. Pérez‐Quintero, Ralf Koebnik, E. DuCharme, S. Sarra, Hinda Doucouré, Ibrahim Keita, Janet Ziegle, Jonathan M. Jacobs, Ricardo Oliva, Ousmane Koïta, Boris Szurek, Valérie Verdier, Jan E. Leach
Software Mentions: 2
Published: over 5 years ago

10.1186/s13062-018-0208-7

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
Cited by: 126
Author(s): Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolić, Rohan B. H. Williams
Software Mentions: 2
Published: over 6 years ago