cran: SAMtool | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giz095

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
Cited by: 45
Author(s): Farah Zaib Khan, Stian Soiland‐Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0244829

Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB
Cited by: 16
Author(s): Ditthawat Nonghanphithak, Orawee Kaewprasert, Pratchakan Chaiyachat, Wipa Reechaipichitkul, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-021-95789-8

Effect of black ginseng and silkworm supplementation on obesity, the transcriptome, and the gut microbiome of diet-induced overweight dogs
Cited by: 10
Author(s): Miey Park, Ki‐Hyun Kim, Varun Jaiswal, Jihee Choi, Ju Lan Chun, Kangmin Seo, Mi-Jin Lee, Hae‐Jeung Lee
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-020-59887-3

Genomic divergence reveals unique populations among Indian Yaks
Cited by: 8
Author(s): S. Jayakumar, M R Vineeth, Tarida Marlin Surya, Kritika Singh, S. P. Dixit, S. K. Niranjan, M. S. Tantia, I. D. Gupta, Dhanalakshmi Ravikumar
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-020-07257-8

Intricate genetic variation networks control the adventitious root growth angle in apple
Cited by: 5
Author(s): Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Software Mentions: 4
Published: almost 4 years ago

10.1093/bioinformatics/btu641

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Cited by: 92
Author(s): Tae-Hyuk Ahn, Juanjuan Chai, Chongle Pan
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-017-09515-4

RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout
Cited by: 13
Author(s): Bam Paneru, Rafet Al-Tobasei, Brett Kenney, Timothy D. Leeds, Mohamed Salem
Software Mentions: 2
Published: about 7 years ago

10.3389/fcimb.2019.00014

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
Cited by: 11
Author(s): Kristine M. Wylie, Todd Wylie, Patrick Minx, David A. Rosen
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2013-14-8-r83

Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function
Cited by: 61
Author(s): Maxim Ivanov, Mart Kals, Marina Kacevska, Isabel Barragán, Kie Kasuga, Anders Rane, Andres Metspalu, Lili Milani, Magnus Ingelman‐Sundberg
Software Mentions: 2
Published: almost 12 years ago

10.18502/ijrm.v13i5.7158

Strategies for whole-exome sequencing analysis in a case series study of familial male infertility
Cited by: 0
Author(s): Masomeh Askari, Dor Mohammad Kordi-Tamandani, Navid Almadani, Mehdi Totonchi
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0172687

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology
Cited by: 10
Author(s): Chandra Shekhar Pareek, Paweł Błaszczyk, Piotr Dziuba, Urszula Czarnik, Leyland Fraser, Przemysław Sobiech, M. Pierzchała, Yaping Feng, Haja N. Kadarmideen, Dibyendu Kumar
Software Mentions: 2
Published: over 7 years ago

10.1186/gb-2010-11-5-r57

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing
Cited by: 127
Author(s): Elizabeth T. Cirulli, Abanish Singh, Kevin V. Shianna, Dongliang Ge, Jason P. Smith, Jessica M. Maia, Erin L. Heinzen, James J. Goedert, David B. Goldstein
Software Mentions: 2
Published: almost 15 years ago

10.3390/microorganisms8050669

A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
Cited by: 1
Author(s): Daniela Becker, Denny Popp, Hauke Harms, Florian Centler
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.17959

Whole-exome sequencing identified genetic risk factors for asparaginase-related complications in childhood ALL patients
Cited by: 30
Author(s): Rachid Abaji, Vincent Gagné, Chang Xu, Jean-François Spinella, Francesco Ceppi, Caroline Laverdière, Jean‐Marie Leclerc, Stephen E. Sallan, Donna Neuberg, Jeffery L. Kutok, Lewis B. Silverman, Daniel Sinnett, Maja Krajinović
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21144880

Somatic Mutation Profiling in Premalignant Lesions of Vulvar Squamous Cell Carcinoma
Cited by: 12
Author(s): Sebastian Zięba, Anne-Floor W. Pouwer, Artur Kowalik, Kamil Zalewski, Natalia Rusetska, Elwira Bakuła‐Zalewska, Janusz Kopczyński, Johanna M.A. Pijnenborg, Joanne A. de Hullu, Magdalena Kowalewska
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.10240

Mutation profiling of 19 candidate genes in acute myeloid leukemia suggests significance of <i>DNMT3A</i> mutations
Cited by: 21
Author(s): Sohee Shin, Seung Tae Lee, Hee‐Jin Kim, Eun Hae Cho, Jong-Won Kim, Silvia Park, Chul Won Jung, Sun‐Hee Kim
Software Mentions: 1
Published: over 8 years ago

10.3389/fpls.2016.01676

Insights into the Sesquiterpenoid Pathway by Metabolic Profiling and De novo Transcriptome Assembly of Stem-Chicory (Cichorium intybus Cultigroup “Catalogna”)
Cited by: 20
Author(s): Giulio Testone, Giovanni Mele, Elisabetta Di Giacomo, Maria Gonnella, Massimiliano Renna, Gian Carlo Tenore, Chiara Nicolodi, Giovanna Frugis, Maria Adelaide Iannelli, Giuseppe Arnesi, Alessandro Schiappa, Donato Giannino
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-6399-1

Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China
Cited by: 21
Author(s): Yan Wang, Lijuan Luo, Qun Li, Hong Wang, Yiqian Wang, Hui Sun, Jianguo Xu, Ruiting Lan, Changyun Ye
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-15-S5-S2

RandAL: a randomized approach to aligning DNA sequences to reference genomes
Cited by: 3
Author(s): Nam S Vo, Quang Tran, Nobal B. Niraula, Vinhthuy Phan
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1797-5

Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data
Cited by: 26
Author(s): Jian Liu, Jingtao Qu, Cong Yang, Danling Tang, Jingwei Li, Hai Long, Rong Tang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0241784

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice
Cited by: 8
Author(s): Artem P. Gureev, Mikhail Syromyatnikov, Daria A. Ignatyeva, Valeria V. Valuyskikh, Sergey A. Solodskikh, Anna V. Panevina, Mariya Gryaznova, Anastasia V. Kokina, Vasily N. Popov
Software Mentions: 1
Published: almost 4 years ago

10.1093/dnares/dsu047

Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing
Cited by: 45
Author(s): Hantao Wang, Xin Jin, Beibei Zhang, Chao Shen, Zhenhua Lin
Software Mentions: 1
Published: almost 10 years ago

10.3390/foods9050608

High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens
Cited by: 8
Author(s): Mikhail Syromyatnikov, Anastasia V. Kokina, Sergey A. Solodskikh, Anna V. Panevina, Е. С. Попов, Vasily N. Popov
Software Mentions: 1
Published: over 4 years ago

10.3389/fendo.2020.00237

DUOX2 and DUOXA2 Variants Confer Susceptibility to Thyroid Dysgenesis and Gland-in-situ With Congenital Hypothyroidism
Cited by: 15
Author(s): Fengqi Wang, Yali Zang, Miaomiao Li, Wenmiao Liu, Yangang Wang, Xiaohong Yu, Hua Li, Fang Wang, Shiguo Liu
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2021.642473

HBOS-CNV: A New Approach to Detect Copy Number Variations From Next-Generation Sequencing Data
Cited by: 3
Author(s): Yang Guo, Shuzhen Wang, Xiguo Yuan
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-16-S17-S3

How genome complexity can explain the difficulty of aligning reads to genomes
Cited by: 6
Author(s): Vinhthuy Phan, Shanshan Gao, Quang Tran, Nam S Vo
Software Mentions: 1
Published: almost 9 years ago

10.3389/fpls.2018.00934

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping
Cited by: 37
Author(s): Laxman Adhikari, Orville M. Lindstrom, Jonathan E. Markham, Ali Missaoui
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2020.573871

Whole-Genome Sequencing: An Effective Strategy for Insertion Information Analysis of Foreign Genes in Transgenic Plants
Cited by: 9
Author(s): Xu‐jing Wang, Yue Jiao, Shuo Ma, Yang Jing, Zhixing Wang
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41438-018-0066-6

Transcriptome driven characterization of curly- and smooth-leafed endives reveals molecular differences in the sesquiterpenoid pathway
Cited by: 63
Author(s): Giulio Testone, Giovanni Mele, Elisabetta Di Giacomo, Gian Carlo Tenore, Maria Gonnella, Chiara Nicolodi, Giovanna Frugis, Maria Adelaide Iannelli, Giuseppe Arnesi, Alessandro Schiappa, Tiziano Biancari, Donato Giannino
Software Mentions: 1
Published: almost 6 years ago

10.1007/s12031-019-01456-z

Identification of De Novo JAK2 and MAPK7 Mutations Related to Autism Spectrum Disorder Using Whole-Exome Sequencing in a Chinese Child and Adolescent Trio-Based Sample
Cited by: 7
Author(s): Jian Jiao, Manxue Zhang, Pengbo Yang, Yan Huang, Xiao Hu, Jia Cai, Chan Yang, Mingjing Situ, Hui Zhang, Lei Fu, Kun-Yi Guo, Yi Huang
Software Mentions: 1
Published: almost 5 years ago

Ecosyste.ms: Papers

Projects: cran: SAMtool

Papers Mentioning SAMtool 30