4.7 Article

Indel detection from DNA and RNA sequencing data with transIndel

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations

Zhifu Sun et al.

BRIEFINGS IN BIOINFORMATICS (2017)

Article Biochemical Research Methods

novoBreak: local assembly for breakpoint detection in cancer genomes

Zechen Chong et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

Jin Zhang et al.

GENOME RESEARCH (2016)

Article Biochemical Research Methods

UCSC Data Integrator and Variant Annotation Integrator

Angie S. Hinrichs et al.

BIOINFORMATICS (2016)

Review Pharmacology & Pharmacy

Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery

Gabriel Wajnberg et al.

EXPERT OPINION ON DRUG DISCOVERY (2016)

Article Biochemistry & Molecular Biology

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Zhongwu Lai et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer

Christine Henzler et al.

NATURE COMMUNICATIONS (2016)

Article Cell Biology

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer

Adam Shlien et al.

CELL REPORTS (2016)

Review Biotechnology & Applied Microbiology

A survey of best practices for RNA-seq data analysis

Ana Conesa et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Integrative Clinical Genomics of Advanced Prostate Cancer

Dan Robinson et al.

Article Biochemistry & Molecular Biology

The Molecular Taxonomy of Primary Prostate Cancer

Adam Abeshouse et al.

Article Biochemistry & Molecular Biology

Targeting the MLL complex in castration-resistant prostate cancer

Rohit Malik et al.

NATURE MEDICINE (2015)

Editorial Material Biotechnology & Applied Microbiology

Enter exitrons

Dorothee Staiger et al.

GENOME BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data

Huilei Xu et al.

BMC GENOMICS (2014)

Article Biotechnology & Applied Microbiology

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Justin M. Zook et al.

NATURE BIOTECHNOLOGY (2014)

Article Biochemical Research Methods

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

Giuseppe Narzisi et al.

NATURE METHODS (2014)

Article Biochemistry & Molecular Biology

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Matthew D. Wilkerson et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

Amie J. Radenbaugh et al.

PLOS ONE (2014)

Article Genetics & Heredity

Reliable Identification of Genomic Variants from RNA-Seq Data

Robert Piskol et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2013)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Tobias Rausch et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

Treatment of Mycoplasma Contamination in Cell Cultures with Plasmocin

Cord C. Uphoff et al.

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2012)

Review Genetics & Heredity

The Human Transcriptome: An Unfinished Story

Mihaela Pertea

GENES (2012)

Article Genetics & Heredity

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Oncology

ZNF238 Is Expressed in Postmitotic Brain Cells and Inhibits Brain Tumor Growth

Valerie M. Tatard et al.

CANCER RESEARCH (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)