Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Authors
Keywords
-
Journal
Biology of Sex Differences
Volume 11, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-07-22
DOI
10.1186/s13293-020-00312-9
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data
- (2019) Timothy H Webster et al. GigaScience
- Distinct molecular etiologies of male and female hepatocellular carcinoma
- (2019) Heini M. Natri et al. BMC CANCER
- Minimap2: pairwise alignment for nucleotide sequences
- (2018) Heng Li BIOINFORMATICS
- RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
- (2018) Shilin Zhao et al. BMC BIOINFORMATICS
- Sex-chromosome dosage effects on gene expression in humans
- (2018) Armin Raznahan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
- (2018) Sophie Lamarre et al. Frontiers in Plant Science
- Y chromosome mosaicism is associated with age-related macular degeneration
- (2018) Felix Grassmann et al. EUROPEAN JOURNAL OF HUMAN GENETICS
- The role of sex in the genomics of human complex traits
- (2018) Ekaterina A. Khramtsova et al. NATURE REVIEWS GENETICS
- Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men
- (2017) Lars A. Forsberg HUMAN GENETICS
- Salmon provides fast and bias-aware quantification of transcript expression
- (2017) Rob Patro et al. NATURE METHODS
- RNA-Seq differential expression analysis: An extended review and a software tool
- (2017) Juliana Costa-Silva et al. PLoS One
- Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits
- (2016) Michela Traglia et al. GENETICS
- The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
- (2016) Swapan Mallick et al. NATURE
- Ensembl 2017
- (2016) Bronwen L. Aken et al. NUCLEIC ACIDS RESEARCH
- Sex Biased Gene Expression Profiling of Human Brains at Major Developmental Stages
- (2016) Lei Shi et al. Scientific Reports
- Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits
- (2016) Michela Traglia et al. GENETICS
- Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
- (2016) Benjamin T. Mayne et al. Frontiers in Genetics
- A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
- (2015) Shanrong Zhao et al. BMC GENOMICS
- The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
- (2015) Ronan Chaligné et al. GENOME RESEARCH
- HISAT: a fast spliced aligner with low memory requirements
- (2015) Daehwan Kim et al. NATURE METHODS
- The human transcriptome across tissues and individuals
- (2015) M. Mele et al. SCIENCE
- The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
- (2015) et al. SCIENCE
- MatchIt: Nonparametric Preprocessing for Parametric Causal Inference
- (2015) Daniel E. Ho et al. Journal of Statistical Software
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Sex differences in cognitive impairment and Alzheimer’s disease
- (2014) Rena Li et al. FRONTIERS IN NEUROENDOCRINOLOGY
- Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
- (2014) Rob Patro et al. NATURE BIOTECHNOLOGY
- Power analysis and sample size estimation for RNA-Seq differential expression
- (2014) Travers Ching et al. RNA
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
- (2014) Charity W Law et al. GENOME BIOLOGY
- Fetal hormonal programming of sex differences in depression: linking women's mental health with sex differences in the brain across the lifespan
- (2014) Jill M. Goldstein et al. Frontiers in Neuroscience
- Reliable Identification of Genomic Variants from RNA-Seq Data
- (2013) Robert Piskol et al. AMERICAN JOURNAL OF HUMAN GENETICS
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- (2013) Y. Liao et al. BIOINFORMATICS
- Comparison of software packages for detecting differential expression in RNA-seq studies
- (2013) F. Seyednasrollah et al. BRIEFINGS IN BIOINFORMATICS
- Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome
- (2013) Avinash M. Veerappa et al. FUNCTIONAL & INTEGRATIVE GENOMICS
- Detecting Evolutionary Strata on the Human X Chromosome in the Absence of Gametologous Y-Linked Sequences
- (2013) Ravi Shanker Pandey et al. Genome Biology and Evolution
- Transcriptome and genome sequencing uncovers functional variation in humans
- (2013) Tuuli Lappalainen et al. NATURE
- The Cancer Genome Atlas Pan-Cancer analysis project
- (2013) John N Weinstein et al. NATURE GENETICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Sry, more than testis determination?
- (2011) Monte E. Turner et al. AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
- BamTools: a C++ API and toolkit for analyzing and managing BAM files
- (2011) D. W. Barnett et al. BIOINFORMATICS
- Thyroid cancer gender disparity
- (2010) Reza Rahbari et al. Future Oncology
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
- (2009) Eran Eden et al. BMC BIOINFORMATICS
- What does the “four core genotypes” mouse model tell us about sex differences in the brain and other tissues?
- (2008) Arthur P. Arnold et al. FRONTIERS IN NEUROENDOCRINOLOGY
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started