Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity

(2020) Nicolas J. Pillon et al.   Nature Communications

Regulation of Proteins in Human Skeletal Muscle: The Role of Transcription

(2020) Pavel A. Makhnovskii et al.   Scientific Reports

Variability in estimated gene expression among commonly used RNA-seq pipelines

(2020) Sonali Arora et al.   Scientific Reports

Skeletal Muscle Extracellular Matrix – What Do We Know About Its Composition, Regulation, and Physiological Roles? A Narrative Review

(2020) Robert Csapo et al.   Frontiers in Physiology

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

(2019) Joanna Zyla et al.   BIOINFORMATICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Benefits of higher resistance‐training volume are related to ribosome biogenesis

(2019) Daniel Hammarström et al.   JOURNAL OF PHYSIOLOGY-LONDON

Acute extracellular matrix, inflammatory and MAPK response to lengthening contractions in elderly human skeletal muscle

(2018) Jacob R. Sorensen et al.   EXPERIMENTAL GERONTOLOGY

Resistance training in young men induces muscle transcriptome-wide changes associated with muscle structure and metabolism refining the response to exercise-induced stress

(2018) Felipe Damas et al.   EUROPEAN JOURNAL OF APPLIED PHYSIOLOGY

Age-specific response of skeletal muscle extracellular matrix to acute resistance exercise: A pilot study

(2018) Barbara Wessner et al.   European Journal of Sport Science

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

(2018) Miriam Payá-Milans et al.   GigaScience

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Rapid switch-off of the human myosin heavy chain IIX gene after heavy load muscle contractions is sustained for at least four days

(2017) J. L. Andersen et al.   SCANDINAVIAN JOURNAL OF MEDICINE & SCIENCE IN SPORTS

Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans

(2017) R. C. Laker et al.   Scientific Reports

Heterogeneity in resistance training-induced muscle strength and mass responses in men and women of different ages

(2016) Juha P. Ahtiainen et al.   AGE

Ribosome biogenesis may augment resistance training-induced myofiber hypertrophy and is required for myotube growth in vitro

(2016) Michael J. Stec et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

One Week of Bed Rest Leads to Substantial Muscle Atrophy and Induces Whole-Body Insulin Resistance in the Absence of Skeletal Muscle Lipid Accumulation

(2016) Marlou L. Dirks et al.   DIABETES

Dose-response relationship between weekly resistance training volume and increases in muscle mass: A systematic review and meta-analysis

(2016) Brad J. Schoenfeld et al.   JOURNAL OF SPORTS SCIENCES

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

(2016) Shiqi Cui et al.   Statistical Applications in Genetics and Molecular Biology

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

(2016) Shiqi Cui et al.   Statistical Applications in Genetics and Molecular Biology

Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness

(2016) Roland W. J. Hangelbroek et al.   Journal of Cachexia Sarcopenia and Muscle

Skeletal muscle homeostasis and plasticity in youth and ageing: impact of nutrition and exercise

(2015) M. S. Brook et al.   Acta Physiologica

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reliable determination of training-induced alterations in muscle fiber composition in human skeletal muscle using quantitative polymerase chain reaction

(2014) S. Ellefsen et al.   SCANDINAVIAN JOURNAL OF MEDICINE & SCIENCE IN SPORTS

Exercise Metabolism and the Molecular Regulation of Skeletal Muscle Adaptation

(2013) Brendan Egan et al.   Cell Metabolism

Transient transcriptional events in human skeletal muscle at the outset of concentric resistance exercise training

(2013) A. J. Murton et al.   JOURNAL OF APPLIED PHYSIOLOGY

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Molecular Networks of Human Muscle Adaptation to Exercise and Age

(2013) Bethan E. Phillips et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults

(2012) Ulrika Raue et al.   JOURNAL OF APPLIED PHYSIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Activation of nuclear factor-κB following muscle eccentric contractions in humans is localized primarily to skeletal muscle-residing pericytes

(2011) Robert D. Hyldahl et al.   FASEB JOURNAL

Sequenced response of extracellular matrix deadhesion and fibrotic regulators after muscle damage is involved in protection against future injury in human skeletal muscle

(2011) Abigail L. Mackey et al.   FASEB JOURNAL

Variability in training-induced skeletal muscle adaptation

(2010) James A. Timmons   JOURNAL OF APPLIED PHYSIOLOGY

High responders to resistance exercise training demonstrate differential regulation of skeletal muscle microRNA expression

(2010) Peter K. Davidsen et al.   JOURNAL OF APPLIED PHYSIOLOGY

Gene-family profiling: a normalization-free real-time RT-PCR approach with increased physiological resolution

(2010) Stian Ellefsen et al.   PHYSIOLOGICAL GENOMICS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Contraction intensity and feeding affect collagen and myofibrillar protein synthesis rates differently in human skeletal muscle

(2009) Lars Holm et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Global Gene Expression in Skeletal Muscle from Well-Trained Strength and Endurance Athletes

(2009) NIGEL K. STEPTO et al.   MEDICINE AND SCIENCE IN SPORTS AND EXERCISE

Improved normalization of real-time reverse transcriptase polymerase chain reaction data using an external RNA control

(2008) Stian Ellefsen et al.   ANALYTICAL BIOCHEMISTRY

IFN-β-regulated genes show abnormal expression in therapy-naïve relapsing–remitting MS mononuclear cells: Gene expression analysis employing all reported protein–protein interactions

(2008) Ken D. Yamaguchi et al.   JOURNAL OF NEUROIMMUNOLOGY