Skeletal muscle transcriptome in healthy aging

[1]  R. Irizarry.  ggplot2 , 2019, Introduction to Data Science.

[2]  W. Kraus,et al.  Longevity‐related molecular pathways are subject to midlife “switch” in humans , 2019, Aging cell.

[3]  L. Ferrucci,et al.  Physical Activity Associated Proteomics of Skeletal Muscle: Being Physically Active in Daily Life May Protect Skeletal Muscle From Aging , 2019, Front. Physiol..

[4]  J. Kobarg,et al.  Fasciculation and elongation zeta proteins 1 and 2: From structural flexibility to functional diversity , 2019, World journal of biological chemistry.

[5]  Hong Chen,et al.  Genetic Variant of MYLK4 Gene and its Association with Growth Traits in Chinese Cattle , 2019, Animal biotechnology.

[6]  R. Sebra,et al.  Genome organization and DNA accessibility control antigenic variation in trypanosomes , 2018, Nature.

[7]  A. Zhavoronkov,et al.  Machine Learning on Human Muscle Transcriptomic Data for Biomarker Discovery and Tissue-Specific Drug Target Identification , 2018, Front. Genet..

[8]  A. Moore,et al.  Plasma proteomic signature of age in healthy humans , 2018, Aging cell.

[9]  Mathias Wilhelm,et al.  A deep proteome and transcriptome abundance atlas of 29 healthy human tissues , 2018, bioRxiv.

[10]  S. Kritchevsky,et al.  Cellular Senescence Biomarker p16INK4a+ Cell Burden in Thigh Adipose is Associated With Poor Physical Function in Older Women , 2018, The journals of gerontology. Series A, Biological sciences and medical sciences.

[11]  G. Sapkota,et al.  The DUF1669 domain of FAM83 family proteins anchor casein kinase 1 isoforms , 2018, Science Signaling.

[12]  Gregor Bieri,et al.  Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain , 2018, Cell reports.

[13]  Hsuan-Yu Chen,et al.  Differences in the frequency of Alzheimer's disease‐associated genomic variations in populations of different races , 2017, Geriatrics & gerontology international.

[14]  M. Tsai,et al.  Dysregulation of nuclear receptor COUP-TFII impairs skeletal muscle development , 2017, Scientific Reports.

[15]  E. Ingelsson,et al.  Fitness, Physical Activity, and Cardiovascular Disease: Longitudinal and Genetic Analyses in the UK Biobank Study , 2017, bioRxiv.

[16]  X. An,et al.  Ten-Eleven Translocation-2 (Tet2) Is Involved in Myogenic Differentiation of Skeletal Myoblast Cells in Vitro , 2017, Scientific Reports.

[17]  Rickey E Carter,et al.  Enhanced Protein Translation Underlies Improved Metabolic and Physical Adaptations to Different Exercise Training Modes in Young and Old Humans. , 2017, Cell metabolism.

[18]  A. Zarbock,et al.  Skap2 is required for β2 integrin–mediated neutrophil recruitment and functions , 2017, The Journal of experimental medicine.

[19]  Zhanjiang Liu,et al.  Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish , 2017, Molecular Genetics and Genomics.

[20]  S. Mowla,et al.  Alternative splicing of the OCC-1 gene generates three splice variants and a novel exonic microRNA, which regulate the Wnt signaling pathway , 2017, RNA.

[21]  M. Tajiri,et al.  The Muscular Dystrophy Gene TMEM5 Encodes a Ribitol β1,4-Xylosyltransferase Required for the Functional Glycosylation of Dystroglycan* , 2016, The Journal of Biological Chemistry.

[22]  M. Tsai,et al.  COUP-TFII regulates satellite cell function and muscular dystrophy. , 2016, The Journal of clinical investigation.

[23]  G. Narasimhan,et al.  Gene expression patterns in transgenic mouse models of hypertrophic cardiomyopathy caused by mutations in myosin regulatory light chain. , 2016, Archives of biochemistry and biophysics.

[24]  Tsippi Iny Stein,et al.  The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses , 2016, Current protocols in bioinformatics.

[25]  C. Mantzoros,et al.  Ciliary neurotrophic factor upregulates follistatin and Pak1, causes overexpression of muscle differentiation related genes and downregulation of established atrophy mediators in skeletal muscle. , 2016, Metabolism: clinical and experimental.

[26]  X. Chen,et al.  Epigenomic Elements Analyses for Promoters Identify ESRRG as a New Susceptibility Gene for Obesity-related Traits , 2016, International Journal of Obesity.

[27]  J. Timmons,et al.  Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness , 2016, Journal of cachexia, sarcopenia and muscle.

[28]  Fang Yu Chou,et al.  Crim1 has cell-autonomous and paracrine roles during embryonic heart development , 2016, Scientific Reports.

[29]  L. Groop,et al.  A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging , 2015, Skeletal Muscle.

[30]  S. Bicciato,et al.  The calcineurin-NFAT pathway controls activity-dependent circadian gene expression in slow skeletal muscle , 2015, Molecular metabolism.

[31]  K. Wagner,et al.  Mammalian Mss51 is a Skeletal Muscle-Specific Gene Modulating Cellular Metabolism , 2015, Journal of neuromuscular diseases.

[32]  C. Gieger,et al.  Identification of Immune-Relevant Factors Conferring Sarcoidosis Genetic Risk. , 2015, American journal of respiratory and critical care medicine.

[33]  W. Kraus,et al.  A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status , 2015, Genome Biology.

[34]  John M. Shelton,et al.  A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance , 2015, Cell.

[35]  M. White.  IRS2 integrates insulin/IGF1 signalling with metabolism, neurodegeneration and longevity , 2014, Diabetes, obesity & metabolism.

[36]  C. Cooper,et al.  Lean Mass, Muscle Strength and Gene Expression in Community Dwelling Older Men: Findings from the Hertfordshire Sarcopenia Study (HSS) , 2014, Calcified Tissue International.

[37]  Hee-Jin Kim,et al.  Genome-wide profiling of the microRNA-mRNA regulatory network in skeletal muscle with aging , 2014, Aging.

[38]  F. Liu,et al.  Tissue‐specific insulin signaling in the regulation of metabolism and aging , 2014, IUBMB life.

[39]  C. Hoffmann,et al.  Human Muscle LIM Protein Dimerizes along the Actin Cytoskeleton and Cross-Links Actin Filaments , 2014, Molecular and Cellular Biology.

[40]  J. Montero,et al.  RNA-sequencing analysis reveals new alterations in cardiomyocyte cytoskeletal genes in patients with heart failure , 2014, Laboratory Investigation.

[41]  L. Ferrucci,et al.  “IDEAL” Aging Is Associated with Lower Resting Metabolic Rate: The Baltimore Longitudinal Study of Aging , 2014, Journal of the American Geriatrics Society.

[42]  Shaodong Guo.  Insulin signaling, resistance, and the metabolic syndrome: insights from mouse models into disease mechanisms. , 2014, The Journal of endocrinology.

[43]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[44]  Aristotelis A. Chatziioannou,et al.  Identifying gender independent biomarkers responsible for human muscle aging using microarray data , 2013, 13th IEEE International Conference on BioInformatics and BioEngineering.

[45]  Yu Jin,et al.  Ten-Eleven Translocation-2 (TET2) Is a Master Regulator of Smooth Muscle Cell Plasticity , 2013, Circulation.

[46]  Ruofeng Wen,et al.  Quantitative Proteomics Using 15N SILAC Mouse , 2013 .

[47]  Rick B. Vega,et al.  Nuclear receptor/microRNA circuitry links muscle fiber type to energy metabolism. , 2013, The Journal of clinical investigation.

[48]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[49]  C. Bouchard,et al.  Molecular Networks of Human Muscle Adaptation to Exercise and Age , 2013, PLoS genetics.

[50]  R. Myers,et al.  Early de novo DNA methylation and prolonged demethylation in the muscle lineage , 2013, Epigenetics.

[51]  Andrej Sali,et al.  Discovery of potent, selective multidrug and toxin extrusion transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling. , 2013, Journal of medicinal chemistry.

[52]  Karen Cheng,et al.  Loss of CDKN2B Promotes p53-Dependent Smooth Muscle Cell Apoptosis and Aneurysm Formation , 2013, Arteriosclerosis, thrombosis, and vascular biology.

[53]  K. Flaherty,et al.  Sarcolipin is a newly identified regulator of muscle-based thermogenesis in mammals , 2012, Nature Medicine.

[54]  G. Galloway,et al.  Association between congenital defects in papillary outgrowth and functional obstruction in Crim1 mutant mice , 2012, The Journal of pathology.

[55]  Kyudong Han,et al.  Identification of ORF sequences and exercise-induced expression change in thoroughbred horse OXCT1 gene. , 2012, Gene.

[56]  Xia Yang.  Use of Functional Genomics to Identify Candidate Genes Underlying Human Genetic Association Studies of Vascular Diseases , 2012, Arteriosclerosis, thrombosis, and vascular biology.

[57]  S. Jakobs,et al.  MINOS1 is a conserved component of mitofilin complexes and required for mitochondrial function and cristae organization , 2012, Molecular biology of the cell.

[58]  S. Bandinelli,et al.  Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing , 2011, Aging cell.

[59]  S. Jiang,et al.  Gene expression profiling suggests a pathological role of human bone marrow-derived mesenchymal stem cells in aging-related skeletal diseases , 2011, Aging.

[60]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[61]  K. Esser,et al.  Aging and microRNA expression in human skeletal muscle: a microarray and bioinformatics analysis. , 2011, Physiological genomics.

[62]  Tom Druet,et al.  Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature , 2011, Nature Genetics.

[63]  R. Hendrickson,et al.  Evaluation of early biomarkers of muscle anabolic response to testosterone , 2011, Journal of cachexia, sarcopenia and muscle.

[64]  Zhiyong Cheng,et al.  Insulin Receptor Substrates Irs1 and Irs2 Coordinate Skeletal Muscle Growth and Metabolism via the Akt and AMPK Pathways , 2010, Molecular and Cellular Biology.

[65]  R. Balice-Gordon,et al.  Investigation of LGI1 as the antigen in limbic encephalitis previously attributed to potassium channels: a case series , 2010, The Lancet Neurology.

[66]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[67]  Wang Hua-qiao,et al.  The expression of EFEMP1 in cervical carcinoma and its relationship with prognosis. , 2010, Gynecologic oncology.

[68]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[69]  Markus G. Manz,et al.  Development of Monocytes, Macrophages, and Dendritic Cells , 2010, Science.

[70]  X. Cui,et al.  Differential genomic responses in old vs. young humans despite similar levels of modest muscle damage after resistance loading. , 2010, Physiological genomics.

[71]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[72]  S. Mekchay,et al.  Proteome Changes in Thai Indigenous Chicken Muscle during Growth Period , 2009, International journal of biological sciences.

[73]  Saskia M Pasedag,et al.  Cell Adhesion and Transcriptional Activity - Defining the Role of the Novel Protooncogene LPP. , 2009, Translational oncology.

[74]  D. Desruisseau,et al.  Skeletal Muscle Contractile Gene (TNNT3, MYH3, TPM2) Mutations Not Found in Vertical Talus or Clubfoot , 2009, Clinical orthopaedics and related research.

[75]  M. Sancristobal,et al.  A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig. , 2008, Animal genetics.

[76]  Takako Sasaki,et al.  Lack of fibulin-3 causes early aging and herniation, but not macular degeneration in mice. , 2007, Human molecular genetics.

[77]  A. Berns,et al.  p15Ink4b is a critical tumour suppressor in the absence of p16Ink4a , 2007, Nature.

[78]  G. Guzman,et al.  Fast skeletal muscle regulatory light chain is required for fast and slow skeletal muscle development , 2007, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[79]  Alan Hubbard,et al.  Resistance Exercise Reverses Aging in Human Skeletal Muscle , 2007, PloS one.

[80]  J. Vajsar,et al.  Walker-Warburg syndrome , 2006, Orphanet journal of rare diseases.

[81]  H. Koistinen,et al.  siRNA-based gene silencing reveals specialized roles of IRS-1/Akt2 and IRS-2/Akt1 in glucose and lipid metabolism in human skeletal muscle. , 2006, Cell metabolism.

[82]  T. Yoshida,et al.  LPP Expression During In Vitro Smooth Muscle Differentiation and Stent-Induced Vascular Injury , 2006, Circulation research.

[83]  D. Hume,et al.  The mononuclear phagocyte system. , 2006, Current opinion in immunology.

[84]  M. L. Greenberg,et al.  Genetic Perturbation of Glycolysis Results in Inhibition of de Novo Inositol Biosynthesis* , 2005, Journal of Biological Chemistry.

[85]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[86]  R. Davoli,et al.  Study of candidate genes for glycolytic potential of porcine skeletal muscle: identification and analysis of mutations, linkage and physical mapping and association with meat quality traits in pigs , 2004, Cytogenetic and Genome Research.

[87]  Miguel Vicente-Manzanares,et al.  Role of the cytoskeleton during leukocyte responses , 2004, Nature Reviews Immunology.

[88]  Y. Yamakoshi,et al.  AMELOGENESIS IMPERFECTA , 2003 .

[89]  G. Paolisso,et al.  Glucose regulation and oxidative stress in healthy centenarians , 2003, Experimental Gerontology.

[90]  D. Maclennan,et al.  Sarcolipin Overexpression in Rat Slow Twitch Muscle Inhibits Sarcoplasmic Reticulum Ca2+ Uptake and Impairs Contractile Function* , 2002, The Journal of Biological Chemistry.

[91]  W. Hauser,et al.  Mutations in LGI1 cause autosomal-dominant partial epilepsy with auditory features , 2002, Nature Genetics.

[92]  K. Burridge,et al.  Leukocyte transendothelial migration: orchestrating the underlying molecular machinery. , 2001, Current Opinion in Cell Biology.

[93]  A. Wei,et al.  Molecular Cloning and Functional Expression of KCNQ5, a Potassium Channel Subunit That May Contribute to Neuronal M-current Diversity* , 2000, The Journal of Biological Chemistry.

[94]  G. Lanfranchi,et al.  TUBA8: A new tissue-specific isoform of alpha-tubulin that is highly conserved in human and mouse. , 2000, Biochemical and biophysical research communications.

[95]  G. Kolle,et al.  CRIM1, a novel gene encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in vertebrate CNS development and organogenesis , 2000, Mechanisms of Development.

[96]  X. Estivill,et al.  Cloning, expression and chromosomal localization of a human testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene. , 1999, Gene.

[97]  G. Shulman,et al.  Disruption of IRS-2 causes type 2 diabetes in mice , 1998, Nature.

[98]  C. Kahn,et al.  Differential regulation of insulin receptor substrates-1 and -2 (IRS-1 and IRS-2) and phosphatidylinositol 3-kinase isoforms in liver and muscle of the obese diabetic (ob/ob) mouse. , 1997, The Journal of clinical investigation.

[99]  W. Ray,et al.  On the origin of the lactate dehydrogenase induced rate effect. , 1984, Biochemistry.

[100]  Meeri Pekkarinen,et al.  Preprocessing and analysis of single-cell RNA-sequencing data , 2018 .

[101]  T. Lumley,et al.  gplots: Various R Programming Tools for Plotting Data , 2015 .

[102]  W. Huber,et al.  Inferring differential exon usage in RNA-Seq data with the DEXSeq package , 2015 .

[103]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[104]  Jisi Ma,et al.  Molecular cloning, sequence identification and expression analysis of novel caprine MYLPF gene , 2012, Molecular Biology Reports.

[105]  Claude Bouchard,et al.  A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype. , 2011, Journal of applied physiology.