Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

[1]  Jason Brunson,et al.  ggalluvial: Layered Grammar for Alluvial Plots , 2020, J. Open Source Softw..

[2]  Johannes Griss,et al.  ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis , 2020, Molecular & Cellular Proteomics.

[3]  Bo Peng,et al.  Erythropoietin and its derivatives: from tissue protection to immune regulation , 2020, Cell Death & Disease.

[4]  Cecelia P. Tamburro,et al.  Genomic Medicine Year in Review: 2019. , 2019, American journal of human genetics.

[5]  P. Ratcliffe,et al.  Mechanisms of hypoxia signalling: new implications for nephrology , 2019, Nature Reviews Nephrology.

[6]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[7]  Gary D Bader,et al.  Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap , 2019, Nature Protocols.

[8]  The Gene Ontology Consortium,et al.  The Gene Ontology Resource: 20 years and still GOing strong , 2018, Nucleic Acids Res..

[9]  S. Wingett,et al.  FastQ Screen: A tool for multi-genome mapping and quality control , 2018, F1000Research.

[10]  Joseph G Ibrahim,et al.  Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences , 2018, bioRxiv.

[11]  J. Shendure,et al.  DNA sequencing at 40: past, present and future , 2017, Nature.

[12]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[13]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[14]  R. Durbin,et al.  Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly , 2016, bioRxiv.

[15]  Gary D. Bader,et al.  AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations , 2016, F1000Research.

[16]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[17]  B. Klaus An end to end workflow for differential gene expression using Affymetrix microarrays , 2016, F1000Research.

[18]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.

[19]  G. Smyth,et al.  ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION. , 2016, The annals of applied statistics.

[20]  Rajan K. Patel,et al.  Blood transcriptional signature of recombinant human erythropoietin administration and implications for antidoping strategies. , 2016, Physiological genomics.

[21]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. , 2015, F1000Research.

[22]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[23]  C. Wilke Streamlined Plot Theme and Plot Annotations for 'ggplot2' , 2015 .

[24]  K. Maiese Erythropoietin and diabetes mellitus. , 2015, World journal of diabetes.

[25]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[26]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[27]  D. Tenen,et al.  Downregulation of RUNX1/CBFβ by MLL fusion proteins enhances hematopoietic stem cell self-renewal. , 2014, Blood.

[28]  Evelien Vaes,et al.  Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes , 2014, BMC Bioinformatics.

[29]  P. Mombaerts,et al.  Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes , 2014, BMC Bioinformatics.

[30]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[31]  Rafael C. Jimenez,et al.  The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..

[32]  M. Kurokawa,et al.  A role for RUNX1 in hematopoiesis and myeloid leukemia , 2013, International Journal of Hematology.

[33]  Rajan K. Patel,et al.  Haemoglobin Mass and Running Time Trial Performance after Recombinant Human Erythropoietin Administration in Trained Men , 2013, PloS one.

[34]  J. Massagué TGFβ signalling in context , 2012, Nature Reviews Molecular Cell Biology.

[35]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[36]  Sorin Draghici,et al.  Down-weighting overlapping genes improves gene set analysis , 2012, BMC Bioinformatics.

[37]  B. May O2/CO2 exchange in erythrocytes , 2012 .

[38]  Martial Saugy,et al.  The athlete biological passport. , 2011, Clinical chemistry.

[39]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[40]  W. Jelkmann Regulation of erythropoietin production , 2011, The Journal of physiology.

[41]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[42]  Wei Shi,et al.  Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips , 2010, Nucleic acids research.

[43]  Rafael A. Irizarry,et al.  A framework for oligonucleotide microarray preprocessing , 2010, Bioinform..

[44]  David M Sabatini,et al.  Defining the role of mTOR in cancer. , 2007, Cancer cell.

[45]  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.

[46]  P. Ghezzi,et al.  Erythropoietin as an antiapoptotic, tissue-protective cytokine , 2004, Cell Death and Differentiation.

[47]  S. Ogawa,et al.  Runx1/AML-1 Ranks as a Master Regulator of Adult Hematopoiesis , 2004, Cell cycle.

[48]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[49]  M. Hofker Faculty Opinions recommendation of PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. , 2003 .

[50]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[51]  F. Lasne,et al.  Recombinant erythropoietin in urine , 2000, Nature.

[52]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[53]  L.,et al.  HEALTH ADMINISTRATION , 1939, The New Zealand medical journal.

[54]  S. Wingett,et al.  FastQ Screen: A tool for multi-genome mapping and quality control , 2018, F1000Research.

[55]  Xing Li,et al.  Quality control of RNA-seq experiments. , 2015, Methods in molecular biology.

[56]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[57]  Dong-er Zhang,et al.  RUNX1 and RUNX1-ETO: roles in hematopoiesis and leukemogenesis. , 2012, Frontiers in bioscience.

[58]  J. Leek Surrogate variable analysis , 2007 .

[59]  D. Holdstock Past, present--and future? , 2005, Medicine, conflict, and survival.