Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

[1]  Database resources of the National Center for Biotechnology Information , 2014, Nucleic Acids Res..

[2]  P. Robinson,et al.  Extension of the sheep sequence space using composite transcriptome assembly of RNA-Seq data in a sheep model for delayed bone healing , 2011 .

[3]  C. Wade,et al.  The sheep genome reference sequence: a work in progress. , 2010, Animal genetics.

[4]  J. Gorman,et al.  Elimination of ischemic mitral regurgitation does not alter long-term left ventricular remodeling in the ovine model. , 2010, The Annals of thoracic surgery.

[5]  G. Duda,et al.  Standard bone healing stages occur during delayed bone healing, albeit with a different temporal onset and spatial distribution of callus tissues. , 2010, Histology and histopathology.

[6]  J. Zwischenberger,et al.  A tetracycline analog improves acute respiratory distress syndrome survival in an ovine model. , 2010, The Annals of thoracic surgery.

[7]  L. Feuk,et al.  Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing , 2010, Genome Biology.

[8]  A. Ciccodicola,et al.  Uncovering the Complexity of Transcriptomes with RNA-Seq , 2010, Journal of biomedicine & biotechnology.

[9]  David B Goldstein,et al.  Screening the human exome: a comparison of whole genome and whole transcriptome sequencing , 2010, Genome Biology.

[10]  T. Nishimura,et al.  Reproductive Ability After Uterine Artery Embolization in a Sheep Model: Observation Over 2 Seasons , 2010, Reproductive Sciences.

[11]  Ying Li,et al.  De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis , 2010, BMC Genomics.

[12]  G. Duda,et al.  The early fracture hematoma and its potential role in fracture healing. , 2010, Tissue engineering. Part B, Reviews.

[13]  C. Clemens,et al.  Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing , 2010, Nucleic acids research.

[14]  Peter N. Robinson,et al.  GOing Bayesian: model-based gene set analysis of genome-scale data , 2010, Nucleic acids research.

[15]  Peter M. Rice,et al.  The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.

[16]  Peter Tiño,et al.  Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays , 2009, BMC Bioinformatics.

[17]  Georg N Duda,et al.  Differential regulation of blood vessel formation between standard and delayed bone healing , 2009, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[18]  G. Duda,et al.  Cellular composition of the initial fracture hematoma compared to a muscle hematoma: A study in sheep , 2009, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[19]  P. Robinson,et al.  Promiscuous and Depolarization‐Induced Immediate‐Early Response Genes Are Induced by Mechanical Strain of Osteoblasts , 2009, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[20]  Georg N Duda,et al.  The challenge of establishing preclinical models for segmental bone defect research. , 2009, Biomaterials.

[21]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[22]  Damian Smedley,et al.  BioMart – biological queries made easy , 2009, BMC Genomics.

[23]  Georg N Duda,et al.  Mechanical induction of critically delayed bone healing in sheep: radiological and biomechanical results. , 2008, Journal of biomechanics.

[24]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[25]  Martin Vingron,et al.  Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration , 2008, Bioinform..

[26]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[27]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[28]  F. Shapiro,et al.  Bone development and its relation to fracture repair. The role of mesenchymal osteoblasts and surface osteoblasts. , 2008, European cells & materials.

[29]  J. Zwischenberger,et al.  Arteriovenous CO2 Removal Improves Survival Compared to High Frequency Percussive and Low Tidal Volume Ventilation in a Smoke/Burn Sheep Acute Respiratory Distress Syndrome Model , 2007, Annals of surgery.

[30]  E. Kirkness,et al.  Using comparative genomics to reorder the human genome sequence into a virtual sheep genome , 2007, Genome Biology.

[31]  P. Robinson,et al.  Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep , 2006, BMC Genomics.

[32]  A. Reddi,et al.  Global gene profiling reveals a downregulation of BMP gene expression in experimental atrophic nonunions compared to standard healing fractures , 2006, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[33]  Georg N Duda,et al.  Instability prolongs the chondral phase during bone healing in sheep. , 2006, Bone.

[34]  G N Duda,et al.  The course of bone healing is influenced by the initial shear fixation stability , 2005, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[35]  Georg N Duda,et al.  Initial vascularization and tissue differentiation are influenced by fixation stability , 2005, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[36]  R. Shofti,et al.  The sheep as a model for coronary artery bypass surgery , 2004, Laboratory animals.

[37]  R. Meyer,et al.  Gene Expression in Older Rats with Delayed Union of Femoral Fractures , 2003, The Journal of bone and joint surgery. American volume.

[38]  M. Spector,et al.  Expression of smooth muscle actin in connective tissue cells participating in fracture healing in a murine model. , 2002, Bone.

[39]  D. Hu,et al.  Molecular aspects of healing in stabilized and non‐stabilized fractures , 2001, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

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

[41]  A. van Lingen,et al.  New segmental long bone defect model in sheep: Quantitative analysis of healing with dual energy X‐ray absorptiometry , 1999, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.

[42]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[44]  A. Piancastelli,et al.  Mineral evolution of bone. , 1996, Biomaterials.

[45]  J. Wark,et al.  The potential of sheep for the study of osteopenia: current status and comparison with other animal models. , 1995, Bone.

[46]  K. Stürmer,et al.  [New aspects of closed intramedullary nailing and marrow cavity reaming in animal experiments. I. The tibia of the sheep, as a model for intramedullar nailing (author's transl)]. , 1980, Unfallheilkunde.

[47]  Georg N Duda,et al.  Insight into the molecular pathophysiology of delayed bone healing in a sheep model. , 2010, Tissue engineering. Part A.

[48]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[49]  Gang Wang,et al.  ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs) , 2007, BMC Genomics.