Anis Karimpour-Fard

Summary

Affiliation: University of Colorado Health Sciences Center
Country: USA

Publications

  1. pmc Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 8:393. 2007
  2. pmc A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray
    Danielle L Leiske
    Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
    BMC Genomics 7:72. 2006
  3. pmc The topology of the bacterial co-conserved protein network and its implications for predicting protein function
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 9:313. 2008
  4. pmc Predicting protein linkages in bacteria: which method is best depends on task
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Bioinformatics 9:397. 2008
  5. pmc Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation
    Alkesh Jani
    Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Physiol Genomics 44:717-27. 2012
  6. pmc Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation
    Allyson G Hindle
    Dept of Cell and Developmental Biology, PO Box 6511, MS 8010, Univ of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
    Am J Physiol Regul Integr Comp Physiol 301:R1440-52. 2011
  7. pmc Multistate proteomics analysis reveals novel strategies used by a hibernator to precondition the heart and conserve ATP for winter heterothermy
    Katharine R Grabek
    Human Medical Genetics Program, Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Physiol Genomics 43:1263-75. 2011
  8. pmc Cross-species cluster co-conservation: a new method for generating protein interaction networks
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 8:R185. 2007
  9. pmc Metabolic changes associated with the long winter fast dominate the liver proteome in 13-lined ground squirrels
    Allyson G Hindle
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
    Physiol Genomics 46:348-61. 2014
  10. pmc A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Hum Genomics 4:421-7. 2010

Collaborators

Detail Information

Publications16

  1. pmc Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 8:393. 2007
    ..The Co-Conservation method, also known as the Phylogenetic profiles method, is a well-established computational tool for predicting functional relationships between proteins...
  2. pmc A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray
    Danielle L Leiske
    Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
    BMC Genomics 7:72. 2006
    ..Moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose genomes may differ substantially in characteristics directly affecting microarray performance...
  3. pmc The topology of the bacterial co-conserved protein network and its implications for predicting protein function
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 9:313. 2008
    ..coli K12. Next, we demonstrate one way in which network connectivity measures and global and local function distribution can be exploited to predict protein function for previously uncharacterized proteins...
  4. pmc Predicting protein linkages in bacteria: which method is best depends on task
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Bioinformatics 9:397. 2008
    ..We also review many previous treatments of these prediction methods, use the latest available annotations, and offer a number of new observations...
  5. pmc Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation
    Alkesh Jani
    Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Physiol Genomics 44:717-27. 2012
    ....
  6. pmc Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation
    Allyson G Hindle
    Dept of Cell and Developmental Biology, PO Box 6511, MS 8010, Univ of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
    Am J Physiol Regul Integr Comp Physiol 301:R1440-52. 2011
    ..This, along with winter elevation of TCA cycle enzymes, suggests that hindlimb muscles are primed for rapid energy production and that carbohydrates are an important fuel for shivering thermogenesis...
  7. pmc Multistate proteomics analysis reveals novel strategies used by a hibernator to precondition the heart and conserve ATP for winter heterothermy
    Katharine R Grabek
    Human Medical Genetics Program, Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Physiol Genomics 43:1263-75. 2011
    ....
  8. pmc Cross-species cluster co-conservation: a new method for generating protein interaction networks
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 8:R185. 2007
    ..We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation...
  9. pmc Metabolic changes associated with the long winter fast dominate the liver proteome in 13-lined ground squirrels
    Allyson G Hindle
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
    Physiol Genomics 46:348-61. 2014
    ..Rather, acetylation contributed to seasonal differences, being highest in winter (specifically in torpor), consistent with fasting physiology and decreased abundance of the mitochondrial deacetylase, SIRT3. ..
  10. pmc A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Hum Genomics 4:421-7. 2010
    ..In this paper, most of the well known algorithms, analysis software and the limitations of that software will be briefly reviewed...
  11. pmc Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development
    Suparna A Sarkar
    Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
    Pancreas 41:962-9. 2012
    ..This study investigated the utility of advanced computational techniques to large-scale genome-based data to identify novel genes that govern murine pancreatic development...
  12. pmc Temporal analysis of mRNA and miRNA expression in transgenic mice overexpressing Arg- and Gly389 polymorphic variants of the β1-adrenergic receptor
    Karen Dockstader
    Division of Cardiology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Physiol Genomics 43:1294-306. 2011
    ....
  13. pmc Gene copy number variation spanning 60 million years of human and primate evolution
    Laura Dumas
    Human Medical Genetics Program, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA
    Genome Res 17:1266-77. 2007
    ....
  14. pmc Regional differences in subcutaneous adipose tissue gene expression
    Charles W Rehrer
    Division of Endocrinology, Metabolism and Diabetes, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
    Obesity (Silver Spring) 20:2168-73. 2012
    ..These results in normal weight healthy women provide a new perspective on regional differences in SAT biology that may have pathophysiologic implications when adiposity increases...
  15. pmc Metabolic cycles in a circannual hibernator
    L Elaine Epperson
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
    Physiol Genomics 43:799-807. 2011
    ..This finding provides new data that strongly support the predictions of a long-standing hypothesis that periodic arousals are necessary to restore metabolic homeostasis...
  16. pmc Lineage-specific gene duplication and loss in human and great ape evolution
    Andrew Fortna
    Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, Colorado, USA
    PLoS Biol 2:E207. 2004
    ....