Daniel Bottomly

Summary

Affiliation: Oregon Health and Science University
Country: USA

Publications

  1. pmc plethy: management of whole body plethysmography data in R
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US
    BMC Bioinformatics 16:134. 2015
  2. pmc HitWalker: variant prioritization for personalized functional cancer genomics
    Daniel Bottomly
    Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
    Bioinformatics 29:509-10. 2013
  3. pmc Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, Oregon, United States of America
    PLoS ONE 6:e17820. 2011
  4. pmc High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
    Nicole A R Walter
    Research and Development Service, Portland VA Medical Center, Portland, OR, USA
    BMC Genomics 10:379. 2009
  5. pmc Therapeutically Targetable ALK Mutations in Leukemia
    Julia E Maxson
    Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, Oregon
    Cancer Res 75:2146-50. 2015
  6. pmc The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits
    Robert Hitzemann
    Portland Alcohol Research Center, Veterans Affairs Medical Center, Portland, 97239, OR, USA
    Mamm Genome 25:12-22. 2014
  7. pmc Utilizing RNA-Seq data for de novo coexpression network inference
    Ovidiu D Iancu
    Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239 3098, USA
    Bioinformatics 28:1592-7. 2012
  8. pmc Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML
    Julia E Maxson
    Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
    N Engl J Med 368:1781-90. 2013
  9. pmc Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
    Nucleic Acids Res 38:5735-45. 2010
  10. doi request reprint Analysis considerations for utilizing RNA-Seq to characterize the brain transcriptome
    Christina L Zheng
    Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, USA Knight Cancer Institute, Oregon Health, Oregon Health and Science University, Portland, Oregon, USA Electronic address
    Int Rev Neurobiol 116:21-54. 2014

Collaborators

Detail Information

Publications12

  1. pmc plethy: management of whole body plethysmography data in R
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US
    BMC Bioinformatics 16:134. 2015
    ....
  2. pmc HitWalker: variant prioritization for personalized functional cancer genomics
    Daniel Bottomly
    Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
    Bioinformatics 29:509-10. 2013
    ..In addition to a ranked list of variants, we have also devised a simple shortest path-based approach of visualizing the results in an intuitive manner to provide biological interpretation...
  3. pmc Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, Oregon, United States of America
    PLoS ONE 6:e17820. 2011
    ....
  4. pmc High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
    Nicole A R Walter
    Research and Development Service, Portland VA Medical Center, Portland, OR, USA
    BMC Genomics 10:379. 2009
    ..With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses...
  5. pmc Therapeutically Targetable ALK Mutations in Leukemia
    Julia E Maxson
    Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, Oregon
    Cancer Res 75:2146-50. 2015
    ..On the basis of our results, we propose that tumors harboring ALK mutations may be therapeutically tractable for personalized treatment of certain aggressive leukemias with ALK inhibitors...
  6. pmc The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits
    Robert Hitzemann
    Portland Alcohol Research Center, Veterans Affairs Medical Center, Portland, 97239, OR, USA
    Mamm Genome 25:12-22. 2014
    ..Each of these issues is discussed, providing an initial framework for complex cross study design and planning. ..
  7. pmc Utilizing RNA-Seq data for de novo coexpression network inference
    Ovidiu D Iancu
    Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239 3098, USA
    Bioinformatics 28:1592-7. 2012
    ..Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal samples, derived its network properties and compared it with microarray-based networks...
  8. pmc Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML
    Julia E Maxson
    Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
    N Engl J Med 368:1781-90. 2013
    ....
  9. pmc Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq
    Daniel Bottomly
    Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
    Nucleic Acids Res 38:5735-45. 2010
    ..Our work provides evidence that Wnt/β-catenin and mitogen signaling pathways intersect directly to regulate a defined set of target genes...
  10. doi request reprint Analysis considerations for utilizing RNA-Seq to characterize the brain transcriptome
    Christina L Zheng
    Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, USA Knight Cancer Institute, Oregon Health, Oregon Health and Science University, Portland, Oregon, USA Electronic address
    Int Rev Neurobiol 116:21-54. 2014
    ..We highlight these to provide an overview of their importance and the impact they can have on downstream interpretation of the brain transcriptome. ..
  11. pmc Androgen receptor promotes ligand-independent prostate cancer progression through c-Myc upregulation
    Lina Gao
    Division of Hematology Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
    PLoS ONE 8:e63563. 2013
    ..Our results define a new link between two critical proteins in prostate cancer - AR and c-Myc - and demonstrate the potential of AR and c-Myc-directed therapies to improve prostate cancer control...