John R Walker

Summary

Affiliation: Genomics Institute of the Novartis Research Foundation
Country: USA

Publications

  1. ncbi request reprint Databases of free expression
    John R Walker
    Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
    Mamm Genome 17:1141-6. 2006
  2. pmc A novel approach to investigate tissue-specific trinucleotide repeat instability
    Jong Min Lee
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
    BMC Syst Biol 4:29. 2010
  3. ncbi request reprint Conditioned opioid withdrawal decreases nociceptin/orphanin FQ levels in the frontal cortex and olfactory tubercle
    John R Walker
    Department of Neuropharmacology, The Scripps Research Institute, La Jolla, CA, USA
    Neuropsychopharmacology 27:203-11. 2002
  4. pmc Applications of a rat multiple tissue gene expression data set
    John R Walker
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Genome Res 14:742-9. 2004
  5. pmc FGFR2 promotes breast tumorigenicity through maintenance of breast tumor-initiating cells
    Sungeun Kim
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS ONE 8:e51671. 2013
  6. doi request reprint Combination therapy targeting both tumor-initiating and differentiated cell populations in prostate carcinoma
    Anna Dubrovska
    The Scripps Research Institute, La Jolla, California 92037, USA
    Clin Cancer Res 16:5692-702. 2010
  7. pmc Gene set enrichment in eQTL data identifies novel annotations and pathway regulators
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS Genet 4:e1000070. 2008
  8. pmc Identification of pathogen genomic variants through an integrated pipeline
    Micah J Manary
    Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
    BMC Bioinformatics 15:63. 2014
  9. pmc A small molecule accelerates neuronal differentiation in the adult rat
    Heiko Wurdak
    The Skaggs Institute of Chemical Biology and Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 107:16542-7. 2010
  10. ncbi request reprint Categorically distinct acute stressors elicit dissimilar transcriptional profiles in the paraventricular nucleus of the hypothalamus
    Teresa M Reyes
    Laboratory of Neuronal Structure and Function, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    J Neurosci 23:5607-16. 2003

Collaborators

Detail Information

Publications42

  1. ncbi request reprint Databases of free expression
    John R Walker
    Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
    Mamm Genome 17:1141-6. 2006
    ..This review highlights the current features and describes examples of two broad categories of mammalian microarray databases: tissue gene expression databases and data warehouses...
  2. pmc A novel approach to investigate tissue-specific trinucleotide repeat instability
    Jong Min Lee
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
    BMC Syst Biol 4:29. 2010
    ..However progress in this area has been hampered by the lack of sensitive high-throughput instability quantification methods and global approaches to identify the underlying factors...
  3. ncbi request reprint Conditioned opioid withdrawal decreases nociceptin/orphanin FQ levels in the frontal cortex and olfactory tubercle
    John R Walker
    Department of Neuropharmacology, The Scripps Research Institute, La Jolla, CA, USA
    Neuropsychopharmacology 27:203-11. 2002
    ..These results shed light on adaptations of endogenous opioid systems to conditioned cues, stress, and withdrawal, all factors that play a role in motivating drug intake...
  4. pmc Applications of a rat multiple tissue gene expression data set
    John R Walker
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Genome Res 14:742-9. 2004
    ..All of these applications of multiple tissue gene expression data sets will play a role in functionally annotating the rat genome...
  5. pmc FGFR2 promotes breast tumorigenicity through maintenance of breast tumor-initiating cells
    Sungeun Kim
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS ONE 8:e51671. 2013
    ....
  6. doi request reprint Combination therapy targeting both tumor-initiating and differentiated cell populations in prostate carcinoma
    Anna Dubrovska
    The Scripps Research Institute, La Jolla, California 92037, USA
    Clin Cancer Res 16:5692-702. 2010
    ..Many studies have sought to determine the underlying differences between bulk tumor and cancer stem cells...
  7. pmc Gene set enrichment in eQTL data identifies novel annotations and pathway regulators
    Chunlei Wu
    Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
    PLoS Genet 4:e1000070. 2008
    ..We believe that the specific molecular hypotheses generated in this study will reveal many additional pathway members and regulators, and that the analysis approaches described herein will be broadly applicable to other eQTL data sets...
  8. pmc Identification of pathogen genomic variants through an integrated pipeline
    Micah J Manary
    Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
    BMC Bioinformatics 15:63. 2014
    ..We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events...
  9. pmc A small molecule accelerates neuronal differentiation in the adult rat
    Heiko Wurdak
    The Skaggs Institute of Chemical Biology and Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 107:16542-7. 2010
    ..Our findings indicate that KHS101 accelerates neuronal differentiation by interaction with TACC3 and may provide a basis for pharmacological intervention directed at endogenous NPCs...
  10. ncbi request reprint Categorically distinct acute stressors elicit dissimilar transcriptional profiles in the paraventricular nucleus of the hypothalamus
    Teresa M Reyes
    Laboratory of Neuronal Structure and Function, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    J Neurosci 23:5607-16. 2003
    ..These global transcriptional profiles inform the search for early (transcription factors) and late (target genes) mechanisms in the modulation of PVH, and generalized CNS, responses to categorically distinct stressors...
  11. pmc Aryl hydrocarbon receptor antagonists promote the expansion of human hematopoietic stem cells
    Anthony E Boitano
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 329:1345-8. 2010
    ..Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy...
  12. pmc Imaging of Plasmodium liver stages to drive next-generation antimalarial drug discovery
    Stephan Meister
    Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
    Science 334:1372-7. 2011
    ..The open-source chemical tools resulting from our effort provide starting points for future drug discovery programs, as well as opportunities for researchers to investigate the biology of exo-erythrocytic forms...
  13. ncbi request reprint A functional genomics approach to the mode of action of apratoxin A
    Hendrik Luesch
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Chem Biol 2:158-67. 2006
    ..We conclude that apratoxin A mediates its antiproliferative activity through the induction of G1 cell cycle arrest and an apoptotic cascade, which is at least partially initiated through antagonism of FGF signaling via STAT3...
  14. pmc A gene atlas of the mouse and human protein-encoding transcriptomes
    Andrew I Su
    The Genomics Institute of the Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 101:6062-7. 2004
    ..We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting...
  15. pmc Regenerative phenotype in mice with a point mutation in transforming growth factor beta type I receptor (TGFBR1)
    Jun Liu
    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 108:14560-5. 2011
    ..This mutant mouse strain provides a unique model to further explore regeneration in mammals and, in particular, the role of TGFBR1 in chondrogenesis and regenerative wound healing...
  16. pmc Identification of the Plasmodium berghei resistance locus 9 linked to survival on chromosome 9
    Selina E R Bopp
    Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
    Malar J 12:316. 2013
    ..As such, the identification of genetic loci associated with susceptibility or resistance may serve to modulate disease severity...
  17. pmc Large-scale analysis of the human and mouse transcriptomes
    Andrew I Su
    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 99:4465-70. 2002
    ..Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations...
  18. pmc Mitotic evolution of Plasmodium falciparum shows a stable core genome but recombination in antigen families
    Selina E R Bopp
    Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
    PLoS Genet 9:e1003293. 2013
    ..falciparum. These results will help improve our understanding of how P. falciparum evolves to evade control efforts within both the individual hosts and large populations...
  19. pmc Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes
    Neekesh V Dharia
    Department of Cell Biology, Institute for Childhood and Neglected Diseases 202, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 107:20045-50. 2010
    ..This analysis provides a data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies...
  20. pmc Identification of small-molecule inducers of pancreatic beta-cell expansion
    Weidong Wang
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:1427-32. 2009
    ..The identification of small molecules that induce beta-cell proliferation suggests that it may be possible to reversibly expand other quiescent cells to overcome deficits associated with degenerative and/or autoimmune diseases...
  21. ncbi request reprint Chronic opioid exposure produces increased heroin self-administration in rats
    John R Walker
    Department of Neuropharmacology, The Scripps Research Institute, CVN 7, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Pharmacol Biochem Behav 75:349-54. 2003
    ..These results suggest that passive administration of morphine sufficient to produce and maintain dependence facilitates escalation in heroin intake...
  22. pmc The role of PTEN/Akt/PI3K signaling in the maintenance and viability of prostate cancer stem-like cell populations
    Anna Dubrovska
    The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:268-73. 2009
    ....
  23. pmc Why are some amyloidoses systemic? Does hepatic "chaperoning at a distance" prevent cardiac deposition in a transgenic model of human senile systemic (transthyretin) amyloidosis?
    Joel N Buxbaum
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    FASEB J 26:2283-93. 2012
    ..Hence systemic (cardiac) TTR deposition may be the direct result of the diminution in the distant chaperoning capacity of the liver related to age or long-standing exposure to misfolded TTR, or both...
  24. pmc Genomewide association analysis in diverse inbred mice: power and population structure
    Phillip McClurg
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Genetics 176:675-83. 2007
    ..These eQTL data confirmed that the MDP is a suitable mapping population for QTL discovery and that eQTL results can serve as a gold standard for relative measures of statistical power...
  25. doi request reprint An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation
    Heiko Wurdak
    The Skaggs Institute of Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell Stem Cell 6:37-47. 2010
    ..TRRAP knockdown also significantly suppressed tumor formation upon intracranial BTIC implantation into mice. Together, these findings support a critical role for TRRAP in maintaining a tumorigenic, stem cell-like state...
  26. doi request reprint Enhanced proteolytic clearance of plasma Aβ by peripherally administered neprilysin does not result in reduced levels of brain Aβ in mice
    John R Walker
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    J Neurosci 33:2457-64. 2013
    ..Taken together, these results suggest a lack of a robust peripheral Aβ efflux sink through which brain amyloid burdens can be therapeutically reduced...
  27. ncbi request reprint Illumination of the melanopsin signaling pathway
    Satchidananda Panda
    Genomics Institute of Novartis Research Foundation, 10675 John J Hopkins Drive, San Diego, CA 92121, USA
    Science 307:600-4. 2005
    ..Melanopsin therefore signals more like an invertebrate opsin than like a classical vertebrate rod-and-cone opsin...
  28. pmc Identification of homeodomain proteins, PBX1 and PREP1, involved in the transcription of murine leukemia virus
    Sheng Hao Chao
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Mol Cell Biol 23:831-41. 2003
    ..Collectively, our results represent the first work demonstrating that the homeodomain proteins PBX1 and PREP1 are cellular factors involved in Moloney MLV transcription regulation...
  29. pmc Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation
    Brooke H Miller
    Department of Neurobiology and Physiology, and Howard Hughes Medical Institute, Northwestern University, Evanston, IL 60208, USA
    Proc Natl Acad Sci U S A 104:3342-7. 2007
    ....
  30. ncbi request reprint Enhanced expression of nicotinamide N-methyltransferase in human papillary thyroid carcinoma cells
    Jimin Xu
    Endocrinology and Diabetes Division, Veterans Affairs Medical Center, University of California School of Medicine, Los Angeles, California 90073, USA
    J Clin Endocrinol Metab 88:4990-6. 2003
    ..These results indicate that NNMT is a potential biomarker for papillary thyroid carcinoma...
  31. ncbi request reprint Early prognosis of the development of renal chronic allograft rejection by gene expression profiling of human protocol biopsies
    Andreas Scherer
    Novartis Institutes for BioMedical Research Transplantation, Novartis Pharma AG, Basel, Switzerland
    Transplantation 75:1323-30. 2003
    ..Oligonucleotide microarray-based approaches have proven to be useful for the diagnosis and prognosis of a variety of diseases and were chosen for the unbiased identification of prognostic biomarkers...
  32. pmc Extinction training regulates neuroadaptive responses to withdrawal from chronic cocaine self-administration
    David W Self
    Department of Psychiatry, The Seay Center for Basic and Applied Research in Psychiatric Illness, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9070 USA
    Learn Mem 11:648-57. 2004
    ..These studies highlight potential benefits for extinction training procedures in the treatment of drug addiction...
  33. pmc Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes
    Stuart M Flechner
    Section of Renal Transplantation, Transplant Center A110, Cleveland Clinic Foundation, Cleveland, OH, USA
    Am J Transplant 4:1475-89. 2004
    ....
  34. pmc Characterization of stanniocalcin 2, a novel target of the mammalian unfolded protein response with cytoprotective properties
    Daisuke Ito
    Department of Neurobiology, Pharmacology, and Physiology, The University of Chicago, Knapp R212, 924 East 57th St, Chicago, IL 60637, USA
    Mol Cell Biol 24:9456-69. 2004
    ..Consequently, induced STC2 expression is an essential feature of survival component of the UPR...
  35. pmc A genomic screen for activators of the antioxidant response element
    Yanxia Liu
    Department of Medicinal Chemistry, University of Florida, 1600 Southwest Archer Road, Gainesville, FL 32610, USA
    Proc Natl Acad Sci U S A 104:5205-10. 2007
    ..This work and other such studies may provide mechanisms for activating the ARE in the absence of general oxidative stress and a yet-unexploited therapeutic approach to degenerative diseases and aging...
  36. pmc Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas
    Zheng Liu
    Department of Computer Science, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
    BMC Syst Biol 1:19. 2007
    ..In this proof-of-concept study, we studied the hypothesis that genes sharing similar three-dimensional expression profiles in the mouse brain are likely to share similar biological functions...
  37. ncbi request reprint Aromatase inhibitors--gene discovery
    William R Miller
    Breast Research Group, University of Edinburgh, Edinburgh, United Kingdom
    J Steroid Biochem Mol Biol 106:130-42. 2007
    ..Changed genes predicting for response showed no concordance with those changed significantly by treatment in the overall group...
  38. ncbi request reprint Identification of the circadian transcriptome in adult mouse skeletal muscle
    John J McCarthy
    Department of Physiology, University of Kentucky, Lexington, Kentucky 40536, USA
    Physiol Genomics 31:86-95. 2007
    ....
  39. ncbi request reprint NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression
    Longlong Yang
    The Hamner Institutes for Health Sciences, 6 Davis Drive, Research Triangle Park, NC 27709 2137, USA
    In Silico Biol 8:47-52. 2008
    ..The NetAtlas plugin is available at http://sourceforge.net/projects/netatlas/...
  40. ncbi request reprint Predicting response and resistance to endocrine therapy: profiling patients on aromatase inhibitors
    William R Miller
    Breast Research Group, University of Edinburgh, Edinburgh, United Kingdom
    Cancer 112:689-94. 2008
    ....
  41. ncbi request reprint Changes in breast cancer transcriptional profiles after treatment with the aromatase inhibitor, letrozole
    William R Miller
    Breast Research Group, University of Edinburgh, Edinburgh, UK
    Pharmacogenet Genomics 17:813-26. 2007
    ..The aim of the study was to identify changes in tumour expression profiling associated with short-term therapy of breast cancer patients with letrozole...
  42. pmc A functional map of NFkappaB signaling identifies novel modulators and multiple system controls
    Thomas A Halsey
    The Hamner Institutes for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709 2137, USA
    Genome Biol 8:R104. 2007
    ..To identify the components and structural features of the NFkappaB network, a series of cell-based, genomic screens was performed using a library of approximately 14,500 full-length genes...