Sergio E Baranzini

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Systems-based medicine approaches to understand and treat complex diseases. The example of multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California, San Francisco, 513 Parnassus Avenue Room S 256, San Francisco, CA 94143 0435, USA
    Autoimmunity 39:651-62. 2006
  2. pmc Revealing the genetic basis of multiple sclerosis: are we there yet?
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave, Room S 256, San Francisco, CA 94143 0435, United States
    Curr Opin Genet Dev 21:317-24. 2011
  3. pmc Detection of identity by descent using next-generation whole genome sequencing data
    Shu Yi Su
    Ernest Gallo Clinic and Research Center, University of California San Francisco, 5858 Horton St, Suite 200, Emeryville, CA 94608, USA
    BMC Bioinformatics 13:121. 2012
  4. doi Genetics of multiple sclerosis: swimming in an ocean of data
    Sergio E Baranzini
    Department of Neurology, University of California, San Francisco, California, USA
    Curr Opin Neurol 25:239-45. 2012
  5. pmc iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks
    Lili Wang
    School of Computing, Queen s University, 25 Union Street, Goodwin Hall, Kingston, Ontario K7L 3N6, Canada
    BMC Bioinformatics 12:380. 2011
  6. pmc Pathway and network-based analysis of genome-wide association studies in multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave Room S 256, San Francisco, CA 94143 0435, USA
    Hum Mol Genet 18:2078-90. 2009
  7. pmc Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0435, USA
    Brain 133:2603-11. 2010
  8. doi The genetics of autoimmune diseases: a networked perspective
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave Room S 256, San Francisco, CA 94143 0435, USA
    Curr Opin Immunol 21:596-605. 2009
  9. pmc Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, University of California at San Francisco, San Francisco, California 94143, USA
    Nature 464:1351-6. 2010
  10. ncbi Modular transcriptional activity characterizes the initiation and progression of autoimmune encephalomyelitis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California, San Francisco, 94143, USA
    J Immunol 174:7412-22. 2005

Detail Information

Publications47

  1. ncbi Systems-based medicine approaches to understand and treat complex diseases. The example of multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California, San Francisco, 513 Parnassus Avenue Room S 256, San Francisco, CA 94143 0435, USA
    Autoimmunity 39:651-62. 2006
    ..The challenge of data integration and modeling of dynamical systems is discussed in the context of disease susceptibility and response to treatment. A theoretical framework that supports the use of combination therapy is also presented...
  2. pmc Revealing the genetic basis of multiple sclerosis: are we there yet?
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave, Room S 256, San Francisco, CA 94143 0435, United States
    Curr Opin Genet Dev 21:317-24. 2011
    ....
  3. pmc Detection of identity by descent using next-generation whole genome sequencing data
    Shu Yi Su
    Ernest Gallo Clinic and Research Center, University of California San Francisco, 5858 Horton St, Suite 200, Emeryville, CA 94608, USA
    BMC Bioinformatics 13:121. 2012
    ..These sequencing data may provide an opportunity to detect IBD with higher resolution than previously possible, potentially enabling the detection of disease causing loci that were previously undetectable with sparser genetic data...
  4. doi Genetics of multiple sclerosis: swimming in an ocean of data
    Sergio E Baranzini
    Department of Neurology, University of California, San Francisco, California, USA
    Curr Opin Neurol 25:239-45. 2012
    ..This review describes the major advances in the genetics of MS with a slight emphasis on data handling and analysis...
  5. pmc iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks
    Lili Wang
    School of Computing, Queen s University, 25 Union Street, Goodwin Hall, Kingston, Ontario K7L 3N6, Canada
    BMC Bioinformatics 12:380. 2011
    ..This integration is essential to capitalize on the value of current and future molecular- and cellular-level data on humans to gain novel insights about health and disease...
  6. pmc Pathway and network-based analysis of genome-wide association studies in multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave Room S 256, San Francisco, CA 94143 0435, USA
    Hum Mol Genet 18:2078-90. 2009
    ..In addition to the immunological pathways previously identified, we report here for the first time the potential involvement of neural pathways in MS susceptibility...
  7. pmc Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0435, USA
    Brain 133:2603-11. 2010
    ..Spectroscopy-based imaging provides a novel quantitative endophenotype for genetic association studies directed towards identifying new factors that contribute to the heterogeneity of clinical expression of multiple sclerosis...
  8. doi The genetics of autoimmune diseases: a networked perspective
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave Room S 256, San Francisco, CA 94143 0435, USA
    Curr Opin Immunol 21:596-605. 2009
    ..The availability of GWAS data allows for a systematic analysis of similarities and differences among several AID. Using this class of approaches the unique genetic landscape for each autoimmune disease can start to be defined...
  9. pmc Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, University of California at San Francisco, San Francisco, California 94143, USA
    Nature 464:1351-6. 2010
    ..These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported...
  10. ncbi Modular transcriptional activity characterizes the initiation and progression of autoimmune encephalomyelitis
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California, San Francisco, 94143, USA
    J Immunol 174:7412-22. 2005
    ..Our study demonstrates the utility of large-scale transcriptional studies and advanced data mining to decipher complex biological processes such as those involved in MS and other neurodegenerative disorders...
  11. ncbi Gene expression profiling in neurological disorders: toward a systems-level understanding of the brain
    Sergio E Baranzini
    Department of Neurology, School of Medicine, University of California, San Francisco, 513 Parnassus Avenue, Medical Sciences Building S 256, San Francisco, CA 94143, USA
    Neuromolecular Med 6:31-51. 2004
    ..Finally, the need for integration of different sources of data is discussed in the context of systems biology and how such integration could result in improved diagnostics, therapies, and disease prevention...
  12. pmc Transcription-based prediction of response to IFNbeta using supervised computational methods
    Sergio E Baranzini
    Department of Neurology, School of Medicine University of California, San Francisco, USA
    PLoS Biol 3:e2. 2005
    ..Large-scale kinetic reverse-transcription PCR, coupled with advanced data-mining efforts, can effectively reveal preexisting and drug-induced gene expression signatures associated with therapeutic effects...
  13. pmc Large-scale gene-expression studies and the challenge of multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, University of California San Francisco, San Francisco, CA 94143 0435, USA
    Genome Biol 3:reviews1027. 2002
    ....
  14. ncbi Uncoupling the roles of HLA-DRB1 and HLA-DRB5 genes in multiple sclerosis
    Stacy J Caillier
    Department of Neurology, University of California, San Francisco, CA 94143, USA
    J Immunol 181:5473-80. 2008
    ..The data underscore the power of the African American MS dataset to identify disease genes by association in a region of high linkage disequilibrium...
  15. pmc Axin2 as regulatory and therapeutic target in newborn brain injury and remyelination
    Stephen P J Fancy
    Department of Pediatrics and Neurosurgery, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
    Nat Neurosci 14:1009-16. 2011
    ..Together, these findings indicate that Axin2 is an essential regulator of remyelination and that it might serve as a pharmacological checkpoint in this process...
  16. pmc Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset
    Pouya Khankhanian
    Department of Neurology, University of California, San Francisco, CA 94143 0435, USA
    BMC Genomics 11:626. 2010
    ..Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions...
  17. ncbi Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosis
    David Otaegui
    University of California San Francisco, San Francisco, CA 94143, USA
    J Immunol 179:4074-82. 2007
    ..The potential role of lactogenic hormones in MS is discussed...
  18. doi Genome-wide pharmacogenomic analysis of the response to interferon beta therapy in multiple sclerosis
    Esther Byun
    Department of Neurology, University of California, San Francisco, San Francisco, CA 94143 0435, USA
    Arch Neurol 65:337-44. 2008
    ..Recombinant interferon beta therapy is widely used to reduce disease activity in multiple sclerosis (MS). However, up to 50% of patients continue to have relapses and worsening disability despite therapy...
  19. pmc A genome-wide association study of brain lesion distribution in multiple sclerosis
    Pierre Antoine Gourraud
    Department of Neurology, School of Medicine, University of California, San Francisco, 675 Nelson Rising Lane, Suite 215, San Francisco, CA 94158, USA
    Brain 136:1012-24. 2013
    ....
  20. pmc Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological event
    Jean Christophe Corvol
    Departments of Neurology and Radiology, University of California, San Francisco, CA 94143 0435, USA
    Proc Natl Acad Sci U S A 105:11839-44. 2008
    ..These results indicate that CIS patients at high risk of conversion have impaired regulation of T cell quiescence, possibly resulting in earlier activation of pathogenic CD4(+) cells...
  21. ncbi Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis
    Lisa F Barcellos
    Division of Epidemiology, School of Public Health, University of California, Berkeley 94720, USA, and Department of Clinical Neurosciences, University of Cambridge, Addenbrooke s Hospital, UK
    Hum Mol Genet 15:2813-24. 2006
    ....
  22. pmc Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data
    Joanne H Wang
    Department of Neurology, University of California San Francisco, San Francisco, CA 94143 0435, USA
    Genome Med 3:3. 2011
    ..Nevertheless, the knowledge of MS genetics remains incomplete, with many risk alleles still to be revealed...
  23. doi The genetics of multiple sclerosis: SNPs to pathways to pathogenesis
    Jorge R Oksenberg
    Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, California 94143 0435, USA
    Nat Rev Genet 9:516-26. 2008
    ....
  24. ncbi Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans
    Guy Haskin Fernald
    School of Medicine, University of California, San Francisco, CA 94143, USA
    J Immunol 178:5076-85. 2007
    ..Implications of this method in the creation of personalized models of response to therapy are discussed...
  25. pmc Sequencing of the IL6 gene in a case-control study of cerebral palsy in children
    Pouya Khankhanian
    Department of Neurology, University of California, 675 Nelson Rising Lane, 94158, San Francisco, CA, USA
    BMC Med Genet 14:126. 2013
    ..This SNP has been associated with other neurological, vascular, and malignant processes as well, often as part of a haplotype block...
  26. doi Parallel states of pathological Wnt signaling in neonatal brain injury and colon cancer
    Stephen P J Fancy
    1 Department of Pediatrics, University of California, San Francisco UCSF, San Francisco, California, USA 2 Department of Neurology, UCSF, San Francisco, California, USA 3 Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA 4
    Nat Neurosci 17:506-12. 2014
    ..These findings suggest a state of pathological high-activity Wnt signaling in human disease tissues that lack predisposing genetic mutation. ..
  27. doi Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, University of California, San Francisco, CA 94143 0435, USA
    Hum Mol Genet 18:767-78. 2009
    ..Gene ontology-based analysis shows a functional dichotomy between genes involved in the susceptibility pathway and those affecting the clinical phenotype...
  28. ncbi Mapping gene activity in complex disorders: Integration of expression and genomic scans for multiple sclerosis
    Guy Haskin Fernald
    Department of Neurology, School of Medicine, University of California, 513 Parnassus Avenue, S 256, San Francisco, CA 94143 0435, USA
    J Neuroimmunol 167:157-69. 2005
    ..Integration of genomic and transcriptional information is a powerful tool to dissect genetic susceptibility in complex multifactorial disorders like MS...
  29. doi The genetics of multiple sclerosis: an up-to-date review
    Pierre Antoine Gourraud
    Department of Neurology, University of California San Francisco, San Francisco, CA 94143 0435, USA
    Immunol Rev 248:87-103. 2012
    ....
  30. pmc Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
    Philip L De Jager
    Division of Molecular Immunology, Center for Neurologic Diseases, Department of Neurology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Nat Genet 41:776-82. 2009
    ....
  31. ncbi Gene expression analysis reveals altered brain transcription of glutamate receptors and inflammatory genes in a patient with chronic focal (Rasmussen's) encephalitis
    Sergio E Baranzini
    Department of Neurology, University of California at San Francisco, 513 Parnassus Avenue, S 256, San Francisco, CA 94143 0435, USA
    J Neuroimmunol 128:9-15. 2002
    ..e. IL1 beta, IgVH, and IL2R gamma among others) and a striking down-regulation of several GluRs, in particular mGluR4. This type of analysis may prove useful in describing the molecular events underlying intractable epilepsy...
  32. doi Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1
    Anne M Slavotinek
    Department of Pediatrics, Division of Genetics, University of California, 533 Parnassus Street, Room U585P, San Francisco, CA 94143 0748, USA
    J Med Genet 48:375-82. 2011
    ..Autosomal recessive inheritance had been assumed because of consanguinity in the Oji-Cre population of Manitoba and reports of affected siblings, but no locus or cytogenetic aberration had previously been described...
  33. pmc In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing
    Dorothee Nickles
    Department of Neurology, University of California San Francisco, San Francisco, CA 94143 0435, USA
    BMC Genomics 13:477. 2012
    ..A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach...
  34. ncbi Genomics and new targets for multiple sclerosis
    Sergio E Baranzini
    University of California, Department of Neurology, School of Medicine, San Francisco, CA 94143 0435, USA
    Pharmacogenomics 6:151-61. 2005
    ..Equally significant, it is likely that locus heterogeneity exists, whereby specific genes influence susceptibility and pathogenesis in some individuals but not in others...
  35. doi Myelin regeneration: a recapitulation of development?
    Stephen P J Fancy
    Departments of Pediatrics and Neurosurgery, Eli and Edyth Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
    Annu Rev Neurosci 34:21-43. 2011
    ..Here we review the current evidence for the recapitulation hypothesis and discuss recent findings in the development and regeneration of myelin in the context of human neurological disease...
  36. pmc Dysregulation of the Wnt pathway inhibits timely myelination and remyelination in the mammalian CNS
    Stephen P J Fancy
    Institute for Regeneration Medicine, Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 23:1571-85. 2009
    ..Evidence of Wnt pathway activity in human MS lesions suggests that its dysregulation might contribute to inefficient myelin repair in human neurological disorders...
  37. pmc Tob1 plays a critical role in the activation of encephalitogenic T cells in CNS autoimmunity
    Ulf Schulze-Topphoff
    Department of Neurology, University of California, San Francisco, CA 94143, USA
    J Exp Med 210:1301-9. 2013
    ..Collectively, our results reveal a critical role for Tob1 in adaptive T cell immune responses that drive development of EAE, thus providing support for the development of Tob1 as a biomarker for demyelinating disease activity...
  38. pmc The molecular signature of therapeutic mesenchymal stem cells exposes the architecture of the hematopoietic stem cell niche synapse
    Enrico Pedemonte
    Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
    BMC Genomics 8:65. 2007
    ..The hematopoietic stem cells (HSCs) niche of the bone marrow is comprised of HSCs, osteoblasts, endothelial cells and a stromal component of non-hematopoietic multipotent cells of mesenchymal origin named "mesenchymal stem cells" (MSCs)...
  39. ncbi Quantitative longitudinal analysis of T cell receptor repertoire expression in HIV-infected patients on antiretroviral and interleukin-2 therapy
    Uma Sriram
    Department of Neurology University of California at San Francisco, California 94143, USA
    AIDS Res Hum Retroviruses 23:741-7. 2007
    ..These results suggest that homeostasis in the T cell receptor repertoire is more robust in those patients who stay on HAART for a long time and confirm the polyclonal stimulating capacity of IL-2...
  40. doi Multiple sclerosis genetics--is the glass half full, or half empty?
    Jorge R Oksenberg
    Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0435, USA
    Nat Rev Neurol 6:429-37. 2010
    ..This Review briefly summarizes well-established concepts of MS epidemiology and susceptibility, and discusses new knowledge emerging from genome-wide association studies...
  41. pmc Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans
    Jorge R Oksenberg
    Department of Neurology, University of California at San Francisco, San Francisco, CA 94143 0435, USA
    Am J Hum Genet 74:160-7. 2004
    ..This finding is unlikely to be solely explained by admixture, since a substantial proportion of the susceptibility chromosomes from African American patients with MS displayed haplotypes consistent with an African origin...
  42. ncbi Dynamic regulation of alternative ATP-binding cassette transporter A1 transcripts
    Jarkko Huuskonen
    Cardiovascular Research Institute, University of California, San Francisco, CA 94143 0130, USA
    Biochem Biophys Res Commun 306:463-8. 2003
    ..In both cell lines class 3 transcript levels were minimal and unchanged. It is shown here for the first time that the regulation of ABCA1 mRNA levels exploits the use of alternative transcription start sites...
  43. ncbi New insights into the genetics of multiple sclerosis
    Sergio E Baranzini
    Department of Neurology, San Francisco School of Medicine, University of California, 94143, USA
    J Rehabil Res Dev 39:201-9. 2002
    ..The identification and characterization of the genes are likely to define the basic etiology of the disease, improve risk assessment, and influence therapeutics...
  44. ncbi The HLA locus and multiple sclerosis in Spain. Role in disease susceptibility, clinical course and response to interferon-beta
    Pablo Villoslada
    Neuroimmunology Unit, Hospital Vall d Hebron, Barcelona, Spain
    J Neuroimmunol 130:194-201. 2002
    ..Similarly, no difference in the distribution of responders and nonresponders to interferon-beta (IFNB) therapy, as defined by primary and secondary end points, was observed when individuals were stratified according to HLA-DR2 status...
  45. doi Evidence for association of chromosome 10 open reading frame (C10orf27) gene polymorphisms and multiple sclerosis
    Robert Goertsches
    Unitat de Neuroimmunologia Clinica, Hospital Universitari Vall d Hebron HUVH, 08035 Barcelona, Spain
    Mult Scler 14:412-4. 2008
    ..Transcript expression in brain lesions from MS patients was increased. These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis...
  46. doi Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets
    May H Han
    Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California 94305, USA
    Nature 451:1076-81. 2008
    ..A proteomic approach illuminated potential therapeutic targets selective for specific pathological stages of MS and implicated participation of the coagulation cascade...
  47. pmc Peroxisome proliferator-activated receptor (PPAR)alpha expression in T cells mediates gender differences in development of T cell-mediated autoimmunity
    Shannon E Dunn
    Department of Neurology and Neurological Studies, and 2Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
    J Exp Med 204:321-30. 2007
    ..These results suggest that males are less prone to develop Th1-mediated autoimmunity because they have higher T cell expression of PPARalpha...