Sergio Baranzini, PhD
Professor
Neurology
School of Medicine

Sergio E. Baranzini earned his degree in clinical biochemistry from the University of Buenos Aires, Argentina, in 1992. He graduated from the same institution in 1997 obtaining a PhD with honors in human molecular genetics. The subject of his PhD thesis was the characterization of genetic mutations leading to Duchenne’s muscular dystrophy.

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Dr. Baranzini then moved to the University of California at San Francisco to specialize in the analysis of complex hereditary diseases, in particular multiple sclerosis. During his postdoctoral stay in UCSF Dr. Baranzini employed state-of-the art methods to explore MS pathogenesis, including immunology, molecular biology, genomics and bioinformatics. Since 2003 Dr. Baranzini is faculty in the Department of Neurology at UCSF, where he currently holds the title of Associate Professor In-Residence. His research involves the large throughout analysis of samples from MS patients to characterize the activity of genes during: i) different stages of the disease (i.e. remission vs. relapse), ii) differential response to treatment (i.e. good responders vs. poor responders), and iii) disease progression (i.e. benign vs. severe). In addition Dr. Baranzini is collaborating with several interdisciplinary teams worldwide to integrate all the available knowledge obtained in different research domains in an approach known as systems biology. Dr Baranzini’s current research involves immunological studies using the EAE model, sequencing of whole genomes and transcriptomes from patients with multiple sclerosis and developing bioinformatics tools to integrate this information with that coming from other high throughput technologies. Dr Baranzini uses a combination of “wet lab” methods including DNA microarrays, proteomics, and laser capture microdissection, in combination with “dry lab” analytical approaches encompassing bioinformatics, complexity theory, and mathematical modeling. Dr. Baranzini has published his research on MS in several top-tier journals like Science, Nature, PNAS, J Immunol, and PLos Biol. He is a member of the American Association of Immunologists, and an elected member of the American Neurological Association. He also serves as an ad-hoc reviewer for many specialized journals.

Awards

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• Barancik Prize for Innovation in Multiple Sclerosis Research, National Multiple Sclerosis Society, 2024
• Neurology Research Incentive Program 2 (N-RIP2), Department of Neurology. UCSF, 2023
• Distinguished Professorship in Neurology I, Department of Neurology. UCSF, 2019
• Stephen C. Reingold award, National Multiple Sclerosis Society (US), 2015
• Endowed Chair in Neurology, Department of Neurology. UCSF, 2010
• Harry Weaver Neuroscience Scholar Award, National Multiple Sclerosis Society (US), 2009-2014
• Advanced Postdoctoral Fellowship, National Multiple Sclerosis Society (US), 2001
• Advanced Graduate Fellowship for research in Molecular Biology, University of Buenos Aires, 1997
• Best Presentation Award. XXVII Genetics Annual Meeting, Argentine Society of Genetics, 1996
• Adolfo Noceti and Atilio Tiscornia Award for ophthalmology research, National Academy of Medicine, Argentina, 1996
• Advanced Graduate Fellowship for research in Molecular Biology, University of Buenos Aires, 1996
• Graduate Fellowship for research in Medical Genetics, University of Buenos Aires, Argentina, 1995
• Graduate Fellowship for research in Molecular Biology, University of Buenos Aires, Argentina, 1993
• Undergraduate scholarship for research in Molecular Biology, University of Buenos Aires, Argentina, 1992

Education & Training

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• Postdoctoral Fellow Neurogenetics University of California, San Francisco 2001
• PhD Biochemistry University of Buenos Aires, Argentina 1997
• BS/MS Biochemistry/Biotechnology University of Buenos Aires, Argentina 1992

Websites

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• My lab site (baranzinilab.ucsf.edu)
• iMSMS (imsms.org)
• Profile at msgenes.ucsf.edu (msgenes.ucsf.edu)

Grants and Projects

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• EVIDARA: Automated Evidential Support from Raw Data for relay agents in Biomedical KG Queries, NIH, 2020-2022
• The genetic basis of progression in multiple sclerosis, NIH, 2017-2021
• Post GWAS approach to identify cell-specific genetic pathways underlying MS risk, NIH, 2014-2019
• Extensive Search for an X-linked Acc Gene, NIH, 1998-1900

Publications (192)

Top publication keywords:
Pattern Recognition, AutomatedMultiple Sclerosis, Relapsing-RemittingMicrobiotaB-LymphocytesGenetic Predisposition to DiseaseComputational BiologyInterferon-betaMultiple SclerosisProtein Interaction MapsEncephalomyelitis, Autoimmune, ExperimentalGenome-Wide Association StudyGene Expression ProfilingMultiple Sclerosis, Chronic ProgressiveSystems BiologyGastrointestinal Microbiome

• Multi-disciplinary research will be the key to stop, restore, and end MS.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2025 Baranzini SE
• Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
  Nature communications 2025 Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, …
• Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation.
  bioRxiv : the preprint server for biology 2025 Jank L, Singh SS, Lee J, Dhukhwa A, Siavoshi F, Joshi D, Minney V, Gupta K, Ghimire S, Deme P, Schoeps VA, Soman K, Ladakis D, Smith M, Borkowski K, Newman J, Baranzini SE, Waubant EL, Fitzgerald KC, …
• Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
  Research square 2024 Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight…
• Artificial intelligence in food and nutrition evidence: The challenges and opportunities.
  PNAS nexus 2024 Bailey RL, MacFarlane AJ, Field MS, Tagkopoulos I, Baranzini SE, Edwards KM, Rose CJ, Schork NJ, Singhal A, Wallace BC, Fisher KP, Markakis K, Stover PJ

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• Biomedical knowledge graph-optimized prompt generation for large language models.
  Bioinformatics (Oxford, England) 2024 Soman K, Rose PW, Morris JH, Akbas RE, Smith B, Peetoom B, Villouta-Reyes C, Cerono G, Shi Y, Rizk-Jackson A, Israni S, Nelson CA, Huang S, Baranzini SE
• Genetics of multiple sclerosis severity: The importance of statistical power in replication studies.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2024 Harroud A, Sawcer SJ, Baranzini SE
• Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency.
  Science translational medicine 2024 Pluvinage JV, Ngo T, Fouassier C, McDonagh M, Holmes BB, Bartley CM, Kondapavulur S, Hurabielle C, Bodansky A, Pai V, Hinman S, Aslanpour A, Alvarenga BD, Zorn KC, Zamecnik C, McCann A, Asencor AI, …
• Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction.
  Nature communications 2024 Siew K, Nestler KA, Nelson C, D'Ambrosio V, Zhong C, Li Z, Grillo A, Wan ER, Patel V, Overbey E, Kim J, Yun S, Vaughan MB, Cheshire C, Cubitt L, Broni-Tabi J, Al-Jaber MY, Boyko V, Meydan C, Barker P,…
• Inflammatory and neurodegenerative serum protein biomarkers increase sensitivity to detect clinical and radiographic disease activity in multiple sclerosis.
  Nature communications 2024 Chitnis T, Qureshi F, Gehman VM, Becich M, Bove R, Cree BAC, Gomez R, Hauser SL, Henry RG, Katrib A, Lokhande H, Paul A, Caillier SJ, Santaniello A, Sattarnezhad N, Saxena S, Weiner H, Yano H, …
• An autoantibody signature predictive for multiple sclerosis.
  Nature medicine 2024 Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Kizer K, Augusto DG, Tubati A, Gomez R, Fouassier C, Gerungan C, Caspar CM, Alexander J, Wapniarski AE, Loudermilk RP, …
• Multiple sclerosis endophenotypes identified by high-dimensional blood signatures are associated with distinct disease trajectories.
  Science translational medicine 2024 Gross CC, Schulte-Mecklenbeck A, Steinberg OV, Wirth T, Lauks S, Bittner S, Schindler P, Baranzini SE, Groppa S, Bellmann-Strobl J, Bünger N, Chien C, Dawin E, Eveslage M, Fleischer V, Gonzalez-…
• Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights.
  Nature aging 2024 Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, …
• What doesn't kill you makes you stronger . . . or does it?
  Multiple sclerosis (Houndmills, Basingstoke, England) 2024 Baranzini SE, Graves JS
• Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset.
  Annals of clinical and translational neurology 2023 Schoeps VA, Zhou X, Horton MK, Zhu F, McCauley KE, Nasr Z, Virupakshaiah A, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Banwell BL, Bar-Or A, Marrie RA, van Domselaar G, O'Mahony J, Mirza AI…
• An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.
  Journal of clinical and translational science 2023 Fecho K, Bizon C, Issabekova T, Moxon S, Thessen AE, Abdollahi S, Baranzini SE, Belhu B, Byrd WE, Chung L, Crouse A, Duby MP, Ferguson S, Foksinska A, Forero L, Friedman J, Gardner V, Glusman G, …
• Inflammatory and neurodegenerative serum protein biomarkers increase sensitivity to detect disease activity in multiple sclerosis.
  medRxiv : the preprint server for health sciences 2023 Chitnis T, Qureshi F, Gehman VM, Becich M, Bove R, Cree BAC, Gomez R, Hauser SL, Henry RG, Katrib A, Lokhande H, Paul A, Caillier SJ, Santaniello A, Sattarnezhad N, Saxena S, Weiner H, Yano H, …
• Locus for severity implicates CNS resilience in progression of multiple sclerosis.
  Nature 2023 International Multiple Sclerosis Genetics Consortium, MultipleMS Consortium
• A Predictive Autoantibody Signature in Multiple Sclerosis.
  medRxiv : the preprint server for health sciences 2023 Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Tubati A, Gomez R, Fouassier C, Gerungan C, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, …
• Early detection of Parkinson's disease through enriching the electronic health record using a biomedical knowledge graph.
  Frontiers in medicine 2023 Soman K, Nelson CA, Cerono G, Goldman SM, Baranzini SE, Brown EG
• Integration of epigenetic and genetic profiles identifies multiple sclerosis disease-critical cell types and genes.
  Communications biology 2023 Ma Q, Shams H, Didonna A, Baranzini SE, Cree BAC, Hauser SL, Henry RG, Oksenberg JR
• Polygenic risk score association with multiple sclerosis susceptibility and phenotype in Europeans.
  Brain : a journal of neurology 2023 Shams H, Shao X, Santaniello A, Kirkish G, Harroud A, Ma Q, Isobe N, University of California San Francisco MS-EPIC Team, Schaefer CA, McCauley JL, Cree BAC, Didonna A, Baranzini SE, Patsopoulos NA, …
• The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
  Bioinformatics (Oxford, England) 2023 Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang …
• Time-aware Embeddings of Clinical Data using a Knowledge Graph.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2023 Soman K, Nelson CA, Cerono G, Baranzini SE
• Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.
  Cell 2022 iMSMS Consortium. Electronic address: sergio.baranzini@ucsf.edu, iMSMS Consortium
• The role of the gut microbiota in multiple sclerosis.
  Nature reviews. Neurology 2022 Correale J, Hohlfeld R, Baranzini SE
• FutureMS cohort profile: a Scottish multicentre inception cohort study of relapsing-remitting multiple sclerosis.
  BMJ open 2022 Kearns PKA, Martin SJ, Chang J, Meijboom R, York EN, Chen Y, Weaver C, Stenson A, Hafezi K, Thomson S, Freyer E, Murphy L, Harroud A, Foley P, Hunt D, McLeod M, O'Riordan J, Carod-Artal FJ, MacDougall…
• Progress toward a universal biomedical data translator.
  Clinical and translational science 2022 Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dancík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, …
• A biomedical open knowledge network harnesses the power of AI to understand deep human biology.
  AI magazine 2022 Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, …
• Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis.
  Journal of the American Medical Informatics Association : JAMIA 2022 Nelson CA, Bove R, Butte AJ, Baranzini SE
• Classification of neurological diseases using multi-dimensional CSF analysis.
  Brain : a journal of neurology 2021 Gross CC, Schulte-Mecklenbeck A, Madireddy L, Pawlitzki M, Strippel C, Räuber S, Krämer J, Rolfes L, Ruck T, Beuker C, Schmidt-Pogoda A, Lohmann L, Schneider-Hohendorf T, Hahn T, Schwab N, Minnerup J,…
• Distinctive waves of innate immune response in the retina in experimental autoimmune encephalomyelitis.
  JCI insight 2021 Cruz-Herranz A, Oertel FC, Kim K, Cantó E, Timmons G, Sin JH, Devereux M, Baker N, Michel B, Schubert RD, Rani L, Cordano C, Baranzini SE, Green AJ
• Childhood obesity and multiple sclerosis: A Mendelian randomization study.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2021 Harroud A, Mitchell RE, Richardson TG, Morris JA, Forgetta V, Davey Smith G, Baranzini SE, Richards JB
• Cell type-specific transcriptomics identifies neddylation as a novel therapeutic target in multiple sclerosis.
  Brain : a journal of neurology 2021 Kim K, Pröbstel AK, Baumann R, Dyckow J, Landefeld J, Kogl E, Madireddy L, Loudermilk R, Eggers EL, Singh S, Caillier SJ, Hauser SL, Cree BAC, UCSF MS-EPIC Team, Schirmer L, Wilson MR, Baranzini SE
• The relative contributions of obesity, vitamin D, leptin, and adiponectin to multiple sclerosis risk: A Mendelian randomization mediation analysis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2021 Harroud A, Manousaki D, Butler-Laporte G, Mitchell RE, Davey Smith G, Richards JB, Baranzini SE
• Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases.
  Life (Basel, Switzerland) 2021 Nelson CA, Acuna AU, Paul AM, Scott RT, Butte AJ, Cekanaviciute E, Baranzini SE, Costes SV
• Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis.
  Science immunology 2020 Pröbstel AK, Zhou X, Baumann R, Wischnewski S, Kutza M, Rojas OL, Sellrie K, Bischof A, Kim K, Ramesh A, Dandekar R, Greenfield AL, Schubert RD, Bisanz JE, Vistnes S, Khaleghi K, Landefeld J, Kirkish …
• Mendelian randomization study shows no causal effects of serum urate levels on the risk of MS.
  Neurology(R) neuroimmunology & neuroinflammation 2020 Harroud A, Richards JB, Baranzini SE
• Levels of brain-derived neurotrophic factor in patients with multiple sclerosis.
  Annals of clinical and translational neurology 2020 Naegelin Y, Saeuberli K, Schaedelin S, Dingsdale H, Magon S, Baranzini S, Amann M, Parmar K, Tsagkas C, Calabrese P, Penner IK, Kappos L, Barde YA
• A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D, University of California, San Francisco MS-EPIC Team, Guo CY,…
• SARS-CoV-2 meta-interactome suggests disease-specific, autoimmune pathophysiologies and therapeutic targets.
  F1000Research 2020 Bellucci G, Ballerini C, Mechelli R, Bigi R, Rinaldi V, Reniè R, Buscarinu MC, Baranzini SE, Madireddy L, Matarese G, Salvetti M, Ristori G
• Vitamin D Regulates MerTK-Dependent Phagocytosis in Human Myeloid Cells.
  Journal of immunology (Baltimore, Md. : 1950) 2020 Clarke J, Yaqubi M, Futhey NC, Sedaghat S, Baufeld C, Blain M, Baranzini S, Butovsky O, Antel J, White JH, Healy LM
• Serum antibodies to phosphatidylcholine in MS.
  Neurology(R) neuroimmunology & neuroinflammation 2020 Sádaba MC, Rothhammer V, Muñoz Ú, Sebal C, Escudero E, Kivisäkk P, Garcia Sanchez MI, Izquierdo G, Hauser SL, Baranzini SE, Oksenberg JR, Álvarez-Lafuente R, Bakshi R, Weiner HL, Quintana FJ
• microRNA and exosome profiling in multiple sclerosis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2020 Mycko MP, Baranzini SE
• Early complement genes are associated with visual system degeneration in multiple sclerosis.
  Brain : a journal of neurology 2019 Fitzgerald KC, Kim K, Smith MD, Aston SA, Fioravante N, Rothman AM, Krieger S, Cofield SS, Kimbrough DJ, Bhargava P, Saidha S, Whartenby KA, Green AJ, Mowry EM, Cutter GR, Lublin FD, Baranzini SE, De …
• Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia.
  Scientific reports 2019 Bonham LW, Steele NZR, Karch CM, Broce I, Geier EG, Wen NL, Momeni P, Hardy J, Miller ZA, Gorno-Tempini ML, Hess CP, Lewis P, Miller BL, Seeley WW, Manzoni C, Desikan RS, Baranzini SE, Ferrari R, …
• Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.
  Nature communications 2019 Nelson CA, Butte AJ, Baranzini SE
• Aberrant oligodendroglial-vascular interactions disrupt the blood-brain barrier, triggering CNS inflammation.
  Nature neuroscience 2019 Niu J, Tsai HH, Hoi KK, Huang N, Yu G, Kim K, Baranzini SE, Xiao L, Chan JR, Fancy SPJ
• Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
  Cell 2019 Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, …
• Silent progression in disease activity-free relapsing multiple sclerosis.
  Annals of neurology 2019 University of California, San Francisco MS-EPIC Team, Cree BAC, Hollenbach JA, Bove R, Kirkish G, Sacco S, Caverzasi E, Bischof A, Gundel T, Zhu AH, Papinutto N, Stern WA, Bevan C, Romeo A, Goodin DS,…
• Insights into microbiome research 6: The role of consortia in studying the role of microbes in health and disease.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2019 Baranzini SE
• Insights into microbiome research 5: Mapping is first but function must come next.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2019 Baranzini SE
• Selective Estrogen Receptor Modulators Enhance CNS Remyelination Independent of Estrogen Receptors.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2019 Rankin KA, Mei F, Kim K, Shen YA, Mayoral SR, Desponts C, Lorrain DS, Green AJ, Baranzini SE, Chan JR, Bove R
• Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
  Cell 2019 Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, …
• Insights into microbiome research 4: The computational analysis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2019 Baranzini SE
• Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria.
  mSystems 2018 Cekanaviciute E, Pröbstel AK, Thomann A, Runia TF, Casaccia P, Katz Sand I, Crabtree E, Singh S, Morrissey J, Barba P, Gomez R, Knight R, Mazmanian S, Graves J, Cree BAC, Zamvil SS, Baranzini SE
• Disease-modifying therapies alter gut microbial composition in MS.
  Neurology(R) neuroimmunology & neuroinflammation 2018 Katz Sand I, Zhu Y, Ntranos A, Clemente JC, Cekanaviciute E, Brandstadter R, Crabtree-Hartman E, Singh S, Bencosme Y, Debelius J, Knight R, Cree BAC, Baranzini SE, Casaccia P
• Insights into microbiome research 2: Experimental design, sample collection, and shipment.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2018 Baranzini SE
• Insights into microbiome research 3: Who's there versus what are they doing?
  Multiple sclerosis (Houndmills, Basingstoke, England) 2018 Baranzini SE
• Protein network analysis reveals selectively vulnerable regions and biological processes in FTD.
  Neurology. Genetics 2018 Bonham LW, Steele NZR, Karch CM, Manzoni C, Geier EG, Wen N, Ofori-Kuragu A, Momeni P, Hardy J, Miller ZA, Hess CP, Lewis P, Miller BL, Seeley WW, Baranzini SE, Desikan RS, Ferrari R, Yokoyama JS, …
• Insights into microbiome research 1: How to choose appropriate controls for a microbiome study in MS?
  Multiple sclerosis (Houndmills, Basingstoke, England) 2018 Baranzini SE
• Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis.
  Annals of neurology 2018 Jia X, Madireddy L, Caillier S, Santaniello A, Esposito F, Comi G, Stuve O, Zhou Y, Taylor B, Kilpatrick T, Martinelli-Boneschi F, Cree BAC, Oksenberg JR, Hauser SL, Baranzini SE
• Mononuclear cell transcriptome changes associated with dimethyl fumarate in MS.
  Neurology(R) neuroimmunology & neuroinflammation 2018 Gafson AR, Kim K, Cencioni MT, van Hecke W, Nicholas R, Baranzini SE, Matthews PM
• Correction: Peroxisome proliferator-activated receptor (PPAR)α expression in T cells mediates gender differences in development of T cell-mediated autoimmunity.
  The Journal of experimental medicine 2018 Dunn SE, Ousman SS, Sobel RA, Zuniga L, Baranzini SE, Youssef S, Crowell A, Loh J, Oksenberg J, Steinman L
• Multiple sclerosis.
  Lancet (London, England) 2018 Thompson AJ, Baranzini SE, Geurts J, Hemmer B, Ciccarelli O
• The microbiome and MS: The influence of the microbiota on MS risk and progression-Session chair summary.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2018 Katz Sand I, Baranzini SE
• Harnessing electronic medical records to advance research on multiple sclerosis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2018 Damotte V, Lizée A, Tremblay M, Agrawal A, Khankhanian P, Santaniello A, Gomez R, Lincoln R, Tang W, Chen T, Lee N, Villoslada P, Hollenbach JA, Bevan CD, Graves J, Bove R, Goodin DS, Green AJ, …
• The Gut Microbiome in Neuromyelitis Optica.
  Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics 2018 Zamvil SS, Spencer CM, Baranzini SE, Cree BAC
• The Role of the Gut Microbiome in Multiple Sclerosis Risk and Progression: Towards Characterization of the "MS Microbiome".
  Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics 2018 Pröbstel AK, Baranzini SE
• The era of GWAS is over - Commentary.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2017 Baranzini SE
• The Genetics of Multiple Sclerosis: From 0 to 200 in 50 Years.
  Trends in genetics : TIG 2017 Baranzini SE, Oksenberg JR
• Systematic integration of biomedical knowledge prioritizes drugs for repurposing.
  eLife 2017 Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE
• Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK,…
• Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Berer K, Gerdes LA, Cekanaviciute E, Jia X, Xiao L, Xia Z, Liu C, Klotz L, Stauffer U, Baranzini SE, Kümpfel T, Hohlfeld R, Krishnamoorthy G, Wekerle H
• Data characterizing the ZMIZ1 molecular phenotype of multiple sclerosis.
  Data in brief 2017 Fewings N, Gatt PN, McKay FC, Parnell GP, Schibeci SD, Edwards J, Basuki MA, Goldinger A, Fabis-Pedrini MJ, Kermode AG, Manrique CP, McCauley JL, Nickles D, Baranzini SE, Burke T, Vucic S, Stewart GJ,…
• The autoimmune risk gene ZMIZ1 is a vitamin D responsive marker of a molecular phenotype of multiple sclerosis.
  Journal of autoimmunity 2017 Fewings NL, Gatt PN, McKay FC, Parnell GP, Schibeci SD, Edwards J, Basuki MA, Goldinger A, Fabis-Pedrini MJ, Kermode AG, Manrique CP, McCauley JL, Nickles D, Baranzini SE, Burke T, Vucic S, Stewart GJ…
• IFN-γ orchestrates mesenchymal stem cell plasticity through the signal transducer and activator of transcription 1 and 3 and mammalian target of rapamycin pathways.
  The Journal of allergy and clinical immunology 2016 Vigo T, Procaccini C, Ferrara G, Baranzini S, Oksenberg JR, Matarese G, Diaspro A, Kerlero de Rosbo N, Uccelli A
• Two missense mutations in SALL4 in a patient with microphthalmia, coloboma, and optic nerve hypoplasia.
  Ophthalmic genetics 2016 Ullah E, Wu D, Madireddy L, Lao R, Ling-Fung Tang P, Wan E, Bardakjian T, Kopinsky S, Kwok PY, Schneider A, Baranzini S, Ansar M, Slavotinek A
• Immune cell-specific transcriptional profiling highlights distinct molecular pathways controlled by Tob1 upon experimental autoimmune encephalomyelitis.
  Scientific reports 2016 Didonna A, Cekanaviciute E, Oksenberg JR, Baranzini SE
• Long-term evolution of multiple sclerosis disability in the treatment era.
  Annals of neurology 2016 University of California, San Francisco MS-EPIC Team:, Cree BA, Gourraud PA, Oksenberg JR, Bevan C, Crabtree-Hartman E, Gelfand JM, Goodin DS, Graves J, Green AJ, Mowry E, Okuda DT, Pelletier D, von …
• Gut microbiome analysis in neuromyelitis optica reveals overabundance of Clostridium perfringens.
  Annals of neurology 2016 Cree BA, Spencer CM, Varrin-Doyer M, Baranzini SE, Zamvil SS
• Association of HLA Genetic Risk Burden With Disease Phenotypes in Multiple Sclerosis.
  JAMA neurology 2016 Isobe N, Keshavan A, Gourraud PA, Zhu AH, Datta E, Schlaeger R, Caillier SJ, Santaniello A, Lizée A, Himmelstein DS, Baranzini SE, Hollenbach J, Cree BA, Hauser SL, Oksenberg JR, Henry RG
• Meta-analysis of genome-wide association studies reveals genetic overlap between Hodgkin lymphoma and multiple sclerosis.
  International journal of epidemiology 2016 Khankhanian P, Cozen W, Himmelstein DS, Madireddy L, Din L, van den Berg A, Matsushita T, Glaser SL, Moré JM, Smedby KE, Baranzini SE, Mack TM, Lizée A, de Sanjosé S, Gourraud PA, Nieters A, Hauser SL…
• A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.
  Science translational medicine 2015 Gustafsson M, Gawel DR, Alfredsson L, Baranzini S, Björkander J, Blomgran R, Hellberg S, Eklund D, Ernerudh J, Kockum I, Konstantinell A, Lahesmaa R, Lentini A, Liljenström HR, Mattson L, Matussek A, …
• Assessing the Power of Exome Chips.
  PloS one 2015 Page CM, Baranzini SE, Mevik BH, Bos SD, Harbo HF, Andreassen BK
• A non-synonymous single-nucleotide polymorphism associated with multiple sclerosis risk affects the EVI5 interactome.
  Human molecular genetics 2015 Didonna A, Isobe N, Caillier SJ, Li KH, Burlingame AL, Hauser SL, Baranzini SE, Patsopoulos NA, Oksenberg JR
• Class II HLA interactions modulate genetic risk for multiple sclerosis.
  Nature genetics 2015 Moutsianas L, Jostins L, Beecham AH, Dilthey AT, Xifara DK, Ban M, Shah TS, Patsopoulos NA, Alfredsson L, Anderson CA, Attfield KE, Baranzini SE, Barrett J, Binder TMC, Booth D, Buck D, Celius EG, …
• iCTNet2: integrating heterogeneous biological interactions to understand complex traits.
  F1000Research 2015 Wang L, Himmelstein DS, Santaniello A, Parvin M, Baranzini SE
• Genetic contribution to multiple sclerosis risk among Ashkenazi Jews.
  BMC medical genetics 2015 Khankhanian P, Matsushita T, Madireddy L, Lizée A, Din L, Moré JM, Gourraud PA, Hauser SL, Baranzini SE, Oksenberg JR
• Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes.
  PLoS computational biology 2015 Himmelstein DS, Baranzini SE
• Genetic associations with brain cortical thickness in multiple sclerosis.
  Genes, brain, and behavior 2015 Matsushita T, Madireddy L, Sprenger T, Khankhanian P, Magon S, Naegelin Y, Caverzasi E, Lindberg RL, Kappos L, Hauser SL, Oksenberg JR, Henry R, Pelletier D, Baranzini SE
• A robust type I interferon gene signature from blood RNA defines quantitative but not qualitative differences between three major IFNβ drugs in the treatment of multiple sclerosis.
  Human molecular genetics 2015 Harari D, Orr I, Rotkopf R, Baranzini SE, Schreiber G
• SNP imputation bias reduces effect size determination.
  Frontiers in genetics 2015 Khankhanian P, Din L, Caillier SJ, Gourraud PA, Baranzini SE
• Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.
  Clinical genetics 2015 Slavotinek AM, Garcia ST, Chandratillake G, Bardakjian T, Ullah E, Wu D, Umeda K, Lao R, Tang PL, Wan E, Madireddy L, Lyalina S, Mendelsohn BA, Dugan S, Tirch J, Tischler R, Harris J, Clark MJ, …
• iPINBPA: an integrative network-based functional module discovery tool for genome-wide association studies.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015 Wang L, Mousavi P, Baranzini SE
• Whole genome sequences of 2 octogenarians with sustained cognitive abilities.
  Neurobiology of aging 2014 Nickles D, Madireddy L, Patel N, Isobe N, Miller BL, Baranzini SE, Kramer JH, Oksenberg JR
• Interferon-beta affects mitochondrial activity in CD4+ lymphocytes: Implications for mechanism of action in multiple sclerosis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2014 Haghikia A, Faissner S, Pappas D, Pula B, Akkad DA, Arning L, Ruhrmann S, Duscha A, Gold R, Baranzini SE, Malhotra S, Montalban X, Comabella M, Chan A
• Prognostic biomarkers of IFNb therapy in multiple sclerosis patients.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2014 Baranzini SE, Madireddy LR, Cromer A, D'Antonio M, Lehr L, Beelke M, Farmer P, Battaglini M, Caillier SJ, Stromillo ML, De Stefano N, Monnet E, Cree BA
• Modules, networks and systems medicine for understanding disease and aiding diagnosis.
  Genome medicine 2014 Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M
• Precision medicine in chronic disease management: The multiple sclerosis BioScreen.
  Annals of neurology 2014 Gourraud PA, Henry RG, Cree BA, Crane JC, Lizee A, Olson MP, Santaniello AV, Datta E, Zhu AH, Bevan CJ, Gelfand JM, Graves JS, Goodin DS, Green AJ, von Büdingen HC, Waubant E, Zamvil SS, Crabtree-…
• PINBPA: cytoscape app for network analysis of GWAS data.
  Bioinformatics (Oxford, England) 2014 Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini SE
• Rituximab efficiently depletes increased CD20-expressing T cells in multiple sclerosis patients.
  Journal of immunology (Baltimore, Md. : 1950) 2014 Palanichamy A, Jahn S, Nickles D, Derstine M, Abounasr A, Hauser SL, Baranzini SE, Leppert D, von Büdingen HC
• The role of antiproliferative gene Tob1 in the immune system.
  Clinical & experimental neuroimmunology 2014 Baranzini SE
• Blood miRNA expression pattern is a possible risk marker for natalizumab-associated progressive multifocal leukoencephalopathy in multiple sclerosis patients.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2014 Muñoz-Culla M, Irizar H, Castillo-Triviño T, Sáenz-Cuesta M, Sepúlveda L, Lopetegi I, López de Munain A, Olascoaga J, Baranzini SE, Otaegui D
• Astrocyte-encoded positional cues maintain sensorimotor circuit integrity.
  Nature 2014 Molofsky AV, Kelley KW, Tsai HH, Redmond SA, Chang SM, Madireddy L, Chan JR, Baranzini SE, Ullian EM, Rowitch DH
• Parallel states of pathological Wnt signaling in neonatal brain injury and colon cancer.
  Nature neuroscience 2014 Fancy SP, Harrington EP, Baranzini SE, Silbereis JC, Shiow LR, Yuen TJ, Huang EJ, Lomvardas S, Rowitch DH
• Naive CD4 T-cell activation identifies MS patients having rapid transition to progressive MS.
  Neurology 2014 Zastepa E, Fitz-Gerald L, Hallett M, Antel J, Bar-Or A, Baranzini S, Lapierre Y, Haegert DG
• A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility.
  Genes and immunity 2014 Damotte V, Guillot-Noel L, Patsopoulos NA, Madireddy L, El Behi M, International Multiple Sclerosis Genetics Consortium, Wellcome Trust Case Control Consortium 2, De Jager PL, Baranzini SE, Cournu-…
• The autoimmune disease-associated transcription factors EOMES and TBX21 are dysregulated in multiple sclerosis and define a molecular subtype of disease.
  Clinical immunology (Orlando, Fla.) 2014 Parnell GP, Gatt PN, Krupa M, Nickles D, McKay FC, Schibeci SD, Batten M, Baranzini S, Henderson A, Barnett M, Slee M, Vucic S, Stewart GJ, Booth DR
• Symposium 2-1  The autoimmunome: Similarities and differences among genetic susceptibility to common immune-related diseases.
  Nihon Rinsho Men'eki Gakkai kaishi = Japanese journal of clinical immunology 2014 Baranzini SE
• Sequencing of the IL6 gene in a case-control study of cerebral palsy in children.
  BMC medical genetics 2013 Khankhanian P, Baranzini SE, Johnson BA, Madireddy L, Nickles D, Croen LA, Wu YW
• Gene expression profiling in MS: a fulfilled promise?
  Multiple sclerosis (Houndmills, Basingstoke, England) 2013 Baranzini SE
• Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
  Nature genetics 2013 International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, …
• Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions.
  Glia 2013 Molofsky AV, Glasgow SM, Chaboub LS, Tsai HH, Murnen AT, Kelley KW, Fancy SP, Yuen TJ, Madireddy L, Baranzini S, Deneen B, Rowitch DH, Oldham MC
• Tob1 plays a critical role in the activation of encephalitogenic T cells in CNS autoimmunity.
  The Journal of experimental medicine 2013 Schulze-Topphoff U, Casazza S, Varrin-Doyer M, Pekarek K, Sobel RA, Hauser SL, Oksenberg JR, Zamvil SS, Baranzini SE
• Opposite roles of NMDA receptors in relapsing and primary progressive multiple sclerosis.
  PloS one 2013 Rossi S, Studer V, Moscatelli A, Motta C, Coghe G, Fenu G, Caillier S, Buttari F, Mori F, Barbieri F, Castelli M, De Chiara V, Monteleone F, Mancino R, Bernardi G, Baranzini SE, Marrosu MG, Oksenberg …
• Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls.
  Human molecular genetics 2013 Nickles D, Chen HP, Li MM, Khankhanian P, Madireddy L, Caillier SJ, Santaniello A, Cree BA, Pelletier D, Hauser SL, Oksenberg JR, Baranzini SE
• Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls.
  American journal of human genetics 2013 International Multiple Sclerosis Genetics Consortium
• Hippocampal demyelination and memory dysfunction are associated with increased levels of the neuronal microRNA miR-124 and reduced AMPA receptors.
  Annals of neurology 2013 Dutta R, Chomyk AM, Chang A, Ribaudo MV, Deckard SA, Doud MK, Edberg DD, Bai B, Li M, Baranzini SE, Fox RJ, Staugaitis SM, Macklin WB, Trapp BD
• A genome-wide association study of brain lesion distribution in multiple sclerosis.
  Brain : a journal of neurology 2013 Gourraud PA, Sdika M, Khankhanian P, Henry RG, Beheshtian A, Matthews PM, Hauser SL, Oksenberg JR, Pelletier D, Baranzini SE
• Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules.
  Neuroscience 2012 Pappas DJ, Gabatto PA, Oksenberg D, Khankhanian P, Baranzini SE, Gan L, Oksenberg JR
• In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing.
  BMC genomics 2012 Nickles D, Madireddy L, Yang S, Khankhanian P, Lincoln S, Hauser SL, Oksenberg JR, Baranzini SE
• The genetics of multiple sclerosis: an up-to-date review.
  Immunological reviews 2012 Gourraud PA, Harbo HF, Hauser SL, Baranzini SE
• Janus-like opposing roles of CD47 in autoimmune brain inflammation in humans and mice.
  The Journal of experimental medicine 2012 Han MH, Lundgren DH, Jaiswal S, Chao M, Graham KL, Garris CS, Axtell RC, Ho PP, Lock CB, Woodard JI, Brownell SE, Zoudilova M, Hunt JF, Baranzini SE, Butcher EC, Raine CS, Sobel RA, Han DK, Weissman I…
• Detection of identity by descent using next-generation whole genome sequencing data.
  BMC bioinformatics 2012 Su SY, Kasberger J, Baranzini S, Byerley W, Liao W, Oksenberg J, Sherr E, Jorgenson E
• Genetics of multiple sclerosis: swimming in an ocean of data.
  Current opinion in neurology 2012 Baranzini SE, Nickles D
• Data integration and systems biology approaches for biomarker discovery: challenges and opportunities for multiple sclerosis.
  Journal of neuroimmunology 2012 Villoslada P, Baranzini S
• iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.
  BMC bioinformatics 2011 Wang L, Khankhanian P, Baranzini SE, Mousavi P
• Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
  Nature 2011 International Multiple Sclerosis Genetics Consortium, Wellcome Trust Case Control Consortium 2, Sawcer S, Hellenthal G, Pirinen M, Spencer CC, Patsopoulos NA, Moutsianas L, Dilthey A, Su Z, Freeman C,…
• Axin2 as regulatory and therapeutic target in newborn brain injury and remyelination.
  Nature neuroscience 2011 Fancy SP, Harrington EP, Yuen TJ, Silbereis JC, Zhao C, Baranzini SE, Bruce CC, Otero JJ, Huang EJ, Nusse R, Franklin RJ, Rowitch DH
• Functional energetics of CD4+-cellular immunity in monoclonal antibody-associated progressive multifocal leukoencephalopathy in autoimmune disorders.
  PloS one 2011 Haghikia A, Perrech M, Pula B, Ruhrmann S, Potthoff A, Brockmeyer NH, Goelz S, Wiendl H, Lindå H, Ziemssen T, Baranzini SE, Käll TB, Bengel D, Olsson T, Gold R, Chan A
• Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1.
  Journal of medical genetics 2011 Slavotinek AM, Baranzini SE, Schanze D, Labelle-Dumais C, Short KM, Chao R, Yahyavi M, Bijlsma EK, Chu C, Musone S, Wheatley A, Kwok PY, Marles S, Fryns JP, Maga AM, Hassan MG, Gould DB, Madireddy L, …
• Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.
  Genome medicine 2011 Wang JH, Pappas D, De Jager PL, Pelletier D, de Bakker PI, Kappos L, Polman CH, Australian and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene), Chibnik LB, Hafler DA, Matthews PM, Hauser …
• Revealing the genetic basis of multiple sclerosis: are we there yet?
  Current opinion in genetics & development 2011 Baranzini SE
• Dynamic, multi-level network models of clinical trials.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2011 Sorani MD, Manley GT, Claude Hemphill J, Baranzini SE
• Myelin regeneration: a recapitulation of development?
  Annual review of neuroscience 2011 Fancy SP, Chan JR, Baranzini SE, Franklin RJ, Rowitch DH
• Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset.
  BMC genomics 2010 Khankhanian P, Gourraud PA, Caillier SJ, Santaniello A, Hauser SL, Baranzini SE, Oksenberg JR
• Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis.
  Brain : a journal of neurology 2010 Baranzini SE, Srinivasan R, Khankhanian P, Okuda DT, Nelson SJ, Matthews PM, Hauser SL, Oksenberg JR, Pelletier D
• Multiple sclerosis genetics--is the glass half full, or half empty?
  Nature reviews. Neurology 2010 Oksenberg JR, Baranzini SE
• Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.
  Nature 2010 Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, …
• The genetics of autoimmune diseases: a networked perspective.
  Current opinion in immunology 2009 Baranzini SE
• Differential micro RNA expression in PBMC from multiple sclerosis patients.
  PloS one 2009 Otaegui D, Baranzini SE, Armañanzas R, Calvo B, Muñoz-Culla M, Khankhanian P, Inza I, Lozano JA, Castillo-Triviño T, Asensio A, Olaskoaga J, López de Munain A
• Longitudinal system-based analysis of transcriptional responses to type I interferons.
  Physiological genomics 2009 Pappas DJ, Coppola G, Gabatto PA, Gao F, Geschwind DH, Oksenberg JR, Baranzini SE
• Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
  Nature genetics 2009 De Jager PL, Jia X, Wang J, de Bakker PI, Ottoboni L, Aggarwal NT, Piccio L, Raychaudhuri S, Tran D, Aubin C, Briskin R, Romano S, International MS Genetics Consortium, Baranzini SE, McCauley JL, …
• Dysregulation of the Wnt pathway inhibits timely myelination and remyelination in the mammalian CNS.
  Genes & development 2009 Fancy SP, Baranzini SE, Zhao C, Yuk DI, Irvine KA, Kaing S, Sanai N, Franklin RJ, Rowitch DH
• Pathway and network-based analysis of genome-wide association studies in multiple sclerosis.
  Human molecular genetics 2009 Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, Wu W, Uitdehaag BM, Kappos L, GeneMSA Consortium, Polman CH, Matthews PM, Hauser SL, Gibson RA, Oksenberg JR, Barnes MR
• Systems biology and its application to the understanding of neurological diseases.
  Annals of neurology 2009 Villoslada P, Steinman L, Baranzini SE
• Incidental MRI anomalies suggestive of multiple sclerosis: the radiologically isolated syndrome.
  Neurology 2008 Okuda DT, Mowry EM, Beheshtian A, Waubant E, Baranzini SE, Goodin DS, Hauser SL, Pelletier D
• Genotype-Phenotype correlations in multiple sclerosis: HLA genes influence disease severity inferred by 1HMR spectroscopy and MRI measures.
  Brain : a journal of neurology 2008 Okuda DT, Srinivasan R, Oksenberg JR, Goodin DS, Baranzini SE, Beheshtian A, Waubant E, Zamvil SS, Leppert D, Qualley P, Lincoln R, Gomez R, Caillier S, George M, Wang J, Nelson SJ, Cree BA, Hauser SL…
• Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
  Human molecular genetics 2008 Baranzini SE, Wang J, Gibson RA, Galwey N, Naegelin Y, Barkhof F, Radue EW, Lindberg RL, Uitdehaag BM, Johnson MR, Angelakopoulou A, Hall L, Richardson JC, Prinjha RK, Gass A, Geurts JJ, Kragt J, …
• Changes in matrix metalloproteinases and their inhibitors during interferon-beta treatment in multiple sclerosis.
  Clinical immunology (Orlando, Fla.) 2008 Comabella M, Río J, Espejo C, Ruiz de Villa M, Al-Zayat H, Nos C, Deisenhammer F, Baranzini SE, Nonell L, López C, Julià E, Oksenberg JR, Montalban X
• Uncoupling the roles of HLA-DRB1 and HLA-DRB5 genes in multiple sclerosis.
  Journal of immunology (Baltimore, Md. : 1950) 2008 Caillier SJ, Briggs F, Cree BA, Baranzini SE, Fernandez-Viña M, Ramsay PP, Khan O, Royal W, Hauser SL, Barcellos LF, Oksenberg JR
• Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological event.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Corvol JC, Pelletier D, Henry RG, Caillier SJ, Wang J, Pappas D, Casazza S, Okuda DT, Hauser SL, Oksenberg JR, Baranzini SE
• The genetics of multiple sclerosis: SNPs to pathways to pathogenesis.
  Nature reviews. Genetics 2008 Oksenberg JR, Baranzini SE, Sawcer S, Hauser SL
• A framework and mechanistically focused, in silico method for enabling rational translational research.
  Summit on translational bioinformatics 2008 Hunt CA, Baranzini S, Matthay MA, Park S
• Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets.
  Nature 2008 Han MH, Hwang SI, Roy DB, Lundgren DH, Price JV, Ousman SS, Fernald GH, Gerlitz B, Robinson WH, Baranzini SE, Grinnell BW, Raine CS, Sobel RA, Han DK, Steinman L
• Evidence for association of chromosome 10 open reading frame (C10orf27) gene polymorphisms and multiple sclerosis.
  Multiple sclerosis (Houndmills, Basingstoke, England) 2008 Goertsches R, Baranzini SE, Morcillo C, Nos C, Camiña M, Oksenberg JR, Montalban X, Comabella M
• Genome-wide pharmacogenomic analysis of the response to interferon beta therapy in multiple sclerosis.
  Archives of neurology 2008 Byun E, Caillier SJ, Montalban X, Villoslada P, Fernández O, Brassat D, Comabella M, Wang J, Barcellos LF, Baranzini SE, Oksenberg JR
• Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosis.
  Journal of immunology (Baltimore, Md. : 1950) 2007 Otaegui D, Mostafavi S, Bernard CC, Lopez de Munain A, Mousavi P, Oksenberg JR, Baranzini SE
• Quantitative longitudinal analysis of T cell receptor repertoire expression in HIV-infected patients on antiretroviral and interleukin-2 therapy.
  AIDS research and human retroviruses 2007 Sriram U, Wong M, Caillier SJ, Hecht FM, Elkins MK, Levy JA, Oksenberg JR, Baranzini SE
• Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans.
  Journal of immunology (Baltimore, Md. : 1950) 2007 Fernald GH, Knott S, Pachner A, Caillier SJ, Narayan K, Oksenberg JR, Mousavi P, Baranzini SE
• The molecular signature of therapeutic mesenchymal stem cells exposes the architecture of the hematopoietic stem cell niche synapse.
  BMC genomics 2007 Pedemonte E, Benvenuto F, Casazza S, Mancardi G, Oksenberg JR, Uccelli A, Baranzini SE
• Peroxisome proliferator-activated receptor (PPAR)alpha expression in T cells mediates gender differences in development of T cell-mediated autoimmunity.
  The Journal of experimental medicine 2007 Dunn SE, Ousman SS, Sobel RA, Zuniga L, Baranzini SE, Youssef S, Crowell A, Loh J, Oksenberg J, Steinman L
• Systems-based medicine approaches to understand and treat complex diseases. The example of multiple sclerosis.
  Autoimmunity 2006 Baranzini SE
• Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis.
  Human molecular genetics 2006 Barcellos LF, Sawcer S, Ramsay PP, Baranzini SE, Thomson G, Briggs F, Cree BC, Begovich AB, Villoslada P, Montalban X, Uccelli A, Savettieri G, Lincoln RR, DeLoa C, Haines JL, Pericak-Vance MA, …
• Predictive modeling of therapy response in multiple sclerosis using gene expression data.
  Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 2006 Mostafavi S, Baranzini S, Oksernberg J, Mousavi P
• Mapping gene activity in complex disorders: Integration of expression and genomic scans for multiple sclerosis.
  Journal of neuroimmunology 2005 Fernald GH, Yeh RF, Hauser SL, Oksenberg JR, Baranzini SE
• Modular transcriptional activity characterizes the initiation and progression of autoimmune encephalomyelitis.
  Journal of immunology (Baltimore, Md. : 1950) 2005 Baranzini SE, Bernard CC, Oksenberg JR
• Genomics and new targets for multiple sclerosis.
  Pharmacogenomics 2005 Baranzini SE, Oksenberg JR
• Longitudinal analysis of B cell repertoire and antibody gene rearrangements during early HIV infection.
  Genes and immunity 2005 Elkins MK, Vittinghoff E, Baranzini SE, Hecht FM, Sriram U, Busch MP, Levy JA, Oksenberg JR, San Francisco Primary Infection Group
• Transcription-based prediction of response to IFNbeta using supervised computational methods.
  PLoS biology 2004 Baranzini SE, Mousavi P, Rio J, Caillier SJ, Stillman A, Villoslada P, Wyatt MM, Comabella M, Greller LD, Somogyi R, Montalban X, Oksenberg JR
• Gene expression profiling in neurological disorders: toward a systems-level understanding of the brain.
  Neuromolecular medicine 2004 Baranzini SE
• Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans.
  American journal of human genetics 2003 Oksenberg JR, Barcellos LF, Cree BA, Baranzini SE, Bugawan TL, Khan O, Lincoln RR, Swerdlin A, Mignot E, Lin L, Goodin D, Erlich HA, Schmidt S, Thomson G, Reich DE, Pericak-Vance MA, Haines JL, Hauser…
• Dynamic regulation of alternative ATP-binding cassette transporter A1 transcripts.
  Biochemical and biophysical research communications 2003 Huuskonen J, Abedin M, Vishnu M, Pullinger CR, Baranzini SE, Kane JP, Fielding PE, Fielding CJ
• Osteopontin polymorphisms and disease course in multiple sclerosis.
  Genes and immunity 2003 Caillier S, Barcellos LF, Baranzini SE, Swerdlin A, Lincoln RR, Steinman L, Martin E, Haines JL, Pericak-Vance M, Hauser SL, Oksenberg JR, Multiple Sclerosis Genetics Group
• Direct deletion analysis in two Duchenne muscular dystrophy symptomatic females using polymorphic dinucleotide (CA)n loci within the dystrophin gene.
  Journal of biochemistry and molecular biology 2003 Giliberto F, Ferreiro V, Dalamón V, Surace E, Cotignola J, Esperante S, Borelina D, Baranzini S, Szijan I
• Pharmacogenomic analysis of interferon receptor polymorphisms in multiple sclerosis.
  Genes and immunity 2003 Sriram U, Barcellos LF, Villoslada P, Rio J, Baranzini SE, Caillier S, Stillman A, Hauser SL, Montalban X, Oksenberg JR
• Large-scale gene-expression studies and the challenge of multiple sclerosis.
  Genome biology 2002 Baranzini SE, Hauser SL
• The HLA locus and multiple sclerosis in Spain. Role in disease susceptibility, clinical course and response to interferon-beta.
  Journal of neuroimmunology 2002 Villoslada P, Barcellos LF, Rio J, Begovich AB, Tintore M, Sastre-Garriga J, Baranzini SE, Casquero P, Hauser SL, Montalban X, Oksenberg JR
• Gene expression analysis reveals altered brain transcription of glutamate receptors and inflammatory genes in a patient with chronic focal (Rasmussen's) encephalitis.
  Journal of neuroimmunology 2002 Baranzini SE, Laxer K, Bollen A, Oksenberg JR
• Analysis of antibody gene rearrangement, usage, and specificity in chronic focal encephalitis.
  Neurology 2002 Baranzini SE, Laxer K, Saketkhoo R, Elkins MK, Parent JM, Mantegazza R, Oksenberg JR
• New insights into the genetics of multiple sclerosis.
  Journal of rehabilitation research and development 2002 Baranzini SE, Oksenberg JR, Hauser SL
• The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease.
  Science (New York, N.Y.) 2001 Chabas D, Baranzini SE, Mitchell D, Bernard CC, Rittling SR, Denhardt DT, Sobel RA, Lock C, Karpuj M, Pedotti R, Heller R, Oksenberg JR, Steinman L
• Multiple sclerosis: genomic rewards.
  Journal of neuroimmunology 2001 Oksenberg JR, Baranzini SE, Barcellos LF, Hauser SL
• Transcriptional analysis of multiple sclerosis brain lesions reveals a complex pattern of cytokine expression.
  Journal of immunology (Baltimore, Md. : 1950) 2000 Baranzini SE, Elfstrom C, Chang SY, Butunoi C, Murray R, Higuchi R, Oksenberg JR
• B cell repertoire diversity and clonal expansion in multiple sclerosis brain lesions.
  Journal of immunology (Baltimore, Md. : 1950) 1999 Baranzini SE, Jeong MC, Butunoi C, Murray RS, Bernard CC, Oksenberg JR
• Carrier detection in Duchenne and Becker muscular dystrophy Argentine families.
  Clinical genetics 1998 Baranzini SE, Giliberto F, Dalamon V, Barreiro C, García-Erro M, Grippo J, Szijan I
• Deletion patterns in Argentine patients with Duchenne and Becker muscular dystrophy.
  Neurological research 1998 Baranzini SE, Giliberto F, Herrera M, Bernath V, Barreiro C, Garcia Erro M, Grippo J, Szijan I
• Clinical, cytogenetic, and molecular testing of Argentine patients with retinoblastoma.
  Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus 1998 Arbetman A, Abdala M, Fandiño A, Herrera J, Baranzini S, Borelina D, Parma D, Manzitti J, Barreiro C, Giliberto F, Szijan I
• Four new polymorphisms in the human dystrophin gene from an Argentinian population.
  Muscle & nerve 1997 Baranzini SE, Lenk U, Szijan I, Speer A
• Patient with an Xp21 contiguous gene deletion syndrome in association with agenesis of the corpus callosum.
  American journal of medical genetics 1997 Baranzini SE, del Rey G, Nigro N, Szijan I, Chamoles N, Cresto JC
• A new point mutation (M313T) in the thyroid hormone receptor beta gene in a patient with resistance to thyroid hormone.
  Thyroid : official journal of the American Thyroid Association 1997 di Fulvio M, Chiesa AE, Baranzini SE, Gruñiero-Papendieck L, Masini-Repiso AM, Targovnik HM