Sergio Baranzini, PhD

Professor in Residence

Neurology

+1 415 502-6865

Sergio E. Baranzini is Distinguished Professor of Neurology I at the University of California San
Francisco (UCSF). He is also a member of the Graduate Program in Bioinformatics, the Institute for
Human Genetics, the Bakar Computational Health Sciences Institute, ImmunoX, and the California
Institute for Quantitative Biology (QB3). He holds the Heidrich Friends and Family endowed chair in
Neurology. Dr. Baranzini earned his degrees in clinical biochemistry (1992) and PhD in human molecular
genetics (1997) from the University of Buenos Aires, Argentina. Dr. Baranzini then moved to UCSF to
specialize in the analysis of complex hereditary diseases, and focused his efforts on multiple sclerosis. His
current research involves the large throughput analysis of samples from MS patients to characterize the
activity of genes during different stages of the disease, differential response to treatment, and disease
progression. In addition, Dr. Baranzini collaborates 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 also 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. He also leads the iMSMS, an international consortium to study the effect of bacterial
populations (microbiota) on MS susceptibility and progression.

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 International Multiple Sclerosis Genetics Consortium,
the American Association of Immunologists, and an elected member of the American Neurological
Association and the International Society of Neuroimmunology. He is also a member of the Editorial
Board of the MS Journal, Neurology and mSystems in addition to serving as an ad-hoc reviewer for
several other scientific publications in including Nature Medicine, PNAS, and the Am J Hum Genet.

Publications:

Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation.

bioRxiv : the preprint server for biology

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, Mangalam A, Haughey N, Kornberg M, Chamling X, Calabresi PA, Bhargava P

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

Research square

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 R

Artificial intelligence in food and nutrition evidence: The challenges and opportunities.

PNAS nexus

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

Biomedical knowledge graph-optimized prompt generation for large language models.

Bioinformatics (Oxford, England)

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)

Harroud A, Sawcer SJ, Baranzini SE

Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency.

Science translational medicine

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, Huynh T, Browne W, Tubati A, Haney MS, Douglas VC, Louine M, Cree BAC, Hauser SL, Seeley W, Baranzini SE, Wells JA, Spudich S, Farhadian S, Ramachandran PS, Gillum L, Hales CM, Zikherman J, Anderson MS, Yazdany J, Smith B, Nath A, Suh G, Flanagan EP, Green AJ, Green R, Gelfand JM, DeRisi JL, Pleasure SJ, Wilson MR

Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction.

Nature communications

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, Arif S, Afsari F, Allen N, Al-Maadheed M, Altinok S, Bah N, Border S, Brown AL, Burling K, Cheng-Campbell M, Colón LM, Degoricija L, Figg N, Finch R, Foox J, Faridi P, French A, Gebre S, Gordon P, Houerbi N, Valipour Kahrood H, Kiffer FC, Klosinska AS, Kubik A, Lee HC, Li Y, Lucarelli N, Marullo AL, Matei I, McCann CM, Mimar S, Naglah A, Nicod J, O'Shaughnessy KM, Oliveira LC, Oswalt L, Patras LI, Lai Polo SH, Rodríguez-Lopez M, Roufosse C, Sadeghi-Alavijeh O, Sanchez-Hodge R, Paul AS, Schittenhelm RB, Schweickart A, Scott RT, Choy Lim Kam Sian TC, da Silveira WA, Slawinski H, Snell D, Sosa J, Saravia-Butler AM, Tabetah M, Tanuwidjaya E, Walker-Samuel S, Yang X, Zhang H, Godovac-Zimmermann J, Sarder P, Sanders LM, Costes SV, Campbell RAA, Karouia F, Mohamed-Alis V, Rodriques S, Lynham S, Steele JR, Baranzini S, Fazelinia H, Dai Z, Uruno A, Shiba D, Yamamoto M, A C Almeida E, Blaber E, Schisler JC, Eisch AJ, Muratani M, Zwart SR, Smith SM, Galazka JM, Mason CE, Beheshti A, Walsh SB

Inflammatory and neurodegenerative serum protein biomarkers increase sensitivity to detect clinical and radiographic disease activity in multiple sclerosis.

Nature communications

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, Baranzini SE

An autoantibody signature predictive for multiple sclerosis.

Nature medicine

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, Eggers EL, Zorn KC, Ananth K, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Sabatino JJ, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BAC, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR

Multiple sclerosis endophenotypes identified by high-dimensional blood signatures are associated with distinct disease trajectories.

Science translational medicine

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-Escamilla G, Gisevius B, Haas J, Kerschensteiner M, Kirstein L, Korsukewitz C, Lohmann L, Lünemann JD, Luessi F, Meyer Zu Hörste G, Motte J, Ruck T, Ruprecht K, Schwab N, Steffen F, Meuth SG, Paul F, Wildemann B, Kümpfel T, Gold R, Hahn T, Zipp F, Klotz L, Wiendl H, German Competence Network Multiple Sclerosis (KKNMS)

Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights.

Nature aging

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, Baranzini S, Sirota M

Commentary: What doesn't kill you makes you stronger . . . or does it?

Multiple sclerosis (Houndmills, Basingstoke, England)

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

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, Bernstein CN, Yeh EA, Casper TC, Lynch SV, Tremlett H, Baranzini S, Waubant E, US Network of Pediatric MS Centers

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

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, Hadlock J, Hanspers K, Hinderer E, Hobbs C, Hyde G, Huang S, Koslicki D, Mease P, Muller S, Mungall CJ, Ramsey SA, Roach J, Rubin I, Schurman SH, Shalev A, Smith B, Soman K, Stemann S, Su AI, Ta C, Watkins PB, Williams MD, Wu C, Xu CH, Biomedical Data Translator Consortium

Inflammatory and neurodegenerative serum protein biomarkers increase sensitivity to detect disease activity in multiple sclerosis.

medRxiv : the preprint server for health sciences

Locus for severity implicates CNS resilience in progression of multiple sclerosis.

Nature

International Multiple Sclerosis Genetics Consortium, MultipleMS Consortium

A Predictive Autoantibody Signature in Multiple Sclerosis.

medRxiv : the preprint server for health sciences

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, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BA, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR

Early detection of Parkinson's disease through enriching the electronic health record using a biomedical knowledge graph.

Frontiers in medicine

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

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

Shams H, Shao X, Santaniello A, Kirkish G, Harroud A, Ma Q, Isobe N, University of California San Francisco MS-EPIC Team, Schaefer C, McCauley JL, Cree BAC, Didonna A, Baranzini SE, Patsopoulos NA, Hauser SL, Barcellos LF, Henry RG, Oksenberg JR

The scalable precision medicine open knowledge engine (SPOKE): A massive knowledge graph of biomedical information.

Bioinformatics (Oxford, England)

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 A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE

Time-aware Embeddings of Clinical Data using a Knowledge Graph.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

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

iMSMS Consortium. Electronic address: [email protected], iMSMS Consortium

The role of the gut microbiota in multiple sclerosis.

Nature reviews. Neurology

Correale J, Hohlfeld R, Baranzini SE

FutureMS cohort profile: a Scottish multicentre inception cohort study of relapsing-remitting multiple sclerosis.

BMJ open

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 NJJ, Baranzini SE, Waldman AD, Connick P, Chandran S

Progress Toward a Universal Biomedical Data Translator.

Clinical and translational science

Fecho K, Thessen AT, 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, Hyde G, Johs A, Su A, Qin G, Zhu Q, Biomedical Data Translator Consortium

A biomedical open knowledge network harnesses the power of AI to understand deep human biology.

AI magazine

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, Huang 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

Nelson CA, Bove R, Butte AJ, Baranzini SE

Classification of neurological diseases using multi-dimensional cerebrospinal fluid analysis.

Brain : a journal of neurology

Distinctive waves of innate immune response in the retina in experimental autoimmune encephalomyelitis.

JCI insight

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)

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

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

The relative contributions of obesity, vitamin D, leptin, and adiponectin to multiple sclerosis risk: A Mendelian randomization mediation analysis.

Multiple sclerosis (Houndmills, Basingstoke, England)

Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases.

Life (Basel, Switzerland)

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

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 G, Liesche-Starnecker F, Ramaglia V, Singh S, Tran EB, Barba P, Zorn K, Oechtering J, Forsberg K, Shiow LR, Henry RG, Graves J, Cree BAC, Hauser SL, Kuhle J, Gelfand JM, Andersen PM, Schlegel J, Turnbaugh PJ, Seeberger PH, Gommerman JL, Wilson MR, Schirmer L, Baranzini SE

Mendelian randomization study shows no causal effects of serum urate levels on the risk of MS.

Neurology(R) neuroimmunology & neuroinflammation

Harroud A, Richards JB, Baranzini SE

Levels of brain-derived neurotrophic factor in patients with multiple sclerosis.

Annals of clinical and translational neurology

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

Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D

SARS-CoV-2 meta-interactome suggests disease-specific, autoimmune pathophysiologies and therapeutic targets.

F1000Research

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)

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

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)

Mycko MP, Baranzini SE

Early complement genes are associated with visual system degeneration in multiple sclerosis.

Brain : a journal of neurology

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 Jager PL, Calabresi PA

Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia.

Scientific reports

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, Yokoyama JS

Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.

Nature communications

Nelson CA, Butte AJ, Baranzini SE

Aberrant oligodendroglial-vascular interactions disrupt the blood-brain barrier, triggering CNS inflammation.

Nature neuroscience

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

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, Burrows K, Robinson HG, Allanach JR, Yam J, Luck H, Campbell DJ, Allman D, Brooks DG, Tomura M, Baumann R, Zamvil SS, Bar-Or A, Horwitz MS, Winer DA, Mortha A, Mackay F, Prat A, Osborne LC, Robbins C, Baranzini SE, Gommerman JL

Silent Progression in Disease Activity-Free Relapsing Multiple Sclerosis.

Annals of neurology

Insights into microbiome research 6: The role of consortia in studying the role of microbes in health and disease.

Multiple sclerosis (Houndmills, Basingstoke, England)

Baranzini SE

Insights into microbiome research 5: Mapping is first but function must come next.

Multiple sclerosis (Houndmills, Basingstoke, England)

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

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

Insights into microbiome research 4: The computational analysis.

Multiple sclerosis (Houndmills, Basingstoke, England)

Baranzini SE

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria.

mSystems

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

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)

Baranzini SE

Insights into microbiome research 3: Who's there versus what are they doing?

Multiple sclerosis (Houndmills, Basingstoke, England)

Baranzini SE

Protein network analysis reveals selectively vulnerable regions and biological processes in FTD.

Neurology. Genetics

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)

Baranzini SE

Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis.

Annals of neurology

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

Gafson AR, Kim K, Cencioni MT, van Hecke W, Nicholas R, Baranzini SE, Matthews PM

Correction: Peroxisome proliferator-activated receptor (PPAR)a expression in T cells mediates gender differences in development of T cell-mediated autoimmunity.

The Journal of experimental medicine

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)

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)

Katz Sand I, Baranzini SE

Harnessing electronic medical records to advance research on multiple sclerosis.

Multiple sclerosis (Houndmills, Basingstoke, England)

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, Baranzini SE, Cree BA, Henry RG, Hauser SL, Gelfand JM, Gourraud PA

The Gut Microbiome in Neuromyelitis Optica.

Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics

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

Pröbstel AK, Baranzini SE

The era of GWAS is over - Commentary.

Multiple sclerosis (Houndmills, Basingstoke, England)

Baranzini SE

The Genetics of Multiple Sclerosis: From 0 to 200 in 50 Years.

Trends in genetics : TIG

Baranzini SE, Oksenberg JR

Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

eLife

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

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, Baranzini SE

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

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

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, Booth DR

The autoimmune risk gene ZMIZ1 is a vitamin D responsive marker of a molecular phenotype of multiple sclerosis.

Journal of autoimmunity

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, Booth DR

IFN-? 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

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

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

Didonna A, Cekanaviciute E, Oksenberg JR, Baranzini SE

Long-term evolution of multiple sclerosis disability in the treatment era.

Annals of neurology

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 Büdingen HC, Zamvil SS, Agrawal A, Caillier S, Ciocca C, Gomez R, Kanner R, Lincoln R, Lizee A, Qualley P, Santaniello A, Suleiman L, Bucci M, Panara V, Papinutto N, Stern WA, Zhu AH, Cutter GR, Baranzini S, Henry RG, Hauser SL

Gut microbiome analysis in neuromyelitis optica reveals overabundance of Clostridium perfringens.

Annals of neurology

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

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

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, Cocco P, Maynadié M, Foretová L, Staines A, Delahaye-Sourdeix M, Li D, Bhatia S, Melbye M, Onel K, Jarrett R, McKay JD, Oksenberg JR, Hjalgrim H

A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.

Science translational medicine

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, Mellergård J, Mendez M, Olsson T, Pujana MA, Rasool O, Serra-Musach J, Stenmarker M, Tripathi S, Viitala M, Wang H, Zhang H, Nestor CE, Benson M

Assessing the Power of Exome Chips.

PloS one

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

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

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, Cotsapas C, D'Alfonso S, Dendrou CA, Donnelly P, Dubois B, Fontaine B, Fugger L, Goris A, Gourraud PA, Graetz C, Hemmer B, Hillert J, Kockum I, Leslie S, Lill CM, Martinelli-Boneschi F, Oksenberg JR, Olsson T, Oturai A, Saarela J, Søndergaard HB, Spurkland A, Taylor B, Winkelmann J, Zipp F, Haines JL, Pericak-Vance MA, Spencer CCA, Stewart G, Hafler DA, Ivinson AJ, Harbo HF, Hauser SL, De Jager PL, Compston A, McCauley JL, Sawcer S, McVean G

iCTNet2: integrating heterogeneous biological interactions to understand complex traits.

F1000Research

Wang L, Himmelstein DS, Santaniello A, Parvin M, Baranzini SE

Genetic contribution to multiple sclerosis risk among Ashkenazi Jews.

BMC medical genetics

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

Himmelstein DS, Baranzini SE

Genetic associations with brain cortical thickness in multiple sclerosis.

Genes, brain, and behavior

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 IFNß drugs in the treatment of multiple sclerosis.

Human molecular genetics

Harari D, Orr I, Rotkopf R, Baranzini SE, Schreiber G

SNP imputation bias reduces effect size determination.

Frontiers in genetics

Khankhanian P, Din L, Caillier SJ, Gourraud PA, Baranzini SE

Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.

Clinical genetics

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, Chervitz S, Patwardhan A, West JM, Ursell P, de Alba Campomanes A, Schneider A, Kwok PY, Baranzini S, Chen RO

iPINBPA: an integrative network-based functional module discovery tool for genome-wide association studies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Wang L, Mousavi P, Baranzini SE

Whole genome sequences of 2 octogenarians with sustained cognitive abilities.

Neurobiology of aging

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)

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)

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

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

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-Hartman E, Nelson S, Baranzini SE, Hauser SL

PINBPA: cytoscape app for network analysis of GWAS data.

Bioinformatics (Oxford, England)

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)

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

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)

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

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

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

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

Damotte V, Guillot-Noel L, Patsopoulos NA, Madireddy L, El Behi M, De Jager PL, Baranzini SE, Cournu-Rebeix I, Fontaine B

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.)

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

Baranzini SE

Sequencing of the IL6 gene in a case-control study of cerebral palsy in children.

BMC medical genetics

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)

Baranzini SE

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.

Nature genetics

Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelcic I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL

Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions.

Glia

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

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

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 JR, Centonze D

Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls.

Human molecular genetics

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

Hippocampal demyelination and memory dysfunction are associated with increased levels of the neuronal microRNA miR-124 and reduced AMPA receptors.

Annals of neurology

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

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

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

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

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

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, Steinman L

Detection of identity by descent using next-generation whole genome sequencing data.

BMC bioinformatics

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

Baranzini SE, Nickles D

Data integration and systems biology approaches for biomarker discovery: challenges and opportunities for multiple sclerosis.

Journal of neuroimmunology

Villoslada P, Baranzini S

iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.

BMC bioinformatics

Wang L, Khankhanian P, Baranzini SE, Mousavi P

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Nature

Sawcer S, Hellenthal G, Pirinen M, Spencer CC, Patsopoulos NA, Moutsianas L, Dilthey A, Su Z, Freeman C, Hunt SE, Edkins S, Gray E, Booth DR, Potter SC, Goris A, Band G, Oturai AB, Strange A, Saarela J, Bellenguez C, Fontaine B, Gillman M, Hemmer B, Gwilliam R, Zipp F, Jayakumar A, Martin R, Leslie S, Hawkins S, Giannoulatou E, D'alfonso S, Blackburn H, Martinelli Boneschi F, Liddle J, Harbo HF, Perez ML, Spurkland A, Waller MJ, Mycko MP, Ricketts M, Comabella M, Hammond N, Kockum I, McCann OT, Ban M, Whittaker P, Kemppinen A, Weston P, Hawkins C, Widaa S, Zajicek J, Dronov S, Robertson N, Bumpstead SJ, Barcellos LF, Ravindrarajah R, Abraham R, Alfredsson L, Ardlie K, Aubin C, Baker A, Baker K, Baranzini SE, Bergamaschi L, Bergamaschi R, Bernstein A, Berthele A, Boggild M, Bradfield JP, Brassat D, Broadley SA, Buck D, Butzkueven H, Capra R, Carroll WM, Cavalla P, Celius EG, Cepok S, Chiavacci R, Clerget-Darpoux F, Clysters K, Comi G, Cossburn M, Cournu-Rebeix I, Cox MB, Cozen W, Cree BA, Cross AH, Cusi D, Daly MJ, Davis E, de Bakker PI, Debouverie M, D'hooghe MB, Dixon K, Dobosi R, Dubois B, Ellinghaus D, Elovaara I, Esposito F, Fontenille C, Foote S, Franke A, Galimberti D, Ghezzi A, Glessner J, Gomez R, Gout O, Graham C, Grant SF, Guerini FR, Hakonarson H, Hall P, Hamsten A, Hartung HP, Heard RN, Heath S, Hobart J, Hoshi M, Infante-Duarte C, Ingram G, Ingram W, Islam T, Jagodic M, Kabesch M, Kermode AG, Kilpatrick TJ, Kim C, Klopp N, Koivisto K, Larsson M, Lathrop M, Lechner-Scott JS, Leone MA, Leppä V, Liljedahl U, Bomfim IL, Lincoln RR, Link J, Liu J, Lorentzen AR, Lupoli S, Macciardi F, Mack T, Marriott M, Martinelli V, Mason D, McCauley JL, Mentch F, Mero IL, Mihalova T, Montalban X, Mottershead J, Myhr KM, Naldi P, Ollier W, Page A, Palotie A, Pelletier J, Piccio L, Pickersgill T, Piehl F, Pobywajlo S, Quach HL, Ramsay PP, Reunanen M, Reynolds R, Rioux JD, Rodegher M, Roesner S, Rubio JP, Rückert IM, Salvetti M, Salvi E, Santaniello A, Schaefer CA, Schreiber S, Schulze C, Scott RJ, Sellebjerg F, Selmaj KW, Sexton D, Shen L, Simms-Acuna B, Skidmore S, Sleiman PM, Smestad C, Sørensen PS, Søndergaard HB, Stankovich J, Strange RC, Sulonen AM, Sundqvist E, Syvänen AC, Taddeo F, Taylor B, Blackwell JM, Tienari P, Bramon E, Tourbah A, Brown MA, Tronczynska E, Casas JP, Tubridy N, Corvin A, Vickery J, Jankowski J, Villoslada P, Markus HS, Wang K, Mathew CG, Wason J, Palmer CN, Wichmann HE, Plomin R, Willoughby E, Rautanen A, Winkelmann J, Wittig M, Trembath RC, Yaouanq J, Viswanathan AC, Zhang H, Wood NW, Zuvich R, Deloukas P, Langford C, Duncanson A, Oksenberg JR, Pericak-Vance MA, Haines JL, Olsson T, Hillert J, Ivinson AJ, De Jager PL, Peltonen L, Stewart GJ, Hafler DA, Hauser SL, McVean G, Donnelly P, Compston A

Axin2 as regulatory and therapeutic target in newborn brain injury and remyelination.

Nature neuroscience

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

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

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, Li C, Cox TC, Smyth I, Chudley AE, Zenker M

Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.

Genome medicine

Wang JH, Pappas D, De Jager PL, Pelletier D, de Bakker PI, Kappos L, Polman CH, Chibnik LB, Hafler DA, Matthews PM, Hauser SL, Baranzini SE, Oksenberg JR

Revealing the genetic basis of multiple sclerosis: are we there yet?

Current opinion in genetics & development

Baranzini SE

Dynamic, multi-level network models of clinical trials.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Sorani MD, Manley GT, Claude Hemphill J, Baranzini SE

Myelin regeneration: a recapitulation of development?

Annual review of neuroscience

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

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

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

Oksenberg JR, Baranzini SE

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.

Nature

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, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF

The genetics of autoimmune diseases: a networked perspective.

Current opinion in immunology

Baranzini SE

Differential micro RNA expression in PBMC from multiple sclerosis patients.

PloS one

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

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

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, Baranzini SE, McCauley JL, Pericak-Vance MA, Haines JL, Gibson RA, Naeglin Y, Uitdehaag B, Matthews PM, Kappos L, Polman C, McArdle WL, Strachan DP, Evans D, Cross AH, Daly MJ, Compston A, Sawcer SJ, Weiner HL, Hauser SL, Hafler DA, Oksenberg JR

Dysregulation of the Wnt pathway inhibits timely myelination and remyelination in the mammalian CNS.

Genes & development

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

Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, Wu W, Uitdehaag BM, Kappos L, 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

Villoslada P, Steinman L, Baranzini SE

Incidental MRI anomalies suggestive of multiple sclerosis: the radiologically isolated syndrome.

Neurology

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

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, Pelletier D

Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.

Human molecular genetics

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, Sombekke M, Vrenken H, Qualley P, Lincoln RR, Gomez R, Caillier SJ, George MF, Mousavi H, Guerrero R, Okuda DT, Cree BA, Green AJ, Waubant E, Goodin DS, Pelletier D, Matthews PM, Hauser SL, Kappos L, Polman CH, Oksenberg JR

Changes in matrix metalloproteinases and their inhibitors during interferon-beta treatment in multiple sclerosis.

Clinical immunology (Orlando, Fla.)

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)

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

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

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

Hunt CA, Baranzini S, Matthay MA, Park S

Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets.

Nature

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)

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

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)

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

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)

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

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

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

Baranzini SE

Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis.

Human molecular genetics

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, Compston A, Hauser SL, Oksenberg JR

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

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

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)

Baranzini SE, Bernard CC, Oksenberg JR

Genomics and new targets for multiple sclerosis.

Pharmacogenomics

Baranzini SE, Oksenberg JR

Longitudinal analysis of B cell repertoire and antibody gene rearrangements during early HIV infection.

Genes and immunity

Elkins MK, Vittinghoff E, Baranzini SE, Hecht FM, Sriram U, Busch MP, Levy JA, Oksenberg JR

Transcription-based prediction of response to IFNbeta using supervised computational methods.

PLoS biology

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

Baranzini SE

Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans.

American journal of human genetics

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 SL

Dynamic regulation of alternative ATP-binding cassette transporter A1 transcripts.

Biochemical and biophysical research communications

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

Caillier S, Barcellos LF, Baranzini SE, Swerdlin A, Lincoln RR, Steinman L, Martin E, Haines JL, Pericak-Vance M, Hauser SL, Oksenberg JR

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

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

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

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

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

Baranzini SE, Laxer K, Bollen A, Oksenberg JR

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Sergio Baranzini, PhD