Oliver Hofmann

Senior Research Scientist (Bioinformatics)

Harvard School of Public Health

I am a Senior Research Scientist in the Department of Biostatistics at HSPH, an Affiliated Faculty member of the HSCI and the Associate Director of the HSPH Bioinformatics Core. I started my research in a molecular biology wetlab environment before switching to natural language processing, database development and curation as part of my PhD thesis, eventually branching out to sequence clustering and pattern recognition as a visiting researcher at deCODE Genetics. My work as a postdoctoral fellow at the South African National Bioinformatics Institute focused on data integration (eVOC ontology), second-generation sequencing analysis and network analysis.

Publications

  • Chronic endotoxin exposure produces airflow obstruction and lung dendritic cell expansion DOI: 10.1165/rcmb.2011-0447OC
  • Population differences in transcript-regulator expression quantitative trait loci DOI: 10.1371/journal.pone.0034286
  • Population differences in transcript-regulator expression quantitative trait loci DOI: 10.1371/journal.pone.0034286
  • Prenatal Lead Levels, Plasma Amyloid β Levels and Gene Expression in Young Adulthood DOI: 10.1289/ehp.1104474
  • Prenatal lead levels, plasma amyloid β levels, and gene expression in young adulthood
  • Prenatal lead levels, plasma amyloid β levels, and gene expression in young adulthood DOI: 10.1289/ehp.1104474
  • The stem cell discovery engine: An integrated repository and analysis system for cancer stem cell comparisons DOI: 10.1093/nar/gkr1051
  • The stem cell discovery engine: An integrated repository and analysis system for cancer stem cell comparisons DOI: 10.1093/nar/gkr1051
  • Toward interoperable bioscience data DOI: 10.1038/ng.1054
  • A functional genomic screen reveals novel host genes that mediate interferon-alpha's effects against hepatitis C virus DOI: 10.1016/j.jhep.2011.07.026
  • Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity DOI: 10.1038/nature09968
  • Capture of MicroRNA-Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling DOI: 10.1371/journal.pgen.1002363
  • The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons DOI: 10.1093/nar/gkr1051
  • A quick guide to large-scale genomic data mining DOI: 10.1371/journal.pcbi.1000779
  • An atlas of combinatorial transcriptional regulation in mouse and man DOI: 10.1016/j.cell.2010.01.044
  • ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level DOI: 10.1093/bioinformatics/btq415
  • Live Coverage of Intelligent Systems for Molecular Biology/European Conference on computational biology (ISMB/ECCB) 2009 DOI: 10.1371/journal.pcbi.1000640
  • Live coverage of scientific conferences using web technologies DOI: 10.1371/journal.pcbi.1000563
  • Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis DOI: 10.1038/ng.609
  • ASTD: The Alternative Splicing and Transcript Diversity database DOI: 10.1016/j.ygeno.2008.11.003
  • miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements DOI: 10.1016/j.molcel.2009.08.020
  • miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements (Supplement) DOI: 10.1016/j.molcel.2009.08.020
  • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line DOI: 10.1038/ng.375
  • ASTD: the Alternative Splicing and Transcript Diversity Database
  • Genome-wide analysis of cancer/testis gene expression DOI: 10.1073/pnas.0810777105
  • Human Proteinpedia enables sharing of human protein data DOI: 10.1038/nbt0208-164
  • Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of myasthenia gravis DOI: 10.1186/1471-2164-9-481
  • Computational selection and prioritization of candidate genes for fetal alcohol syndrome DOI: 10.1186/1471-2164-8-389
  • Simplified ontologies allowing comparison of developmental mammalian gene expression DOI: 10.1186/gb-2007-8-10-r229
  • The LIFEdb database in 2006 DOI: 10.1093/nar/gkj139
  • Concept-based annotation of enzyme classes DOI: 10.1093/bioinformatics/bti284
  • BRENDA: a resource for enzyme data and metabolic information DOI: 10.1016/S0968-0004(01)02027-8
  • BRENDA: a resource for enzyme data and metabolic information DOI: 10.1016/S0968-0004(01)02027-8
  • A Quick Guide to Large-Scale Genomic Data Mining DOI: 10.1371/journal.pcbi.1000779
  • A Quick Guide to Large-Scale Genomic Data Mining DOI: 10.1371/journal.pcbi.1000779
  • Simplified ontologies allowing comparison of developmental mammalian gene expression DOI: 10.1186/gb-2007-8-10-r229
  • Simplified ontologies allowing comparison of developmental mammalian gene expression DOI: 10.1186/gb-2007-8-10-r229

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Co-workers & collaborators

Brad Chapman

Brad Chapman

Oliver Hofmann's public data