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    Henrik Bengtsson, PhD, MS

    TitleAssociate Professor
    SchoolUCSF School of Medicine
    DepartmentEpidemiology & Biostatistics
    Address550 16th. Street
    San Francisco CA 94158
    Phone415-514-8033
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Capurso D, Bengtsson H, Segal MR. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res. 2016 Mar 18; 44(5):2028-35. PMID: 26869583.
        View in: PubMed
      2. Segal MR, Bengtsson HL. Reconstruction of 3D genome architecture via a two-stage algorithm. BMC Bioinformatics. 2015; 16:373. PMID: 26553003; PMCID: PMC4638111.
      3. Pollett S, Wood N, Boscardin WJ, Bengtsson H, Schwarcz S, Harriman K, Winter K, Rutherford G. Validating the Use of Google Trends to Enhance Pertussis Surveillance in California. PLoS Curr. 2015; 7. PMID: 26543674; PMCID: PMC4626035.
      4. Soroceanu L, Matlaf L, Khan S, Akhavan A, Singer E, Bezrookove V, Decker S, Ghanny S, Hadaczek P, Bengtsson H, Ohlfest J, Luciani-Torres MG, Harkins L, Perry A, Guo H, Soteropoulos P, Cobbs CS. Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma. Cancer Res. 2015 Aug 1; 75(15):3065-76. PMID: 26239477; PMCID: PMC4526117 [Available on 08/01/16].
      5. Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 2014 Dec; 24(12):2022-32. PMID: 25236618; PMCID: PMC4248318.
      6. Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Res. 2013; 2:264. PMID: 24701342; PMCID: PMC3968891.
      7. Ortiz-Estevez M, Aramburu A, Bengtsson H, Neuvial P, Rubio A. CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. Bioinformatics. 2012 Jul 1; 28(13):1793-4. PMID: 22576175; PMCID: PMC3381965.
      8. Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R. Querying genomic databases: refining the connectivity map. Stat Appl Genet Mol Biol. 2012; 11(2). PMID: 22499690.
        View in: PubMed
      9. Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG. Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res. 2011 Nov 15; 17(22):7024-34. PMID: 22068658; PMCID: PMC3226754.
      10. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2724-9. PMID: 22003129; PMCID: PMC3286973.
      11. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 30; 474(7353):609-15. PMID: 21720365; PMCID: PMC3163504.
      12. Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011 Aug 1; 27(15):2038-46. PMID: 21666266; PMCID: PMC3137217.
      13. White S, Ohnesorg T, Notini A, Roeszler K, Hewitt J, Daggag H, Smith C, Turbitt E, Gustin S, van den Bergen J, Miles D, Western P, Arboleda V, Schumacher V, Gordon L, Bell K, Bengtsson H, Speed T, Hutson J, Warne G, Harley V, Koopman P, Vilain E, Sinclair A. Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. PLoS One. 2011; 6(3):e17793. PMID: 21408189; PMCID: PMC3049794.
      14. Sutton E, Hughes J, White S, Sekido R, Tan J, Arboleda V, Rogers N, Knower K, Rowley L, Eyre H, Rizzoti K, McAninch D, Goncalves J, Slee J, Turbitt E, Bruno D, Bengtsson H, Harley V, Vilain E, Sinclair A, Lovell-Badge R, Thomas P. Identification of SOX3 as an XX male sex reversal gene in mice and humans. J Clin Invest. 2011 Jan; 121(1):328-41. PMID: 21183788; PMCID: PMC3007141.
      15. Ortiz-Estevez M, Bengtsson H, Rubio A. ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. Bioinformatics. 2010 Aug 1; 26(15):1827-33. PMID: 20529889; PMCID: PMC2913655.
      16. Bengtsson H, Neuvial P, Speed TP. TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics. 2010; 11:245. PMID: 20462408; PMCID: PMC2894037.
      17. Carmichael CL, Wilkins EJ, Bengtsson H, Horwitz MS, Speed TP, Vincent PC, Young G, Hahn CN, Escher R, Scott HS. Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes. Br J Haematol. 2010 Aug; 150(3):382-5. PMID: 20456351.
        View in: PubMed
      18. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010 May 18; 17(5):510-22. PMID: 20399149; PMCID: PMC2872684.
      19. Jongmans MC, Kuiper RP, Carmichael CL, Wilkins EJ, Dors N, Carmagnac A, Schouten-van Meeteren AY, Li X, Stankovic M, Kamping E, Bengtsson H, Schoenmakers EF, van Kessel AG, Hoogerbrugge PM, Hahn CN, Brons PP, Scott HS, Hoogerbrugge N. Novel RUNX1 mutations in familial platelet disorder with enhanced risk for acute myeloid leukemia: clues for improved identification of the FPD/AML syndrome. Leukemia. 2010 Jan; 24(1):242-6. PMID: 19946261.
        View in: PubMed
      20. Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics. 2009 Sep 1; 25(17):2149-56. PMID: 19535535; PMCID: PMC2734319.
      21. Bengtsson H, Ray A, Spellman P, Speed TP. A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics. 2009 Apr 1; 25(7):861-7. PMID: 19193730; PMCID: PMC2660872.
      22. Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics. 2008 Mar 15; 24(6):759-67. PMID: 18204055.
        View in: PubMed
      23. Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr; 8(2):485-99. PMID: 17189563.
        View in: PubMed
      24. Bengtsson H, Hössjer O. Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. BMC Bioinformatics. 2006; 7:100. PMID: 16509971; PMCID: PMC1534066.
      25. Bengtsson A, Bengtsson H. Microarray image analysis: background estimation using quantile and morphological filters. BMC Bioinformatics. 2006; 7:96. PMID: 16504173; PMCID: PMC1525206.
      26. Bengtsson H, Jönsson G, Vallon-Christersson J. Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinformatics. 2004 Nov 12; 5:177. PMID: 15541170; PMCID: PMC539274.
      27. Bengtsson H. . Low-level analysis of microarray data, PhD thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University. 2004.
      28. Bengtsson H. . The R.oo package - Object-Oriented Programming with References Using Standard R Code. 3rd International Workshop on Distributed Statistical Computing (DSC 2003), Kurt Hornik and Friedrich Leisch and Achim Zeileis (Eds.). 2003.
      29. Bengtsson H, Calder B, Mian IS, Callow M, Rubin E, Speed TP. Identifying differentially expressed genes in cDNA microarray experiments authors. Sci Aging Knowledge Environ. 2001 Dec 19; 2001(12):vp8. PMID: 14602959.
        View in: PubMed
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