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Henrik Bengtsson, PhD, MS

Title(s)Associate Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
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. Pamela Paris, Matthew R. Cooperberg, Janet Cowan, Karla Lindquist, Yasuko Kobayashi, Jeff Simko, Henrik Bengtsson, Khushboo L Singh, Lisa F. Newcomb, Daniel W. Lin, Peter Carroll. A multibiomarker approach to predict prostate cancer pathology outcomes. Journal of Clinical Oncology. 2019 Mar 1; 37(7_suppl):58-58.
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    2. Segal MR, Bengtsson HL. Improved accuracy assessment for 3D genome reconstructions. BMC Bioinformatics. 2018 05 30; 19(1):196. PMID: 29848293.
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    3. Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi MK, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon DA, Costello JF. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol. 2018 04 09; 20(5):632-641. PMID: 29077933.
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    4. Puri S, Roy N, Russ HA, Leonhardt L, French EK, Roy R, Bengtsson H, Scott DK, Stewart AF, Hebrok M. Replication confers ß cell immaturity. Nat Commun. 2018 02 02; 9(1):485. PMID: 29396395.
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    5. Stephanie Hilz, Samuel J Shelton, Llewellyn Jalbert, Hang K Wong, Tali Mazor, Chibo Hong, Josie Hayes, Tracy Luks, Henrik Bengtsson, Annette Molinaro, Michael McDermott, Mitchel S Berger, Daniel Lim, Aaron Diaz, Joanna J Phillips, Susan Chang, Sarah Nelson, Michael C Oldham, Joseph Costello. GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi99-vi99.
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    6. Nguyen HG, Welty C, Lindquist K, Ngo V, Gilbert E, Bengtsson H, Magi-Galluzzi C, Jean-Gilles J, Yao J, Cooperberg M, Messing E, Klein EA, Carroll PR, Paris PL. Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy. J Urol. 2018 03; 199(3):719-725. PMID: 28941923.
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    7. Mazor T, Chesnelong C, Pankov A, Jalbert LE, Hong C, Hayes J, Smirnov IV, Marshall R, Souza CF, Shen Y, Viswanath P, Noushmehr H, Ronen SM, Jones SJM, Marra MA, Cairncross JG, Perry A, Nelson SJ, Chang SM, Bollen AW, Molinaro AM, Bengtsson H, Olshen AB, Weiss S, Phillips JJ, Luchman HA, Costello JF. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. Proc Natl Acad Sci U S A. 2017 10 03; 114(40):10743-10748. PMID: 28916733.
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    8. Hao Nguyen, Christopher Welty, Karla Lindquist, Vy Ngo, Elizabeth Gilbert, Henrik Bengtsson, Cristina Magi-Galluzzi, Jerome Jean Gilles, Jorge Yao, Matthew Cooperberg, Edward Messing, Eric Klein, Peter Carroll, Pamela Paris. PD71-05 VALIDATION OF GEMCAP AS A DNA BASED BIOMARKER TO PREDICT PROSTATE CANCER RECURRENCE AFTER RADICAL PROSTATECTOMY. The Journal of Urology. 2017 Apr 1; 197(4):e1357.
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    9. Hao Gia Nguyen, Christopher Welty, Karla Lindquist, Vy Ngo, Elizabeth Gilbert, Henrik Bengtsson, Cristina Magi-Galluzzi, Jerome Jean-Gilles, Jorge Yao, Matthew R. Cooperberg, Edward M. Messing, Eric A. Klein, Peter Carroll, Pamela Paris. Validation of GEMCaP as a DNA based biomarker to predict disease recurrence in patients undergoing prostatectomy for prostate cancer. Journal of Clinical Oncology. 2017 Feb 20; 35(6_suppl):58-58.
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    10. Tali Mazor, Llewellyn Jalbert, Aleksandr Pankov, Chibo Hong, Josie Hayes, Ivan Smirnov, Roxanne Marshall, Arie Perry, Sarah Nelson, Susan Chang, Andrew Bollen, Annette Molinaro, Henrik Bengtsson, Adam Olshen, Joanna Phillips, Joseph Costello. GENT-05. DELETION OR AMPLIFICATION OF MUTANT IDH1 IS ASSOCIATED WITH EXTREME DNA HYPOMETHYLATION AND MALIGNANT PROGRESSION. Neuro-Oncology. 2016 Nov 1; 18(suppl_6):vi74-vi74.
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    11. 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.
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    12. Simon Pollett, Nicholas Wood, W. John Boscardin, Henrik Bengtsson, George Rutherford. Validating the Use of Google Enquiry Metadata to Enhance Pertussis Surveillance in Australia. Open Forum Infectious Diseases. 2015 Dec 9; 2(suppl_1):1818.
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    13. Segal MR, Bengtsson HL. Reconstruction of 3D genome architecture via a two-stage algorithm. BMC Bioinformatics. 2015 Nov 09; 16:373. PMID: 26553003.
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    14. Tali Mazor, Brett E. Johnson, Matt Grimmer, Chibo Hong, Emily G. Hamilton, Lindsey E. Jones, Ana Xavier-Magalhães, Ivan V. Smirnov, Henrik Bengtsson, Adam B. Olshen, Kevin Petrecca, Andrew W. Bollen, Mitchel S. Berger, Barry S. Taylor, Sarah J. Nelson, Manish K. Aghi, Jennifer L. Clarke, Joanna J. Phillips, Susan M. Chang, Joseph F. Costello. GENO-25HYPERMUTATION AND MALIGNANT PROGRESSION IN AN EXPANDED COHORT OF TEMOZOLOMIDE-TREATED LOW-GRADE GLIOMA PATIENTS. Neuro-Oncology. 2015 Nov 1; 17(suppl_5):v97-v97.
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    15. 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 Oct 19; 7. PMID: 26543674.
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    16. 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 01; 75(15):3065-76. PMID: 26239477.
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    17. 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.
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    18. 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.
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    19. Won Kim, Adam Foye, Henrik Bengtsson, Hyunsung John Kim, Barry S. Taylor, Nader Pourmand, Phillip G. Febbo. Feasibility of RNA sequencing to detect TMPRSS2:ERG fusions following laser capture microdissection of prostate cancer. Journal of Clinical Oncology. 2013 Feb 20; 31(6_suppl):76-76.
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    20. 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 01; 28(13):1793-4. PMID: 22576175.
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    21. Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R. Querying genomic databases: refining the connectivity map. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(2). PMID: 22499690.
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    22. 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.
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    23. 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.
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    24. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. PMID: 21720365.
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    25. 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 01; 27(15):2038-46. PMID: 21666266.
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    26. 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 Mar 07; 6(3):e17793. PMID: 21408189.
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    27. Pierre Neuvial, Henrik Bengtsson, Terence P. Speed. Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies. Handbook of Statistical Bioinformatics. 2011 Jan 1; 225-255.
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    28. 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.
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    29. Ortiz-Estevez M, Bengtsson H, Rubio A. ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. Bioinformatics. 2010 Aug 01; 26(15):1827-33. PMID: 20529889.
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    30. 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 May 12; 11:245. PMID: 20462408.
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    31. 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.
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    32. 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.
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    33. 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.
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    34. 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 01; 25(17):2149-56. PMID: 19535535.
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    35. 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 01; 25(7):861-7. PMID: 19193730.
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    36. 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.
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    37. 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.
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    38. 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 Mar 01; 7:100. PMID: 16509971.
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    39. Bengtsson A, Bengtsson H. Microarray image analysis: background estimation using quantile and morphological filters. BMC Bioinformatics. 2006 Feb 28; 7:96. PMID: 16504173.
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    40. 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.
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    41. Bengtsson H.. Low-level analysis of microarray data, PhD thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University. 2004.
    42. 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.
    43. 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.
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