University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Henrik Bengtsson, PhD, MS

Henrik Bengtsson, PhD, MS

Assistant Professor, Dept. of Epidemiology & Biostatistics, UCSF

Selected Publications

  1. Segal MR, Bengtsson HL. Improved accuracy assessment for 3D genome reconstructions. BMC Bioinformatics. 2018 May 30; 19(1):196.
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  2. 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 Apr 09; 20(5):632-641.
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  3. 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.
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  4. 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. 2017 Sep 20.
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  5. 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 Oct 03; 114(40):10743-10748.
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  6. 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.
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  7. Segal MR, Bengtsson HL. Reconstruction of 3D genome architecture via a two-stage algorithm. BMC Bioinformatics. 2015 Nov 09; 16:373.
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  8. 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.
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  9. 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.
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  10. 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.
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  11. Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Res. 2013; 2:264.
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  12. 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.
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  13. 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).
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  14. 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.
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  15. 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.
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  16. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15.
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  17. 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.
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  18. 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.
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  19. 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.
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  20. 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.
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