Henrik Bengtsson, PhD, MS
Associate Professor
Epidemiology & Biostatistics
School of Medicine

Websites

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• Epidemiology & Biostatistics (epibiostat.ucsf.edu)
• The Aroma Project (aroma-project.org)
• Futureverse - A Unifying Parallelization Framework in R for Everyone (futureverse.org)
• GitHub (github.com)
• UCSF Computational Biology and Informatics (cbi.ucsf.edu)

Publications (55)

Top publication keywords:
ChromosomesHigh-Throughput Nucleotide SequencingAlgorithmsGenomeOligonucleotide Array Sequence AnalysisSoftwareDNA, Single-StrandedChromatinGenomicsMolecular ConformationDNA, CircularGene Expression ProfilingGenome, HumanGene DosageAlleles

• Metabolites from blood and formalin-fixed, paraffin-embedded tissue from participants with low- and high-grade prostate cancer: a pilot study.
  Frontiers in oncology 2026 Graff RE, Bengtsson HL, Suh JH, Olshen AB, Wang EY, Allen RM, Van Blarigan EL, Kenfield SA, Cowan JE, Carroll PR, Simko J, Chan JM
• SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences.
  PloS one 2026 Pereira H, Silva PC, Davis MW, Abraham L, Babnigg G, Bengtsson H, Johansson B
• SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences.
  bioRxiv : the preprint server for biology 2024 Pereira H, Silva PC, Davis MW, Abraham L, Babnigg G, Bengtsson H, Johansson B
• Futureverse - Worry-Free Parallelization in R
  Biometric Bulletin 2023 Henrik Bengtsson
• Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics.
  Cancer research 2023 Ding YC, Song H, Adamson AW, Schmolze D, Hu D, Huntsman S, Steele L, Patrick CS, Tao S, Hernandez N, Adams CD, Fejerman L, Gardner K, Nápoles AM, Pérez-Stable EJ, Weitzel JN, Bengtsson H, Huang FW, …

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• A Unifying Framework for Parallel and Distributed Processing in R using Futures
  The R Journal 2021 Henrik Bengtsson
• A Unifying Framework for Parallel and Distributed Processing in R using Futures.
  The R Journal 2021 Henrik Bengtsson
• Multiple Tissue Biomarkers Independently and Additively Predict Prostate Cancer Pathology Outcomes.
  European urology 2020 Cooperberg MR, Cowan JE, Lindquist KJ, Kobayashi Y, Simko JP, Bengtsson H, Singh K, Ngo V, Avila A, Newcomb LF, Tretriakova M, Lin DW, Stone S, Carroll PR, Paris PL
• Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature.
  Experimental hematology 2020 Fitch B, Roy R, Geng H, Montecino-Rodriguez E, Bengtsson H, Gaillard C, Hiam K, Casero D, Olshen AB, Dorshkind K, Kogan SC
• GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA
  Neuro-oncology 2019 Hilz, Stephanie and Hong, Chibo and Jalbert, Llewellyn and Mazor, Tali and Martin, Michael and Kumar, Anupam and Shelton, Samuel and Wong, Karen and Hayes, Josie and Yu, Yao and Zhang, Michael and …
• A multibiomarker approach to predict prostate cancer pathology outcomes.
  Journal of Clinical Oncology 2019 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
• Improved accuracy assessment for 3D genome reconstructions.
  BMC bioinformatics 2018 Segal MR, Bengtsson HL
• Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas.
  Neuro-oncology 2018 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,…
• Replication confers β cell immaturity.
  Nature communications 2018 Puri S, Roy N, Russ HA, Leonhardt L, French EK, Roy R, Bengtsson H, Scott DK, Stewart AF, Hebrok M
• GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS.
  Neuro-Oncology 2017 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, …
• Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy.
  The Journal of urology 2017 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
• Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1.
  Proceedings of the National Academy of Sciences of the United States of America 2017 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, …
• Validation of GEMCaP as a DNA based biomarker to predict disease recurrence in patients undergoing prostatectomy for prostate cancer.
  Journal of Clinical Oncology 2017 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…
• Genetic Subtypes of Human Pediatric ALLs Show Gene Expression Differences That Parallel Those Observed in Mouse B1 and B2 Progenitors, Suggesting Divergent Developmental Origins.
  Blood 2016 Scott C. Kogan, Huimin Geng, Ritu Roy, Encarnacion Montecino-Rodriguez, Coline M Gaillard, Kamir Hiam, Henrik Bengtsson, David Casero, Adam B Olshen, Kenneth Dorshkind
• GENT-05. DELETION OR AMPLIFICATION OF MUTANT IDH1 IS ASSOCIATED WITH EXTREME DNA HYPOMETHYLATION AND MALIGNANT PROGRESSION.
  Neuro-Oncology 2016 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…
• Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.
  Nucleic acids research 2016 Capurso D, Bengtsson H, Segal MR
• Validating the Use of Google Enquiry Metadata to Enhance Pertussis Surveillance in Australia.
  Open Forum Infectious Diseases 2015 Simon Pollett, Nicholas Wood, W. John Boscardin, Henrik Bengtsson, George Rutherford
• Reconstruction of 3D genome architecture via a two-stage algorithm.
  BMC bioinformatics 2015 Segal MR, Bengtsson HL
• GENO-25HYPERMUTATION AND MALIGNANT PROGRESSION IN AN EXPANDED COHORT OF TEMOZOLOMIDE-TREATED LOW-GRADE GLIOMA PATIENTS.
  Neuro-Oncology 2015 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, …
• Validating the Use of Google Trends to Enhance Pertussis Surveillance in California.
  PLoS currents 2015 Pollett S, Wood N, Boscardin WJ, Bengtsson H, Schwarcz S, Harriman K, Winter K, Rutherford G
• Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma.
  Cancer research 2015 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
• Abstract 3426: A novel approach to copy number assessment by whole genome sequencing reveals extensive spatial heterogeneity in diffuse low-grade glioma.
  Molecular and Cellular Biology 2014 Ilari Scheinin, Hinke F. van Thuijl, Daoud Sie, Hendrik F. van Essen, Paul P. Eijk, Francois Rustenburg, Ahmed Idbaih, Agusti Alentorn, Gerrit A. Meijer, Mark A. van der Wiel, Henrik Bengtsson, Adam …
• 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 research 2014 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
• illuminaio: An open source IDAT parsing tool for Illumina microarrays.
  F1000Research 2013 Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD
• Feasibility of RNA sequencing to detect TMPRSS2:ERG fusions following laser capture microdissection of prostate cancer.
  Journal of Clinical Oncology 2013 Won Kim, Adam Foye, Henrik Bengtsson, Hyunsung John Kim, Barry S. Taylor, Nader Pourmand, Phillip G. Febbo
• CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
  Bioinformatics (Oxford, England) 2012 Ortiz-Estevez M, Aramburu A, Bengtsson H, Neuvial P, Rubio A
• Abstract 5079: A genomic copy number biomarker to identify oral cancer patients at low risk for metastasis.
  Molecular and Cellular Biology 2012 Aditi Bhattacharya, Antoine M. Snijders, Ritu Roy, Gregory Hamilton, Jesse Paquette, Taku Tokuyasu, Henrik Bengtsson, Richard CK Jordan, Adam Olshen, Daniel Pinkel, Brian L. Schmidt, Donna G. …
• Querying genomic databases: refining the connectivity map.
  Statistical applications in genetics and molecular biology 2012 Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R
• Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2011 Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG
• Subtype and pathway specific responses to anticancer compounds in breast cancer.
  Proceedings of the National Academy of Sciences of the United States of America 2011 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, …
• Integrated genomic analyses of ovarian carcinoma.
  Nature 2011 Cancer Genome Atlas Research Network
• Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.
  Bioinformatics (Oxford, England) 2011 Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE
• Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis.
  PloS one 2011 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, …
• Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies.
  Handbook of Statistical Bioinformatics 2011 Pierre Neuvial, Henrik Bengtsson, Terence P. Speed
• Identification of SOX3 as an XX male sex reversal gene in mice and humans.
  The Journal of clinical investigation 2010 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, …
• ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
  Bioinformatics (Oxford, England) 2010 Ortiz-Estevez M, Bengtsson H, Rubio A
• TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.
  BMC bioinformatics 2010 Bengtsson H, Neuvial P, Speed TP
• Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes.
  British journal of haematology 2010 Carmichael CL, Wilkins EJ, Bengtsson H, Horwitz MS, Speed TP, Vincent PC, Young G, Hahn CN, Escher R, Scott HS
• Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.
  Cancer cell 2010 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 …
• Novel RUNX1 mutations in familial platelet disorder with enhanced risk for acute myeloid leukemia: clues for improved identification of the FPD/AML syndrome.
  Leukemia 2009 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, …
• A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.
  Bioinformatics (Oxford, England) 2009 Bengtsson H, Wirapati P, Speed TP
• A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
  Bioinformatics (Oxford, England) 2009 Bengtsson H, Ray A, Spellman P, Speed TP
• Estimation and assessment of raw copy numbers at the single locus level.
  Bioinformatics (Oxford, England) 2008 Bengtsson H, Irizarry R, Carvalho B, Speed TP
• Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.
  Biostatistics (Oxford, England) 2006 Carvalho B, Bengtsson H, Speed TP, Irizarry RA
• Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method.
  BMC bioinformatics 2006 Bengtsson H, Hössjer O
• Microarray image analysis: background estimation using quantile and morphological filters.
  BMC bioinformatics 2006 Bengtsson A, Bengtsson H
• Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.
  BMC bioinformatics 2004 Bengtsson H, Jönsson G, Vallon-Christersson J
• Low-level analysis of microarray data, PhD thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University
  Low-level analysis of microarray data, PhD thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University 2004 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 Bengtsson H
• Identifying differentially expressed genes in cDNA microarray experiments authors.
  Science of aging knowledge environment : SAGE KE 2001 Bengtsson H, Calder B, Mian IS, Callow M, Rubin E, Speed TP