Henrik Bengtsson

Henrik Bengtsson

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Henrik Bengtsson

Henrik Bengtsson

Publications by authors named "Henrik Bengtsson"

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42Publications

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Improved accuracy assessment for 3D genome reconstructions.

BMC Bioinformatics 2018 05 30;19(1):196. Epub 2018 May 30.

Division of Bioinformatics, Department of Epidemiology and Biostatistics, UCSF, 16th Street, San Francisco, 94158, USA.

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http://dx.doi.org/10.1186/s12859-018-2214-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977474PMC
May 2018

Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy.

J Urol 2018 03 20;199(3):719-725. Epub 2017 Sep 20.

Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, California. Electronic address:

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http://dx.doi.org/10.1016/j.juro.2017.09.071DOI Listing
March 2018

Replication confers β cell immaturity.

Nat Commun 2018 02 2;9(1):485. Epub 2018 Feb 2.

Diabetes Center, Department of Medicine, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41467-018-02939-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797102PMC
February 2018

Pollutant Concentrations and Toxic Effects on the Red Alga Ceramium tenuicorne of Sediments from Natural Harbors and Small Boat Harbors on the West Coast of Sweden.

Arch Environ Contam Toxicol 2016 Apr 30;70(3):583-94. Epub 2016 Jan 30.

Department of Environmental Science and Analytical Chemistry (ACES), Stockholm University, 10691, Stockholm, Sweden.

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http://link.springer.com/content/pdf/10.1007%2Fs00244-016-02
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http://link.springer.com/10.1007/s00244-016-0262-z
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http://dx.doi.org/10.1007/s00244-016-0262-zDOI Listing
April 2016

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.

Nucleic Acids Res 2016 Mar 10;44(5):2028-35. Epub 2016 Feb 10.

Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA

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http://dx.doi.org/10.1093/nar/gkw070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797302PMC
March 2016

Reconstruction of 3D genome architecture via a two-stage algorithm.

BMC Bioinformatics 2015 Nov 9;16:373. Epub 2015 Nov 9.

Division of Bioinformatics, Department of Epidemiology and Biostatistics, University of California, 550 16th Street, San Francisco, 94158, CA, USA.

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http://dx.doi.org/10.1186/s12859-015-0799-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4638111PMC
November 2015

Altered expression of myelin-associated inhibitors and their receptors after traumatic brain injury in the mouse.

Restor Neurol Neurosci 2014 ;32(5):717-31

Department of Neuroscience, Neurosurgery, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.3233/RNN-140419DOI Listing
July 2015

Interacting chemokine signals regulate dendritic cells in acute brain injury.

PLoS One 2014 25;9(8):e104754. Epub 2014 Aug 25.

Department of Neuroscience, Developmental Neuroscience, Biomedical Center, Uppsala University, Uppsala, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143236PMC
May 2015

illuminaio: An open source IDAT parsing tool for Illumina microarrays.

F1000Res 2013 4;2:264. Epub 2013 Dec 4.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA ; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.12688/f1000research.2-264.v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968891PMC
April 2014

Querying genomic databases: refining the connectivity map.

Stat Appl Genet Mol Biol 2012 Jan 6;11(2). Epub 2012 Jan 6.

University of California-San Francisco, CA, USA.

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http://dx.doi.org/10.2202/1544-6115.1715DOI Listing
January 2012

Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.

Clin Cancer Res 2011 Nov 8;17(22):7024-34. Epub 2011 Nov 8.

Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-11-1944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226754PMC
November 2011

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

Bioinformatics 2011 Aug 11;27(15):2038-46. Epub 2011 Jun 11.

Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137217PMC
August 2011

Identification of SOX3 as an XX male sex reversal gene in mice and humans.

J Clin Invest 2011 Jan 22;121(1):328-41. Epub 2010 Dec 22.

School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, South Australia, Australia.

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http://dx.doi.org/10.1172/JCI42580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3007141PMC
January 2011

ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.

Bioinformatics 2010 Aug 6;26(15):1827-33. Epub 2010 Jun 6.

Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913655PMC
August 2010

Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders.

Eur J Neurosci 2010 Mar;31(5):852-63

Department of Neuroscience, Developmental Neuroscience, Biomedical Center, Uppsala University, PO Box 593, SE-751 24 Uppsala, Sweden.

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http://doi.wiley.com/10.1111/j.1460-9568.2010.07105.x
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http://dx.doi.org/10.1111/j.1460-9568.2010.07105.xDOI Listing
March 2010

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.

Bioinformatics 2009 Sep 17;25(17):2149-56. Epub 2009 Jun 17.

Department of Statistics, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734319PMC
September 2009

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.

Bioinformatics 2009 Apr 4;25(7):861-7. Epub 2009 Feb 4.

Department of Statistics, Life Sciences Division, University of California, Lawrence Berkeley National Laboratory, Berkeley, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660872PMC
April 2009

Type I collagen alpha1 Sp1 polymorphism and the risk of cruciate ligament ruptures or shoulder dislocations.

Am J Sports Med 2008 Dec 31;36(12):2432-6. Epub 2008 Jul 31.

Department of Surgical Sciences, Section of Orthopedics, University Hospital, Uppsala, Sweden.

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http://journals.sagepub.com/doi/10.1177/0363546508320805
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http://dx.doi.org/10.1177/0363546508320805DOI Listing
December 2008

Distinct cellular patterns of upregulated chemokine expression supporting a prominent inflammatory role in traumatic brain injury.

J Neurotrauma 2008 Aug;25(8):959-74

Department of Neuroscience, Developmental Neuroscience, Biomedical Center, Uppsala University, Uppsala, Sweden.

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http://www.liebertpub.com/doi/10.1089/neu.2008.0562
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http://dx.doi.org/10.1089/neu.2008.0562DOI Listing
August 2008

Generation and characterization of a Gdf1 conditional null allele.

Genesis 2008 Jul;46(7):368-72

Department of Neuroscience, Uppsala University, Biomedical Center, Uppsala, Sweden.

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http://dx.doi.org/10.1002/dvg.20408DOI Listing
July 2008

Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.

Biostatistics 2007 Apr 22;8(2):485-99. Epub 2006 Dec 22.

Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/biostatistics/kxl042DOI Listing
April 2007

Increasing incidence of ruptured abdominal aortic aneurysm: a population-based study.

J Vasc Surg 2006 Aug;44(2):237-43

Department of Vascular Diseases, Malmö University Hospital, Malmö, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S074152140600763
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http://dx.doi.org/10.1016/j.jvs.2006.04.037DOI Listing
August 2006

Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method.

BMC Bioinformatics 2006 Mar 1;7:100. Epub 2006 Mar 1.

Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Box 118, SE-221 00 Lund, Sweden.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534066PMC
March 2006

Microarray image analysis: background estimation using quantile and morphological filters.

BMC Bioinformatics 2006 Feb 28;7:96. Epub 2006 Feb 28.

Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Box 118, SE-221 00 Lund, Sweden.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525206PMC
February 2006

Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.

BMC Bioinformatics 2004 Nov 12;5:177. Epub 2004 Nov 12.

Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Box 118, SE-221 00 Lund, Sweden.

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http://dx.doi.org/10.1186/1471-2105-5-177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539274PMC
November 2004

Transgenic expression of Cre recombinase from the tyrosine hydroxylase locus.

Genesis 2004 Oct;40(2):67-73

Department of Neuroscience, Developmental Neuroscience Unit, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden.

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http://doi.wiley.com/10.1002/gene.20065
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http://dx.doi.org/10.1002/gene.20065DOI Listing
October 2004