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Futureverse - Worry-Free Parallelization in R. Biometric Bulletin. 2023; 3(40):8-10.
Henrik Bengtsson. . View Publication.
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Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics. Cancer Res. 2023 08 01; 83(15):2600-2613.
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, Neuhausen SL, Ziv E. PMID: 37145128; PMCID: PMC10390863.
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PubMed Mentions:
1 Fields:
Translation:
HumansCells
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A Unifying Framework for Parallel and Distributed Processing in R using Futures. The R Journal. 2021; 13(2):273-291.
Henrik Bengtsson. . View Publication.
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A Unifying Framework for Parallel and Distributed Processing in R using Futures. The R Journal. 2021 Jan 1; 13(2):208.
Bengtsson BH. .
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Multiple Tissue Biomarkers Independently and Additively Predict Prostate Cancer Pathology Outcomes. Eur Urol. 2021 01; 79(1):141-149.
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. PMID: 33148472.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature. Exp Hematol. 2020 10; 90:65-71.e1.
Fitch B, Roy R, Geng H, Montecino-Rodriguez E, Bengtsson H, Gaillard C, Hiam K, Casero D, Olshen AB, Dorshkind K, Kogan SC. PMID: 32946981; PMCID: PMC7606616.
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PubMed Mentions:
6 Fields:
Translation:
HumansAnimalsCells
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GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA. Neuro-oncology. 2019; 21(6).
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 Luks, Tracy and Olson, Marram and Lafontaine, Marisa and Shai, Anny and Bengtsson, Henrik and Olshen, Adam and Molinaro, Annette and McDermott, Michael and Chang, Edward and Hervey-Jumper, Shawn and Berger, Mitchel and Lim, Daniel and Diaz, Aaron and Lupo, Janine and Phillips, Joanna and Chang, Susan and Nelson, Sarah and Oldham, Michael and Costello, Joseph. View Publication.
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A multibiomarker approach to predict prostate cancer pathology outcomes. Journal of Clinical Oncology. 2019 Mar 1; 37(7_suppl):58-58.
Paris PP, Cooperberg CM, Cowan CJ, Lindquist LK, Kobayashi KY, Simko SJ, Bengtsson BH, Singh SK, Newcomb NL, Lin LD, Carroll CP. .
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Improved accuracy assessment for 3D genome reconstructions. BMC Bioinformatics. 2018 05 30; 19(1):196.
Segal MR, Bengtsson HL. PMID: 29848293; PMCID: PMC5977474.
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PubMed Mentions:
6 Fields:
Translation:
AnimalsCells
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Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol. 2018 04 09; 20(5):632-641.
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. PMID: 29077933; PMCID: PMC5892142.
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PubMed Mentions:
17 Fields:
Translation:
Humans
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Replication confers β cell immaturity. Nat Commun. 2018 02 02; 9(1):485.
Puri S, Roy N, Russ HA, Leonhardt L, French EK, Roy R, Bengtsson H, Scott DK, Stewart AF, Hebrok M. PMID: 29396395; PMCID: PMC5797102.
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PubMed Mentions:
76 Fields:
Translation:
AnimalsCells
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GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi99-vi99.
Hilz HS, Shelton SS, Jalbert JL, Wong WH, Mazor MT, Hong HC, Hayes HJ, Luks LT, Bengtsson BH, Molinaro MA, McDermott MM, Berger BM, Lim LD, Diaz DA, Phillips PJ, Chang CS, Nelson NS, Oldham OM, Costello CJ. .
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Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy. J Urol. 2018 03; 199(3):719-725.
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. PMID: 28941923.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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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.
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. PMID: 28916733; PMCID: PMC5635900.
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PubMed Mentions:
76 Fields:
Translation:
HumansCells
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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.
Nguyen NH, Welty WC, Lindquist LK, Ngo NV, Gilbert GE, Bengtsson BH, Magi-Galluzzi MC, Jean-Gilles JJ, Yao YJ, Cooperberg CM, Messing ME, Klein KE, Carroll CP, Paris PP. .
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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 Dec 2; 128(22):1741-1741.
Kogan KS, Geng GH, Roy RR, Montecino-Rodriguez ME, Gaillard GC, Hiam HK, Bengtsson BH, Casero CD, Olshen OA, Dorshkind DK. .
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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.
Mazor MT, Jalbert JL, Pankov PA, Hong HC, Hayes HJ, Smirnov SI, Marshall MR, Perry PA, Nelson NS, Chang CS, Bollen BA, Molinaro MA, Bengtsson BH, Olshen OA, Phillips PJ, Costello CJ. .
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Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res. 2016 Mar 18; 44(5):2028-35.
Capurso D, Bengtsson H, Segal MR. PMID: 26869583; PMCID: PMC4797302.
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PubMed Mentions:
14 Fields:
Translation:
AnimalsCells
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Validating the Use of Google Enquiry Metadata to Enhance Pertussis Surveillance in Australia. Open Forum Infectious Diseases. 2015 Dec 9; 2(suppl_1):1818.
Pollett PS, Wood WN, Boscardin BW, Bengtsson BH, Rutherford RG. .
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Reconstruction of 3D genome architecture via a two-stage algorithm. BMC Bioinformatics. 2015 Nov 09; 16:373.
Segal MR, Bengtsson HL. PMID: 26553003; PMCID: PMC4638111.
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PubMed Mentions:
14 Fields:
Translation:
HumansAnimalsCells
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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.
Mazor MT, Johnson JB, Grimmer GM, Hong HC, Hamilton HE, Jones JL, Xavier-Magalhães XA, Smirnov SI, Bengtsson BH, Olshen OA, Petrecca PK, Bollen BA, Berger BM, Taylor TB, Nelson NS, Aghi AM, Clarke CJ, Phillips PJ, Chang CS, Costello CJ. .
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Validating the Use of Google Trends to Enhance Pertussis Surveillance in California. PLoS Curr. 2015 Oct 19; 7.
Pollett S, Wood N, Boscardin WJ, Bengtsson H, Schwarcz S, Harriman K, Winter K, Rutherford G. PMID: 26543674; PMCID: PMC4626035.
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PubMed Mentions:
12
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Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma. Cancer Res. 2015 Aug 01; 75(15):3065-76.
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. PMID: 26239477; PMCID: PMC4526117.
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PubMed Mentions:
51 Fields:
Translation:
HumansAnimalsCells
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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.
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. PMID: 25236618; PMCID: PMC4248318.
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PubMed Mentions:
180 Fields:
Translation:
HumansCells
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illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Res. 2013; 2:264.
Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. PMID: 24701342; PMCID: PMC3968891.
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PubMed Mentions:
38 Fields:
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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.
Kim KW, Foye FA, Bengtsson BH, Kim KH, Taylor TB, Pourmand PN, Febbo FP. .
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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.
Ortiz-Estevez M, Aramburu A, Bengtsson H, Neuvial P, Rubio A. PMID: 22576175; PMCID: PMC3381965.
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PubMed Mentions:
12 Fields:
Translation:
Humans
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Abstract 5079: A genomic copy number biomarker to identify oral cancer patients at low risk for metastasis. Molecular and Cellular Biology. 2012 Apr 15; 5079-5079.
Bhattacharya BA, Snijders SA, Roy RR, Hamilton HG, Paquette PJ, Tokuyasu TT, Bengtsson BH, Jordan JR, Olshen OA, Pinkel PD, Schmidt SB, Albertson AD. .
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Querying genomic databases: refining the connectivity map. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(2).
Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R. PMID: 22499690.
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PubMed Mentions:
7 Fields:
Translation:
Humans
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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.
Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG. PMID: 22068658; PMCID: PMC3226754.
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PubMed Mentions:
28 Fields:
Translation:
Humans
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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.
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. PMID: 22003129; PMCID: PMC3286973.
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PubMed Mentions:
282 Fields:
Translation:
HumansCells
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Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15.
Cancer Genome Atlas Research Network. PMID: 21720365; PMCID: PMC3163504.
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PubMed Mentions:
3815 Fields:
Translation:
HumansCells
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Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011 Aug 01; 27(15):2038-46.
Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. PMID: 21666266; PMCID: PMC3137217.
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PubMed Mentions:
68 Fields:
Translation:
Humans
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Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. PLoS One. 2011 Mar 07; 6(3):e17793.
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. PMID: 21408189; PMCID: PMC3049794.
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PubMed Mentions:
53 Fields:
Translation:
HumansAnimalsCells
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Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies. Handbook of Statistical Bioinformatics. 2011 Jan 1; 225-255.
Neuvial NP, Bengtsson BH, Speed ST. .
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Identification of SOX3 as an XX male sex reversal gene in mice and humans. J Clin Invest. 2011 Jan; 121(1):328-41.
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. PMID: 21183788; PMCID: PMC3007141.
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PubMed Mentions:
93 Fields:
Translation:
HumansAnimalsCells
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ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. Bioinformatics. 2010 Aug 01; 26(15):1827-33.
Ortiz-Estevez M, Bengtsson H, Rubio A. PMID: 20529889; PMCID: PMC2913655.
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PubMed Mentions:
10 Fields:
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TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics. 2010 May 12; 11:245.
Bengtsson H, Neuvial P, Speed TP. PMID: 20462408; PMCID: PMC2894037.
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PubMed Mentions:
34 Fields:
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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.
Carmichael CL, Wilkins EJ, Bengtsson H, Horwitz MS, Speed TP, Vincent PC, Young G, Hahn CN, Escher R, Scott HS. PMID: 20456351.
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PubMed Mentions:
8 Fields:
Translation:
HumansCells
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Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010 May 18; 17(5):510-22.
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, Cancer Genome Atlas Research Network. PMID: 20399149; PMCID: PMC2872684.
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PubMed Mentions:
1223 Fields:
Translation:
HumansCells
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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.
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. PMID: 19946261.
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PubMed Mentions:
39 Fields:
Translation:
Humans
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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.
Bengtsson H, Wirapati P, Speed TP. PMID: 19535535; PMCID: PMC2734319.
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PubMed Mentions:
87 Fields:
Translation:
HumansCells
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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.
Bengtsson H, Ray A, Spellman P, Speed TP. PMID: 19193730; PMCID: PMC2660872.
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PubMed Mentions:
23 Fields:
Translation:
Humans
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Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics. 2008 Mar 15; 24(6):759-67.
Bengtsson H, Irizarry R, Carvalho B, Speed TP. PMID: 18204055.
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PubMed Mentions:
78 Fields:
Translation:
Cells
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Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr; 8(2):485-99.
Carvalho B, Bengtsson H, Speed TP, Irizarry RA. PMID: 17189563.
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PubMed Mentions:
127 Fields:
Translation:
Humans
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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.
Bengtsson H, Hössjer O. PMID: 16509971; PMCID: PMC1534066.
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PubMed Mentions:
13 Fields:
Translation:
Humans
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Microarray image analysis: background estimation using quantile and morphological filters. BMC Bioinformatics. 2006 Feb 28; 7:96.
Bengtsson A, Bengtsson H. PMID: 16504173; PMCID: PMC1525206.
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PubMed Mentions:
4 Fields:
Translation:
HumansAnimals
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Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinformatics. 2004 Nov 12; 5:177.
Bengtsson H, Jönsson G, Vallon-Christersson J. PMID: 15541170; PMCID: PMC539274.
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PubMed Mentions:
22 Fields:
Translation:
Cells
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Low-level analysis of microarray data, PhD thesis, Centre for Mathematical Sciences, Division of Mathematical Statistics, Lund University. 2004.
Bengtsson H.
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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. View Publication.
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Identifying differentially expressed genes in cDNA microarray experiments authors. Sci Aging Knowledge Environ. 2001 Dec 19; 2001(12):vp8.
Bengtsson H, Calder B, Mian IS, Callow M, Rubin E, Speed TP. PMID: 14602959.
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PubMed Mentions: Fields:
Translation:
AnimalsCells