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Presentations

Below are selected presentations related to aroma-project.org and/or related statistical methods by us.

2012

2012-12-14: Henrik Bengtsson, aroma.seq: Bringing sequence analysis to the Aroma Framework, Bioconductor European Developers' Workshop 2012, UZH/ETH Zurich, 20+5 minutes.
Slides (35): pdf [0.6Mb]

2011

2011-10-27: Henrik Bengtsson, Single Tumor-Normal Pair Parent-Specific Copy Number Analysis, Workshop II: Transcriptomics and Epigenomics, IPAM, UCLA, Los Angeles, CA, 55 minutes.
Slides (35+6): pdf [2.3Mb]

2011-07-28: Henrik Bengtsson, Single Tumor-Normal Pair Parent-Specific Copy Number Analysis, BioC2011, Seattle, WA, 45 minutes.
Slides (34): pdf [2.1Mb]

2011-06-21: Henrik Bengtsson, Single Tumor-Normal Pair Parent-Specific Copy Number Analysis, Session I6 (IMS) on 'Statistical Methods for High-Throughput Genomic Assays', WNAR 2011, San Luis Obispo, CA, 25 minutes.
Slides (28): pdf [1.7Mb]

2011-03-22: Henrik Bengtsson, Enhanced power for segmenting parent-specific copy numbers, Session #99 on 'Assessing DNA Copy Number Variation from High-Throughput Technologies', ENAR 2011, Miami, FL, 25 minutes.
Slides (25): pdf [1.8Mb]

2011-03-10: Henrik Bengtsson, Analysis of SNP arrays for parent-specific copy numbers, Quantitative Biology Discussion Group (QBDG), Helen Diller Family Comprehensive Cancer Center, UCSF, 60 minutes.

2010

2010-11-10: Henrik Bengtsson, Greatly improved parent-specific tumor copy numbers with DNA microarrays when a matched normal is available, International Cancer Genome Consortium (ICGC), conference call, 60 minutes.

2010-09-30: Pierre Neuvial, Statistical analysis of single nucleotide polymorphism microarrays in cancer studies, Workshop in Biostatistics, Stanford University, CA.
Slides (60): pdf [7.7Mb].

2010-08-18: Pierre Neuvial, Greatly improved allele-specific tumor copy numbers with DNA microarrays when a matched normal is available, CSB 2010 (International Conference on Computational Systems Bioinformatics), Stanford University, CA, USA.
Slides (9+7): pdf [1.0Mb].

2010-04-14: Pierre Neuvial, On detecting and calling DNA copy number alterations in cancer samples from genotyping microarrays, Institut Curie, Paris.
Slides (46): pdf [2.1Mb].

2009

2009-10-01: Pierre Neuvial, TumorBoost: Normalization of allele-specific tumor copy numbers in paired tumor/normal, designs for genotyping microarrays, Statistics and Genomics Seminar, UC Berkeley, CA, USA.
Slides (36): pdf [2.1Mb].

2009-10-13: Henrik Bengtsson, Improved copy number analysis, Department of Epidemiology & Biostatistics, University of California, San Francisco (UCSF), CA.
Slides (46): pdf [4.6Mb].

2009-03-16: Henrik Bengtsson, A Single-Array Preprocessing Method for Estimating Full-Resolution Raw Copy Numbers from all Affymetrix Genotyping Arrays, Comprehending Copy Number Variation (Tools, Applications and Results), Cambridge Health Institute, March 16, 2009, San Diego, CA.
Slides (39): ppt [0.8Mb], pdf [0.8Mb]. Handouts: 6up.pdf [0.7Mb]

2008

2008-12-16: Henrik Bengtsson, Low-Level Copy Number Analysis (CRMA v2 preprocessing), CEIT Workshop on SNP arrays, Dec 15-17, 2008, San Sebastian, Spain.
Slides (96): ppt [2.0Mb], pdf [2.1Mb]

2008-12-15: Henrik Bengtsson, Low-Level Copy Number Analysis (Part 1-Background, Part 2-Simple preprocessing, Part 3-aroma.affymetrix), CEIT Workshop on SNP arrays, Dec 15-17, 2008, San Sebastian, Spain.
Slides (64): ppt [10.1Mb], pdf [6.6Mb]

2008-04-24: Henrik Bengtsson, aroma.affymetrix - Processing very large Affymetrix data sets in bounded memory (Working with Large Datasets), BioC 2008 developers meeting, Lausanne, Switzerland.
Slides: ppt [531kb], pdf [445kb]

2008-01-24: Henrik Bengtsson, Copy-number estimation on the latest generation of high-density oligonucleotide microarrays, Mathematical Biosciences Institute, The Ohio State University.
Slides: ppt [4.3Mb], pdf [1.9Mb]

2007

2007-09-13: Henrik Bengtsson, Estimating chromosomal copy numbers from Affymetrix SNP & CN chips, Statistics and Genomics Seminar, UC Berkeley.
Slides: ppt [3.3Mb], pdf [1.7Mb]

2007-08-07: Henrik Bengtsson, aroma.affymetrix - Analysis of small to very large Affymetrix data sets, BioC2007 lab session, 13:00-15:00, August 7, 2007, Fred Hutchinson Cancer Research Center, Seattle, US.
Slides: pdf [0.5Mb], Suppl. slides: pdf [0.9Mb], ppt [3.4Mb]
Cut'n'paste code: src [9kb]

2007-05-31: Henrik Bengtsson, Copy-number estimation using Robust Multichip Analysis.
Thursday May 31, 2007 @ 9:30-10:45, INSERM Workshop #177 on Statistical Methods and novel strategies to search for genes involved in common diseases, Londe-Les-Maures (Toulon), France.
http://ist.inserm.fr/BASIS/elgis/fqmat/atelier/SDF?DOC_NUM=177

2007-04-21: Henrik Bengtsson, Enhanced method for identifying copy-number aberrations in small to very large oligonucleotide microarray data sets.
Saturday April 21, 2007 @ 13:30-14:00, Affymetrix Low Level Workshop, Oakland Marriott City Center, Oakland, 2007.
http://www.affymetrix.com/corporate/events/low_level_workshop/2007_04_low_level_workshop.affx

2007-01-08: Henrik Bengtsson, Crash course: Using aroma.affymetrix for copy-number analysis.
Monday January 8, 2007 @ 13:30-16:00, Bioinformatics, WEHI, Melbourne.
http://www.maths.lth.se/bioinformatics/calendar/20070108b/

2006

2006-09-28: Henrik Bengtsson, Package aroma.affymetrix - How to analyze huge Affymetrix data sets in R on a notebook.
Thursday September 28, 2006 @ 16:00-17:00, Statistics and Genomics
Seminar, 1011 Evans Hall, University of California, Berkeley
http://www.maths.lth.se/bioinformatics/calendar/20060928b/