Joint Meetings

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The Cancer Center Biostatistics and Bioinformatics Cores have regularly scheduled meetings and seminars. These seminars are related to biostatistics, computing, informatics, or related areas, preferably in the area of cancer, but not necessarily.


Date Speaker Topic
December 18, 2009 Siddhartha Basu, Ph.D.
Research Associate
Center for Genetic Medicine

dictyBase: a model organism database’s latest expansion for hosting multiple genomes

dictyBase is a unique genomics resource that provides unified access to the curated information and experimental data for the model organism Dictyostelium discoideum. D. discoideum is widely used by biomedical researchers to study a broad range of biological aspects such as development, differentiation, cell signaling, motility and molecular mechanism of disease. Since it inception more than six years ago, dictyBase has been widely adopted as the definitive database for Dictyostelium researchers, and for other bioinformatics and model organism communities.

In recent years, numerous other Dictyostelid genomes have either fully been sequenced or are close to completion. Currently, dictybase is expanding to integrate these genomes to provide an infrastructure for comparative genomics of similar genomes. This is especially powerful since dictyBase is a manually curated database and annotations based on experimental evidence in D. discoideum can be propagated to all orthologs in the related organisms. Furthermore, curation in dictyBase is facilitated by having access to gene models of the related organisms for comparison.

The existing dictyBase infrastructure and website will be reviewed along with a discussion of how the infrastructure will be expanded to accommodate new genomes. In this multi-genome setup, each genome will have its own web address using its species name as a unique identifier. Each genome by default will host a genome browser and a gene page with a similar look and feel of the main dictyBase user interface. Each of the added genomes will be available for blast search for doing cross-species comparison. Dictyostelium purpurem is the first genome to be released in this multi-genome setup at dictyBase.

November 20, 2009 Joseph Kang, Ph.D.
Assistant Professor
Preventive Medicine

A strategy to identify differential marginal associations based on recursive partitioning methods: a machine doctor’s view of a population cohort

A marginal association between a putative cause and its related outcome for an entire study population can be described as mixtures of associations among subgroups. Given this fact, for example, at least three groups may be exhaustively explored with respect to the statistical significance and the direction of associations: significantly positive, significantly negative, or non-significant. It is relatively easy to evaluate the direction and the degree of associations across subgroups that had been determined a priori. However, as dimensions of the co-variates that describe the differential subgroups increase and as the knowledge of them remains still at an early stage of a clinical investigation, the statistical identification of those groups becomes imperative. For this purpose, we employ a Recursive Partitioning technique that has been immensely developed in various scientific communities during the past decades. In this talk, a Recursive Partitioning strategy is introduced to identify subgroups whose marginal associations are influenced by co-variates whose characteristics are fairly complex yet clinically important. We discuss simulation study results and analyses based on a cardiovascular data set of young adults.

Key words: marginal association, confounding effect, recursive partitioning

October 16, 2009 Pan Du, Ph.D.
Research Assistant Professor
Northwestern University Medical School
NUCATS Institute

Annotating the Human Genome with Disease Ontology: Algorithm

This talk will discuss the procedure of annotating human genome using Disease Ontology (DO) and existing challenges. A novel method is proposed to improve the DO annotation. To facilitate the application of DO to the functional analysis, a lighter version of DO (DOLite) was constructed using computational methods plus expert curation. The performance of these implementations has been evaluated by public datasets and multiple internal projects at Northwestern University. A website application of DOLite, FunDO, has been implemented to facilitate the translational research. The application of FunDO has lead to the discovery of an existing drug for potential treatment of new diseases.
September 18, 2009 David Were
Systems Analyst/Programmer
Northwestern University Medical School
NUCATS Institute
Accrual Reporting with eNOTIS

July 17, 2009 Borko Jovanovic, Ph.D.
Associate Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20090717_Jovanovic.B&B.July.2009.pdf Statistics in Translation]

June 19, 2009 Jennifer (Allen) Pacheco
Senior Systems Analyst
Northwestern University Medical School
Center for Genetic Medicine
[Slides20090619_UsingEDW_forGWAS_inc_recruit.pdf A re-usable EDW use case: from case/conrol algorithm development, to recruitment, to reporting, for GWAS (Genome-wide Association Studdies)]

May 15, 2009 Kwang-Youn Kim, Ph.D
Assistant Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20090515_Biostat_Seminar_2009-05-15_final_for_email.pdf Variations in the Genome]

March 20, 2009 Juned Siddique, Ph.D
Assistant Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20090320_biostat_bioinformatics_siddique.pdf Slides - Missing Data in Longitudinal Trials: Analytic Issues]

[Slides20090320 missing_data_in_longitudinal_trials.pdf Paper - Missing Data in Longitudinal Trials: Analytic Issues]
February 20, 2009 Eric Just
Senior Data Architect
Northwestern University Medical School
NUCATS
[Slides20090220_EDW Overview Bioinform.pdf The Northwestern Medicine Enterprise Data Warehouse: Empowering Research at FSM]
January 16, 2009 Luis Amaral, Ph.D
Associate Professor
Northwestern University
Chemical and Biological Engineering
December 19, 2008 Abel Kho, M.D.
Assistant Professor
Northwestern University Medical School
General Internal Medicine
[Slides20081219_Biostats_12_19_08.pdf Antibiotic Resistance and the Compelling Case for Health Information Exchange]
November 21, 2008 Denise Scholtens, Ph.D.
Assistant Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20081121_GSEAoverview.pdf Topics in Gene Set Enrichment Analysis]
October 17, 2008 Brian Chamberlain
Systems Analyst/Programmer
Northwestern University Medical School
NUCATS
[Slides20081017_NIH Informed Consent Authoring Tool (show).pdf Informed consent authoring - Let Sherpa do it]
August 15, 2008 Sean Whitaker
Data Security Analyst
Northwestern University Medical School
RHLCCC
[Slides20080815_psc-biostat-demo.pdf Managing patients on clinical trials using Patient Study Calendar]
July 18, 2008 Ed Wang, Ph.D.
Associate Professor
Northwestern University Medical School
Department of Surgery
[Slides20080717_Preventive_medicine_talk.pdf Study Design and Analytical Strategy for Evidence Based Health Care Research]
June 20, 2008 Simon Lin, M.D.
Assistant Professor
Northwestern University Medical School
Bioinformatics Core
Working with Very Large Datasets
May 16, 2008 Borko Jovanovic, Ph.D.
Associate Professor
Northwestern University Medical School
Department of Preventive Medicine
[Jovanovic.Phase1.Talk.May2008.pdf CRM, EWOC and other Phase I designs, hands on]
March 21, 2008 Dorothy Dunlop, Ph.D.
Research Associate Professor
Northwestern University Medical School
Institute for Healthcare Studies and Division of Rheumatology
[gee2008.pdf Regression Analysis of Longitudinal Data]
February 15, 2008 Warren Kibbe, Ph.D.
Research Associate Professor
Northwestern University Medical School
RHLCCC
Director, Bioinformatics Core
[Slides20080313_nuID Annotations 2008.pdf Annotation of Illumina and Affymetrix microarrays using RefSeq and nuIDs]
November 16, 2007 Joan Chmiel, Ph.D.
Daniel Erickson, MBA
Professor; Database Team Leader
Northwestern University Medical School
Department of Preventive Medicine
[Slides20071116-macs.pdf Studies of HIV-related Cancers in the MACS: Computerized Interviews, Epidemiologic Designs and Analyses]
October 21, 2007 Andrew Winter
Software Architect
Northwestern University Medical School
RHLCCC
An Update on the Northwestern Medicine Enterprise Data Warehouse - One Year Later.
September 21, 2007 Angela Fought, M.S.
Ed Vonesh, Ph.D.
Statistical Analyst II; Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20070817_Prostate Biopsy Research v3_final.pdf Prostate Screening and Biopsy Research]
August 17, 2007 Sean Whitaker
Data Security Analyst
Northwestern University Medical School
RHLCCC
[Slides20070817_Biostat.pdf caAERS: An Open Source tool for Capturing and Reporting Adverse Events ]
July 20, 2007 Paul Yarnold, Ph.D.
Research Professor of Medicine
Northwestern University Medical School
Department of Emergency Medicine
The use of hierarchically optimal classification tree analysis in medical research: The first decade
June 15, 2007 Pan Du
Senior Bioinformatics Analyst
Northwestern University Medical School
RHLCCC
[Slides20070622_lumiVST.pdf Towards an Optimized Illumina Microarray Data Analysis Pipeline]
April 20, 2007 Eric Just
Bioinformatics Software Engineer
Northwestern University Medical School
Center for Genetic Medicine
[Slides20070420_EJ-biostat_bioinform.pdf Object-oriented Access to Chado Sequence and Feature Data Using Modware]
March 16, 2007 Elizabeth Hahn, MA
Assistant Professor
Northwestern University Medical School
Preventive Medicine
[Slides20070316_Hahn_nu_nic_0307.pdf Methodological Challenges in Analyzing Patient-Reported Outcomes]
February 16, 2007 Simon Lin, M.D.
Assistant Professor
Northwestern University Medical School
Bioinformatics Core
[Slides20070216-nuID.pdf nuID: A Novel Identifier for Oligos, Ideal for Oligonucleotide-based Microarrays]
January 19, 2007 Alfred W. Rademaker, Ph.D.
Professor
Northwestern University Medical School
Department of Preventive Medicine
[Slides20070119-Phase_II_01-19-07WEB.pdf Cancer Clinical Trials: Extensions and Alternatives]
December 15, 2006 Rhett Sutphin
System Analyst
Northwestern University Medical School
RHLCCC
[Slides20061215-mzHDF.pdf mzHDF for High-throughput Proteomics Data]
November 17, 2006 Michelle Holko, Ph.D.
Postdoctoral Fellow
Northwestern University Medical School
Department of Preventive Medicine
Analysis of Interferon Stimulated Gene Expression Profiles in Renal Cell Cancer
October 20, 2006 Andrew Winter
Software Architect
Northwestern University Medical School
RHLCCC
[Slides20061020-EDW.pdf An Introduction to the Enterprise Data Warehouse for the McGaw Medical Center of Northwestern University]
September 18, 2006 Denise Scholtens, Ph.D.
Assistant Professor
Northwestern University Medical School
Department of Preventive Medicine
Likelihood Approaches for Estimating Local Network Features
July 26, 2006 Warren Kibbe, Ph.D.
Research Associate Professor
Northwestern University Medical School
RHLCCC
Director, Bioinformatics Core
[Slides20060726-caBIG.pdf caBIG: What is it?]
June 16, 2006 Irene Helenowski, M.S.
Statistical Analyst / Programmer 2
Northwestern University Medical School
Department of Preventive Medicine
[Slides20060616-Helenowski.pdf Examining the Effect of Biomarkers in Terms of Compartmentalization and a Continuous Variable]
May 19, 2006 Pan Du, Ph.D.
Senior Bioinformatics Analyst
Northwestern University Medical School
RHLCCC
[Slides20060519-peakDetection_presentation.pdf Improved Peak Detection in Mass Spectrometry Spectrum by Incorporating Continuous Wavelet Transform-based Pattern Matching]
April 21, 2006 Joan S. Chmiel, Ph.D.
Alfred W. Rademaker, Ph.D.
Professors
Northwestern University Medical School
Department of Preventive Medicine
[WHI_Slides_04-21-06.pdf Statistical Considerations in the Women's Health Initiative (WHI) Clinical Trial]
March 17, 2006 Eric Just
Bioinformatics Software Engineer
Northwestern University Medical School
Center for Genetic Medicine
[Slides2006-03_EJ-biostat_bioinform.pdf dictyMart: A Powerful Query Interface for dictyBase Based on BioMart]
February 17, 2006 Tony Chiang, M.S.
Research Scientist
Fred Hutchinson Cancer Research Center
Program in Computational Biology

[ScISI02172006.pdf Creating In][ScISI02172006.pdf Silico Interactomes]

January 20, 2006 John Osborne, MSc.
Northwestern University Medical School
RHLCCC
[DiseaseOntologyApplications.pdf Disease Ontology and its Applications]
December 16, 2005 Ji-Ping Wang, Ph.D.
Assistant Professor
Northwestern University
Department of Statistics
[Slides20051216-genecapturepredicition.pdf Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries]
November 18, 2005 Xijin Ge
Northwestern University Medical School
Analytical assessment of the significance of transcription factor binding sites for detecting transcriptional mechanisms from microarray data
October 21, 2005 Hongmei Jiang, Ph.D.
Assistant Professor
Northwestern University
Department of Statistics
A Two-Step Procedure for Multiple Pairwise Comparisons in Microarray Experiments
September 16, 2005 Everett Zhou, Ph.D.
Research Associate-Bioinformatics Programmer
University of North Carolina
Computer Applications in Genetics/Bioinformatics
August 19, 2005 Yong Zeng, Ph.D. and Spencer Huang, Ph.D.
Northwestern University Medical School
Department of Preventive Medicine
Gene Expression Profiling for Pediatric Renal Tumors
July 15, 2005 Eric Just
Bioinformatics Software Engineer
Northwestern University Medical School
Center for Genetic Medicine
[2005-07_EJ-biostat_bioinform.pdf dictyBase: Towards a Generic Model Organism Database]
June 17, 2005 Eric G. Bremer
Research Associate Professor
Northwestern University Medical School
Neurological Surgery
[eb_research_hour.pdf Grid Enabled Data/Text Mining for Systems Biology Knowledge Base Development]
May 20, 2005 Warren Kibbe, Ph.D.
Research Associate Professor
Northwestern University Medical School
RHLCCC
Director, Bioinformatics Core
[21CFR-Part11-HIPAA.pdf HIPAA and 21 CFR Part 11 ]
April 15, 2005 Alfred Rademaker, Ph.D.
Professor
Northwestern University Medical School
Department of Preventive Medicine
Director of Cancer Center Biostatistics Core
[Phase_II_04-15-05_FINAL.pdf The design and analysis of Phase II cancer studies]
March 18, 2005 Simon Lin, M.D.
Assistant Professor
Northwestern University Medical School
Bioinformatics Core
[proteomics.pdf Mass spectrometry based proteomics and metabolomics]
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