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November 23, 2009
12:30-2:00 PM
HSPH
Bldg 2, Room 426
| Identifying Common Copy Number Variants (CNVs) at a 500 Base-Pair Resolution
Correlated and High-Dimensional Data Seminar
Charles Lee, Ph.D., FACMG
Director of Cytogenetics, Harvard Cancer Center
Associate Professor, Harvard Medical School
Associate Faculty Member, MIT Broad Institute
Clinical Cytogeneticist, Brigham and Women’s Hospital
We have developed two tiling oligonucleotide array sets (a 42 million NimbleGen array set and a 24 million Agilent array set) to identify and characterize common copy number variants (CNVs) at a 500 bp resolution. Insights into mutational mechanisms and disease association studies will also be discussed.
A pizza lunch will be served
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November 23, 2009
3:30pm-5:30pm
HSPH
Kresge LL6
| Genome Browsing with Ensembl
PQG series: Tutorials For Analyzing Quantitative 'Omic Data
Paul Bain, Harvard Medical School
Ensembl provides unified access to genomic information and annotation for more than 50 eukaryotic species. Learn how to find gene and genomic-related information, from splice sites to SNPs and more. We'll also explore the data mining tool BioMart that provides access to Ensembl data in bulk with hands-on exercises.
http://www.hsph.harvard.edu/pqg/events/tutorials-short-courses.html
NO RSVP REQUIRED. Participation is open to the HSPH community and is on a first-come first serve basis. Please note that all participants need to have an existing HSPH ID and password to access the computers.
For more information on this tutorial series, please contact Aditi Hazra at
This e-mail address is being protected from spambots, you need JavaScript enabled to view it
To be added to the PQG email list, please contact Shaina Andelman at
This e-mail address is being protected from spambots, you need JavaScript enabled to view it
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December 4, 2009
12:30-1:30pm
HSPH
Bldg 2, rm 426
| Impact of Timing of Starting Treatment Following Infection with Application to Initiating HAART in HIV Positive Patients
HIV Working Group
Judith Lok, Ph.D.
Assistant Professor, Department of Biostatistics, Harvard School of Public Health
ABSTRACT: Using observational data, we estimate the effect of treatment regimes that initiate treatment depending on time since infection. The main complication with observational data is that treatment was not randomly assigned. E.g., if sicker patients were treated earlier, this may lead to underestimation of the effect of treatment, or even reverse a possible effect. Our identifying assumption is that there are no unmeasured confounders. We develop a new class of Structural Nested Models (SNMs) to estimate the impact of time of initiation of treatment after infection on an outcome measured one year after initiation, compared to the effect of not initiating treatment.
We illustrate our methods using the AIEDRP Core01 database on HIV. The current standard of care in HIV positive patients is Highly Active Anti-Retroviral Treatment (HAART). However, it is unknown yet what is the best time to start HAART, and guidelines are changing. Perhaps postponing HAART is beneficial, because it postpones the time patients experience side effects or develop drug resistance, and hence might improve the patients' long term prognosis. However, it is unknown how long initiation of HAART can safely be postponed without irreversible immune system damage. We investigate the effect of initiating HAART at different times following HIV infection on immune reconstitution measured one year after initiation.
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December 4, 2009
2:00-3:30pm
HSPH
Bldg 2, rm 426
| Statistical Methods in Air Pollution Epidemiology
Statistical Methods in Epidemiology Working Group
Francesca Dominici, Ph.D.
Professor, Department of Biostatistics, Harvard School of Public Health
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December 7, 2009
2:30 p.m.
DFCI
CLSB 11081
| In advance of the SABCS, Meredith Regan (Senior Research Scientist, DFCI and HSPH) will present two short talks.
Adjusting for selective crossover in analyses of letrozole vs. tamoxifen in the BIG 1-98 trial.
and
Factors predictive of treatment benefit from letrozole in postmenopausal patients with hormone receptor-positive breast cancer: results from BIG 1-98.
BIG 1-98 is a double-blind randomized trial comparing 5yrs of Let (Letx5), Tam (Tamx5) and sequences of Let and Tam as adjuvant endocrine therapy for postmenopausal women with endocrine-responsive breast cancer. Initial results (presented Jan05) demonstrated the superiority of Let over Tam in significantly prolonging disease-free survival (DFS) and reducing the risk of relapse in distant sites. Following these results, investigators were informed of the treatment allocation for patients (pts) randomized to Tamx5, and 25% of pts selectively crossed over to Let.
Centrally-assessed ER, PgR, HER2, and Ki-67 have been evaluated individually as potential predictive factors for treatment selection. These and other factors such as age, tumor size, tumor grade, number of involved lymph nodes, and peritumoral vessel invasion are considered together, in a composite score, to consider treatment selection. |
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December 8, 2009
6:30pm light dinner
7:00pm presentation
Buckingham Browne & Nichols Upper School,
Cambridge
| Statistical Methods in Public Health Practice: Case Studies in Influenza and BioSurveillance
Boston Chapter of the ASA
Al Ozonoff, Boston University School of Public Health
Registration http://ozonoff.eventbrite.com/
Directions http://www.bbns.org/contact/directions
Most events require advance reservation. See the latest newsletter for details.
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December 17, 2009
3:30-4:30pm
DFCI
Smith 964
| Geographical Genomics, Canalization, and the Origins of Human Disease
2009/2010 Center for Cancer Computational Biology Seminar Series Greg Gibson
Professor, Georgia Institute of Technology CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu |
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January 7, 2009
12:30-1:30pm
DFCI
CLSB 11081
| Automated High-dimensional Flow Cytometric Data Analysis
Biostatistics and Computational Biology Monthly Seminar
Saumyadipta Pyne, Department of Medical Oncology, Dana-Farber Cancer Institute.
Abstract: Flow cytometric analysis allows rapid single cell interrogation of surface and intracellular determinants by measuring fluorescence intensity of fluorophore-conjugated reagents. The availability of new platforms, allowing detection with increasing number of markers that can be used in parallel, has challenged the traditional technique of identifying cell populations by manual gating and has resulted in a growing need for the development of automated, high-dimensional analytical methods.
We present a new computational platform, FLAME, based on novel multivariate parametric modeling approach to address the complexities of high-dimensional cytometric data with rigor and without the need for projection to lower dimensions. We show examples of FLAME's ability to detect rare populations, to model robustly in the presence of outliers and skew, and to perform the critical task of registering cell populations across samples which enables comparison of cohorts across different time points and phenotypes. Recently, FLAME has been incorporated with the GenePattern package of Broad Institute. The advance will facilitate the application of flow cytometry to new, complex biological and clinical problems.
Click here for article.
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January 8, 2010
2:00-3:00PM HSPH
Bldg 2, room 426 | Assessing risk in families with cancer
Statistical Methods in Epidemiology Working Group Giovanni Parmigiani, Ph.D.
Professor and Chair, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health |
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January 21, 2010
3:30-4:30pm
DFCI
Smith 964
| Title TBA (I have some cool stuff I can only talk about once it’s published!)
2009/2010 Center for Cancer Computational Biology Seminar Series Rafael Irizarry
Professor of Biostatistics, Bloomberg School of Public Health
The Johns Hopkins University CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu
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January 29, 2010
12:30-1:30pm
HSPH
Bldg 2, rm 426
| Metabolic Complications of HIV and Antiretroviral Medications in Children and Adolescents
HIV Working Group
Jane Lindsey, Ph.D. and Denise Jacobson, Ph.D.
Senior Research Scientists, Department of Biostatistics, Harvard School of Public Health and The Center for Biostatistics in AIDS Research
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February 5, 2010
2:30-4:00pm
HSPH
Bldg 2, room 426
| Improving the reliability of diagnostic tests in population-based agreement models
Statistical Methods in Epidemiology Working Group
Kerrie Nelson
MGH Biostatistics
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February 6, 2010
10:00-4:00pm
Boston University School of Public Health
| Short Course: Measurement Error: Models, Methods and Applications
Boston Chapter of the ASA
John Buonaccorsi, University of Massachusetts, Amherst
Registration http://bcasa-buonaccorsi.eventbrite.com/
Most events require advance reservation. See the latest newsletter for details. |
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February 18, 2010
3:30-4:30pm
DFCI
Smith 964
| Mapping Sequences from Next-Generation Sequencing Machines: Challenges and Solutions
2009/2010 Center for Cancer Computational Biology Seminar Series Steven Salzberg
Director, Center for Bioinformatics and Computational Biology
Phillip H. and Catherine C. Horvitz Professor, Department of Computer Science, University of Maryland CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu
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March 5, 2010
2:00-3:30pm
HSPH
Bldg 2, room 426
| Landmark prediction of survival
Statistical Methods in Epidemiology Working Group
Layla Parast
HSPH, Dept of Biostatistics
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March 18, 2010
3:30-4:30pm
DFCI
Smith 964
| Analytical Challenges in Interpreting mRNA-Seq Data
2009/2010 Center for Cancer Computational Biology Seminar Series Sandrine Dudoit
Associate Professor of Biostatistics and Statistics
Chair and Head Graduate Advisor, Graduate Group in Biostatistics, University of California, Berkeley CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu
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April 9, 2010
2:00-3:30pm
HSPH
Bldg 2, room 426
| Fair assessment of variation in logistic regression models
Statistical Methods in Epidemiology Working Group
Yves Christien
Harvard University, Dept of Statistics
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April 15, 2010
3:30-4:30pm
DFCI
Smith 964
| Using Functional Genomics Data to Discover Novel Biology and Understand Disease
2009/2010 Center for Cancer Computational Biology Seminar Series Olga Troyanskaya
Associate Professor Lewis-Sigler Institute for Integrative Genomics
and Department of Computer Science, Princeton University CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu |
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May 7,2010
2:30pm – 4:00pm
HSPH
Bldg2, room 426
| Survival point estimate prediction in matched and non-matched case-control
subsample designed study
Statistical Methods in Epidemiology Working Group
Annette Molinaro
Yale University, Dept of Biostatistics
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May 20, 2010
3:30-4:30pm
DFCI
Smith 964
| How the Cell Looks at the Genome
2009/2010 Center for Cancer Computational Biology Seminar Series Tim Hughes
Professor, Banting and Best Department of Medical Research
and Department of Molecular Genetics, University of Toronto CCCB: From Data to Knowledge, From Knowledge to Understanding
http://cccb.dfci.harvard.edu |
Announcements | |
August 2009
| Xihong Lin named 2009 Myrto Lefkopoulou Distinguished Lecturer at HSPH
The Department of Biostatistics, Harvard School of Public Health, has named Xihong Lin¸ Ph.D., Professor of Biostatistics at Harvard School of Public Health, Department of Biostatistics, as the 2009 Myrto Lefkopoulou Distinguished Lecturer. Professor Lin will present a lecture entitled "Statistical Issues and Challenges in Analyzing High-throughput 'Omics Data in Population-based Studies" on September 3, 2009 at 4 p.m. at the Harvard School of Public Health in the Kresge Building, Room G2.
The lectureship was established in perpetuity in memory of Dr. Myrto Lefkopoulou, a faculty member and graduate of Harvard School of Public Health. Dr. Lefkopoulou tragically died of cancer in 1992 at the age of 34 after a courageous two-year battle. She was deeply beloved by friends, students, and faculty.
Each year the Myrto Lefkopoulou Lectureship is awarded to a promising statistician who has made contributions to either collaborative or methodologic research in the applications of statistical methods to biology or medicine and/or has shown excellence in the teaching of Biostatistics. Ordinarily, the lectureship is given to a statistician within 15 years of receiving an earned doctorate. |
September 14-18, 2009
Mathematical Biosciences Institute
The Ohio State University
| Workshop 1: Network Biology: Understanding Metabolic and Protein Interactions
Organizers: Laszlo Barabasi and Eivind Almaas
SPEAKERS
Reka Albert (Physics, Pennsylvania State)
Eivind Almaas (Biotechnology, NUST)
Albert-Laszlo Barabasi (Physics, Northeastern)
Frank Doyle (Chemical Engineering, UC Santa Barbara)
Mark Gerstein (Molecular Biophysics, Biochemistry, & Computer Science, Yale)
Ravi Iyengar (Pharmacology & Systems Therapeutics, MSSM)
Nevan Krogan (Cellular & Molecular Pharmacology, UC San Francisco)
Chad Myers (Computer Science & Engineering, U Minnesota)
Jason Papin (Biomedical Engineering, U Virginia)
John Quackenbush (Biostatistics & Computational Biology, Dana-Farber Cancer Inst.)
Eytan Ruppin (Computer Science, Tel Aviv)
Eugene Shakhnovich (Chemistry & Chemical Biology, Harvard)
Jorg Stelling (Biosystems Science & Engineering, ETH Zurich)
Gregory Stephanopoulos (Chemical Engineering, MIT)
Marc Vidal (Cancer Biology, CCSB)
The MBI receives major funding from the National Science Foundation Division of Mathematical Sciences and is supported by The Ohio State University.
The Mathematical Biosciences Institute adheres to the AA/EOE guidelines.
To apply for this event: http://www.mbi.osu.edu |
October 2009
| The Department of Biostatistics at the Harvard School of Public Health together with statisticians from the pharmaceutical industry and the FDA is organizing the 2009 Non-Clinical Biostatistics Conference, which will take place this October at the Med School Conference Center. You can find detailed information at the conference website, www.ncb2009.org. Its theme is Statistical Methodologies: Key to Discovery, Safety Assessment and Development.
This is a unique opportunity for those interested in non-clinical biostatistics. It is in fact the first conference in the U.S. fully dedicated to this topic, and it will bring together a large number of statisticians working in drug discovery, pharmacology, safety, and chemical development.
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Opportunities | |
| | Discovery Future Fellowships The Australian government has announced funding for 'Future Fellowships' - four-year appointments for international researchers to work in Australia. The fellowships can be taken up at any of many different academic institutes and research organizations.
http://www.arc.gov.au/ncgp/futurefel/future_default.htm |
