Northwestern University

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Mar
27
Tue 12:00 PM

BIDS Seminar: Rosemary Braun, PhD, MPH - Faculty Research (TimeStamp: A Universal Method for Robust Detection of Circadian State from Gene Expression)

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When: Tuesday, March 27, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: - Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Co-Sponsor(s):
Northwestern Institute on Complex Systems (NICO)

Category: Lectures & Meetings

Description:

Abstract: Determining the state of an individual's internal physiological clock has important implications for precision medicine, from diagnosing neurological disorders to optimizing drug delivery.  To be useful, such a test must be accurate, minimally burdensome to the patient, and robust to differences in patient protocols, sample collection, and assay technologies. TimeStamp is a novel machine--learning approach to predict physiological time based on gene expression in human blood.  A powerful feature is TimeStamp's generalizability, enabling it to be applied to samples from disparate studies and yield highly accurate results despite systematic differences between the studies.  This quality is unique amongst expression--based predictors, and addresses a major challenge in the development of reliable and clinically useful biomarker tests.

About BIDS: These talks include visiting lecturers, presentations on research by BIDS faculty and trainees, as well as presentations about informatics tools and resources to support research.

Apr
3
Tue 12:00 PM

BIDS Seminar: Theresa Walunas, PhD - Faculty Research (Using an Integrated Medical Records Dataset to Explore Health Outcomes in Patients with Autoimmune Disease)

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When: Tuesday, April 3, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: - Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Category: Lectures & Meetings

Description:

Medical record data is a rich source of information that can be used to better understand health outcomes for patients with complex conditions, such as autoimmune disease.  However, people with complex diseases often seek care in multiple institutions, making it difficult to get a complete picture of their care and health outcomes from single health system data repositories. Integrated medical records from multiple healthcare institutions represent an opportunity to develop a more complete picture of complex patients and their care. We examined the impact of receiving care in multiple locations on health outcomes for people with systemic lupus erythematosus using a novel local integrated medical record dataset, the Chicago HealthLNK data repository.  Using this dataset, we were able to demonstrate that care fragmentation is associated with increased risk of severe comorbidities and develop a model for examining the role of care fragmentation in other complex multi-system disease. 

About Biomedical Informatics Data Science (BIDS): These talks include visiting lecturers, presentations on research by BIDS faculty and trainees, as well as presentations about informatics tools and resources to support research.

Apr
10
Tue 12:00 PM

BIDS Seminar (CANCELLED due to Computational Research Day 2018)

CANCELLED

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When: Tuesday, April 10, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: - Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Category: Lectures & Meetings

Description:

Cancelled due to Computational Research Day 2018.

Apr
17
Tue 12:00 PM

BIDS Seminar: Jiping Wang, PhD - Faculty Research (Normalization of Transcript Degradation Improves Accuracy in RNA-seq Analysis)

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When: Tuesday, April 17, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: - Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Category: Lectures & Meetings

Description:

Abstract: RNA-sequencing (RNA-seq) is a powerful high-throughput tool to profile transcriptional activities in cells. The observed read counts can be biased by various factors such that they do not accurately represent the true relative abundance of mRNA transcript abundance. Normalization is a critical step to ensure unbiased comparison of gene expression between samples or conditions. Here we show that the gene-specific heterogeneity of transcript degradation pattern across samples presents a common and major source of unwanted variation, and it may substantially bias the results in gene expression analysis. Most existing normalization approaches focused on global adjustment of systematic bias are ineffective to correct for this bias. We propose a novel method based on matrix factorization over-approximation that allows quantification of RNA degradation of each gene within each sample. The estimated degradation index scores are used to build a pipeline named DegNorm (stands for degradation normalization) to adjust read count for RNA degradation heterogeneity on a gene-by-gene basis while simultaneously controlling sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of real RNA-seq data and simulated data.

About Biomedical Informatics Data Science (BIDS): These talks include visiting lecturers, presentations on research by BIDS faculty and trainees, as well as presentations about informatics tools and resources to support research.

Apr
24
Tue 12:00 PM

BIDS Seminar: Cancelled

CANCELLED

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When: Tuesday, April 24, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: - Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Category: Lectures & Meetings

Description:

This event is cancelled for today.