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Thursday, 24 April 2014
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GBCB Seminar: Text mining for biocuration of bacterial infectious disease
Thu, Apr 24, 4:00pm - 
VBI Movie Series featuring “The Waiting Room”
Mon, May 26, 6:00pm - 
VBI Movie Series featuring “WALL-E”
Mon, May 19, 6:00pm - 
VBI Movie Series featuring “The Matrix”
Mon, May 12, 6:00pm - 
VBI Movie Series featuring “E.T.
Mon, May 05, 6:00pm - 
VBI Movie Series featuring “Brazil”
Mon, Apr 28, 6:00pm - 
Life Sci Seminar: Combining Next-Generation Phenotyping with Panomics—A New Standard for ...
Fri, May 09, 12:20pm -  1:20pm
Life Sci Seminar: Outer Membrane Biogenesis in Gram-Negative Bacteria
Fri, May 02, 12:20pm -  1:20pm
Life Sci Seminar: Dr. Mark Estelle
Fri, Apr 25, 12:20pm -  1:20pm

Speaker: Dan Sullivan, GBCB Doctoral Candidate

Advisors: Dr. Rebecca Wattam, VBI and Dr. David Bevan, Dept. of Biochemistry

Title: Text Mining for Biocuration of Bacterial Infectious Disease

Time and Location: Thursday, April 24, 4:00pm, VBI Conference Center, 1015 Life Science Circle

Abstract: Specialty gene sets, such as virulence factors and antibiotic resistance genes, are of particular interest to infectious disease researchers.  Much of the information about specialty genes’ function is described in literature but unavailable as structured data in bioinformatics databases.  The steadily increasing volume of literature makes it difficult to manually find relevant papers and extract assertion sentences about specialty genes. This presentation describes efforts to build and an automatic classifier for such sentences. Experiments were conducted to assess the impact of the imbalance of positive and negative examples in source documents on classification; develop a support vector machine (SVM) classifier using term frequency-inverse document frequency (TF-IDF) representation of text; and assess the marginal benefit of additional training examples on the quality of the classifier. Analysis of learning curves indicates that additional training examples will not likely improve the quality of the classifier. We discuss options for other text representation schemes to investigate in order to improve the quality of the classifier as measured by F-score.

References:
(1) Pyysalo S, O. T., Cho H-, Sullivan D, Mao C, Sobral B, et al. (2010). "Towards Event Extraction from Full Texts on Infectious Diseases" Proceedings of the 2010 Workshop on Biomedical Natural Language Processing. Uppsala, Sweden: Association for Computational Linguistics: 132-140.

(2) Basu, A., C. Walters, et al. (2003). Support vector machines for text categorization. System Sciences, 2003. Proceedings of the 36th Annual Hawaii International Conference on, IEEE.

(3) Pedregosa, F. a. V., G. and Gramfort, A. and Michel, V., B. a. G. and Thirion, O. and Blondel, M. and Prettenhofer, P., et al. (2011). "Scikit-learn: Machine Learning in Python." Journal of Machine Learning Research 12: 2825--2830.

VBI Movie Series

Title: The Waiting Room

Time and Location: Monday, May 26, 6:00pm, free popcorn, welcome to friends and family!

About: The theme for the series is "Visions of the Future" and I'd like to discuss not only the background dystopian view almost all of the directors take, but the evolution of the role of the protagonist as a hero.

Contact: Kathy O'Hara, kohara1@vbi.vt.edu

VBI Movie Series

Title: WALL-E

Time and Location: Monday, May 19, 6:00pm, free popcorn, welcome to friends and family!

About: The theme for the series is "Visions of the Future" and I'd like to discuss not only the background dystopian view almost all of the directors take, but the evolution of the role of the protagonist as a hero.

Contact: Kathy O'Hara, kohara1@vbi.vt.edu

VBI Movie Series

Title: The Matrix

Time and Location: Monday, May 12, 6:00pm, free popcorn, welcome to friends and family!

About: The theme for the series is "Visions of the Future" and I'd like to discuss not only the background dystopian view almost all of the directors take, but the evolution of the role of the protagonist as a hero.

Contact: Kathy O'Hara, kohara1@vbi.vt.edu

VBI Movie Series

Title: E.T.

Time and Location: Monday, May 5, 6:00pm, free popcorn, welcome to friends and family!

About: The theme for the series is "Visions of the Future" and I'd like to discuss not only the background dystopian view almost all of the directors take, but the evolution of the role of the protagonist as a hero.

Contact: Kathy O'Hara, kohara1@vbi.vt.edu

VBI Movie Series

Title: Forbidden Planet

Time and Location: Monday, April 28, 6:00pm, free popcorn, welcome to friends and family!

About: The theme for the series is "Visions of the Future" and I'd like to discuss not only the background dystopian view almost all of the directors take, but the evolution of the role of the protagonist as a hero.

Contact: Kathy O'Hara, kohara1@vbi.vt.edu

Speaker: Dr. Szilard Voros

Title: Combining Next-Generation Phenotyping with Panomics-- A New Standard for Biomarker and Drug Discovery

Time and Location: Friday, May 9, 12:20pm, VBI Conference Center, 1015 Life Science Circle


Contact Information: Dr. Tim Howland, thowland@vt.edu

Life Science seminar schedule

Abstract:
We present a comprehensive and integrated approach for biomarker and target
discovery that addresses the shortcomings of current approaches to investigate diseaserelevant
pathways. By combining next-generation phenotyping through the use of
advanced imaging with panomics, we investigate and analyze comprehensive,
multidimensional biological networks. Our current focus is atherosclerosis in
cardiovascular diseases.

Company Description:
About Global Genomics Group (G3)
G3 is a life sciences company investigating biological pathways that lead to the
development of diseases to identify novel diagnostic biomarkers and therapeutic targets.
G3 combines next generation phenotyping with panomics (a collective use of multi-tissue
genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics,
lipoprotein proteomics and glycomics) and intregated, system-biology-based
bioinformatics.

Speaker: Dr. Thomas Silhavy, Princeton University

Title: Outer Membrane Biogenesis in Gram-Negative Bacteria

Time and Location: Friday, May 2, 12:20pm, VBI Conference Center, 1015 Life Science Circle


Contact Information: Dr. Ann Stevens, ams@vt.edu

Life Science seminar schedule
 

Abstract: The outer membrane (OM) of Gram-negative bacteria functions as a protective barrier.  It is unusual because the OM bilayer is asymmetric; the inner leaflet is composed of phospholipids, but the outer leaflet is made of lipopolysaccharide (LPS).  Two kinds of proteins are found in the OM.  Lipoproteins are inserted into the inner leaflet of the OM by posttranslationally attached lipid moieties.  Integral OM proteins are b-barrel proteins (OMPs).  All of the components of the OM are synthesized inside the cell.  They must be transported to, and assembled in the OM in the correct orientation to maintain barrier function, and all of this takes place outside the cytoplasm where there is no obvious energy source, such as ATP.

I will present a brief history of how the differences between Gram-positive and Gram-negative bacteria led to the discovery of the outer membrane.  Then I will describe how we have used genetic analysis to identify and characterize the cellular components required for LPS and OMP biogenesis.  After discussing what is known about these essential cellular processes, I will focus on the genetic approaches we are taking to probe the mechanism by which β-barrel assembly machine folds and inserts OMPs into the OM.  My talk will focus on the remarkable insights provided by extragenic suppressors.

Speaker: Dr. Mark Estelle

Title: tbd

Time and Location: Friday, April 25, 12:20pm, VBI Conference Center, 1015 Life Science Circle


Contact Information: Dr. Zach Nimchuk, znimchuk@vt.edu

Life Science seminar schedule