CBCB Seminar Series

Most CBCB seminars are held from 2 p.m. until 3:15 p.m. on Thursdays in the CBCB seminar room, 3118 at Biomolecular Sciences Building #296
Some external seminars are listed here. These, and some other exceptions, will have a different time and/or place.
For directions to CBCB please scroll down.

2:00 p.m., Friday, April 9, 2010

Title: "Transcript Assembly and Abundance Estimation with High-Throughput RNA Sequencing"

By: Cole Trapnell, CBCB

Venue: 3118 in CBCB (our usual venue)

Speaker information: Cole Trapnell will be presenting his PhD thesis

2:00 p.m., Thursday, April 15, 2010

RECOMB 2010 Practice Talks

Venue: 3118 Biomolecular Sciences directions

Title (RECOMB 2010 Practice Talk): "Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs"

Authors: Barna Saha, Allison Hoch, Samir Khuller, Louiqa Raschid and Xiao-Ning Zhang

Speaker: Barna Saha, a third year Computer Science graduate student working with Samir Khuller on algorithm design and analysis.

Abstract: We focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph. We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time. We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time. In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well. We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR). A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns. Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses. We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.
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Title (RECOMB 2010 Practice Talk): "Extracting between-pathway models from E-MAP interactions using expected graph compression"

Speaker: David Kelley

Abstract: Genetic interactions (such as synthetic lethal interactions) have become quantifiable on a large-scale using the epistatic miniarray profile (E-MAP) method. An E-MAP allows the construction of a large, weighted network of both aggravating and alleviating genetic interactions between genes. By clustering genes into modules and establishing relationships between those modules, we can discover compensatory pathways. We introduce a general framework for applying greedy clustering heuristics to probabilistic graphs.We use this framework to apply a graph clustering method called graph summarization to an E-MAP that targets yeast chromosome biology. This results in a new method for clustering E-MAP data that we call Expected Graph Compression (EGC). We validate modules and compensatory pathways using enriched Gene Ontology annotations and a novel method based on correlated gene expression from a comprehensive collection of expression experiments. EGC finds a number of modules that are not found by any of the previous methods to cluster E-MAP data. Further, EGC uncovers core submodules contained within several previously found modules, suggesting that EGC can reveal the finer structure of E-MAP networks.

2:00 p.m., Thursday, April 29, 2010

Title: "Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings"

Speaker: Konstantin Berlin, a finishing PhD student in Computer Science

Venue: 3118 Biomolecular Sciences directions

Scheduled Events

    Upcoming:
  • Sept. 8, 2011: Sean Eddy, Janelia Farm, HHMI

Past Events


Other Events


Directions

More detailed transportation options to CBCB can be found here.

From the Capital Beltway to Parking Lot:
  • take Capital Beltway (I-495) Exit 25 and turn onto Baltimore Avenue (US Route 1) South
  • go two miles south on Baltimore Ave and enter the main gate at Campus Drive
  • take the right lane into campus and make first right turn onto Paint Branch Drive
  • stop at the first stop sign then pass Stadium Drive on the left
  • stop at the second stop sign then pass Parking Lot XX2 on the right
  • look for the Paint Branch Drive Visitor Lot on the left
  • turn left onto Technology Drive and park in the Paint Branch Drive Visitor Lot


From Parking Lot to CBCB:
  • the back of the Biomolecular Sciences Building #296 faces this parking lot
  • walk around to the front of the building and using the keypad near the front door
  • dial the number of one of the CBCB staff members in order to gain entrance to the building
  • CBCB is located on the third floor of the Biomolecular Sciences Building #296