CBG Seminar Series

Most CBCB seminars are now held jointly with the Computational Biology, Bioinformatics and Genomics Concentration Area within the Biological Sciences Graduate Program.
Starting in the fall of 2011, CBG seminars are usually scheduled for noon in the seminar room of the Biosciences Research Building (room 1103). This time slot is shared with seminars hosted by the Molecular and Cellular Biology graduate program.

Some external seminars of interest to CBCB, some informal seminars, and research in progress, are held in CBCB (directions, Google map: bit.ly/CBCB-Gmap; the seminar room is 3118).

2:00 pm Thursday, September 8, 2011

Title: " HMMER: a new generation of homology search software"

By: Sean Eddy

Venue: 1103 Biosciences Research Bldg.

Abstract:Database homology searching might be the most important application in computational molecular biology, and since the 1990s, BLAST has been our main workhorse. Since BLAST's introduction, theoretical advances have been made in applying probabilistic inference methods to homology searches using hidden Markov model (HMM) approaches. General adoption of probabilistic methods has been limited by some key problems, including the fact that the popular HMM implementations (including my HMMER software) are computationally demanding. I will talk about HMMER3, a new generation of HMMER that aims to even more fully deploy probabilistic inference technology on homology searches, while at the same time attaining (and perhaps soon surpassing) BLAST's speed.

Speaker information:Sean Eddy is a group leader at Janelia Farm.
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Noon Wednesday, September 14, 2011

Title: Next Generation Sequencing Launch
Illumina representatives will present the new next generation sequencing facility. Lunch will be served.

Summary: Following a brief introduction about the launch of the University of Maryland's next generation sequencing core (Regier/El-Sayed), the Illumina genomics specialist (Al-Awar) will present an overview of some applications of the Illumina sequencing technology including DNA-seq, RNA-seq, CHiP-seq and small RNA sequencing. The last segment (El-Sayed/Regier)will focus on operational details of the core, scientific consultation, placing orders and primary analysis workflow.

Speaker information:
Next Generation Sequencing core at University of Maryland, College Park and IBBR:  Najib El-Sayed and Jerry Regier
Illumina:  Umayma Al-Awar and John Donaldson

Noon Monday, September 26, 2011 (A related BEES seminar)

Title: "Deep sequencing surveys of microbes and genes involved with honey bee disease"

By: Scott Cornman

Speaker information: Dr. Scott Cornman is in the USDA-ARS.

2:00 pm Thursday, October 6, 2011

Title: "Distinct modes of transcription factor binding and chromatin dynamics."

By: Xiaole Shirley Liu

Summary: The application of ChIP-seq and DNase-seq in recent years has greatly expedited the mechanistic understanding of transcriptional and epigenetic regulation. Although epigenetic profiles are often considered a reflection of the overall transcriptional activities, the dynamics of epigenetic profiles can be effectively mined to reveal novel transcriptional mechanisms. I will introduce approaches using the dynamics of H3K4me2 ChIP-seq and DNase-seq to infer in vivo transcription factor binding. I will also discuss its application to prostate and breast cancer cell lines to reveal distinct mode of estrogen receptor and androgen receptor binding and chromatin dynamics.

Speaker information: Xiaole Shirley Liu is Associate Professor of Biostatistics in the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and the Department of Biostatistics, Harvard School of Public Health

Noon Wednesday, October 26, 2011

Title: "Evolution of sex-biased gene expression in Caenorhabditis"

By: Cristel Thomas

Speaker information: Cristel Thomas, an MOCB graduate student in the Haag laboratory, will be presenting her Ph.D. thesis.

1:30 pm Tuesday, November 22, 2011

Title: "Characterizing and Predicting Gene-Composition Variation Among Bacterial Genomes"

By: Joshua Weitz

Venue: CBCB, 3118 Biomolecular Sciences Building (#296)

Summary: The discovery of variable gene content of genomes of closely related bacteria has radically re-shaped our understanding of microbial species identity. In this talk, I discuss recent progress in characterizing and predicting variability in gene composition among bacterial genomes. I will review as well as introduce metrics to characterize the heterogeneous distribution of genes within genomes. I will also present a neutral model of genome evolution that can reproduce the gene-composition variation observed in bacterial pathogens.

Speaker information: Joshua S. Weitz is an Assistant Professor in the School of Biology at the Georgia Institute of Technology. Dr. Weitz has an adjunct appointment in the School of Physics and is program faculty in the Bioengineering Interdisciplinary Graduate Program.
Weitz Lab

Noon Monday, November 28, 2011 (A related BEES seminar)

Title: "Evolution of new proteins in E. coli genomes"

By: Guoqin Yu

Speaker information: Dr. Guoqin Yu is a Postdoctoral Associate with IBBR and NIST.

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