Presentation Schedule

The HuGe group meets weekly on Monday at 2:00pm in the 4th Floor Computer Science Conference room(SB4.01.10). Anyone is welcome to attend to hear our discussion on current techniques and topics.

Each week we present 1-2 current papers in the field of bioinformatics. Here is our presentation schedule for this semester. Check back weekly for changes.

Spring 2007

• 04/19/07: Ph.D. Thesis defense
  Presenter: Kihoon Yoon
  
• 04/05/07: Meeting cancelled (bioinformatics candidate presentation)
• 03/27/07: Meeting cancelled (bioinformatics candidate presentation)
• 03/19/07: Meeting cancelled (bioinformatics candidate presentation).
  
• 03/05/07: Prediction-Based Fingerprints of Protein–Protein Interactions.
  Presenter: Mark Doderer
  Paper, Slides
• 02/19/07:
  Presenter: Kihoon Yoon
  
• 02/12/07: SAGA: A Subgraph Matching Tool for Biological Graphs.
  Presenter: Angela Dean
  Paper, Slides
• 02/05/07: Dynamic Modeling of Cis-Regulatory Circuits And Gene Expression Prediction ViaCross-Gene Identification.
  Presenter: Eddie Salinas
  Paper, Slides
• 02/19/07: Gene Networks for low-dose radiation using Graph Theoretical Algorithms.
  Presenter: Sree Phani Kishore Devineni
  Paper
• 02/12/07:Adaptively inferring human transcriptional subnetworks.
  Presenter: Amitava Karmaker
  Paper, Slides
• 02/05/07: Presentation of Functional impact of missense variants in BRCA1 predicted by supervised learning.
  Presenter: Mark Doderer
  Paper, Slides
• 01/29/07: Meeting cancelled.
  

Fall 2006

• 12/04/06: CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data.
  Presenter: Amitava Karmaker
  Paper
  
• 11/27/06: A computational study of off A computational study of off-target target effects of RNA interference
  Presenter: Kihoon Yoon
  Paper
  
• 11/20/2006 : Meeting cancelled
  
  
• 11/13/06:
  Presenter: Mark Doderer
  Paper:
  
• 11/06/06: Breast cancer classification and prognosis based on gene expression profiles from a population-based study
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 10/30/06: Database Review
  Presenter: Kihoon Yoon
  
  
• 10/23/06:
  Presenter: Mark Doderer
  
  
• 10/16/06: MicroRNA’s as oncogenes and tumor suppressors
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 10/09/06: GOAnno: GO annotation based on multiple alignment
  Presenter: Mark Doderer
  Paper,
• 10/02/2006 : Predicting protein interaction sites: binding hot-spots in protein–protein and protein–ligand interfaces
  Presenter: Kihoon Yoon
  Paper
  
• 09/12/2006 : Applied Bioinformatics for the Identification of Regulatory Elements
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 09/05/2006: Protein Function Prediction Survey
  Presenter: Mark Doderer
  Paper1, Paper2,Paper3, Slides
  

Spring 2006

• 05/02/2006 : Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 04/25/2006 : A role for the exosome in the in vivo degradation of unstable mRNAs
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 04/18/2006 : Meeting cancelled
  
  
• 04/11/2006 : PhD Proposal Presentation (SB 03.01.02)
  Presenter: Kihoon Yoon
  
  
• 04/04/2006 : Cellular and subcellular localization of the membrane proteins
  Presenter: Mark Doderer
  Paper, Slides
  
• 03/28/2006: Conditional gene expression by controlling translation
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 03/21/2006 : Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 03/14/2006 : Detecting Protein-Protein Interactions in the Intact Cell
  Presenter: Mark Doderer
  Paper, Slides
  
• 03/07/2006 : Meeting cancelled
  
  
• 02/28/2006 : Meeting cancelled
  
  
• 02/21/2006: Rapid techniques for DNA extraction from routinely processed archival tissue for use in PCR
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 02/14/2006: Comprehensive in silico functional specification of mouse retina transcripts
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 02/07/2006: SPdb: a signal peptide database
  Presenter: Mark Doderer
  Paper, Slides
  
• 01/31/2006: Overview of Bioinfomatics
  Presenter: Stephen Kwek
  
  

Fall 2005

• 02/28/2006 : Meeting cancelled
  
  
• 10/04/2005: Secondary structure prediction with support vector machines
  Presenter: John Salinas
  Paper, Slides
  
• 09/13/2005 : Meeting cancelled
  
  
• 09/06/2005: Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 08/30/2005:
  Presenter: Ben Truitt
  

Spring 2005

• 05/04/2005 : Predicting genetic regulatory response using classification
  Presenter: John Andrichak
  Paper, Slides
  
• 05/04/2005 : Predicting genetic regulatory response using classification
  Presenter: John Andrichak
  Paper, Slides
  
• 05/04/2005: Clustering of DNA Sequences in Human Promoters
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 04/25/2005: Computational identification of promoters and first exons in the human genome
  Presenter: Erhan John Kartaltepe
  Paper, Slides
  
• 04/20/2005 : Meeting cancelled
  
  
• 04/13/2005: PhD Proposal Presentation (SB 03.01.02)
  Presenter: Rehan Akbani
  
  
• 04/06/2005: Computational Gene Prediction Using Multiple Sources of Evidence
  Presenter: Amitava Karmaker
  Paper, Slides
  
• 03/30/2005 :An overview on predicting the subcellular location of a protein
  Presenter: Mark Doderer
  Paper, Slides
  
• 03/30/2005 : Support vector machine approach for protein subcellular localization prediction
  Presenter: John Salinas
  Paper, Slides
  
• 03/23/2005 : The biology of eukaryotic promoter prediction - a review
  Presenter: Ben Truitt
  Paper, Slides
  
• 03/09/2005 : Meeting cancelled , CSB deadline
  
  
• 03/02/2005 : Meeting cancelled
  
  
• 02/23/2005 : Techniques for Recognition of Translation Initiation Sites
  Presenter: Rehan Akbani
  Paper, Slides
  
• 02/16/2005 : Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
  Presenter:Paulie Pena
  Paper, Slides
  
• 02/16/2005 : Prediction of phosphorylation sites using SVMs
  Presenter:Jessamin Yu
  Paper, Slides
  
• 02/09/2005: CART Classification of Human 5' UTR Sequences
  Presenter: Erhan John Kartaltepe
  Paper, Slides
  
• 02/02/2005: Predicting subcellular localization of proteins using machine-learned classifiers
  Presenter: Kihoon Yoon
  Paper, Slides
  
• 01/26/2005: Bioinformatics overview
  Presenter: Stephen Kwek
  
  
• 01/19/2005: Bioinformatics overview
  Presenter: Stephen Kwek