Bioinformatics Journal Club at CHRF                     

Bioinformatics journal club meetings take place each Friday at 11 a.m. in the Research Foundation building, 8th floor, room 8551 (unless announced otherwise). The purpose of the journal club is to discuss recent papers relevant for bioinformatics, computational biology and other quantitative biomedical studies. We also have informal research talks and other forms of exchanging information on an ad hoc basis.  Right now, most of the people who attend the meetings are from the Division of Biomedical Informatics. Of course, everyone is welcome to join us (please contact Jarek Meller in order to add your name to our mailing list). 

If possible, copies of the papers to be discussed will be available for downloading at our Web Editor site. If you want to send a message to our mailing list (please use only for matters related to journal club), please use our mail submission page. Below is our tentative schedule for the next several months.

    Literature watch (first Friday of each month), covering the following journals:

Applications of Statistics in Molecular Biology (Mario Medvedovic)

Biostatistics (Mario Medvedovic)

Machine Learning (Rafal Adamczak)

IEEE Transactions on Neural Networks (Rafal Adamczak)

Nature (Michael Wagner)

Proteomics (Michael Wagner)

Bioinformatics (Aleksey Porollo)

Journal of Computational Chemistry (Aleksey Porollo)

BMC Bioinformatics (Xiangdong Liu)

Molecular Cell (Walter Jessen)

Genome Research (Anil Jegga)

Trends in Molecular Biology (Anil Jegga)

Science (Jarek Meller)

Journal of Molecular Biology (Sergio Kaiser)

Proteins: Structure, Function and Bioinformatics (Jarek Meller)

PNAS (Theresa Setty and Sue Kong)

Medical Informatics (Lukasz Itert)

IEEE Transactions on Artificial Intelligence (Lukasz Itert)

Journal of Computational Biology (Siva Sivaganesan)

Nucleic Acid Research (Walter Jessen)

Of course, if you find an interesting paper in another journal, please bring it on!

    Informal talks focused on our own research projects (every second Friday of each month):

October '04 - Michael Wagner, "Outpatient scheduling simulation model"

November '04 - John Pestian/Lukasz Itert

December '04 - Mario Medvedovic

January '05 - Siva Sivaganesan

February '05 - Anil Jegga

March '05 - Rafal Adamczak

April '05 - Jarek Meller

May '05 - Bruce Aronow

Titles and abstracts to be announced.

    Selected papers (reviews, research papers etc. on a specific subject) to be presented and discussed every third Friday of each month:

October '04 - Jarek Meller - models of protein pathways

November '04 -  Walter Jessen - gene expression profiling in colorectal cancer

December '04 - Ranga Chandra -  systems biology

January '05 -  Bhuvana Sakthivel - ???

February '05 - Aleksey Porollo - identification of protein-protein interaction sites

March '05 - Brad Slaven - gene finding in newly sequenced genomes

April '05 - Sergio Kaiser - ???

May '05 - Johannes  Freudenberg - across platform normalization of gene expression data

June '05 - Sue Kong - ???

The actual papers to be discussed will be available for downloading at our Web Editor site (when accessing via this link you will only be able to browse its content, but not edit it).

The remaining Fridays will be used on ad hoc basis for invited talks, interviews and joint meetings with other divisions at CHRF. Separate announcements will follow. See you in our conference room on the 8th floor of the Research Foundation building!

So far we have had the following guests this year:

Artem Evdokimov (P&G), October `04, "Impact of structural biology on early-stage drug design, case study of methionine aminopeptidase"

John Rugg (CCHMC), October `04, "Topics in clinical informatics and scheduling"

Last year's topics (2003/2004 academic year):

Informal talks focused on our own research projects (every second Friday of each month):

October '03 - Mario Medvedovic (Bayesian approach to clustering of microarray gene expression and other data)

November '03 - Rafal Adamczak (Solvent accessibility prediction with neural network based regression)

January '04 - Aleksey Porollo (Prediction of protein-protein interaction interfaces)

February '04 - Michael Wagner (Classification of prostate cancer subtypes using mass spec proteomic data)

April '04 - Lukasz Itert (Medical text processing)

Selected papers (every third Friday of each month):

October '03 - Zhongming Yang - models of regulatory pathways

November '03 - Lukasz Itert - advances in text mining

January '04 - Anil Jegga - advances in DNA sequence analysis

February '04 - Aleksey Porollo - XML in bioinformatics

April '04 - Rafal Adamczak - advances in Neural Networks

May '04 - Mario Medvedovic - clustering techniques for bioinformatics

June '04 - Jarek Meller - advances in protein structure prediction

Author: Jarek Meller