Below is a list of papers recommended at the monthly journal sessions. Feel free to add more at the end, or to comment on these.


Yvonne Edwards (24 Aug 2007)

BUSINESS OFFICE FEATURE: Microarray Technologies: Bench to Bedside

Emma Hitt

Science 317:1101-1106 (24 August 2007)


Jacky Pallas (17 Aug 2007)

Structure-based activity prediction for an enzyme of unknown function

Johannes C. Hermann1, Ricardo Marti-Arbona2, Alexander A. Fedorov3, Elena Fedorov3, Steven C. Almo3, Brian K. Shoichet1 & Frank M. Raushel2

Nature 448, 775-779 (16 August 2007)


Jacky Pallas (13 Aug 2007)

"Divergence of Transcription Factor Binding Sites Across Related Yeast Species"

Anthony R. Borneman,... Mark Gerstein, Michael Snyder

Science, Vol. 317. no. 5839, pp. 815 - 819

Comment: ChIP-chip analysis of yeast species identifies TFBS differences. Materials and Methods here

Two papers from PLoS ONE discuss methods for handling short DNA sequences. The first describes an alternative to MegaBlast for matches 14-30 nt sequences to genomes. The second is a new assembly protocol designed specifically for the output of the new generation seequencing machines.

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

Christian Iseli1, Giovanna Ambrosini Philipp Bucher C. Victor Jongeneel

PLoS ONE

Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

Andreas Sundquist, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, Serafim Batzoglou

PLoS ONE


Anna Lobley (4th Aug 2005)

"Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions"

Ramon Aragues, Andrej Sali, Jaume Bonet, Marc Marti-Renom, Baldomero Oliva

PLoS Comp Biol


Some from Jacky Pallas (12th January 2006):

"PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny" by Rahul Siddharthan Eric D. Siggia1, Erik van Nimwegen PLoS Computational Biology

"Genome-Wide Associations of Gene Expression Variation in Humans" by Barbara E. Stranger, and ..., and Emmanouil T. Dermitzakis1 PLoS Genetics December 2005

"The importance of sequence diversity in the aggregation and evolution of proteins" by Caroline F. Wright1, Sarah A. Teichmann2, Jane Clarke3 and Christopher M. Dobson Nature 438, 878-881 (8 December 2005)

"Genetics in the Age of Systems Biology" by Peter Robin Hiesinger and Bassem A. Hassan Cell 29 Dec 2006 Essay: explores how classical approaches such as forward genetics fit into this emerging framework

"Time to Organize the Bioinformatics Resourceome" by Nicola Cannata, Emanuela Merelli, Russ B. Altman PLoS Comp Biol Dec 05 Perspectives


From Stefano Lise, 12th January 2006:

"Protein Structure Prediction: Inroads to Biology" by Donald Petrey and Barry Honig Molecular Cell Vol. 20, pp 811-819 (2005)


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