This page lists the papers that are presented each week. When you know which paper(s) you will be presenting, please edit the corresponding link below. Start by clicking the 'editPage' link above, and then use this as a template for adding new entries:

replacing the four UPPER-CASE strings with the paper details and URL.

Also, for the monthly journal sessions, anybody/everybody can add any recommended papers to the corresponding section.

30th October 2008 Chair: Kevin Bryson#

Speaker: Antonis Koussounadis

"Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks."

Fuchs A, Kirschner A, Frishman D.


16th October 2008 Chair: Yvonne Edwards#

Speaker: Sonia Shah

"Computational prediction of human proteins that can be secreted into bloodstream"

Juan Cui, Qi Liu, David Puett, Ying Xu


9th October 2008 Chair: Tim Nugent#

Speaker: Rand Hindi

"An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields"

Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, Jos� N. Onuchic

Proteins: Structure, Function, and Bioinformatics

11 September 2008 Chair: Sonia Shah#

Speaker: Tim Nugent

"Molecular dynamics simulations and membrane protein structure quality"

Anthony Ivetac and Mark S. P. Sansom

European Biophysics Journal, Volume 37, Number 4, April 2008

31 July 2008 Chair: Iain Fairclough#

Speaker: Yvonne Edwards

"Protein Disorder Is Positively Correlated with Gene Expression in Escherichia coli"

Oleg Paliy, Shawn M. Gargac, Yugong Cheng, Vladimir N. Uversky, and A. Keith Dunker

J. Proteome Res., 7 (6), 2234?2245, 2008.

15 May 2008 Chair: Jacky Pallas#

Speaker: Iain Fairclough

"Network-based global inference of human disease genes."

Wu X, Jiang R, Zhang MQ, Li S.

Molecular Systems Biology 4:189

21st February 2008 Chair: Dan Roden#

Speaker: Kevin Bryson

"A modular network model of aging"

Huiling Xue, Bo Xian, Dong Dong, Kai Xia, Shanshan Zhu, Zhongnan Zhang, Lei Hou, Qingpeng Zhang, Yi Zhang & Jing-Dong J Han

Molecular Systems Biology 3:147

14th February 2008 Chair: Iain Fairclough#

Speaker: Melissa Pentony

Jikui Song, Lian-Wang Guo, Hakim Muradov, Nikolai O. Artemyev, Arnold E. Ruoho, and John L. Markley.

Intrinsically disordered {gamma}-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure.

PNAS 2008 105(5):1505-1510

24th January 2008 Chair: Tim Nugent#

Speaker: Jacky Pallas

Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo L�pez, Nick Goldman, Ari L�ytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer Harrow and Alfonso Valencia.

Determination and validation of principal gene products

Bioinformatics 2008 24(1):11-17; doi:10.1093

17th January 2008 Chair: Sean Ward#

Speaker: Rand Hindi

Jean-Francois Taly , Antoine Marin and Jean-Francois Gibrat Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

BMC Bioinformatics 2008, 9:6 doi:10.1186/1471-2105-9-6

13th December 2007 Chair: Michael Sadowski#

Speaker: Kevin Bryson

Ingemar Andr�, Philip Bradley, Chu Wang, and David Baker Prediction of the structure of symmetrical protein assemblies

PNAS 2007 104: 17656-17661

28th November 2007 Chair: Anna Lobley#

Speaker: Stefano Lise

Alexandra Shulman-Peleg*, *Maxim Shatsky*, *Ruth Nussinov* and *Haim J. Wolfson* Spatial chemical conservation of hot spot interactions in protein-protein complexes

BMC Biology 2007, *5**:*43

15th November 2007 Chair: Jacky Pallas#

Speaker: Antonis Koussounadis

Maguitman AG, Rechtsteiner A, Verspoor K, Strauss CE, Rocha LM. "Large-scale testing of bibliome informatics using Pfam protein families."

Pac Symp Biocomput. 2006;:76-87. PMID: 17094229

8th November 2007 Chair: Tim Nugent#

Speaker: Sonia Shah

"A systems biology approach for pathway level analysis" by Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R.

Genome Res. 2007 17(10):1537-45.

18th October 2007 Chair: Stefano Lise#

Speaker: Tim Nugent

"Toward high-resolution prediction and design of transmembrane helical protein structures" by P. Barth, J. Schonbrun and D. Baker

PNAS October 2, 2007 vol. 104 no. 40 15682-15687

13th September 2007 Chair: Dan Roden#

Speaker: Melissa Pentony

"Natively Unstructured Loops Differ from Other Loops" by Avner Schlessinger, Jinfeng Liu & Burkhard Rost

PLOS Comp. Biol. July 2007 Volume 3 Issue 7

26th July 2007 Chair: Tim Nugent#

Speaker: Matthew Trotter

"Nearest Neighbor Networks: clustering expression data based on gene neighborhoods." by Huttenhower C, et al.

BMC Bioinformatics, 8:250. (2007)

12th July 2007 Chair: Yvonne Edwards#

Speaker: Dan Roden

"Predicting functionally important residues from sequence conservation" by John A. Capra and Mona Singh."

Bioinformatics, 2007,Epub ahead of print

28th June 2007 Chair: Stefano Lise#

Speaker: Michael Sadowski

"Ab initio modeling of small proteins by iterative TASSER simulations."

by Wu S., Skolnick J and Zhang Y.

BMC Bioinformatics, 2007, 5:17

21st June 2007 Chair: Jacky Pallas#

Speaker: Anna Lobley

"The 2006 Automated Function Prediction Meeting"

BMC Bioinformatics, 2007, Vol. 8, suppl. 4, S1

Paper1 SVM Fold BMC Bioinformatics 2007, 8(Suppl 4):S2

Paper2 Ligand binding site prediction BMC Bioinformatics 2007, 8(Suppl 4):S9

14th June 2007 Chair: Anna Lobley#

Speaker: Sonia Shah

"Identifying Tissue Specific Differential Gene Expression and Exon Splicing using Exon arrays"

UKAffy conference talk

6th June 2007 Chair: #

Speaker: Kevin Bryson

"Genome-Wide Mapping of in Vivo Protein-DNA Interactions"

by Johnson et al.

Science, 2007 May 31; Epub ahead of print

17th May 2007 Chair: Kevin Bryson#

Speaker: Antonis Koussounadis

"Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations"

by Van Vooren et al.

Nucleic Acids Research, 2007, Vol. 35, No. 8 *2533-2543*

19th April 2007 Chair: Antonis Koussounadis #

Speaker: Stefano Lise

"Network-based prediction of protein function"

by Roded Sharan, Igor Ulitsky, & Ron Shamir

Molecular Systems Biology 3:88

19th April 2007 Chair: Sonia Shah#

Speaker: Rand Hindi

"Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials"

by Dmitry Rykunov, András Fiser

Proteins 67(3):559-568

19th April 2007 Chair: Kevin Bryson#

Speaker: Matthew Trotter

"Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms"

by Chiang JH and Chao SY

BMC Bioinformatics 2007 Mar 14;8(1):91

22nd March 2007 Chair: Rand Hindi#

Speaker: Anna Lobley

"A New Method to Measure the Semantic Similarity of GO Terms"

by Wang J, Zhidian D, Payattakool R, Yu P S and Chen CF Bioinformatics

15th March 2007 Chair: Melissa Pentony#

Speaker: Yvonne Edwards

"Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters"

by D. Baek, C. Davis, B. Ewing, D. Gordon and P. Green

Genome Research (2007) 17(2)

8th March 2007 Chair: Michael Sadowski#

Speaker: Tim Nugent

Tim will be talking about transmembrane proteins with reference to this paper on reentrant regions:

"Structural Classification and Prediction of Reentrant Regions in ?-Helical Transmembrane Proteins: Application to Complete Genomes" by H�kan Viklunda, Erik Gransetha and Arne Elofsson

Journal of Molecular Biology Volume 361, Issue 3 , 18 August 2006

22nd February 2007 Chair: Tim Nugent#

Speaker: Melissa Pentony

Melissa will be talking about the prevalence of disorder in the recently characterised proteomes and essential proteins of E. coli and S. cerevisiae, with reference to the following paper:

"Prevalent Structural Disorder in E. coli and S. cerevisiae Proteomes" by Peter Tompa, Zsuzsanna Dosztayi and Istvan Simon

J. Proteome Res., 5 (8), 1996 -2000, 2006.

15th February 2007 Chair: Dan Roden#

Speaker: Michael Sadowski

Sid will be talking about the adaptation of proteins to extreme temperature conditions, with particular reference to the following paper:

"Relative Tolerance of Mesostable & Thermostable Protein Homologs to Extensive Mutation" by Besenmatter, Kast & Hilvert.

Proteins 66:500-506 (2007)

8th February 2007 Chair: Yvonne Edwards#

Speaker: Sonia Shah

I'll be talking about exon array analysis and will also discuss the paper by Xing et al:

"Probe selection and expression index computation of affymetrix exon arrays"


25th January 2007 Chair: Jacky Pallas#

Speaker: Kevin Bryson

I'm going to give a personal overview of what I understand by the term 'systems biology', supplemented by the following paper:

"The intricate side of systems biology"

Eberhard Voit, Ana Rute Neves, Helena Santos


16th January 2007 Chair: Anna Lobley#

Speaker: Dan Roden

"Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights"

Philip M. Kim, Long J. Lu, Yu Xia, Mark B. Gerstein


14th December 2006 Chair: Michael Sadowski#

Speaker: Dan Frampton

"Predicting domain-domain interactions using a parsimony approach" Katia S Guimar�es, Raja Jothi, Elena Zotenko, Teresa M Przytycka

Genome Biology

23th November 2006 Chair: Dan Frampton#

Speaker: Sonia Shah

"Model-based analysis of tiling-arrays for ChIP-chip" W. Evan Johnson et al. 2006


10th November 2006 Chair: Stefano Lise#

Speaker: Anna Lobley

"Characterisation and prediction of protein-protein interactions within and between complexes" Sprinzak et al 2006


26th October 2006 Chair: Sonia Shah#

Speaker: Melissa Pentony

"Analysis of Molecular Recognition Features (MoRFs)" by Mohan et al 2006

JMB 362:1043

19th October 2006 Chair: Dan Roden#

Speaker: Jacky Pallas

An introduction to the new microarray technology: genome tiling, methylation and ChIP-on-chip

Three papers which discuss biological applications for this technology are:

1. "Transcriptional maps of 10 human chromosomes at 5-nt resolution" by Cheng et al 2005, Science 308:1149

2. "Genome-wide analysis of estrogen receptor binding sites" by Carroll et al 2006, Nature Genetics Adv. Pub.

3. "Genome-wide high resolution mapping and functional analysis of DNA methylation in Arabidopsis" by Zhang et al 2006 Cell, 126:1189-1201

12th October 2006 Chair: Michael Sadowski#

Speaker : Matthew Trotter

Baker SG, Kramer BS

"Identifying genes that contribute most to good classification in microarrays" BMC Bioinf 7:407

Lewin A, Grieve IC

"Grouping gene ontology terms to improve the assessment of gene set enrichment in microarray data" BMC Bioinf 7:426

Oba S, Ishii S

"Semi-supervised discovery of differential genes" BMC Bioinf 7:414

28th September 2006 Chair: Melissa Pentony#

Speaker 1: Stefano Lise

"Protein-Protein Interactions More Conserved within Species than across Species"

Sven Mika and Burkhard Rost

PLoS Computational Biology Vol. 2, No. 7, e79

Speaker 2: Michael Sadowski

"Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance"

Djurdjevic DP & Biggs MJ

J Comput Chem 27:1177-1195

14th September 2006 Chair: Kevin Bryson#

Speaker 1: Anna Lobley

"Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes"

S. Datta and S. Datta

BMC Bioinformatics Aug 31;7(1):397


7th September 2006 Chair: Anna Lobley#

Speaker 1: Melissa Pentony

"Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes"

Chad Haynes, Christopher J. Oldfield, Fei Ji, Niels Klitgord, Michael E. Cusick, Predrag Radivojac, Vladimir N. Uversky, Marc Vidal, Lilia M. Iakoucheva

PLOS Computational Biology 2006, 2(8)

Speaker 2: Sonia Shah

"Transcriptional network dynamics in macrophage activation"

Roland Nilsson, Vladimir B. Bajic, Harukazu Suzuki, Diego di Bernardo, Johan Bj�rkegren, Shintaro Katayama, James F. Reid, Matthew J. Sweet, Manuela Gariboldi, Piero Carninci et al.

Genomics 2006, 88(2)


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« This page (revision-1) was last changed on 29-Oct-2008 21:56 by UnknownAuthor