ASAP-IOL

Interdisciplinary Optimization and Decision Making

Journal Club

General Information

§ Once a month, members of the Interdisciplinary Optimization and Decision Making Journal Club hold a lunch time meeting to discuss papers of common interest

§ At these meeting one member of the group makes a 20-30 minute slide presentation of a published paper (usually not one of their own papers)

§ The presentation is often followed by a lively discussion of the paper

§ All members are required to attend the Club meeting

§ Other members of the University are welcome to participate

§ If you would like to join the Journal Club then please contact the club coordinator for more information

Frequency	Once per month
Timing	12:30 on the third Friday of each month
Location	Room C1 Computer Science Building Jubilee Campus, NG8 1BB University of Nottingham
Contact	Azhar Ali Shah

Schedule of Presentations

Speaker, Date, Time & Venue	Title
Enrico Glaab 18^th June 2010	TBA
Jack Chaplin 22 July 2010	TBA
Fran Romero-Campero 20 August 2010	TBA
Pawel Widera 17^th September	TBA
Claudio F. Lima 15^th Oct 2010	TBA
Azhar A. Shah 19^th Nov 2010	TBA
Jonathan Blakes 17 Dec 2010	TBA
Andrew J Parkes 21 Jan 2011	TBA
Maria Franco 18 Feb 2011	TBA

Past Presentations

Speaker, Date	Title
German Terrazas Angulo 20^th Nov 2009	"Forming ordered structures in ternary, photosensitive blends through the use of masks", By Pratyush Dayal et al., Soft Matter, 2009, 5, 1205 - 1213 Full Paper:
Jonathan Blakes 18^th Sep 2009	"Agile Computer Control of a Complex Experiment", Gael Varoquaux, Computing in Science & Engineering (March/April 2008) 20-25 Full Paper:
Fran Romero-Campero ASAP 19^th June 2009	“Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops”, Joshua W Williamset al., Molecular Systems Biology 4 Article number: 234. Full Paper:
Azhar Ali Shah 20^th Mar 2009	“Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space”, Yaniv Loewenstein et al., Bioinformatics 2008 24(13):i41-i49 Full Paper:
Petros Kountouris Chemistry 20^th Feb 2009	“Real-value prediction of backbone torsion angles”, Bin Xue et al. (2008), Proteins: Structure, Function, and Bioinformatics; 72(1): 427-433
James Smaldon ASAP 16^th Jan 2009	“On the way towards ‘basic autonomous agents’: Stochastic simulations of minimal lipid–peptide cells”,  Ruiz-Mirazo et al. (2008), Biosystems 91(2): 374-387 Full Paper
Stephen Hamby Chemistry 21^st Nov 2008, @ 12:30	“Protein conformational flexibility prediction using machine Learning”, Oleg Trott et al. (2008), Journal of Magnetic Resonance 192:37—47 Full Paper
Pooja Jain Chemistry 17^th October 2008	“Inferring Function Using Patterns of Native Disorder in Proteins”, Lobley A et al. (2007), PLoS Comput Biol 3(8): e162 Full Paper
Peter Siepmann ASAP 19^th Sep 2008, @ 12:30	“Automatic identification of music performers with learning ensembles”, by E Stamatatosa, Artificial Intelligence, 165(1), pp. 37-56, 2005. Slides , Full Paper
Mike Stout, ASAP 15^th August 2008, @ 12:30	Postponed due to summer holidays
Jaume Bacardit ASAP 18^th July 2008, @ 12:30	Post postponed due to conferences (GECCO)
Daniel Barthel ASAP ^20th June 2008, @ 12:30	Postponed due to RAD2008
Jonathan Blakes ASAP 16^th May 2008, @ 12:30	Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases, /Elf J and Ehrenberg M,/ Systems Biology. 2. 2004 (pdf) (slides)
Pawel Widera ASAP 18^th April 2008, @ 12:30	“Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home”, Das et. al., Proteins: Structure, Function, and Bioinformatics, 2007, 69, 118-128 (pdf), (Slides)
Gemma Danks Biology Department University of York 28^th Mar 2008, @ 12:30	“Developing L-systems models of protein folding”, LNCS, Volume 4648/2007 Full Paper
Fran Romero-Campero ASAP 15^th Feb 2008, @ 12:30	“Network motifs: theory and experimental approaches”, Alon U, Nat Rev Genet. 2007 Jun;8(6):450-61 Full Paper
Haydn Williams Chemistry 18^th Jan 2008, @ 12:30	“Molecular Dynamics Simulations on the Oligomer-Formation Process of the GNNQQNY Peptide from Yeast Prion Protein Sup35”, Zhuqing Zhang et. al. Biophysical Journal 93:1484-1492 (2007) Full Paper
Natalio Krasnogor ASAP 21^st Dec 2007	Postponed due to Christmas holidays
Craig Bruce Chemistry, 16^th Nov 2007, @ 12:30	‘A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification Qingliang’ , Li Andreas Bender et. al., J. Chem. Inf. Model., 47 (5), 1776 -1786, 2007. Complete Paper
Azhar Ali Shah ASAP, 19^th Oct 2007, @ 12:30		'Rapid methods for comparing protein structures and scanning structure databases' Carugo, Current Bioinformatics 2006;1(1):75-83 Complete Paper
Petros Kountouris Chemistry 21^st Sept 2007, @ 12:30 Room: C1, Computer Science		‘Support vector machines for prediction of dihedral angle regions’ , Zimmermann et al., Bioinformatics 2006; 22(24):3009-3015 Complete Paper
James Smaldon ASAP 17^th August 2007, @ 12:30 Room: C1, Computer Science		‘A vesicle bioreactor as a step toward an artificial cell assembly’ Vincent Noireaux et al. PNAS 2004; 101(51): 17669-17674 Full Paper
Stephen Hamby Chemistry 20^th July 2007, @ 12:30 Room: C1, Computer Science		'Glycan classification with tree kernals' By: Yoshiro Yamashi et. Al., Bioinformatics 2007;23(10) Complete Paper
Andrew Parkes 15^th Jun 2007, @ 12:30 Room: C1, Computer Science	“A systematic comparison and evaluation of biclustering methods for gene expression data” By: Amela Prelic et. al., Bioinformatics, Vol.22(9), 2006 Complete Paper
Peter Siepmann ASAP, 18^th May 2007, @ 12:30 Room: C1, Computer Science	“A comprehensive survey of fitness approximation in evolutionary computation”, Complete Paper
Dr. Gavin Brown, Computer Science, University of Manchester 27^th April 2007	Managing Ensemble Diversity with the Bias/Variance Decomposition Tutorials
Mike Stout, ASAP 27^th April 2007	Water in protein structure prediction
Jaume Bacardit ASAP 16 Mar 2007	Observer-Invariant Histopathology using Genetics-Based Machine Learning
James Marshall Computer Science University of Bristol 23 Feb 2007	Noise, cost and speed-accuracy trade-offs: decision making in a decentralized system. [PDF] Weighting waiting in collective decision-making. Behavioral Ecology and Sociobiology (in press) [PDF]
Tim Kovacs Computer Science, University of Bristol 23Feb 2007	Strength or Accuracy? Credit assignment in Classifier Systems
Daniel Barthel ASAP 16 Feb 2007	Total Evidence, Consensus, and Bat Phylogeny: A Distance-Based Approach
Pawel Widera ASAP 15 Dec 2006	The Framsticks system: versatile simulator of 3D agents and their evolution
German Terrazas ASAP 27th Oct 2006	Artificial Chemistries - A Review [Slides]
Andrew Parkes ASAP 22nd September 2006	Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses [Slides] A tutorial on Hidden Markov Models and selected applications in speech recognition
Peter Siepmann ASAP 11th August 2006	Nanocell logic gates for molecular computing, [Slides]
Dr. PierLuigi Frisco  14^th June 2006	Computing and modeling with conformon-P systems
Dr. Marian Gheorghe University of Sheffield 14^th June 2006	A formal language-based approach in biology
Dr. Colin Johnson University of Kent 31^st March 2006	What can automatic programming learn from theoretical computer science
Dr. Alex Freitas University of Kent 31^st March 2006	Predicting post-synaptic activity in proteins with data mining.
Chris Martin Department of Physics 3^rd March 2006	Drying-mediated self-assembly of nanoparticles Nanoparticle Networks on Silicon: Self-Organized or Disorganized?
Adam Sweetman, Department of Physics 3^rd March 2006	Temperature-dependent Monte Carlo simulations of thin metal film growth and percolation Effect of a STM tip on the surface-diffusion measurement: A Monte Carlo study
Mike Stout ASAP 17^th February 2006	The language of genes PART 2: Searls DB
Mike Stout ASAP 27th January 2006	The language of genes PART 1: Searls DB
Dr. Samad Ahmadi School of Computing De Montfort University Leicester 29^th November 2005	Search Algorithms for Clustering
Natalio Krasnogor ASAP 18^th November 2005	Murphys Law
Steven Gustafson 21^st October 2005	On Testing Heuristics and Computational Experiments in Computer Science. See: Hooker 1995
Daniel Barthel ASAP 23^rd Sept.  2005	On Cluster Validation Techniques [Slides]
German Terrazas ASAP 22^nd July 2005	Soft Machines: Nanotechnology and Life [Slides]
Jaume Bacardit ASAP 17^th June 2005	Extracted Global Structure Makes Local Building Block Processing Effective in XCS [Slides]
Scott Littlewood 20th May 2005	Multi colony ant algorithms.
Lin Li ASAP 15th April 2005	Rhombic Dodecahedron Shape for Self-Assembling Robots

Club Members

Name	Research Interests
Natalio Krasnogor	Evolutionary Algorithms Heuristics and Metaheuristics Bioinformatics System Self-Assembly Natural Computation Computational Nature
Jaume Bacardit	Bioinformatics Evolutionary Computation Learning Classifier Systems
Lin Li	System Self-Assembly Bioinformatics
Scott Littlewood	Simplified Models of Protein Structure Prediction Ant Colonies inspired systems
German Terrazas Angulo	Software Self  Assembly Simulation
Peter Siepmann	Bioinformatics
Mike Stout	Functional Programming Protein Structure Prediction Evolutionary Computation
Adam Sweetman
Randall Owen	Lattice Model Proteins Functional Programming
Andrew Parkes	Space Allocation
Jerry Swan	Mathematics
Pawel Widera	Bioinformatics
Linda Fiaschi	Bioinformatics
Jonathan Hirst	ab initio calculations of the electronic excited states of molecules electronic structure and circular dichroism of proteins protein folding and evolution bioinformatics computer-aided drug design drug resistance
James Smaldon	Computation and modeling of artificial chemical cells
Azhar Ali Shah	Bioinformatics and Grid Computing
John Woodward	Hyperheuristics
Juan Ramn Gonzlez Gonzlez	Bioinformatics
Stephen Hamby Chemistry	?
Petros Kountouris Chemistry	Bioinformatics Protein Structure Prediction
Haydn Williams Chemistry	Molecular Dynamic Simulations Forced Unfolding of Protein
Pooja Jain Chemistry	Bioinformatics Modeling and Optimization Protein Structure Prediction Protein 3D-Strcutre signature identification
Jonathon Blakes ASAP	Inforbiotics
Francisco R Campero ASAP	Inforbiotics
Enrico Glaab ASAP	LCS for microarray data analysis
Maria Franco ASAP	Learning Classifier Systems

Past Members

Name	Research Interests
Steven Gustafson	Evolutionary Computation
Itziar Frades	Bioinformatics
Daniel Barthel	Bioinformatics
Craig Bruce Chemistry	Cheminformatics Machine learning techniques QSAR High Performance Computing (HPC)

Tuesday, 08 June 2010

Azhar Ali Shah

aas@cs.nott.ac.uk