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program
Tuesday 21 September 2010
20.00 – 21.30 Welcome reception at conference venue
Wednesday 22 September 2010 (10 papers)
9:00–9:30 Arrival and Registration
9:30–9:45 Conference Welcome (Elena Marchiori)
9:45–11:00 Session A: Tutorials MA1 (Concettina Guerra) / MA2 (Neil Lawrence)
11:00–11:30 Coffee Break
11:30–12:45 Session B: Tutorials MB1 (Dick de Ridder) / MB2 (Clarisse Dhaenens)
12:45–14:00 Lunch Break
14:00–15:00 Plenary Lecture 1 (Rita Casadio)
15:00–16:00 Session C: Molecular Structure Prediction MC1–MC4 (chair Frederico Divina)
- A Matrix Algorithm for RNA Secondary Structure Prediction
S.P.T. Krishnan, Mushfique Junayed Khurshid, and Bharadwaj Veeravalli
- Exploiting Long-range Dependencies in Protein β-sheet secondary structure prediction
Yizhao Ni and Mahesan Niranjan
- Alpha Helix Prediction based on Evolutionary Computation
Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar Ruiz, and Gualberto Asencio Cortés
- An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps
Stefano Teso, Cristina Di Risio, Andrea Passerini, and Roberto Battiti
16:00–16:30 Tea and Biscuits
16:30–18:00 Session D: Learning Methods for Gene Expression and Mass Spectrometry Data MD1–MD6 (chair George Lee)
- Semi-Supervised Graph Embedding Scheme with Active Learning (SSGEAL): Classifying High Dimensional Biomedical Data
George Lee and Anant Madabhushi
- Iterated Local Search for Biclustering of Microarray Data
Wassim Ayadi, Mourad Elloumi, and Jin-Kao Hao
- Biologically-aware Latent Dirichlet Allocation (BaLDA) for the Classification of Expression Microarray
Alessandro Perina, Pietro Lovato, Vittorio Murino, and Manuele Bicego
- Measuring the Quality of Shifting and Scaling Patterns in Biclusters
Beatriz Pontes, Raúl Giráldez, and Jesús S. Aguilar-Ruiz
- Frequent Episode Mining to Support Pattern Analysis in Developmental Biology
Ronnie Bathoorn, Monique Welten, Michael Richardson, Arno Siebes, and Fons J. Verbeek
- Time Series Gene Expression Data Classification via L1-norm Temporal SVM
Carlotta Orsenigo and Carlo Vercellis
18:00–23:00 Poster Session (Buffet available)
Thursday 23 September 2010 (13 papers)
9:00–10:00 Plenary Lecture 2 (Florence d’Alché-Buc)
10:00–10:45 Session A: Classification of Biological Sequences TA1–TA3 (chair Jennifer Smith)
- Joint Loop End Modeling Improves Covariance Model Based Non-coding RNA Gene Search
Jennifer Smith
- Structured Output Prediction of Anti-Cancer Drug Activity
Hongyu Su, Markus Heinonen, and Juho Rousu
- SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context
Norman E. Davey, Niall J. Haslam, Denis C. Shields, and Richard J. Edwards
10:45–11:15 Coffee Break
11:15–12:45 Session B: Classification of Biological Sequences TB1–TB6 (chair Witold Dyrka)
- Sequence-based Prediction of Protein Secretion Success in Aspergillus niger
Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J.T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos, and Dick de Ridder
- Machine Learning Study of DNA Binding by Transcription Factors from the LacI family
Gennady G. Fedonin and Mikhail S. Gelfand
- Towards 3D modeling of Interacting TM Helix Pairs Based on Classification of Helix Pair Sequence
Witold Dyrka, Jean-Christophe Nebel, and Malgorzata Kotulska
- Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations
Gökhan Yavaş, Mehmet Koyutürk, and Thomas LaFramboise
- Preservation of Statistically Significant patterns in Multiresolution 0-1 Data
Prem Raj Adhikari and Jaakko Hollmén
- Novel Machine Learning Methods for MHC Class I Binding Prediction
Christian Widmer, Nora C. Toussaint, Yasemin Altun, Oliver Kohlbacher, and Gunnar Rätsch
12:45–14:00 Lunch Break
14:00–15:00 Plenary Lecture 3 (Daniel Huson)
15:00–16:00 Session C: Unsupervised Learning Methods for Biological Sequences TC1–TC4 (chair Andrew Wong)
- SIMCOMP: A Hybrid Soft Clustering of Metagenome Reads
Shruthi Prabhakara and Raj Acharya
- The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings
Elijah Myers, Paul S. Fisher, Keith Irwin, Jinsuk Baek, and Joao Setubal
- An Algorithm to Find All Identical Motifs in Multiple Biological Sequences
Ashish Kishor Bindal, R. Sabarinathan, J. Sridhar, D. Sherlin, and K. Sekar
- Discovery of Non-induced Patterns from Sequences
Andrew K.C. Wong, Dennis Zhuang, Gary C.L. Li, and En-Shiun Annie Lee
16:00–16:30 Tea and Biscuits
16:30–21:30 Conference Banquet at Burgers Zoo in Arnhem
Friday 24 September 2010 (15 papers)
9:00–10:00 Plenary Lecture 4 (Natasa Przulj)
10:00–11:00 Session A: Unsupervised Learning Methods for Biological Sequences WA1-WA4 (chair Rasa Jurgenelaite)
- Exploring Homology Using the Concept of Three-State Entropy Vector
Armando J. Pinho, Sara P. Garcia, Paulo J.S.G. Ferreira, Vera Afreixo, Carlos A.C. Bastos, António J.R. Neves, and João M.O.S. Rodrigues
- A Maximum-Likelihood Formulation and EM Algorithm for the Protein Multiple Alignment Problem
Valentina Sulimova, Nikolay Razin, Vadim Mottl, Ilya Muchnik, and Casimir Kulikowski
- Polynomial Supertree Methods Revisited
Malte Brinkmeyer, Thasso Griebel, and Sebastian Böcker
- Enhancing Graph Database Indexing By Suffix Tree Structure
Vincenzo Bonnici, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, and Dennis Shasha
11:00–11:15 Coffee Break
11:15–12:45 Session B: Protein Protein Interaction and Network Inference WB1–WB6 (chair Luis Rueda)
- Biological Protein-protein Interaction Prediction using Binding Free Energies and Linear Dimensionality Reduction
Luis Rueda, Carolina Garate, Sridip Banerjee, and Md. Mominul Aziz
- Employing Publicly Available Biological Expert Knowledge from Protein-Protein Interaction Information
Kristine A. Pattin, Jiang Gui, and Jason H. Moore
- SFFS-MR: A Floating Search Strategy for GRNs Inference
Fabrício M. Lopes, David C. Martins-Jr., Junior Barrera, and Roberto M. Cesar-Jr.
- Revisiting the Voronoi description of Protein-Protein interfaces: Algorithms
Frederic Cazals
- MC4: A Tempering Algorithm for Large-sample Network Inference
Daniel James Barker, Steven M. Hill, and Sach Mukherjee
- Flow-based Bayesian Estimation of Nonlinear Differential Equations for Modeling Biological Network
Nicolas Brunel and Florence d’Alché-Buc
12:45–14:00 Lunch Break
14:00–15:15 Session C: Bioimaging WC1–WC5 (chair Scott Doyle)
- Sub-grid and Spot Detection in DNA Microarray Images using Optimal Multi-level Thresholding
Iman Rezaeian and Luis Rueda
- Quantification of Cytoskeletal Protein Localization from High-Content Images
Shiwen Zhu, Paul Matsudaira, Roy Welsch, and Jagath C. Rajapakse
- Pattern Recognition for High Throughput Zebrafish Imaging using Genetic Algorithm Optimization
Alexander E. Nezhinsky and Fons J. Verbeek
- Consensus of Ambiguity: Theory of Active Learning for Biomedical Image Analysis Applications
Scott Doyle and Anant Madabhushi
- Semi-supervised Learning of Sparse Linear Models in Mass Spectral Imaging
Fabian Ojeda, Marco Signoretto, Raf Van de Plas, Etienne Waelkens, Bart De Moor, and Johan A.K. Suykens
15:15–15:30 Conference Closing
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