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GENSIPS 2009
TECHNICAL PROGRAM
Sunday, May 17, 2009
| 1:00-2:00 |
University Ballroom CD |
| Tutorial 1: Inferring Biological Networks from Diverse Data |
Instructor: Chad Myers, Computer Science, University of Minnesota, Minneapolis, USA |
| 2:00-3:00 |
University Ballroom CD |
| Tutorial 2: Information-Theoretic Methods for Reverse Engineering of Gene Regulatory Networks |
Instructor: Olgica Milenkovic, University of Illinois at Urbana-Champaign, USA |
| 3:00-3:30 |
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Coffee Break |
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| 3:30-5:30 |
University Ballroom CD |
| Poster Session 1: Identification and Classification of Genomic Structure |
Chair: Ulisses M. Braga-Neto, Texas A&M University |
| Parameswaran Ramachandran, Wu-Sheng Lu, and Andreas Antoniou |
Tuning Technique for the Location of Hot Spots in Proteins Using A Bandpass Notch Digital Filter |
POSTER |
| Sitanshu Sekhar Sahu1 and Ganapati Panda |
A New Approach for Identification of Hot Spots in Proteins Using S-Transform Filtering |
POSTER |
| Ranadip Pal, Aniruddha Datta and Edward Dougherty |
Quantification of data extraction noise in Probabilistic Boolean Network Modeling |
POSTER |
| Nilanjana Banerjee, Yasser alSafadi, Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski |
TOWARDS IDENTIFICATION OF THEMATIC OVERLAPS IN GENE SETS |
POSTER |
| Chao Sima, Thang Vu, Ulisses M. Braga-Neto and Edward R. Dougherty |
BOLSTERED ERROR ESTIMATOR WITH FEATURE SELECTION |
POSTER |
| Babak Faryabi, Golnaz Vahedi, Jean-Francois Chamberland, Aniruddha Datta, Edward R. Dougherty |
Open-Loop Feedback Intervention: Control of Gene Regulatory Networks with Unmeasurable Context |
POSTER |
| L. Yu and S. Marshal |
THE PARTITION OF TEMPORAL GENE EXPRESSION SEQUENCE USING DISCRETE WAVELET TRANSFORM FOR MODELLING |
POSTER |
| Xiyi Hang, Wei Dai, Fang-Xiang Wu and Olgcia Milenkovic |
SUBSPACE PURSUIT FOR GENE PROFILE CLASSIFICAITON |
POSTER |
| Sara Nasser, Glen J. Weiss, Aarati R. Ranade and Seungchan Kim |
IN-SILICO CONDITIONING OF MICRORNA TO IDENTIFY POTENTIAL BIOMARKERS FROM SERUM FOR PANCREATIC CANCER |
POSTER |
| Aparna Gorthi, Ravi Jain, Nevenka Dimitrova |
A Machine Learning Approach for Classifying Histone Modifications |
POSTER |
| M. Fiasché1, M. Cuzzola, M. Cacciola, G. Megali, R. Fedele, P. Iacopino, F.C. Morabito |
A NEURAL NETWORK MODEL FOR EARLY DIAGNOSIS OF ACUTE GVHD BASED ON GENE EXPRESSION DATA |
POSTER |
| 6:00-7:00 |
University Ballroom A |
| Welcome Reception |
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Monday, May 18, 2009
| 7:00-8:00 |
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| Continental Breakfast |
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| 8:00-9:00 |
University Ballroom CD |
| Plenary Talk 1: Gary P. Schroth, Illlumina Inc., San Diego, USA |
Title: Enabling Genome Biology with Next-Generation DNA Sequencing
Chair: Peter Beyerlein, University of Wildau, Germany |
| 9:00-10:00 |
University Ballroom CD |
| Tutorial 3: Deciphering Cancer Genetics: Promise of Personalized Medicine |
Instructor: Shahab Asgharzadeh, Medicine, USC, Los Angeles, USA |
| 10:00-10:15 |
University Ballroom CD |
| Coffee Break |
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| 10:15-12:00 |
University Ballroom CD |
| Lecture Session 1: Gene Regulatory Networks |
Chair: Gaurav Sharma, University of Rochester |
| Xiaoning Qian1, Edward R. Dougherty |
Control-compatible State Reduction for Boolean Networks |
LECTURE |
| Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, and Edward Dougherty |
CRITICAL BOOLEAN NETWORKS REQUIRE MINIMAL INTERVENTION RATE |
LECTURE |
| Zhouyi Xu and Xiaodong Cai |
Modified K-Leap Method for Stochastic Simulation of Genetic Networks with Small Number of Molecules |
LECTURE |
| David C. Martins-Jr, Evaldo A. de Oliveira, Paulo J. S. Silva, Ronaldo F. Hashimoto |
Revealing temporal genetic regulatory networks from steady-state distributions |
LECTURE |
| Carlos H. A. Higa, Ronaldo F. Hashimoto, Roberto Hirata Jr., Nina S. T. Hirata and Carlos S. Santos |
INFERENCE OF REGULATORY NETWORK USING TEMPORAL COEFFICIENT OF DETERMINATION OBTAINED FROM ERGODIC MARKOV CHAINS |
LECTURE |
| 10:15-12:00 |
Faculty Room |
| Special Session 1: RNA Sequence Analysis & Noncoding RNA Prediction |
Organizer and Chair: Byung-Jun Yoon, Texas A&M University |
| Gustavo Glusman |
MINING “JUNK” DNA TO FIND HIDDEN TRANSCRIPTIONAL GEM |
LECTURE |
| Juan Caballero and Gustavo Glusman |
ENHANCING GENE DETECTION WITH COMPUTER GENERATED INTERGENIC REGIONS |
LECTURE |
| Arif Harmanci, Gaurav Sharma, and David Mathews |
Joint Stochastic Sampling for RNA Secondary Structure Prediction |
LECTURE |
| Byung-Jun Yoon |
Simple Alignment Constraints for Efficient Alignment of RNA Sequences Using Family-Specific Models |
LECTURE |
| Hui Liu, Dong Yue, Yidong Chen, and Yufei Huang |
A comprehensive study of a SVM-based miRNA target prediction algorithm |
LECTURE |
| 12:00-1:00 |
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| Lunch |
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| 1:00-2:00 |
University Ballroom CD |
| Plenary Talk 2: Wen-Hsiung Li, University of Chicago, Chicago, USA, and Biodiversity Research Center, Academia Sinica, Taiwan |
Title: Computational problems in genomics
Chair: Gaurav Sharma, University of Rochester |
| 2:00-3:00 |
University Ballroom CD |
| Tutorial 4: Modeling and Analysis of Biochemical Reaction Systems: Current Techniques and Future Challenges |
Instructor: John Goutisas, Center for Imaging Science, The Johns Hopkins University, Baltimore, USA |
| 3:00-3:30 |
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| Coffee Break |
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| 3:30-4:30 |
University Ballroom CD |
| Lecture Session 2: Linear Classification in Genomic Signal Processing |
Chair: Ulisses M. Braga-Neto, Texas A&M University |
| Amin Zollanvari, Ulisses M. Braga-Neto and Edward R. Dougherty |
SAMPLE SIZE CALCULATION FROM SPECIFIED RMS OF THE RESUBSTITUTION ERROR FOR LINEAR CLASSIFIERS |
LECTURE |
| Thang T. Vu1, Ulisses M. Braga-Neto1 and Edward R. Dougherty |
BAGGING DEGRADES THE PERFORMANCE OF LINEAR DISCRIMINANT CLASSIFIERS |
LECTURE |
| Lingyan Sheng, Antonio Ortega, Roger Pique-Regi, Shahab Asgharzadeh |
TREELETS AS FEATURE TRANSFORMATION TOOL FOR BLOCK DIAGONAL LINEAR DISCRIMINATION |
LECTURE |
| 3:30-5:30 |
University Ballroom B |
| Poster Session 2: Modeling and Analysis of Genomic Structure |
Chair: Stephen Marshall, University of Strathclyde |
| Ranadip Pal |
Analyzing Steady State Probability Distributions of Context-Sensitive Probabilistic Boolean Networks |
POSTER |
| Hossein Zare, Mostafa Kaveh, and Arkady B. Khodursky |
ENTROPY-BASED ANALYSIS OF CHIP-SEQUENCING DATA |
POSTER |
| Vibha Mane, M´onica F. Bugallo, Petar M. Djuri´ |
STOCHASTIC MODELING OF SECOND ORDER REACTIONS USING A MOMENT PROPAGATION METHOD |
POSTER |
| Albert Oliveras-Vergés |
MAXIMUM LIKELIHOOD FACTOR ANALYSIS IN MALARIA CYTOKINE ANALYSIS AND MODELLING |
POSTER |
| Le Yu, Steven Watterson, Stephen Marshall and Peter Ghazal |
A GENERAL MODEL FOR INFERRING A BOOLEAN NETWORK WITH PERTURBATION FROM SPARSE GENE EXPRESSION DATA |
POSTER |
| Ronaldo Fumio Hashimoto, Henrique Stagni and Carlos Henrique Aguena Higa |
BUDDING YEAST CELL CYCLE MODELED BY CONTEXT-SENSITIVE PROBABILISTIC BOOLEAN NETWORK |
POSTER |
| Noushin Ghaffari, Ivan Ivanov, and Edward Dougherty |
A COD BASED REDUCTION ALGORITHM FOR BOOLEAN AND PROBABILISTIC BOOLEAN NETWORKS |
POSTER |
| Fabr´icio M. Lopes1;2, David C. Martins-Jr1 and Roberto M. Cesar-Jr |
Comparative study of GRN's inference methods based on feature selection by mutual information |
POSTER |
| Liming Wang and Dan Schonfeld |
Consistency in Representation and Transformation of Genomic Sequences |
POSTER |
| 6:00-7:30 |
University Ballroom A |
| Dinner |
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Tuesday, May 19, 2009
| 7:00-8:00 |
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| Continental Breakfast |
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| 8:00-9:00 |
University Ballroom CD |
| Plenary Talk 3: Yves Lussier, University of Chicago, Chicago, USA |
Title: Using Phenomic Networks for Therapeutic Target and Biomarker Discovery
Chair: Nevenka Dimitrova, Philips Research Labs |
| 9:00-10:00 |
University Ballroom CD |
| Lecture Session 3: Temporal Analysis of Genomic Data |
Chair: Nidhal Bouaynaya, University of Arkansas at Little Rock |
| Mahsuni Gokdemir and Haris Vikalo |
A PARTICLE FILTERING ALGORITHM FOR PARAMETER ESTIMATION IN REAL-TIME BIOSENSOR ARRAYS |
LECTURE |
| Raman Arora, Colin Dewey and William A. Sethares |
Reconstructing latent periods in genome sequences with insertions and deletions |
LECTURE |
| Nidhal Bouaynaya, Dan Schonfeld and Radhakrishnan Nagarajan |
ANALYSIS OF TEMPORAL GENE EXPRESSION PROFILES USING TIME-DEPENDENT MUSIC ALGORITHM |
LECTURE |
| 9:00-10:00 |
Faculty Room |
| Special Session 2: Plant genomic: Current trends and opportunities for signal processing |
Organizer and Chair: Alain B. Tchagang, Institute for Information Technology, Montreal |
| Lin Wang1, 2, Fumiaki Katagiri1 and Jane Glazebrook1 |
ARABIDOPSIS DEFENSE RESPONSE AGAINST PSEUDOMONAS SYRINGAE - EFFECTS OF MAJOR REGULATORY GENES AND THE IMPACT OF CORONATINE |
LECTURE |
| Viviane Tchonang Leuche and Ahmed Tewfik |
COMPUTATIONAL ANALYSIS OF FUNCTIONALLY RELATED GENES IN MOUSE RESPONSE TO PLASMODIUM CHABAUDI |
LECTURE |
| Alain Tchagang, Hugo Bérubé, Ziying Liu, Sieu Phan, Fazel Famili, and Youlian Pan |
TOWARDS THE RECONSTRUCTION OF BRASSICA NAPUS SEED DEVELOPMENT FA METABOLISM DYNAMIC REGULATORY MAP |
LECTURE |
| 10:00-10:15 |
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| Coffee Break |
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| 10:15-12:00 |
University Ballroom CD |
| Lecture Session 3: Stochastic Modeling and Simulation of Genomic Data |
Chair: Haris Vikalo, University of Texas at Austin |
| Abdullah K. Alqallaf, Ahmed H. Tewfik, Paula Krakowiak, Flora Tassone, Ryan Davis, Robin
Hansen, Irva Hertz-Picciotto, Isaac Pessah, Jeff Gregg and Scott B. Selleck |
IDENTIFYING PATTERNS OF COPY NUMBER VARIANTS IN CASE-CONTROL STUDIES OF HUMAN GENETIC DISORDERS |
LECTURE |
| Abdullah K. Alqallaf1, Ahmed H. Tewfik1, and Scott B. Sell |
GENETIC VARIATION DETECTION USING MAXIMUM LIKELIHOOD ESTIMATOR |
LECTURE |
| Sang Hyun Lee, Haris Vikalo and Sriram Vishwanath |
Message-passing for motif finding |
LECTURE |
| Sahar M.Monfared, Vikram Krishnamurthy Fellow, IEEE1 and Bruce Cornell |
STOCHASTIC MODELING AND SIGNAL PROCESSING OF NANO-SCALE PROTEIN-BASED BIOSENSORS |
LECTURE |
| Shreepriya Das, Haris Vikalo and Arjang Hassibi |
Stochastic Modeling of Reaction Kinetics in Biosensors using the Fokker Planck Equation |
LECTURE |
| 10:15-12:00 |
Faculty Room |
| Special Session 3: Data mining and machine learning applications in bioinformatics and systems biology |
Organizers and Chairs: Chad Myers, Rui Kuang, University of Minnesota |
| Matthew Hibbs |
The effects of pre-processing and parameter choices on similarity searches through large gene expression data collections |
LECTURE |
| Jeremy Bellay, Benjamin VanderSluis, Yungil Kim, Sunayan Bandyopadhyay1, and Chad L. Myers |
Characterization of systems-level organization through mining large-scale genetic interaction networks |
LECTURE |
| Gaurav Pandey, Gowtham Atluri, Gang Fang, Rohit Gupta, Michael Steinbach and Vipin Kumar |
Association Analysis Techniques for Analyzing Complex Biological Data Sets |
LECTURE |
| Thanh Ngo and Rui Kuang |
Partial profile alignment kernels for protein classification |
LECTURE |
| Ze Tian, TaeHyun Hwang and Rui Kuang |
A HYPERGRAPH-BASED LEARNING ALGORITHM FOR CLASSIFYING ARRAYCGH DATA WITH SPATIAL PRIOR |
LECTURE |
| 12:00-1:00 |
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| Lunch |
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| 1:00-2:00 |
University BallRoom CD |
| Plenary Talk 4: Andreas S. Beutler, Mayo Clinic, Minnepolis, USA |
Title: Transcriptome Reprogramming in Chronic Pain Mapped by RNA-seq
Chair: Peter Beyerlein, University of Wildau, Germany |
| 2:00-3:00 |
Faculty Foom |
| Special Session 4: Static & Dynamic Disease Modeling |
Organizer and Chair: Peter Beyerlein, University of Wildau, Germany |
| Stephanie Tscherneck, Sarah Strunk, Christian Schmidt, Paul Hammer1, Ronny Amberg, Chong Wang, Rainer Gillert, Antje Krause, Gabriele Petznick and Peter Beyerlein1 |
On the Mutual Information Between Interaction Perplexity and Function of Proteins |
LECTURE |
| Herman Sontrop , Ren´e van den Ham , Perry Moerland, Marcel Reinders and Wim Verhaegh |
A sensitivity analysis of microarray feature selection and classification under measurement noise |
LECTURE |
| Christian Schmidt, Carsten Krumbiegel, Katja Waterstradt, Gabriele Petznick, Holger Schafer, Kerstin Schnurr |
Expectation-Maximization-Estimation of Mixture Densities for Electron-Spin-Resonance-Analysis of Albumin |
LECTURE |
| 3:00-3:30 |
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| Coffee Break |
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| 3:30-4:30 |
University BallRoom CD |
| Special Session 5: Dynamic Pathway Modeling in Biological Systems: A Crossroad for Drug Discovery and Disease Mechanisms |
Organizer and Chair: Shipra Agrawal, Institute for Bioinformatics and Applied biotechnology and Nevenka Dimitrova, Philips Research Labs |
| Sivaraman Balakrishnan, Oznur Tastan, Jaime Carbonell and Judith Klein-Seetharaman |
COMMUNICATION INTERCEPTION OF HUMAN SIGNAL TRANSDUCTION PATHWAYS BY HUMAN IMMUNODEFICIENCY VIRUS-1 |
LECTURE |
| Smita Mohanty and N.Srinivasan |
HOW EFFECTIVE IS THE DATA ON CO-OCCURRENCE OF DOMAINS IN MULTI-DOMAIN PROTEINS IN PREDICTION OF PROTEIN-PROTEIN INTERACTIONS? |
LECTURE |
| Urmi Sengupta1, Sanchaita Ukil, Nevenka Dimitrova2 and Shipra Agrawal |
Identification of Altered Regulatory Pathways in Diabetes Type II and Complications through Expression Networks |
LECTURE |
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