Workshop on Genomic Signal Processing and Statistics (GENSIPS)

PROCEEDINGS

Table of Contents

 

 

WELCOMING MESSAGE

 

KEYNOTE ADDRESS FOLDER

 

Jeremy K. Nicholson, Department of Biological Chemistry, Faculty of Medicine, Imperial College of Science Technology and Medicine, London University, UK. "Metabolic Modeling Approaches to Further the Understanding of Differential Gene Function and Disease Processes." Abstract

 

 

INVITED PRESENTATIONS FOLDER

 

Adam Arkin, Departments of Chemisty and Bioengineering, University of California at Berkeley, USA. Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways. Abstract

 

Michael Brent, Department of Computer Science, Washington University in St. Louis, USA. Improving gene structure prediction by combining the intrinsic genome signal with the signal from natural selection. Abstract

  

J. Patrick Fitch, Lawrence Livermore Laboratory, USA. Biosignatures of Pathogen and Host. Joint work with B.A. Chromy, C.E. Forde, E. Garcia, S.N. Gardner, P.P. Gu, T.A. Kuczmarksi, C.F. Melius, S.L. McCutchen-Maloney, F.P. Milanovich, V.L. Motin, L.L. Ott, A.A. Quong, J.N. Quong, J.M. Rocco, T.R. Slezak, B.A. Sokhansanj, E.A. Vitalis, A.T. Zemia and P.M. McCreedy, Lawrence Livermore Laboratory, USA. Abstract

  

Bradford W. Gibson, Buck Institute for Age Research and Department of Pharmaceutical Chemistry, University of California at San Francisco, USA. Redefining Proteomics: Completing the Human Mitochondrial Proteome to High-Throughput Tertiary Structure Assignments of Novel Proteins. Abstract

 

Jun Liu, Department of Statistics, Harvard University, USA.Motif Regressor: Towards the Integration of Sequence Motif Discovery and Microarray Analysis. Abstract

 

Elaine Mardis, Genome Sequencing Center, Washington University School of Medicine, USA.DNA Sequencing:Present Status and Future Challenges. Abstract

 

Robert H. Waterston, Genome Sequencing Center, Washington University School of Medicine, USA.The Human and Mouse Genomes:A Comparison. Abstract

 

Bruce Weir, North Carolina State University, USA. "Genome Scans for Human Disease Genes." Abstract

 

Mike West, Institute of Statistics and Decision Sciences, Duke University."Factor Models and Predictive Trees in Molecular Phenotyping." Abstract

 

Fred Wright, Department of Biostatistics, University of North Carolina at Chapel Hill, USA. The Analysis of Oligonucleotide Arrays: A Signal Processing Viewpoint. Abstract

 

C. F. Jeff Wu, Department of Statistics and Department of Industrial and Operations Engineering, University of Michigan, USA. Use of the Normal Probability Plot to Identify Significant Effects for Microarray Data. Abstract

 

 

 

CONTRIBUTED PAPERS FOLDER

 

Poster Session I

Test of Origin Site (oriC) and Terminus (terC) of Replication by Wavelet Analysis in Bacteria,J. Song, T. Ware and S.-L. Liu, Department of Microbiology and Infectious Diseases, Department of Mathematics and Probability, University of Calgary, Canada.....CP1-01

Microarray Image Compression and the Effect of Compression Loss, Rebecka Jornsten, Bin Yu, Wei Wang and Kannan Ramchandran, Department of Statistics, Department of Electrical Engineering and Computer Science, University of California at Berkeley, USA; Computer Science Department, University of North Carolina, USA.....CP1-02

Using HMMs to Quantify Signals from DNA Driven Through a Nanometer-Scale Pore, Vincent Stanford and John Kasianowicz, National Institute of Standards and Technology Information Access Division,  National Institute of Standards and Technology Biotechnology Division, USA.....CP1-03

Discriminant Eigengels: A Statistical Approach to 2-D Gel Analysis, Xiaoran Mo and Roland Wilson, Department of Computer Science, University of Warwick, UK.....CP1-04

A Strategy for Identifying Putative Causes of Gene Expression Variation in Human Cancer, Sampsa Hautaniemi, Markus Ringn‰r, P„ivikki Kauraniemi, Anne Kallioniemi, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Institute of Signal Processing, Tampere University of Technology, Finland; Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, USA; Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Finland; Biomedicum Biochip Center PL63, Finland.....CP1-06

Locally Linear Projection (LLP), Xiaoming Huo and Jihong Chen, School of Industrial and System Engineering, Georgia Institute of Technology, USA.....CP1-07

Complexity: Software Tools for Analysis of Information Measures of Genetic Texts, Yury Orlov, V. P. Filippov, V.N. Potapov, N.A. Kolchanov, Institute of Cytology and Genetics, Russia; Sobolev Institute of Mathematics, Russia.....CP1-08

Clustering Gene Expression Data with Min-Max-Median Initialized Fuzzy C-Means Algorithms, Xue-Wen Chen, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.....CP1-09

Nonlinear Correlation for the Analysis of Gene Expression Data, Karen M. Bloch and Gonzalo R. Arce, DuPont Company; Department of Electrical and Computer Engineering, University of Delaware, USA.....CP1-10

Constrained Independent Component Analysis of DNA Microarray Signals, Xuejun Liao and Lawrence Carin, Department of Electrical and Computer Engineering, Duke University, USA.....CP1-11

Classification of Gene Expression Data by Pairwise Comparisons, George Michailidis, Department of Statistics, University of Michigan, USA.....CP1-12

Posterior Pareto Front Analysis for Gene Filtering, Alfred Hero andG. Fleury, Department of Electrical Engineering and Computer Science, Department of Biomedical Engineering, Department of Statistics, University of Michigan, USA; Đcole Sup‰rieure d'Đlectricit‰, Service des Mesures, France.....CP1-13

Iterative Deconvolution for Automatic Basecalling of the DNA Electrophoresis Time Series, Xiao-Ping Zhang and Daniel Allison, Applied Biosystems, Applera Corporation, USAŕ.CP1-14

Applying Logistic Regression and RVm to Achieve Accurate Probabilistic Cancer Diagnosis from Gene Expression Profiles, Balaji Krishnapuram, Alexander Hartemink and Lawrence Carin, Department of Electrical Engineering, Department of Computer Science, Duke University, USA.....CP1-15

Hidden Markov Models for DNA Sequencing, Petros Boufounos, Sameh El-Difrawy and Dan Ehrlich, Research Laboratory for Electronics, Massachusetts Institute of Technology, USA; Whitehead Institute for Biomedical Research, USA.....CP1-16

Poster Session II

Fast Segmentation and Lossy-to-Lossless Compression of DNA Microarray Images, Jianping Hua, Zixiang Xiong, Qiang Wu and Kenneth Castleman, Department of Electrical Engineering, Texas A&M University, USA; Advanced Digital Imaging Research, USA.....CP2-01

Gene and Exon Prediction using Allpass-Based Filters, Palghat Vaidyanathan and Byung-Jun Yoon, Department of Electrical Engineering, California Institute of Technology, USA.....CP2-02

Enhancement, Classification and Compression of Chromosome Images, Zixiang Xiong, Qiang Wu and Kenneth Castlemen, Department of Electrical Engineering, Texas A&M University, USA; Advanced Digital Imaging Research, USA.....CP2-03

A Coding Theory Framework for Genetic Sequence Analysis, Elebeoba May, M. A. Vouk, D. L. Bitzer and D. I. Rosnick, Computational Biology Department, Sandia National Laboratories, USA; Department of Computer Science, North Carolina State University, USA.....CP2-04

An Analytical Solution to the Mobility Shifts Corrections Problem for DNA Chromatograms, Sameh El-Difrawy and Elias S. Manolakos, Communications and Digital Signal Processing (CDSP) Center, Department of Electrical and Computer Engineering, Northeastern University, USA.....CP2-05

Computational Identification of Exons in DNA with a Hidden Markov Model, Daniel Nicorici, Jaakko Astola and Ioan Tabus, Tampere International Center for Signal Processing, Tampere University of Technology, Finland.....CP2-06

Skyline Normalization of DNA Chromatograms by Regression, Lucio Andrade and Elias S. Manolakos, Communications and Digital Signal Processing Center (CDSP), Department of Electrical and Computer Engineering, Northeastern University, USA.....CP2-07

New Approaches to Genome Sequence Analysis Based on Digital Signal Processing, John A. Berger, Sanjit K. Mitra, Marco Carli and Alessandro Neri, Department of Electrical and Computer Engineering, University of California at Santa Barbara, USA; Department of Electrical Engineering, University of Rome TRE, Italy.....CP2-08

Protein Retrieval by Matching 3D Surfaces, Shann-Ching Chen and Tsuhan Chen, Department of Electrical and Computer Engineering, Carnegie Mellon University, USA.....CP2-09

Escherichia coli Protein Coding Sequence Detection by Analysis of Free Energy Periodicity, David Rosnick, D. Bitzer, M. Vouk and E. May, Department of Computer Science, North Carolina State University, USA; Computational Biology Department, Sandia National Laboratories, USA.....CP2-10

A Computational Model for Simulating Continuous Time Boolean Networks, Hakan Ůktem, Ronald Pearson, Olli Yli-Harja, Daniel Nicorici, Juha Kesseli, Harri Lahdesmaki, Karen Egiazarian and Jaakko Astola, Institute of Signal Processing, Tampere University of Technology, Finland.....CP2-11

Signaling Efficiency of Kinetic Proofreading in T-cells, John Keane and Les Atlas, Department of Electrical Engineering, Cell Systems Initiative, Department of Bioengineering, University of Washington, USA.....CP2-12

Construction of Genomic Networks using Mutual-Information Clustering and Reversible- Jump MCMC Predictor Design, Xiaobo Zhou, Xiaodong Wang and Edward R. Dougherty, Department of Electrical Engineering, Texas A&M University, USA; Department of Electrical Engineering, Columbia University, USA; Department of Pathology, University of Texas, USA.....CP2-13

Using Error-Correcting Design to Improve cDNA Microarray Performance, Alexei Osadtchi, Arshad Khan, Richard M. Leahy and Desmond J. Smith, Signal and Image Processing Institute, University of Southern California, USA;Department of Molecular Pharmacology, University of California at Los Angeles School of Medicine, USA.....CP2-14

Automated Image Analysis for DNA Fingerprinting, Daniel R. Fuhrmann, Robert H. Waterston, John D. McPherson, Readman Chiu, Jacqueline E. Schein and Marco A. Marra, Department of Electrical Engineering, Washington University in St. Louis, USA; Genome Sequencing Center, Washington University School of Medicine, USA; Genome Sciences Center, British Columbia Cancer Agency, Canada.....CP2-15

NMR Signal Processing with Wavelet Denoising, Wei Liang, J. M. Macdonald and Hamid Krim, North Carolina State University, USA.....CP2-16