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TABLE OF CONTENTS
Issue No. 01 - January-March (vol. 7)
ISSN: 1545-5963
PAPERS

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data (Abstract)

H. Hagen , Univ. of Kaiserslautern, Kaiserslautern, Germany
J. Malik , Dept. of Electr. Eng. & Comput. Sci., Univ. of California, Berkeley, CA, USA
D.W. Knowles , Life Sci. Div., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
M.B. Eisen , Dept. of Mol. & Cell Biol., Univ. of California, Berkeley, Berkeley, CA, USA
S.V.E. Keranen , Genomics Div., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
C.L. Luengo Hendriks , Centre for Image Anal., Swedish Univ. of Agric. Sci., Uppsala, Sweden
C.C. Fowlkes , Donald Bren Sch. of Inf. & Comput. Sci., Univ. of California, Irvine, CA, USA
M.D. Biggin , Genomics Div., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
E.W. Bethel , Comput. Res. Div., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
B. Hamann , Dept. of Comput. Sci., Univ. of California, Davis, Davis, CA, USA
Min-Yu Huang , Dept. of Comput. Sci., Univ. of California, Davis, Davis, CA, USA
G.H. Weber , Dept. of Mol. & Cell Biol., Univ. of California, Berkeley, Berkeley, CA, USA
O. Rubel , Centre for Image Anal., Swedish Univ. of Agric. Sci., Uppsala, Sweden
pp. 1
EDITORIAL

Editor's Note (HTML)

pp. 1
PAPERS

Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution (Abstract)

Liang-Wei Gong , University of Valencia University of Valencia University of Yale, Burjassot Burjassot New Haven
Ester Díaz , University of Valencia University of Valencia University of Yale, Burjassot Burjassot New Haven
Guillermo Ayala , University of Valencia University of Valencia University of Yale, Burjassot Burjassot New Haven
María Elena Díaz , University of Valencia University of Valencia University of Yale, Burjassot Burjassot New Haven
Derek Toomre , University of Valencia University of Valencia University of Yale, Burjassot Burjassot New Haven
pp. 2-11

BioExtract Server—An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data (Abstract)

Carolyn J. Lawrence , USDA-ARS Iowa State University, Ames
Doug Jennewein , University of South Dakota, Vermillion
Michael K. Bergman , VisualMetrics Corporation, Coralville
Volker Brendel , Iowa State University, Ames
Carol Lushbough , University of South Dakota, Vermillion
pp. 12-24

Feature Selection for Gene Expression Using Model-Based Entropy (Abstract)

Shenghuo Zhu , NEC Laboratories America, Cupertino
Tao Li , Florida International University, Miami
Dingding Wang , Florida International University, Miami
Kai Yu , NEC Laboratories America, Cupertino
Yihong Gong , NEC Laboratories America, Cupertino
pp. 25-36

Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions (Abstract)

Petri Pehkonen , University of Kuopio, Kuopio
Garry Wong , University of Kuopio, Kuopio
Petri Törönen , University of Helsinki, Kuopio
pp. 37-49

Multidimensional Profiling of Cell Surface Proteins and Nuclear Markers (Abstract)

Bahram Parvin , Lawrence Berkeley National Laboratory, Berkeley
Mary Helen Barcellos-Hoff , New York University Langone School of Medicine
Paul Yaswen , Lawrence Berkeley National Laboratory, Berkeley
Kumari Andarawewa , University of Virginia, Charlottesville
Ju Han , Lawrence Berkeley National Laboratory, Berkeley
Hang Chang , Lawrence Berkeley National Laboratory, Berkeley
pp. 80-90

Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis (Abstract)

Purvesh Khatri , Wayne State University, Detriot
Sorin Drăghici , Wayne State University, Detriot
Arina Done , Wayne State University, Detriot
Bogdan Done , Wayne State University, Detriot
pp. 91-99

Sparse Support Vector Machines with L_{p} Penalty for Biomarker Identification (Abstract)

Ming T. Tan , University of Maryland, Baltimore
Zhenqiu Liu , University of Maryland, Baltimore
Shili Lin , Ohio State University, Columbus
pp. 100-107

A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification (Abstract)

Yukyee Leung , The University of Hong Kong , HK
Yeungsam Hung , The University of Hong Kong, HK
pp. 108-117

Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics (Abstract)

Milos Hauskrecht , University of Pittsburgh, Pittsburgh
Richard Pelikan , University of Pittsburgh, Pittsburgh
pp. 126-137

Exploratory Consensus of Hierarchical Clusterings for Melanoma and Breast Cancer (Abstract)

Pritha Mahata , University of Newcastle, Australia, Newcastle
pp. 138-152

Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm (Abstract)

Miguel C. Teixeira , Lisbon Technical University, Lisboa
Sara C. Madeira , Universidade da Beira Interior, Covilhã, KDBIO Group, INESC-ID, Lisbon, and Lisbon Technical University, Lisboa
Isabel Sá-Correia , Lisbon Technical University, Lisboa
Arlindo L. Oliveira , KDBIO Group, INESC-ID, Libson and Lisbon Technical University, Lisboa
pp. 153-165

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci (Abstract)

Elchanan Mossel , UC Berkeley, Berkeley
Sebastien Roch , Microsoft Research, Redmond
pp. 166-171

On the Importance of Comprehensible Classification Models for Protein Function Prediction (Abstract)

Daniela C. Wieser , European Bioinformatics Institute, Cambridge
Rolf Apweiler , European Bioinformatics Institute, Cambridge
Alex A. Freitas , University of Kent, Canterbury
pp. 172-182
SHORT PAPERS

Approximate Maximum Parsimony and Ancestral Maximum Likelihood (Abstract)

Fabio Pardi , EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge
Noga Alon , Tel Aviv University, Tel Aviv
Anat Rapoport , Tel Aviv University, Tel Aviv
Benny Chor , Tel Aviv University, Tel Aviv
pp. 183-187
REVIEWERS LIST

2009 Reviewer's List (PDF)

pp. 188-190
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