Bioinformatics

DISCOVERY NOTES:

Deepak Grover, Mitali Mukerji, Pankaj Bhatnagar, K. Kannan, and Samir K. Brahmachari

Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 813-817; doi:10.1093/bioinformatics/bth005 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Ruslan I. Sadreyev and Nick V. Grishin

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 818-828; doi:10.1093/bioinformatics/btg485 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chun Tang, Aidong Zhang, and Murali Ramanathan

ESPD: a pattern detection model underlying gene expression profiles
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 829-838; doi:10.1093/bioinformatics/btg486 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, and Naftali Kaminski

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 839-846; doi:10.1093/bioinformatics/btg487 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. B. Vilim, R. M. Cunningham, B. Lu, P. Kheradpour, and F. J. Stevens

Fold-specific substitution matrices for protein classification
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 847-853; doi:10.1093/bioinformatics/btg492 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dung-Tsa Chen, Sue-Hwa Lin, and Seng-jaw Soong

Gene selection for oligonucleotide array: an approach using PM probe level data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 854-862; doi:10.1093/bioinformatics/btg493 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yuichiro Hourai, Tatsuya Akutsu, and Yutaka Akiyama

Optimizing substitution matrices by separating score distributions
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 863-873; doi:10.1093/bioinformatics/btg494 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jens Nilsson, Thoas Fioretos, Mattias Höglund, and Magnus Fontes

Approximate geodesic distances reveal biologically relevant structures in microarray data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 874-880; doi:10.1093/bioinformatics/btg496 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Florian Frommlet, Andreas Futschik, and Malgorzata Bogdan

On the significance of sequence alignments when using multiple scoring matrices
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 881-887; doi:10.1093/bioinformatics/btg498 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xiaohong Huang, Wei Pan, Soon Park, Xinqiang Han, Leslie W. Miller, and Jennifer Hall

Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 888-894; doi:10.1093/bioinformatics/btg499 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Minghua Deng, Zhidong Tu, Fengzhu Sun, and Ting Chen

Mapping gene ontology to proteins based on protein–protein interaction data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 895-902; doi:10.1093/bioinformatics/btg500 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zheng Rong Yang and Kuo-Chen Chou

Predicting the linkage sites in glycoproteins using bio-basis function neural network
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 903-908; doi:10.1093/bioinformatics/bth001 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Qing Zhou and Jun S. Liu

Modeling within-motif dependence for transcription factor binding site predictions
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 909-916; doi:10.1093/bioinformatics/bth006 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ming Ouyang, William J. Welsh, and Panos Georgopoulos

Gaussian mixture clustering and imputation of microarray data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 917-923; doi:10.1093/bioinformatics/bth007 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Aniruddha Datta, Ashish Choudhary, Michael L. Bittner, and Edward R. Dougherty

External control in Markovian genetic regulatory networks: the imperfect information case
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 924-930; doi:10.1093/bioinformatics/bth008 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Dugas, S. Merk, S. Breit, and P. Dirschedl

mdclust—exploratory microarray analysis by multidimensional clustering
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 931-936; doi:10.1093/bioinformatics/bth009 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Scott, G. Lu, M. Hallett, and D. Y. Thomas

The Hera database and its use in the characterization of endoplasmic reticulum proteins
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 937-944; doi:10.1093/bioinformatics/bth010 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Morgan N. Price and Eleanor Rieffel

Finding coexpressed genes in counts-based data: an improved measure with validation experiments
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 945-952; doi:10.1093/bioinformatics/bth011 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael E. Smoot, Stephanie A. Guerlain, and William R. Pearson

Visualization of near-optimal sequence alignments
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 953-958; doi:10.1093/bioinformatics/bth013 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kyongbum Lee, Daehee Hwang, Tadaaki Yokoyama, George Stephanopoulos, Gregory N. Stephanopoulos, and Martin L. Yarmush

Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 959-969; doi:10.1093/bioinformatics/bth015 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xing Han and Wenjun Kang

Sequence analysis and membrane partitioning energies of -helical antimicrobial peptides
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 970-973; doi:10.1093/bioinformatics/bth027 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Michael L. Tress, Osvaldo Graña, and Alfonso Valencia

SQUARE—determining reliable regions in sequence alignments
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 974-975; doi:10.1093/bioinformatics/bth032 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nelson Young, Zhan Chang, and David S. Wishart

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 976-978; doi:10.1093/bioinformatics/bth033 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Peter N. Robinson, Andreas Wollstein, Ulrike Böhme, and Brad Beattie

Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 979-981; doi:10.1093/bioinformatics/bth040 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Hall and L. Stern

A rapid method for illustrating features in both coding and non-coding regions of a genome
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 982-983; doi:10.1093/bioinformatics/bth042 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kishore R. Sakharkar and Vincent T. K. Chow

Exploring genome architecture through GOV: a WWW-based gene order visualizer
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 984-985; doi:10.1093/bioinformatics/bth046 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrew C.R. Martin

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 986-988; doi:10.1093/bioinformatics/bth048 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ahmed A. Majeed, Niyaz Ahmed, K. Rajender Rao, S. Ghousunnissa, Farhana Kauser, Buddhaditta Bose, H. A. Nagarajaram, V. M. Katoch, Debby V. Cousins, Leonardo A. Sechi, Robert H. Gilman, and Seyed E. Hasnain

AmpliBASE MT^TM: a Mycobacterium tuberculosis diversity knowledgebase
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 989-992; doi:10.1093/bioinformatics/bth051 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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