Bioinformatics

The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism
pp. 257-263(7)
Authors: Iyer, Lakshminarayan M.; Burroughs, A. Maxwell; Aravind, L.

Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
pp. 264-268(5)
Authors: Cordes, Matthew H. J.; Binford, Greta J.

Highly consistent patterns for inherited human diseases at the molecular level
pp. 269-277(9)
Authors: López-Bigas, Núria; Blencowe, Benjamin J.; Ouzounis, Christos A.

A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli
pp. 278-284(7)
Authors: Idicula-Thomas, Susan; Kulkarni, Abhijit J.; Jayaraman, Valadi K.; Balaji, Petety V.

Application of latent semantic analysis to protein remote homology detection
pp. 285-290(6)
Authors: Dong, Qi-wen; Wang, Xiao-long; Lin, Lei

An extensible automated protein annotation tool: standardizing input and output using validated XML
pp. 291-296(6)
Authors: Deevi, S. Vishnu V.; Martin, Andrew C. R.

Mean curvature as a major determinant of β-sheet propensity
pp. 297-302(6)
Authors: Koh, Eunhee; Kim, Taehyo; Cho, Hyun-soo

Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
pp. 303-309(7)
Authors: Cao, Baoqiang; Porollo, Aleksey; Adamczak, Rafal; Jarrell, Mark; Meller, Jaroslaw

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms
pp. 310-316(7)
Authors: Glynn, Earl F.; Chen, Jie; Mushegian, Arcady R.

A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer
pp. 317-325(9)
Authors: Zhang, Wensheng; Rekaya, Romdhane; Bertrand, Keith

Maximum significance clustering of oligonucleotide microarrays
pp. 326-331(6)
Authors: de Ridder, Dick; Staal, Frank J. T.; van Dongen, Jacques J. M.; Reinders, Marcel J. T.

A bi-dimensional regression tree approach to the modeling of gene expression regulation
pp. 332-340(9)
Authors: Ruan, Jianhua; Zhang, Weixiong

Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
pp. 341-345(5)
Author: Beerli, Peter

Conservation analysis of large biochemical networks
pp. 346-353(8)
Authors: Vallabhajosyula, Ravishankar Rao; Chickarmane, Vijay; Sauro, Herbert M.

DNAVis: interactive visualization of comparative genome annotations
pp. 354-355(2)
Authors: Fiers, Mark W. E. J.; van de Wetering, Huub; Peeters, Tim H. J. M.; van Wijk, Jarke J.; Nap, Jan-Peter

Paircoil2: improved prediction of coiled coils from sequence
pp. 356-358(3)
Authors: McDonnell, A. V.; Jiang, T.; Keating, A. E.; Berger, B.

Identification of plant microRNA homologs
pp. 359-360(2)
Authors: Dezulian, Tobias; Remmert, Michael; Palatnik, Javier F.; Weigel, Detlef; Huson, Daniel H.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences
pp. 361-362(2)
Authors: Sobreira, Tiago José P.; Durham, Alan M.; Gruber, Arthur

apTreeshape: statistical analysis of phylogenetic tree shape
pp. 363-364(2)
Authors: Bortolussi, Nicolas; Durand, Eric; Blum, Michael; François, Olivier

BALLView: a tool for research and education in molecular modeling
pp. 365-366(2)
Authors: Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter

PAGE: phase-shifted analysis of gene expression
pp. 367-368(2)
Authors: Leung, Elo; Bushel, Pierre R.

Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data
pp. 369-370(2)
Author: Valentini, Giorgio

2SNP: scalable phasing based on 2-SNP haplotypes
pp. 371-373(3)
Authors: Brinza, Dumitru; Zelikovsky, Alexander

Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization
pp. 374-375(2)
Authors: Dogrusoz, U.; Erson, E. Z.; Giral, E.; Demir, E.; Babur, O.; Cetintas, A.; Colak, R.

SubLoc: a server/client suite for protein subcellular location based on SOAP
pp. 376-377(2)
Authors: Chen, Hu; Huang, Ni; Sun, Zhirong

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search
pp. 378-380(3)
Authors: Ding, Jing; Hughes, LaRon M.; Berleant, Daniel; Fulmer, Andy W.; Wurtele, Eve Syrkin

REDfly: a Regulatory Element Database for Drosophila
pp. 381-383(3)
Authors: Gallo, Steven M.; Li, Long; Hu, Zihua; Halfon, Marc S.