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ORCIDBioinformatics, Volume 22
Volume 22, Number 1, January 2006
- Alex Bateman
:
Bioinformatics - The new home for protein sequence motifs. 2
- Dorit Amikam, Michael Y. Galperin:
PilZ domain is part of the bacterial c-di-GMP binding protein. 3-6
- Nusrat Rabbee, Terence P. Speed:
A genotype calling algorithm for affymetrix SNP arrays. 7-12
- Miao Zhang, Warren Gish:
Improved spliced alignment from an information theoretic approach. 13-20 - Kyle L. Jensen, Mark P. Styczynski, Isidore Rigoutsos, Gregory Stephanopoulos:
A generic motif discovery algorithm for sequential data. 21-28 - Weichun Huang, David M. Umbach, Leping Li:
Accurate anchoring alignment of divergent sequences. 29-34 - Zasha Weinberg, Walter L. Ruzzo:
Sequence-based heuristics for faster annotation of non-coding RNA families. 35-39
- Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam:
Inferring functional information from domain co-evolution. 40-49
- Marta Blangiardo, Simona Toti, Betti Giusti, Rosanna Abbate, Alberto Magi, Filippo Poggi, Luciana Rossi, Francesca Torricelli, Annibale Biggeri:
Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data. 50-57 - Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen:
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. 58-67 - Xiaoyan Leng, Hans-Georg Müller:
Classification using functional data analysis for temporal gene expression data. 68-76 - Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang:
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. 77-87 - Hao Helen Zhang, Jeongyoun Ahn, Xiaodong Lin, Cheolwoo Park:
Gene selection using support vector machines with non-convex penalty. 88-95
- Huai Li, Ming Zhan:
Systematic intervention of transcription for identifying network response to disease and cellular phenotypes. 96-102
- Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu:
BioThesaurus: a web-based thesaurus of protein and gene names. 103-105
- Ismael Navas-Delgado, Maria del Mar Rojano-Muñoz, Sergio Ramírez, Antonio J. Pérez-Pulido, Eduardo Andrés León, José Francisco Aldana Montes, Oswaldo Trelles:
Intelligent client for integrating bioinformatics services. 106-111
- Åsa Pérez-Bercoff, Johan Koch, Thomas R. Bürglin:
LogoBar: bar graph visualization of protein logos with gaps. 112-114 - Colas Schretter, Michel C. Milinkovitch:
OligoFaktory: a visual tool for interactive oligonucleotide design. 115-116
- Tom M. W. Nye, Pietro Liò, Walter R. Gilks:
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. 117-119 - Vivek Gopalan, Wei-Gang Qiu, Michael Z. Chen, Arlin Stoltzfus:
Nexplorer: phylogeny-based exploration of sequence family data. 120-121
- Alan R. Dabney:
ClaNC: point-and-click software for classifying microarrays to nearest centroids. 122-123
- Xinglai Ji, Ying Xu:
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation. 124-126
Volume 22, Number 2, January 2006
- Victor de Lorenzo, Luis Serrano, Alfonso Valencia:
Synthetic Biology: challenges ahead. 127-128
- Jean-Christophe Gelly, Alexandre G. de Brevern, Serge A. Hazout:
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. 129-133
- Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
WindowMasker: window-based masker for sequenced genomes. 134-141 - James J. Gordon, Michael W. Towsey, James M. Hogan, Sarah A. Mathews, Peter Timms:
Improved prediction of bacterial transcription start sites. 142-148
- I. Mihalek, I. Res, Olivier Lichtarge:
A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins. 149-156 - Leelavati Narlikar, Alexander J. Hartemink:
Sequence features of DNA binding sites reveal structural class of associated transcription factor. 157-163 - Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin:
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. 164-171
- Hetunandan Kamisetty, Chris Bailey-Kellogg, Gopal Pandurangan:
An efficient randomized algorithm for contact-based NMR backbone resonance assignment. 172-180 - Jan E. Gewehr, Ralf Zimmer:
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. 181-187 - Wei Xie, Nikolaos V. Sahinidis:
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem. 188-194 - Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede:
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. 195-201
- Francesca Martella:
Classification of microarray data with factor mixture models. 202-208 - Anshuman Gupta, Costas D. Maranas, Réka Albert:
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. 209-214 - Mizanur R. Khondoker, Chris A. Glasbey, Bruce J. Worton:
Statistical estimation of gene expression using multiple laser scans of microarrays. 215-219
- Zhaohui S. Qin, Shyam Gopalakrishnan, Gonçalo R. Abecasis:
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. 220-225
- Ashish Choudhary, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
Intervention in a family of Boolean networks. 226-232 - Barbara A. Novak, Ajay N. Jain:
Pathway recognition and augmentation by computational analysis of microarray expression data. 233-241
- Do-Hoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, Sun Kim:
COMPAM : visualization of combining pairwise alignments for multiple genomes. 242-244
- Ljubomir J. Buturovic:
PCP: a program for supervised classification of gene expression profiles. 245-247
- Anaïs Baudot, David Martin, Pierre Mouren, François Chevenet, Alain Guénoche, Bernard Jacq, Marie-Christine Brun:
PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks. 248-250 - Jo Criel, Elena Tsiporkova:
Gene Time Echipression Warper: a tool for alignment, template matching and visualization of gene expression time series. 251-252
- Mahender Kumar Singh, Shilpy Srivastava, G. P. S. Raghava, Grish C. Varshney:
HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies. 253-255
Volume 22, Number 3, February 2006
- Lakshminarayan M. Iyer, A. Maxwell Burroughs, L. Aravind:
The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. 257-263
- Matthew H. J. Cordes, Greta J. Binford:
Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria. 264-268
- Núria López-Bigas, Benjamin J. Blencowe, Christos A. Ouzounis:
Highly consistent patterns for inherited human diseases at the molecular level. 269-277
- Susan Idicula-Thomas, Abhijit J. Kulkarni, Bhaskar D. Kulkarni, Valadi K. Jayaraman, Petety V. Balaji:
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. 278-284 - Qiwen Dong, Xiaolong Wang, Lei Lin:
Application of latent semantic analysis to protein remote homology detection. 285-290 - S. Vishnu V. Deevi, Andrew C. R. Martin:
An extensible automated protein annotation tool: standardizing input and output using validated XML. 291-296
- Eunhee Koh, Taehyo Kim, Hyun-soo Cho:
Mean curvature as a major determinant of ß-sheet propensity. 297-302 - Baoqiang Cao, Aleksey A. Porollo, Rafal Adamczak, Mark Jarrell, Jaroslaw Meller:
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. 303-309
- Earl F. Glynn, Jie Chen, Arcady R. Mushegian:
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. 310-316 - Wensheng Zhang, Romdhane Rekaya, Keith Bertrand:
A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer. 317-325 - Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders:
Maximum significance clustering of oligonucleotide microarrays. 326-331 - Jianhua Ruan, Weixiong Zhang:
A bi-dimensional regression tree approach to the modeling of gene expression regulation. 332-340
- Peter Beerli:
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. 341-345
- Ravishankar Rao Vallabhajosyula, Vijay Chickarmane, Herbert M. Sauro:
Conservation analysis of large biochemical networks. 346-353
- Mark W. E. J. Fiers, Huub van de Wetering, Tim H. J. M. Peeters, Jarke J. van Wijk, Jan Peter Nap:
DNAVis: interactive visualization of comparative genome annotations. 354-355
- A. V. McDonnell, Taijiao Jiang, Amy E. Keating, Bonnie Berger:
Paircoil2: improved prediction of coiled coils from sequence. 356-358 - Tobias Dezulian, Michael Remmert, Javier F. Palatnik, Detlef Weigel, Daniel H. Huson:
Identification of plant microRNA homologs. 359-360 - Tiago José P. Sobreira, Alan M. Durham, Arthur Gruber:
TRAP: automated classification, quantification and annotation of tandemly repeated sequences. 361-362
- Nicolas Bortolussi, Eric Durand, Michael G. B. Blum, Olivier François:
apTreeshape: statistical analysis of phylogenetic tree shape. 363-364
- Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher:
BALLView: a tool for research and education in molecular modeling. 365-366
- Elo Leung, Pierre R. Bushel:
PAGE: phase-shifted analysis of gene expression. 367-368 - Giorgio Valentini:
Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data. 369-370
- Dumitru Brinza, Alexander Zelikovsky:
2SNP: scalable phasing based on 2-SNP haplotypes. 371-373
- Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak:
Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization. 374-375
- Hu Chen, Ni Huang, Zhirong Sun:
SubLoc: a server/client suite for protein subcellular location based on SOAP. 376-377 - Jing Ding, Laron M. Hughes, Daniel Berleant, Andy W. Fulmer, Eve Syrkin Wurtele:
PubMed Assistant: a biologist-friendly interface for enhanced PubMed search. 378-380 - Steven M. Gallo, Long Li, Zihua Hu, Marc S. Halfon:
REDfly: a Regulatory Element Database for Drosophila. 381-383
Volume 22, Number 4, February 2006
- Jiexin Zhang, Li Zhang, Kevin R. Coombes:
Gene sequence signatures revealed by mining the UniGene affiliation network. 385-391 - Xiang Guo, Kay Tatsuoka, Rongxiang Liu:
Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. 392-399 - Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio:
Quality classification of tandem mass spectrometry data. 400-406
- András Kocsor, Attila Kertész-Farkas, László Kaján, Sándor Pongor:
Application of compression-based distance measures to protein sequence classification: a methodological study. 407-412 - Yao-ming Huang, Christopher Bystroff:
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. 413-422 - Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel:
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. 423-429 - Tilman Sauer, Ekaterina Shelest, Edgar Wingender:
Evaluating phylogenetic footprinting for human-rodent comparisons. 430-437 - Joseph M. Volpe, Lindsay G. Cowell, Thomas B. Kepler:
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. 438-444 - Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo:
CMfinder - a covariance model based RNA motif finding algorithm. 445-452
- Elodie Duprat, Marie-Paule Lefranc, Olivier Gascuel:
A simple method to predict protein-binding from aligned sequences - application to MHC superfamily and ß2-microglobulin. 453-459 - Simon W. Ginzinger, Johannes Fischer:
SimShift: Identifying structural similarities from NMR chemical shifts. 460-465
- Lexin Li:
Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information. 466-471 - Baolin Wu:
Differential gene expression detection and sample classification using penalized linear regression models. 472-476
- Eugene P. van Someren, B. L. T. Vaes, W. T. Steegenga, Anneke M. Sijbers, Koen J. Dechering, Marcel J. T. Reinders:
Least absolute regression network analysis of the murine osteoblast differentiation network. 477-484
- Siddhartha Basu, Erich Bremer, Chun Zhou, Daniel F. Bogenhagen:
MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation. 485-492
- Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, Dag Harmsen:
Ridom TraceEdit: a DNA trace editor and viewer. 493-494 - Derek Huntley, Angela Baldo, Saurabh Johri, Marek J. Sergot:
SEAN: SNP prediction and display program utilizing EST sequence clusters. 495-496 - Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, Graziano Pesole:
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. 497-499 - Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, Robert Giegerich:
RNAshapes: an integrated RNA analysis package based on abstract shapes. 500-503
- John Eargle, Dan Wright, Zaida Luthey-Schulten:
Multiple Alignment of protein structures and sequences for VMD. 504-506
- Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey:
EDGE: extraction and analysis of differential gene expression. 507-508 - Michael Mueller, Anuj Goel, Manjula Thimma, Nicholas J. Dickens, Timothy J. Aitman, Jonathan Mangion:
eQTL Explorer: integrated mining of combined genetic linkage and expression experiments. 509-511
- B. L. Browning:
FLOSS: flexible ordered subset analysis for linkage mapping of complex traits. 512-513
- Henning Schmidt, Mats Jirstrand:
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. 514-515
Volume 22, Number 5, March 2006
- Daniel Dalevi, Devdatt P. Dubhashi, Malte Hermansson:
Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures. 517-522 - Guojun Yang, Timothy C. Hall:
HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana. 523-526
- Giuseppe D'Auria, Ravindra Pushker, Francisco Rodríguez-Valera:
IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. 527-531 - Wolfgang P. Lehrach, Dirk Husmeier, Christopher K. I. Williams:
A regularized discriminative model for the prediction of protein-peptide interactions. 532-540 - Matthew Rabinowitz, Lance Myers, Milena Banjevic, Albert Chan, Joshua Sweetkind-Singer, Jessica Haberer, Kelly McCann, Roland Wolkowicz:
Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization. 541-549
- Andreas Henschel, Wan Kyu Kim, Michael Schroeder:
Equivalent binding sites reveal convergently evolved interaction motifs. 550-555
- Alexander Ploner, Stefano Calza, Arief Gusnanto, Yudi Pawitan:
Multidimensional local false discovery rate for microarray studies. 556-565 - Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio:
Improving missing value estimation in microarray data with gene ontology. 566-572
- Miguel Pérez-Enciso:
Multiple association analysis via simulated annealing (MASSA). 573-580
- Yoram Louzoun, Lev Muchnik, Sorin Solomon:
Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW. 581-588
- Roberto Amato, Angelo Ciaramella, Natalia Deniskina, Carmine Del Mondo, Diego di Bernardo, Ciro Donalek, Giuseppe Longo, Giuseppe Mangano, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, Roberto Tagliaferri:
A multi-step approach to time series analysis and gene expression clustering. 589-596 - Jung-Jae Kim, Zhuo Zhang, Jong-Chan Park, See-Kiong Ng:
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature. 597-605 - Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey:
Inferring global levels of alternative splicing isoforms using a generative model of microarray data. 606-613
- Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler:
Local RNA base pairing probabilities in large sequences. 614-615 - Leighton Pritchard, Jennifer A. White, Paul R. J. Birch, Ian K. Toth:
GenomeDiagram: a python package for the visualization of large-scale genomic data. 616-617
- Andrew Smith, John-Marc Chandonia, Steven E. Brenner:
ANDY: a general, fault-tolerant tool for database searching on computer clusters. 618-620
- Dominik Gront, Andrzej Kolinski:
BioShell - a package of tools for structural biology computations. 621-622 - Mikhail A. Lomize, Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg:
OPM: Orientations of Proteins in Membranes database. 623-625
- Bradley M. Hemminger, Billy Saelim, Patrick F. Sullivan:
TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. 626-627
- Colin S. Gillespie, Darren J. Wilkinson, Carole J. Proctor, Daryl P. Shanley, Richard J. Boys, Thomas B. L. Kirkwood:
Tools for the SBML Community. 628-629