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ORCIDBMC Bioinformatics, Volume 7
Volume 7, 2006
- Micah Hamady, Erin Peden, Rob Knight
, Ravinder Singh:
Fast-Find: A novel computational approach to analyzing combinatorial motifs. 1 - Pall F. Jonsson, Tamara Cavanna, Daniel Zicha, Paul A. Bates:
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. 2 - Ramón Díaz-Uriarte, Sara Alvarez de Andrés:
Gene selection and classification of microarray data using random forest. 3 - Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell:
Application of machine learning in SNP discovery. 4 - Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides:
The comprehensive updated regulatory network of Escherichia coli K-12. 5 - Giacomo Gamberoni, Sergio Storari, Stefano Volinia:
Finding biological process modifications in cancer tissues by mining gene expression correlations. 6 - Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi:
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. 7 - Staal Amund Vinterbo, Stephan Dreiseitl, Lucila Ohno-Machado:
Approximation properties of haplotype tagging. 8 - Feng-Biao Guo, Chun-Ting Zhang:
ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. 9 - James A. Casbon, Gavin E. Crooks, Mansoor A. S. Saqi:
A high level interface to SCOP and ASTRAL implemented in Python. 10 - Andrean Goede, Elke Michalsky, Ulrike Schmidt, Robert Preissner:
SuperMimic - Fitting peptide mimetics into protein structures. 11 - Zihua Hu, Gail R. Willsky:
Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies. 12 - Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li, Zhuchu Chen:
Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice. 13 - Oliver Sander, Ingolf Sommer, Thomas Lengauer:
Local protein structure prediction using discriminative models. 14 - James J. Yang, Mark C. K. Yang:
An improved procedure for gene selection from microarray experiments using false discovery rate criterion. 15 - Markus Brameier, Josien Haan, Andrea Krings, Robert M. MacCallum:
Automatic discovery of cross-family sequence features associated with protein function. 16 - Brian Tjaden:
An approach for clustering gene expression data with error information. 17 - Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He, Yi-Xue Li:
In silico discovery of human natural antisense transcripts. 18 - Morgan N. Price, Adam P. Arkin, Eric J. Alm:
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. 19 - Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang, Kexuan Tang:
Prediction of protein structural class with Rough Sets. 20 - Patrick Durand, Laurent Labarre, Alain Meil, Jean-Louis Divol, Yves Vandenbrouck, Alain Viari, Jérôme Wojcik:
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. 21 - Alexei A. Adzhubei, Jon K. Laerdahl, Anna V. Vlasova:
preAssemble: a tool for automatic sequencer trace data processing. 22 - Li-Xuan Qin, Richard P. Beyer, Francesca N. Hudson, Nancy J. Linford, Daryl E. Morris, Kathleen F. Kerr:
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. 23 - Kyaw Tun, Pawan K. Dhar, Maria Concetta Palumbo, Alessandro Giuliani:
Metabolic pathways variability and sequence/networks comparisons. 24 - Jason C. Ting, Ying Ye, George H. Thomas, Ingo Ruczinski, Jonathan Pevsner:
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. 25 - Xia Li, Shaoqi Rao, Wei Jiang, Chuanxing Li, Yun Xiao, Zheng Guo, Qingpu Zhang, Lihong Wang, Lei Du, Jing Li, Li Li, Tianwen Zhang, Qing K. Wang:
Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling. 26 - Hongbo Zhu, Francisco S. Domingues, Ingolf Sommer, Thomas Lengauer:
NOXclass: prediction of protein-protein interaction types. 27 - Nicolas Thierry-Mieg:
A new pooling strategy for high-throughput screening: the Shifted Transversal Design. 28 - Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Derek Phillips:
Recrafting the neighbor-joining method. 29 - Ming Yi, Jay D. Horton, Jonathan C. Cohen, Helen H. Hobbs, Robert M. Stephens:
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. 30 - Bradford C. Powell, Clyde A. Hutchison III:
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. 31 - Xian Wang, Ao Li, Zhaohui Jiang, Huanqing Feng:
Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme. 32 - Erdahl T. Teber, Edward Crawford, Kent B. Bolton, Derek Van Dyk, Peter R. Schofield, Vimal Kapoor, W. Bret Church:
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. 33 - Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris N. Kholodenko, Ernst Dieter Gilles:
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. 34 - Kyoungmi Kim, Grier P. Page, T. Mark Beasley, Stephen Barnes, Katherine E. Scheirer, David B. Allison:
A proposed metric for assessing the measurement quality of individual microarrays. 35 - Domenico Catalano, Flavio Licciulli, Antonio Turi, Giorgio Grillo, Cecilia Saccone, Domenica D'Elia:
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. 36 - Xiao I. Liu, Neeraj Korde, Ursula Jakob, Lars I. Leichert:
CoSMoS: Conserved Sequence Motif Search in the proteome. 37 - Hao-Teng Chang, Tun-Wen Pai, Tan-Chi Fan, Bo-Han Su, Pei-Chih Wu, Chuan Yi Tang, Chun-Tien Chang, Shi-Hwei Liu, Margaret Dah-Tsyr Chang:
A reinforced merging methodology for mapping unique peptide motifs in members of protein families. 38 - Alison A. Motsinger, Stephen L. Lee, George Mellick, Marylyn D. Ritchie:
GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. 39 - Xiaobo Zhou, James Chou, Stephen T. C. Wong:
Protein structure similarity from principle component correlation analysis. 40 - Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano:
Discovering semantic features in the literature: a foundation for building functional associations. 41 - Harald Barsnes, Svein-Ole Mikalsen, Ingvar Eidhammer:
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. 42 - Tim Van den Bulcke, Koen Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor, Kathleen Marchal:
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. 43 - Ryung S. Kim, Hongkai Ji, Wing Hung Wong:
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. 44 - Olivier Croce, Michaël Lamarre, Richard Christen:
Querying the public databases for sequences using complex keywords contained in the feature lines. 45 - Wen-Yu Chung, Réka Albert, István Albert, Anton Nekrutenko, Kateryna D. Makova:
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. 46 - Ross I. Brinkworth, Alan L. Munn, Bostjan Kobe:
Protein kinases associated with the yeast phosphoproteome. 47 - James A. Casbon, Mansoor A. S. Saqi:
On single and multiple models of protein families for the detection of remote sequence relationships. 48 - Jeanette N. McClintick, Howard J. Edenberg:
Effects of filtering by Present call on analysis of microarray experiments. 49 - Xing Qiu, Yuanhui Xiao, Alexander Gordon, Andrei Yakovlev:
Assessing stability of gene selection in microarray data analysis. 50 - Kristofer Hallén, Johan Björkegren, Jesper Tegnér:
Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations. 51 - Bor-Sen Chen, Yu-Chao Wang:
On the attenuation and amplification of molecular noise in genetic regulatory networks. 52 - Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich:
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. 53 - Pedro Carmona-Saez, Monica Chagoyen, Andrés Rodríguez Moreno, Oswaldo Trelles, José María Carazo, Alberto D. Pascual-Montano:
Integrated analysis of gene expression by association rules discovery. 54 - Michael Baitaluk, Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray, Amarnath Gupta:
PathSys: integrating molecular interaction graphs for systems biology. 55 - Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles:
A methodology for the structural and functional analysis of signaling and regulatory networks. 56 - Yanan Yu, Mya Breitbart, Pat McNairnie, Forest Rohwer:
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. 57 - Bin Zheng, David C. McLean Jr., Xinghua Lu:
Identifying biological concepts from a protein-related corpus with a probabilistic topic model. 58 - Hemant Ishwaran, J. Sunil Rao, Udaya B. Kogalur:
BAMarrayTM: Java software for Bayesian analysis of variance for microarray data. 59 - Kim W. Carter, Pamela A. McCaskie, Lyle J. Palmer:
JLIN: A java based linkage disequilibrium plotter. 60 - Phillip McClurg, Mathew T. Pletcher, Tim Wiltshire, Andrew I. Su:
Comparative analysis of haplotype association mapping algorithms. 61 - Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack:
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. 62 - Claes R. Andersson, Anders Isaksson, Mats G. Gustafsson:
Bayesian detection of periodic mRNA time profiles without use of training examples. 63 - Christoph Gille, Peter N. Robinson:
HotSwap for bioinformatics: A STRAP tutorial. 64 - Svetlana A. Shabalina, Alexey N. Spiridonov, Aleksey Y. Ogurtsov:
Computational models with thermodynamic and composition features improve siRNA design. 65 - Hanno Teeling, Frank Oliver Glöckner:
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. 66 - Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. 67 - Mikael Bodén, Zheng Yuan, Timothy L. Bailey:
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. 68 - Feng He, An-Ping Zeng:
In search of functional association from time-series microarray data based on the change trend and level of gene expression. 69 - Aaron Birkland, Golan Yona:
BIOZON: a system for unification, management and analysis of heterogeneous biological data. 70 - Paul Shafer, Timothy Isganitis, Golan Yona:
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. 71 - Zuozhou Chen, Weilin Wang, Xuefeng Bruce Ling, Jane Jijun Liu, Liangbiao Chen:
GO-Diff: Mining functional differentiation between EST-based transcriptomes. 72 - Daniel P. Berrar, Ian Bradbury, Werner Dubitzky:
Instance-based concept learning from multiclass DNA microarray data. 73 - Brandon W. Higgs, Jennifer W. Weller, Jeffrey L. Solka:
Spectral embedding finds meaningful (relevant) structure in image and microarray data. 74 - Andrew E. Firth, Chris M. Brown:
Detecting overlapping coding sequences in virus genomes. 75 - Chengpeng Bi, Peter K. Rogan:
BIPAD: A web server for modeling bipartite sequence elements. 76 - Donglin Liu, Joel H. Graber:
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. 77 - Pedro Carmona-Saez, Roberto D. Pascual-Marqui, Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano:
Biclustering of gene expression data by non-smooth non-negative matrix factorization. 78 - Gareth A. Palidwor, Emmanuel G. Reynaud, Miguel A. Andrade-Navarro:
Taxonomic colouring of phylogenetic trees of protein sequences. 79 - Jie Wu, Zhenjun Hu, Charles DeLisi:
Gene annotation and network inference by phylogenetic profiling. 80 - G. W. Patton, Robert M. Stephens, I. A. Sidorov, X. Xiao, Richard A. Lempicki, Dimiter S. Dimitrov, Robert H. Shoemaker, G. Tudor:
Transcriptomic response to differentiation induction. 81 - Alistair R. R. Forrest, Darrin F. Taylor, J. Lynn Fink, M. Milena Gongora, Cameron Flegg, Rohan D. Teasdale, Harukazu Suzuki, Mutsumi Kanamori, Chikatoshi Kai, Yoshihide Hayashizaki, Sean M. Grimmond:
PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. 82 - Jing Huang, Wen Wei, Joyce Chen, Jane Zhang, Guoying Liu, Xiaojun Di, Rui Mei, Shumpei Ishikawa, Hiroyuki Aburatani, Keith W. Jones, Michael H. Shapero:
CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. 83 - Grier P. Page, Jode W. Edwards, Gary L. Gadbury, Prashanth Yelisetti, Jelai Wang, Prinal Trivedi, David B. Allison:
The PowerAtlas: a power and sample size atlas for microarray experimental design and research. 84 - Joshua S. Yuan, Ann Reed, Feng Chen, C. Neal Stewart Jr.:
Statistical analysis of real-time PCR data. 85 - Ricardo Z. N. Vêncio, Tie Koide, Suely L. Gomes, Carlos A. de B. Pereira:
BayGO: Bayesian analysis of ontology term enrichment in microarray data. 86 - Delong Liu, Shyamal D. Peddada, Leping Li, Clarice R. Weinberg:
Phase analysis of circadian-related genes in two tissues. 87 - Jonathan P. Bollback:
SIMMAP: Stochastic character mapping of discrete traits on phylogenies. 88 - Michael E. Bradley, Steven A. Benner:
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins. 89 - Shann-Ching Chen, Robert F. Murphy:
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. 90 - Sudhir Varma, Richard Simon:
Bias in error estimation when using cross-validation for model selection. 91 - Richard Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Jieh Hsiang, Ting-Yi Sung, Wen-Lian Hsu:
Various criteria in the evaluation of biomedical named entity recognition. 92 - Howard M. Salis, Vassilios Sotiropoulos, Yiannis N. Kaznessis:
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers. 93 - Stefan M. Stanley, Timothy L. Bailey, John S. Mattick:
GONOME: measuring correlations between GO terms and genomic positions. 94 - E. Ke Tang, Ponnuthurai N. Suganthan, Xin Yao:
Gene selection algorithms for microarray data based on least squares support vector machine. 95 - Anders Bengtsson, Henrik Bengtsson:
Microarray image analysis: background estimation using quantile and morphological filters. 96 - Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. 97 - Patrick Martin, Kim E. Boulukos, Philippe Pognonec:
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance. 98 - Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs:
Determination of strongly overlapping signaling activity from microarray data. 99 - Henrik Bengtsson, Ola Hössjer:
Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. 100 - Yian Ann Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhard O. Voit, Jonas S. Almeida:
A multivariate prediction model for microarray cross-hybridization. 101 - Richard P. Auburn, Roslin R. Russell, Bettina Fischer, Lisa A. Meadows, Santiago Sevillano Matilla, Steven Russell:
SimArray: a user-friendly and user-configurable microarray design tool. 102 - Arthur Chun-Chieh Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, Mu-Fen Hsieh:
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. 103 - Joan Teyra, Andreas Doms, Michael Schroeder, M. Teresa Pisabarro:
SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. 104 - Roel G. W. Verhaak, Frank J. T. Staal, Peter J. M. Valk, Bob Löwenberg, Marcel J. T. Reinders, Dick de Ridder:
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. 105 - Robert Tibshirani:
A simple method for assessing sample sizes in microarray experiments. 106 - Rasmus Goll, Trine Olsen, Guanglin Cui, Jon Florholmen:
Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR. 107 - Teresa W. Haynes, Debra J. Knisley, Edith Seier, Yue Zou:
A quantitative analysis of secondary RNA structure using domination based parameters on trees. 108 - Björn H. Junker, Christian Klukas, Falk Schreiber:
VANTED: A system for advanced data analysis and visualization in the context of biological networks. 109 - Michael Spitzer, Stefan Lorkowski, Paul Cullen, Alexander Sczyrba, Georg Fuellen:
IsoSVM - Distinguishing isoforms and paralogs on the protein level. 110 - Scott A. Becker, Nathan D. Price, Bernhard O. Palsson:
Metabolite coupling in genome-scale metabolic networks. 111 - Hidenori Inaoka, Yutaka Fukuoka, Isaac S. Kohane:
Lower expression of genes near microRNA in C. elegans germline. 112 - Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel:
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. 113 - Victor X. Jin, Gregory A. Singer, Francisco J. Agosto-Perez, Sandya Liyanarachchi, Ramana V. Davuluri:
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. 114