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BMCBI
2006

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AMDA: an R package for the automated microarray data analysis

13 years 11 months ago

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Background: Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and...

Mattia Pelizzola, Norman Pavelka, Maria Foti, Paol...

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Id	Views	Title	Status

1	374	AMDA: an R package for the automated microarray data analysis	claim
2	249	Gene functional similarity search tool (GFSST)	claim
3	242	Predicting residue-wise contact orders in proteins by support vector regression	claim
4	240	Statistical analysis of real-time PCR data	claim
5	239	Applying dynamic Bayesian networks to perturbed gene expression data	claim
6	233	AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies	claim
7	223	PSMIX: an R package for population structure inference via maximum likelihood method	claim
8	216	Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data	claim
9	213	CoXpress: differential co-expression in gene expression data	claim
10	211	Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme	claim
11	207	A new measure for functional similarity of gene products based on Gene Ontology	claim
12	205	Application of Petri net based analysis techniques to signal transduction pathways	claim
13	203	Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data	claim
14	203	Independent component analysis reveals new and biologically significant structures in micro array data	claim
15	202	Spectral embedding finds meaningful (relevant) structure in image and microarray data	claim
16	202	Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks	claim
17	202	DWARF - a data warehouse system for analyzing protein families	claim
18	201	Gene selection algorithms for microarray data based on least squares support vector machine	claim
19	200	Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data	claim
20	199	PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments	claim
21	198	Gene selection and classification of microarray data using random forest	claim
22	195	Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities	claim
23	195	CAFTAN: a tool for fast mapping, and quality assessment of cDNAs	claim
24	194	Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems	claim
25	192	Analysis of circular genome rearrangement by fusions, fissions and block-interchanges	claim
26	190	VANTED: A system for advanced data analysis and visualization in the context of biological networks	claim
27	190	SNPs3D: Candidate gene and SNP selection for association studies	claim
28	187	Detecting outliers when fitting data with nonlinear regression - a new method based on robust nonlinear regression and the false discovery rate	claim
29	186	Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method	claim
30	184	PathSys: integrating molecular interaction graphs for systems biology	claim
31	184	PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm	claim
32	183	Mining gene expression data by interpreting principal components	claim
33	182	A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila	claim
34	182	AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis	claim
35	181	The comprehensive updated regulatory network of Escherichia coli K-12	claim
36	181	Automatic pathway building in biological association networks	claim
37	181	Array2BIO: from microarray expression data to functional annotation of co-regulated genes	claim
38	180	The Gaggle: An open-source software system for integrating bioinformatics software and data sources	claim
39	180	Building multiclass classifiers for remote homology detection and fold recognition	claim
40	179	Multiscale Hy3S: Hybrid stochastic simulation for supercomputers	claim
41	179	Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression	claim
42	178	Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables	claim
43	178	GOLEM: an interactive graph-based gene-ontology navigation and analysis tool	claim
44	178	MannDB - A microbial database of automated protein sequence analyses and evidence integration for protein characterization	claim
45	175	Parameter estimation for stiff equations of biosystems using radial basis function networks	claim
46	174	CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays	claim
47	174	Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration	claim
48	173	Kernel-based distance metric learning for microarray data classification	claim
49	172	BioWarehouse: a bioinformatics database warehouse toolkit	claim
50	172	Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information	claim
51	172	A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data	claim
52	171	The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies	claim
53	171	The Autoimmune Disease Database: a dynamically compiled literature-derived database	claim
54	170	Biclustering of gene expression data by non-smooth non-negative matrix factorization	claim
55	169	Finding biological process modifications in cancer tissues by mining gene expression correlations	claim
56	169	Comparative analysis of haplotype association mapping algorithms	claim
57	169	Beyond microarrays: Finding key transcription factors controlling signal transduction pathways	claim
58	169	Machine learning techniques in disease forecasting: a case study on rice blast prediction	claim
59	169	Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction	claim
60	167	GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions	claim
61	167	The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci	claim
62	166	Extraction of phylogenetic network modules from the metabolic network	claim
63	166	SEQOPTICS: a protein sequence clustering system	claim
64	166	bioNMF: a versatile tool for non-negative matrix factorization in biology	claim
65	165	Improved variance estimation of classification performance via reduction of bias caused by small sample size	claim
66	165	A stable gene selection in microarray data analysis	claim
67	165	Validation and functional annotation of expression-based clusters based on gene ontology	claim
68	165	Improving the quality of protein structure models by selecting from alignment alternatives	claim
69	164	BIOZON: a system for unification, management and analysis of heterogeneous biological data	claim
70	164	Evaluation of clustering algorithms for gene expression data	claim
71	164	Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier	claim
72	163	Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features	claim
73	161	A novel approach to phylogenetic tree construction using stochastic optimization and clustering	claim
74	161	Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome	claim
75	161	miTarget: microRNA target gene prediction using a support vector machine	claim
76	161	A method for rapid similarity analysis of RNA secondary structures	claim
77	160	MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation	claim
78	160	Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources	claim
79	159	Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures	claim
80	159	EpiJen: a server for multistep T cell epitope prediction	claim
81	159	ProtRepeatsDB: a database of amino acid repeats in genomes	claim
82	159	EVEREST: automatic identification and classification of protein domains in all protein sequences	claim
83	159	MultiSeq: unifying sequence and structure data for evolutionary analysis	claim
84	158	Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change	claim
85	158	Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data	claim
86	157	Determination of the minimum number of microarray experiments for discovery of gene expression patterns	claim
87	157	Comparison of protein interaction networks reveals species conservation and divergence	claim
88	156	Bayesian models for pooling microarray studies with multiple sources of replications	claim
89	156	Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models	claim
90	156	GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data	claim
91	156	Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments	claim
92	155	AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data	claim
93	155	A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates	claim
94	155	CAVER: a new tool to explore routes from protein clefts, pockets and cavities	claim
95	155	Analysis of promoter regions of co-expressed genes identified by microarray analysis	claim
96	154	An improved procedure for gene selection from microarray experiments using false discovery rate criterion	claim
97	154	Analysis with respect to instrumental variables for the exploration of microarray data structures	claim
98	154	Automated recognition of malignancy mentions in biomedical literature	claim
99	154	Agile methods in biomedical software development: a multi-site experience report	claim
100	153	Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling	claim
101	153	2DDB - a bioinformatics solution for analysis of quantitative proteomics data	claim
102	153	The 3of5 web application for complex and comprehensive pattern matching in protein sequences	claim
103	153	Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method	claim
104	153	Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments	claim
105	153	Automatic document classification of biological literature	claim
106	152	Predicting deleterious nsSNPs: an analysis of sequence and structural attributes	claim
107	152	Amplification of the Gene Ontology annotation of Affymetrix probe sets	claim
108	152	A two-stage approach for improved prediction of residue contact maps	claim
109	151	Modeling Sage data with a truncated gamma-Poisson model	claim
110	151	Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues	claim
111	150	Instance-based concept learning from multiclass DNA microarray data	claim
112	150	Protein structure similarity from principle component correlation analysis	claim
113	150	TreeDyn: towards dynamic graphics and annotations for analyses of trees	claim
114	150	Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains	claim
115	150	CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes	claim
116	150	Cluster analysis of protein array results via similarity of Gene Ontology annotation	claim
117	149	REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance	claim
118	149	Curation of viral genomes: challenges, applications and the way forward	claim
119	149	HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics	claim
120	149	Identification of biomarkers from mass spectrometry data using a "common" peak approach	claim
121	148	Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data	claim
122	148	Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores	claim
123	147	A hidden Markov model approach for determining expression from genomic tiling micro arrays	claim
124	147	A case study in pathway knowledgebase verification	claim
125	147	QPath: a method for querying pathways in a protein-protein interaction network	claim
126	147	Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data	claim
127	147	The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases	claim
128	146	Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training	claim
129	146	A critical review of PASBio's argument structures for biomedical verbs	claim
130	146	Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE	claim
131	146	GeneTools - application for functional annotation and statistical hypothesis testing	claim
132	146	A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls	claim
133	145	GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes	claim
134	145	Querying the public databases for sequences using complex keywords contained in the feature lines	claim
135	145	Fast-Find: A novel computational approach to analyzing combinatorial motifs	claim
136	144	Development and implementation of an algorithm for detection of protein complexes in large interaction networks	claim
137	144	More robust detection of motifs in coexpressed genes by using phylogenetic information	claim
138	144	methBLAST and methPrimerDB: web-tools for PCR based methylation analysis	claim
139	144	ProFAT: a web-based tool for the functional annotation of protein sequences	claim
140	144	Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences	claim
141	143	Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms	claim
142	143	IsoSVM - Distinguishing isoforms and paralogs on the protein level	claim
143	143	Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction	claim
144	143	Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences	claim
145	142	PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size	claim
146	142	Improving the Performance of SVM-RFE to Select Genes in Microarray Data	claim
147	142	Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis	claim
148	142	RDMAS: a web server for RNA deleterious mutation analysis	claim
149	141	Identification of consensus RNA secondary structures using suffix arrays	claim
150	141	Maximum common subgraph: some upper bound and lower bound results	claim
151	141	Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences	claim
152	141	The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case	claim
153	141	Visual setup of logical models of signaling and regulatory networks with ProMoT	claim
154	140	MACSIMS : multiple alignment of complete sequences information management system	claim
155	140	Feature selection using Haar wavelet power spectrum	claim
156	140	SNP-PHAGE - High throughput SNP discovery pipeline	claim
157	139	DNA Molecule Classification Using Feature Primitives	claim
158	139	Integrated functional visualization of eukaryotic genomes	claim
159	139	Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost	claim
160	138	Determination of strongly overlapping signaling activity from microarray data	claim
161	138	Approximation properties of haplotype tagging	claim
162	137	INTEGRATOR: interactive graphical search of large protein interactomes over the Web	claim
163	137	Biologically relevant effects of mRNA amplification on gene expression profiles	claim
164	137	Chaos game representation for comparison of whole genomes	claim
165	137	Sigma: multiple alignment of weakly-conserved non-coding DNA sequence	claim
166	137	GOPET: A tool for automated predictions of Gene Ontology terms	claim
167	137	A classification-based framework for predicting and analyzing gene regulatory response	claim
168	137	Improving the accuracy of protein secondary structure prediction using structural alignment	claim
169	137	Cell_motility: a cross-platform, open source application for the study of cell motion paths	claim
170	137	A maximum likelihood framework for protein design	claim
171	137	Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences	claim
172	137	Curation of complex, context-dependent immunological data	claim
173	137	Bounded search for de novo identification of degenerate cis-regulatory elements	claim
174	136	Metric for Measuring the Effectiveness of Clustering of DNA Microarray Expression	claim
175	136	Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis	claim
176	136	EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences	claim
177	135	TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes	claim
178	135	Correcting ligands, metabolites, and pathways	claim
179	135	iHAP - integrated haplotype analysis pipeline for characterizing the haplotype structure of genes	claim
180	134	Application of machine learning in SNP discovery	claim
181	134	An approach for clustering gene expression data with error information	claim
182	134	A statistical score for assessing the quality of multiple sequence alignments	claim
183	133	Choosing negative examples for the prediction of protein-protein interactions	claim
184	133	An integrated approach to the prediction of domain-domain interactions	claim
185	133	Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae	claim
186	133	Web-based analysis of the mouse transcriptome using Genevestigator	claim
187	132	Length-dependent prediction of protein intrinsic disorder	claim
188	132	Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays	claim
189	132	Genome-wide DNA polymorphism analyses using VariScan	claim
190	131	Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span	claim
191	131	SIMAGE: simulation of DNA-microarray gene expression data	claim
192	131	The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison	claim
193	131	Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations	claim
194	131	inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons	claim
195	130	CARMA: A platform for analyzing microarray datasets that incorporate replicate measures	claim
196	130	Identifying biological concepts from a protein-related corpus with a probabilistic topic model	claim
197	130	MicroTar: predicting microRNA targets from RNA duplexes	claim
198	130	Docking protein domains in contact space	claim
199	130	An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices	claim
200	130	An accurate and interpretable model for siRNA efficacy prediction	claim
201	130	Spatial normalization of array-CGH data	claim
202	130	4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing	claim
203	130	Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping	claim
204	129	BIPAD: A web server for modeling bipartite sequence elements	claim
205	129	Independent Component Analysis-motivated Approach to Classificatory Decomposition of Cortical Evoked Potentials	claim
206	129	EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity	claim
207	129	Functional clustering of yeast proteins from the protein-protein interaction network	claim
208	129	Identifying genes that contribute most to good classification in microarrays	claim
209	129	A literature-based similarity metric for biological processes	claim
210	129	Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps	claim
211	129	Fast index based algorithms and software for matching position specific scoring matrices	claim
212	128	Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice	claim
213	128	An interactive tool for visualization of relationships between gene expression profiles	claim
214	128	Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches	claim
215	128	New directions in biomedical text annotation: definitions, guidelines and corpus construction	claim
216	128	Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments	claim
217	128	Comparative assessment of performance and genome dependence among phylogenetic profiling methods	claim
218	128	Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it	claim
219	127	Automatic discovery of cross-family sequence features associated with protein function	claim
220	127	On the attenuation and amplification of molecular noise in genetic regulatory networks	claim
221	127	Exploring supervised and unsupervised methods to detect topics in biomedical text	claim
222	127	Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions	claim
223	127	Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks	claim
224	127	Using local gene expression similarities to discover regulatory binding site modules	claim
225	127	A graph-search framework for associating gene identifiers with documents	claim
226	127	PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens	claim
227	126	Effect of data normalization on fuzzy clustering of DNA microarray data	claim
228	126	OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments	claim
229	126	A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data	claim
230	126	A joint model of regulatory and metabolic networks	claim
231	126	Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data	claim
232	126	Genomes as geography: using GIS technology to build interactive genome feature maps	claim
233	126	JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow	claim
234	126	A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors	claim
235	125	Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation	claim
236	125	Automated functional classification of experimental and predicted protein structures	claim
237	125	Evaluating different methods of microarray data normalization	claim
238	125	Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow	claim
239	124	ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes	claim
240	124	Detection of divergent genes in microbial aCGH experiments	claim
241	124	Network-based de-noising improves prediction from microarray data	claim
242	124	HybGFS: a hybrid method for genome-fingerprint scanning	claim
243	124	The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line	claim
244	124	Predicting transcription factor binding sites using local over-representation and comparative genomics	claim
245	123	How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results	claim
246	123	Computational models with thermodynamic and composition features improve siRNA design	claim
247	123	Characterizing disease states from topological properties of transcriptional regulatory networks	claim
248	123	An Automated Method for Rapid Identification of Putative Gene Family Members in Plants	claim
249	123	Permutation test for periodicity in short time series data	claim
250	123	SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology	claim
251	122	A multivariate prediction model for microarray cross-hybridization	claim
252	122	A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks	claim
253	122	A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets	claim
254	122	CoSMoS: Conserved Sequence Motif Search in the proteome	claim
255	122	BioMoby extensions to the Taverna workflow management and enactment software	claim
256	122	PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data	claim
257	122	Genome comparison using Gene Ontology (GO) with statistical testing	claim
258	122	Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle	claim
259	121	Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package	claim
260	121	Splice site identification using probabilistic parameters and SVM classification	claim
261	121	Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions	claim
262	120	Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins	claim
263	120	An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse	claim
264	120	A factor analysis model for functional genomics	claim
265	120	Optimizing amino acid substitution matrices with a local alignment kernel	claim
266	120	SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces	claim
267	120	Classification of protein quaternary structure by functional domain composition	claim
268	120	Projections for fast protein structure retrieval	claim
269	120	The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy	claim
270	119	Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies	claim
271	119	A methodology for the structural and functional analysis of signaling and regulatory networks	claim
272	119	LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates	claim
273	119	Hidden Markov Model Variants and their Application	claim
274	119	Evaluation of microarray data normalization procedures using spike-in experiments	claim
275	118	Microarray image analysis: background estimation using quantile and morphological filters	claim
276	118	A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images	claim
277	118	Exploration of biological network centralities with CentiBiN	claim
278	118	Identification of gene expression patterns using planned linear contrasts	claim
279	118	Low degree metabolites explain essential reactions and enhance modularity in biological networks	claim
280	118	Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration	claim
281	118	Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats	claim
282	118	Predicting the effect of missense mutations on protein function: analysis with Bayesian networks	claim
283	118	Automatic generation of gene finders for eukaryotic species	claim
284	118	Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis	claim
285	117	Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale)	claim
286	117	The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees	claim
287	117	SigFlux: A novel network feature to evaluate the importance of proteins in signal transduction networks	claim
288	117	G-InforBIO: integrated system for microbial genomics	claim
289	117	Gene Designer: a synthetic biology tool for constructing artificial DNA segments	claim
290	117	A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics	claim
291	117	Incorporating background frequency improves entropy-based residue conservation measures	claim
292	116	HotSwap for bioinformatics: A STRAP tutorial	claim
293	116	JColorGrid: software for the visualization of biological measurements	claim
294	116	Gene annotation and network inference by phylogenetic profiling	claim
295	116	Whole genome association mapping by incompatibilities and local perfect phylogenies	claim
296	116	ROKU: a novel method for identification of tissue-specific genes	claim
297	116	TaxMan: a taxonomic database manager	claim
298	116	Integrative missing value estimation for microarray data	claim
299	116	Cluster analysis for DNA methylation profiles having a detection threshold	claim
300	116	A model-based approach to selection of tag SNPs	claim
301	116	MICA: desktop software for comprehensive searching of DNA databases	claim
302	116	Optimized mixed Markov models for motif identification	claim
303	115	SimArray: a user-friendly and user-configurable microarray design tool	claim
304	115	MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa	claim
305	115	RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers	claim
306	115	The accuracy of several multiple sequence alignment programs for proteins	claim
307	115	Detecting recombination in evolving nucleotide sequences	claim
308	115	AgdbNet - antigen sequence database software for bacterial typing	claim
309	115	Multivariate curve resolution of time course microarray data	claim
310	114	A high level interface to SCOP and ASTRAL implemented in Python	claim
311	114	Empirical validation of the S-Score algorithm in the analysis of gene expression data	claim
312	114	Taxonomic colouring of phylogenetic trees of protein sequences	claim
313	114	Evaluation and comparison of mammalian subcellular localization prediction methods	claim
314	114	A methodology for global validation of microarray experiments	claim
315	114	A direct comparison of protein interaction confidence assignment schemes	claim
316	114	Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle	claim
317	114	BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences	claim
318	114	Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa	claim
319	114	PROMPT: a protein mapping and comparison tool	claim
320	114	Impact of RNA structure on the prediction of donor and acceptor splice sites	claim
321	113	In silico discovery of human natural antisense transcripts	claim
322	113	QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species	claim
323	113	GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima	claim
324	112	GENOMEMASKER package for designing unique genomic PCR primers	claim
325	112	Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins	claim
326	112	MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences	claim
327	112	A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database	claim
328	112	Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data	claim
329	112	Phylophenetic properties of metabolic pathway topologies as revealed by global analysis	claim
330	112	A correlated motif approach for finding short linear motifs from protein interaction networks	claim
331	112	Protein disorder prediction by condensed PSSM considering propensity for order or disorder	claim
332	112	Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease	claim
333	112	Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins	claim
334	111	SIMMAP: Stochastic character mapping of discrete traits on phylogenies	claim
335	111	Development of an unbiased statistical method for the analysis of unigenic evolution	claim
336	111	PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions	claim
337	111	Using ESTs to improve the accuracy of de novo gene prediction	claim
338	111	Tools for integrated sequence-structure analysis with UCSF Chimera	claim
339	111	High throughput profile-profile based fold recognition for the entire human proteome	claim
340	110	preAssemble: a tool for automatic sequencer trace data processing	claim
341	110	Bias in error estimation when using cross-validation for model selection	claim
342	110	Design of a combinatorial DNA microarray for protein-DNA interaction studies	claim
343	110	Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae	claim
344	110	CpGcluster: a distance-based algorithm for CpG-island detection	claim
345	109	Integrated analysis of gene expression by association rules discovery	claim
346	109	An integrated system for genetic analysis	claim
347	109	A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions	claim
348	109	GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease	claim
349	109	iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website	claim
350	109	HaploRec: efficient and accurate large-scale reconstruction of haplotypes	claim
351	108	An improved map of conserved regulatory sites for Saccharomyces cerevisiae	claim
352	108	RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits	claim
353	108	A new pooling strategy for high-throughput screening: the Shifted Transversal Design	claim
354	108	Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress	claim
355	108	FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries	claim
356	108	NOXclass: prediction of protein-protein interaction types	claim
357	108	Improved Chou-Fasman method for protein secondary structure prediction	claim
358	108	SPIDer: Saccharomyces protein-protein interaction database	claim
359	108	Gene function classification using Bayesian models with hierarchy-based priors	claim
360	108	Probe set algorithms: is there a rational best bet?	claim
361	107	A reinforced merging methodology for mapping unique peptide motifs in members of protein families	claim
362	107	Simplifying gene trees for easier comprehension	claim
363	107	Evaluation of methods for oligonucleotide array data via quantitative real-time PCR	claim
364	107	CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies	claim
365	107	Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum	claim
366	106	Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method	claim
367	106	GONOME: measuring correlations between GO terms and genomic positions	claim
368	106	Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach	claim
369	106	Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index	claim
370	106	Gene and protein nomenclature in public databases	claim
371	105	Integrative investigation of metabolic and transcriptomic data	claim
372	105	CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks	claim
373	105	Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence	claim
374	104	GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes	claim
375	104	SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools	claim
376	104	Semi-supervised discovery of differential genes	claim
377	104	MANET: tracing evolution of protein architecture in metabolic networks	claim
378	104	Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila	claim
379	103	Correction of scaling mismatches in oligonucleotide microarray data	claim
380	103	Domain-based small molecule binding site annotation	claim
381	103	Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice	claim
382	103	Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves	claim
383	103	Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression	claim
384	103	Accelerating the reconstruction of genome-scale metabolic networks	claim
385	103	Improving missing value imputation of microarray data by using spot quality weights	claim
386	103	Meta-All: a system for managing metabolic pathway information	claim
387	102	UVPAR: fast detection of functional shifts in duplicate genes	claim
388	102	Protein secondary structure prediction for a single-sequence using hidden semi-Markov models	claim
389	102	Predicting population coverage of T-cell epitope-based diagnostics and vaccines	claim
390	102	Prediction of protein structural class with Rough Sets	claim
391	102	SNA - a toolbox for the stoichiometric analysis of metabolic networks	claim
392	102	MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria	claim
393	102	Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells	claim
394	102	Taking U out, with two nucleases?	claim
395	101	SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms	claim
396	101	SuperMimic - Fitting peptide mimetics into protein structures	claim
397	101	Local protein structure prediction using discriminative models	claim
398	101	How repetitive are genomes?	claim
399	101	Hierarchical modularity of nested bow-ties in metabolic networks	claim
400	101	Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives	claim
401	101	On the persistence of supplementary resources in biomedical publications	claim
402	101	A combined approach to data mining of textual and structured data to identify cancer-related targets	claim
403	100	DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions	claim
404	100	Design of microarray probes for virus identification and detection of emerging viruses at the genus level	claim
405	100	Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm	claim
406	100	STAR: predicting recombination sites from amino acid sequence	claim
407	100	Using the nucleotide substitution rate matrix to detect horizontal gene transfer	claim
408	100	Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas	claim
409	100	Empirical array quality weights in the analysis of microarray data	claim
410	99	MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers	claim
411	99	A proposed metric for assessing the measurement quality of individual microarrays	claim
412	99	MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools	claim
413	99	Genetic algorithm learning as a robust approach to RNA editing site prediction	claim
414	98	In search of functional association from time-series microarray data based on the change trend and level of gene expression	claim
415	98	JLIN: A java based linkage disequilibrium plotter	claim
416	98	Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server	claim
417	98	Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation	claim
418	98	The Secrets of a Functional Synapse - From a Computational and Experimental Viewpoint	claim
419	98	Optimised amino acid specific weighting factors for unbound protein docking	claim
420	98	Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements	claim
421	97	Choosing the best heuristic for seeded alignment of DNA sequences	claim
422	97	AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation	claim
423	97	PDA: Pooled DNA analyzer	claim
424	97	A comparative analysis of the information content in long and short SAGE libraries	claim
425	97	Goulphar: rapid access and expertise for standard two-color microarray normalization methods	claim
426	97	REEF: searching REgionally Enriched Features in genomes	claim
427	97	Selecting normalization genes for small diagnostic microarrays	claim
428	96	Bayesian detection of periodic mRNA time profiles without use of training examples	claim
429	96	Individualized markers optimize class prediction of microarray data	claim
430	96	Structure alignment based on coding of local geometric measures	claim
431	95	A quantitative analysis of secondary RNA structure using domination based parameters on trees	claim
432	95	XcisClique: analysis of regulatory bicliques	claim
433	95	A simple method for assessing sample sizes in microarray experiments	claim
434	95	Estimate haplotype frequencies in pedigrees	claim
435	95	Discrete profile comparison using information bottleneck	claim
436	95	Predicting DNA-binding sites of proteins from amino acid sequence	claim
437	94	Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition	claim
438	94	Metabolite coupling in genome-scale metabolic networks	claim
439	94	STEM: a tool for the analysis of short time series gene expression data	claim
440	94	Protein Ranking by Semi-Supervised Network Propagation	claim
441	94	Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology	claim
442	94	Novel knowledge-based mean force potential at the profile level	claim
443	94	Dynamic variable selection in SNP genotype autocalling from APEX microarray data	claim
444	94	Noise-injected neural networks show promise for use on small-sample expression data	claim
445	94	Simulation of microarray data with realistic characteristics	claim
446	94	Genepi: a blackboard framework for genome annotation	claim
447	93	Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR	claim
448	93	Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor	claim
449	93	A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database	claim
450	92	Recrafting the neighbor-joining method	claim
451	92	Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays	claim
452	92	Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs	claim
453	92	Systematic assignment of thermodynamic constraints in metabolic network models	claim
454	92	A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes	claim
455	92	Demonstration of two novel methods for predicting functional siRNA efficiency	claim
456	91	Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06)	claim
457	91	Cheminformatics methods for novel nanopore analysis of HIV DNA termini	claim
458	91	Empirical study of supervised gene screening	claim
459	91	PeanutMap: an online genome database for comparative molecular maps of peanut	claim
460	91	In silico identification of putative promoter motifs of White Spot Syndrome Virus	claim
461	90	The PowerAtlas: a power and sample size atlas for microarray experimental design and research	claim
462	90	Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data	claim
463	90	BayGO: Bayesian analysis of ontology term enrichment in microarray data	claim
464	90	An improved ant colony algorithm with diversified solutions based on the immune strategy	claim
465	90	A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity	claim
466	89	A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event	claim
467	89	ORENZA: a web resource for studying ORphan ENZyme activities	claim
468	89	SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera	claim
469	88	Protein kinases associated with the yeast phosphoproteome	claim
470	88	A two-sample Bayesian t-test for microarray data	claim
471	88	Effect of various normalization methods on Applied Biosystems expression array system data	claim
472	88	RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes	claim
473	87	Prediction of indirect interactions in proteins	claim
474	87	Trends in life science grid: from computing grid to knowledge grid	claim
475	87	MathDAMP: a package for differential analysis of metabolite profiles	claim
476	87	XML schemas for common bioinformatic data types and their application in workflow systems	claim
477	87	Phylogeny based discovery of regulatory elements	claim
478	87	Computational expression deconvolution in a complex mammalian organ	claim
479	86	Microbial identification by mass cataloging	claim
480	86	The impact of sample imbalance on identifying differentially expressed genes	claim
481	86	MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution	claim
482	86	Integrated siRNA design based on surveying of features associated with high RNAi effectiveness	claim
483	86	PHY*FI: fast and easy online creation and manipulation of phylogeny color figures	claim
484	86	Identification of QTLs controlling gene expression networks defined a priori	claim
485	85	On single and multiple models of protein families for the detection of remote sequence relationships	claim
486	85	Quality control for terms and definitions in ontologies and taxonomies	claim
487	85	An application of statistics to comparative metagenomics	claim
488	85	Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock	claim
489	85	Identification of physicochemical selective pressure on protein encoding nucleotide sequences	claim
490	85	Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data	claim
491	85	SVM-based prediction of caspase substrate cleavage sites	claim
492	85	Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy	claim
493	85	On the statistical assessment of classifiers using DNA microarray data	claim
494	84	Phase analysis of circadian-related genes in two tissues	claim
495	84	Representation of target-bound drugs by computed conformers: implications for conformational libraries	claim
496	84	Evaluation of clustering algorithms for protein-protein interaction networks	claim
497	84	Inferring topology from clustering coefficients in protein-protein interaction networks	claim
498	84	SVRMHC prediction server for MHC-binding peptides	claim
499	83	Bacterial genotyping by 16S rRNA mass cataloging	claim
500	82	Selection of antisense oligonucleotides based on multiple predicted target mRNA structures	claim
501	82	Transcriptomic response to differentiation induction	claim
502	82	Profiling alternatively spliced mRNA isoforms for prostate cancer classification	claim
503	82	A method for computing the overall statistical significance of a treatment effect among a group of genes	claim
504	82	Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions	claim
505	82	Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus	claim
506	81	Multipolar representation of protein structure	claim
507	81	Lower expression of genes near microRNA in C. elegans germline	claim
508	81	Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs	claim
509	81	A fisheye viewer for microarray-based gene expression data	claim
510	81	V-MitoSNP: visualization of human mitochondrial SNPs	claim
511	80	Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets	claim
512	80	An analysis of the Sargasso Sea resource and the consequences for database composition	claim
513	80	Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts	claim
514	80	Quantification of the variation in percentage identity for protein sequence alignments	claim
515	79	GO-Diff: Mining functional differentiation between EST-based transcriptomes	claim
516	79	Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator	claim
517	79	The effects of multiple features of alternatively spliced exons on the KA/KS ratio test	claim
518	78	An evaluation of human protein-protein interaction data in the public domain	claim
519	78	Modelling study of dimerization in mammalian defensins	claim
520	78	Subfamily logos: visualization of sequence deviations at alignment positions with high information content	claim
521	78	IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model	claim
522	76	Coloring the Mu transpososome	claim
523	76	XRate: a fast prototyping, training and annotation tool for phylo-grammars	claim
524	75	A fast SCOP fold classification system using content-based E-Predict algorithm	claim
525	75	Improving the specificity of high-throughput ortholog prediction	claim
526	75	A machine learning strategy to identify candidate binding sites in human protein-coding sequence	claim
527	74	Effects of filtering by Present call on analysis of microarray experiments	claim
528	74	Protein protein interactions, evolutionary rate, abundance and age	claim
529	74	An unsupervised classification scheme for improving predictions of prokaryotic TIS	claim
530	74	Establishing bioinformatics research in the Asia Pacific	claim
531	73	Browsing repeats in genomes: Pygram and an application to non-coding region analysis	claim
532	72	Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis	claim
533	72	Selecting effective siRNA sequences by using radial basis function network and decision tree learning	claim
534	71	MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics	claim
535	69	Retrieval with gene queries	claim
536	68	Detecting overlapping coding sequences in virus genomes	claim
537	68	Haplotype-based quantitative trait mapping using a clustering algorithm	claim
538	67	Assessing stability of gene selection in microarray data analysis	claim
539	67	Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus	claim
540	67	A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification	claim
541	65	mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code	claim
542	65	Particle simulation approach for subcellular dynamics and interactions of biological molecules	claim
543	65	A fast parallel algorithm for finding the longest common sequence of multiple biosequences	claim
544	64	GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins	claim
545	64	FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis	claim
546	64	In silico modelling of hormone response elements	claim
547	64	MIMOX: a web tool for phage display based epitope mapping	claim
548	63	Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics	claim
549	62	Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations	claim
550	61	Various criteria in the evaluation of biomedical named entity recognition	claim
551	61	A scalable machine-learning approach to recognize chemical names within large text databases	claim
552	61	A probabilistic classifier for olfactory receptor pseudogenes	claim
553	60	PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory	claim
554	60	Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes	claim
555	59	Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data	claim
556	58	GeneLibrarian: an effective gene-information summarization and visualization system	claim
557	57	Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris	claim
558	57	Mining expressed sequence tags identifies cancer markers of clinical interest	claim
559	54	Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae	claim
560	53	Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network	claim
561	53	A specialized learner for inferring structured cis-regulatory modules	claim
562	51	Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine	claim
563	50	Metabolic pathways variability and sequence/networks comparisons	claim
564	46	Mapping data elements to terminological resources for integrating biomedical data sources	claim
565	45	A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB	claim

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