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2005

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A method for aligning RNA secondary structures and its application to RNA motif detection

13 years 4 months ago

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Background: Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure a...

Jianghui Liu, Jason Tsong-Li Wang, Jun Hu, Bin Tia...

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Id	Views	Title	Status

1	306	A method for aligning RNA secondary structures and its application to RNA motif detection	claim
2	302	CGHPRO - A comprehensive data analysis tool for array CGH	claim
3	292	Atlas - a data warehouse for integrative bioinformatics	claim
4	253	The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks	claim
5	251	Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation	claim
6	250	FiatFlux - a software for metabolic flux analysis from 13C-glucose experiments	claim
7	246	ParPEST: a pipeline for EST data analysis based on parallel computing	claim
8	223	Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling	claim
9	212	PAGE: Parametric Analysis of Gene Set Enrichment	claim
10	201	A comparative study of discriminating human heart failure etiology using gene expression profiles	claim
11	201	Principal component analysis for predicting transcription-factor binding motifs from array-derived data	claim
12	198	Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks	claim
13	196	Chemistry in Bioinformatics	claim
14	190	Species-specific analysis of protein sequence motifs using mutual information	claim
15	190	An Entropy-based gene selection method for cancer classification using microarray data	claim
16	189	Quantitative inference of dynamic regulatory pathways via microarray data	claim
17	189	A sentence sliding window approach to extract protein annotations from biomedical articles	claim
18	187	JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases	claim
19	180	arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays	claim
20	179	MARS: Microarray analysis, retrieval, and storage system	claim
21	178	A quantization method based on threshold optimization for microarray short time series	claim
22	173	Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis	claim
23	169	MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes	claim
24	169	Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality	claim
25	169	An adaptive method for cDNA microarray normalization	claim
26	167	Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes	claim
27	163	Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system	claim
28	163	Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data	claim
29	163	CoaSim: A flexible environment for simulating genetic data under coalescent models	claim
30	162	Accelerated probabilistic inference of RNA structure evolution	claim
31	161	Non-linear mapping for exploratory data analysis in functional genomics	claim
32	160	Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot	claim
33	159	Columba: an integrated database of proteins, structures, and annotations	claim
34	158	Automated generation of heuristics for biological sequence comparison	claim
35	157	Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser	claim
36	157	Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method	claim
37	156	DynGO: a tool for visualizing and mining of Gene Ontology and its associations	claim
38	156	A new dynamical layout algorithm for complex biochemical reaction networks	claim
39	155	Mining protein function from text using term-based support vector machines	claim
40	154	GObar: A Gene Ontology based analysis and visualization tool for gene sets	claim
41	153	A comparative review of estimates of the proportion unchanged genes and the false discovery rate	claim
42	153	Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control	claim
43	153	Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text	claim
44	152	CoPub Mapper: mining MEDLINE based on search term co-publication	claim
45	152	GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments	claim
46	152	An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem	claim
47	152	Ranking the whole MEDLINE database according to a large training set using text indexing	claim
48	152	Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER	claim
49	151	stam - a Bioconductor compliant R package for structured analysis of microarray data	claim
50	151	ProMiner: rule-based protein and gene entity recognition	claim
51	150	Discover protein sequence signatures from protein-protein interaction data	claim
52	150	Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi	claim
53	149	The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function	claim
54	148	Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments	claim
55	148	NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae	claim
56	147	GATA: a graphic alignment tool for comparative sequence analysis	claim
57	147	Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants	claim
58	145	CAGER: classification analysis of gene expression regulation using multiple information sources	claim
59	144	Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements	claim
60	144	GeneRank: Using search engine technology for the analysis of microarray experiments	claim
61	143	Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries	claim
62	143	Evaluation of BioCreAtIvE assessment of task 2	claim
63	142	transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences	claim
64	142	CLU: A new algorithm for EST clustering	claim
65	142	High performance workflow implementation for protein surface characterization using grid technology	claim
66	141	Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis	claim
67	141	A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models	claim
68	140	JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture	claim
69	140	Dissecting systems-wide data using mixture models: application to identify affected cellular processes	claim
70	138	Detailed protein sequence alignment based on Spectral Similarity Score (SSS)	claim
71	137	ArrayQuest: a web resource for the analysis of DNA microarray data	claim
72	137	A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities	claim
73	137	A standard curve based method for relative real time PCR data processing	claim
74	136	Automatic detection of false annotations via binary property clustering	claim
75	136	Identification of clustered microRNAs using an ab initio prediction method	claim
76	136	Gene/protein name recognition based on support vector machine using dictionary as features	claim
77	135	A robust two-way semi-linear model for normalization of cDNA microarray data	claim
78	134	Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)	claim
79	134	Ancestral sequence alignment under optimal conditions	claim
80	134	Systematic feature evaluation for gene name recognition	claim
81	134	Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists	claim
82	133	Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops	claim
83	133	Ab initio identification of putative human transcription factor binding sites by comparative genomics	claim
84	132	Kalign - an accurate and fast multiple sequence alignment algorithm	claim
85	132	Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein	claim
86	132	CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis	claim
87	131	Functional annotation by identification of local surface similarities: a novel tool for structural genomics	claim
88	131	Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases	claim
89	131	Regularized Least Squares Cancer Classifiers from DNA microarray data	claim
90	130	Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test	claim
91	130	Squid - a simple bioinformatics grid	claim
92	130	MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data	claim
93	128	Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process	claim
94	127	Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"	claim
95	127	Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification	claim
96	127	Are scale-free networks robust to measurement errors?	claim
97	126	GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA	claim
98	126	Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models	claim
99	126	An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments	claim
100	126	HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms	claim
101	125	Multiple sequence alignments of partially coding nucleic acid sequences	claim
102	125	DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment	claim
103	125	Query3d: a new method for high-throughput analysis of functional residues in protein structures	claim
104	125	A simple approach for protein name identification: prospects and limits	claim
105	125	Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling	claim
106	124	Evaluating concentration estimation errors in ELISA microarray experiments	claim
107	124	Internet-based profiler system as integrative framework to support translational research	claim
108	124	ErmineJ: Tool for functional analysis of gene expression data sets	claim
109	124	Probabilistic annotation of protein sequences based on functional classifications	claim
110	124	Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection	claim
111	123	PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability	claim
112	122	ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences	claim
113	122	GenClust: A genetic algorithm for clustering gene expression data	claim
114	122	FACT - a framework for the functional interpretation of high-throughput experiments	claim
115	122	Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein	claim
116	122	Bayesian coestimation of phylogeny and sequence alignment	claim
117	122	Computational verification of protein-protein interactions by orthologous co-expression	claim
118	122	Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine	claim
119	122	A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks	claim
120	122	A neural strategy for the inference of SH3 domain-peptide interaction specificity	claim
121	122	Finding genomic ontology terms in text using evidence content	claim
122	121	Evaluation of gene importance in microarray data based upon probability of selection	claim
123	121	Automated methods of predicting the function of biological sequences using GO and BLAST	claim
124	121	Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data	claim
125	121	Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)	claim
126	120	Robust detection of periodic time series measured from biological systems	claim
127	120	SpectralNET - an application for spectral graph analysis and visualization	claim
128	120	pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties	claim
129	120	Harshlight: a "corrective make-up" program for microarray chips	claim
130	120	A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools	claim
131	119	The distance-profile representation and its application to detection of distantly related protein families	claim
132	119	A protein domain interaction interface database: InterPare	claim
133	119	AnovArray: a set of SAS macros for the analysis of variance of gene expression data	claim
134	119	GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures	claim
135	119	Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society	claim
136	118	Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes	claim
137	118	Feature selection and nearest centroid classification for protein mass spectrometry	claim
138	118	Variation in structural location and amino acid conservation of functional sites in protein domain families	claim
139	118	Vestige: Maximum likelihood phylogenetic footprinting	claim
140	117	Graph-representation of oxidative folding pathways	claim
141	117	An SVM-based system for predicting protein subnuclear localizations	claim
142	117	Differentiation of regions with atypical oligonucleotide composition in bacterial genomes	claim
143	117	An evaluation of GO annotation retrieval for BioCreAtIvE and GOA	claim
144	117	HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research	claim
145	116	WEBnm@: a web application for normal mode analyses of proteins	claim
146	116	Can Zipf's law be adapted to normalize microarrays?	claim
147	116	SuperLigands - a database of ligand structures derived from the Protein Data Bank	claim
148	116	Which gene did you mean?	claim
149	116	Dynamic covariation between gene expression and proteome characteristics	claim
150	116	A computational approach for identifying pathogenicity islands in prokaryotic genomes	claim
151	116	Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set	claim
152	115	SUPERFICIAL - Surface mapping of proteins via structure-based peptide library design	claim
153	115	Graphical representation of ribosomal RNA probe accessibility data using ARB software package	claim
154	115	Statistical distributions of optimal global alignment scores of random protein sequences	claim
155	115	MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays	claim
156	114	Signal transduction pathway profiling of individual tumor samples	claim
157	114	AutoFACT: An Automatic Functional Annotation and Classification Tool	claim
158	114	Quality determination and the repair of poor quality spots in array experiments	claim
159	114	Extension of Lander-Waterman theory for sequencing filtered DNA libraries	claim
160	114	Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity	claim
161	114	A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins	claim
162	113	Normal uniform mixture differential gene expression detection for cDNA microarrays	claim
163	113	PentaPlot: A software tool for the illustration of genome mosaicism	claim
164	113	Alternative splicing and protein function	claim
165	113	Pathway level analysis of gene expression using singular value decomposition	claim
166	113	Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks	claim
167	113	Microarray scanner calibration curves: characteristics and implications	claim
168	112	Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds	claim
169	112	Towards precise classification of cancers based on robust gene functional expression profiles	claim
170	112	Visualization methods for statistical analysis of microarray clusters	claim
171	112	Integration of the Gene Ontology into an object-oriented architecture	claim
172	112	"Harshlighting" small blemishes on microarrays	claim
173	112	Web services and workflow management for biological resources	claim
174	111	Improving interoperability between microbial information and sequence databases	claim
175	110	Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information	claim
176	110	Considerations when using the significance analysis of microarrays (SAM) algorithm	claim
177	110	ProGenExpress: Visualization of quantitative data on prokaryotic genomes	claim
178	109	Genome comparison without alignment using shortest unique substrings	claim
179	109	Automation of gene assignments to metabolic pathways using high-throughput expression data	claim
180	108	The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases	claim
181	108	SplitTester: software to identify domains responsible for functional divergence in protein family	claim
182	108	A linear memory algorithm for Baum-Welch training	claim
183	108	Storing, linking, and mining microarray databases using SRS	claim
184	107	A stepwise framework for the normalization of array CGH data	claim
185	107	Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach	claim
186	107	An edit script for taxonomic classifications	claim
187	107	ProbeMaker: an extensible framework for design of sets of oligonucleotide probes	claim
188	107	Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines	claim
189	106	A multistep bioinformatic approach detects putative regulatory elements in gene promoters	claim
190	106	SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution	claim
191	106	Thesaurus-based disambiguation of gene symbols	claim
192	106	ESTree db: a Tool for Peach Functional Genomics	claim
193	105	SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management	claim
194	105	Secondary structure assignment that accurately reflects physical and evolutionary characteristics	claim
195	104	Scoring functions for transcription factor binding site prediction	claim
196	104	A statistical approach for array CGH data analysis	claim
197	104	Wildfire: distributed, Grid-enabled workflow construction and execution	claim
198	104	An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention	claim
199	103	SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms	claim
200	103	Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery	claim
201	103	Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments	claim
202	103	MicroGen: a MIAME compliant web system for microarray experiment information and workflow management	claim
203	102	Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis	claim
204	102	The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications	claim
205	102	Genomic multiple sequence alignments: refinement using a genetic algorithm	claim
206	102	BioCreAtIvE Task1A: entity identification with a stochastic tagger	claim
207	102	Modelling the interaction of steroid receptors with endocrine disrupting chemicals	claim
208	101	MASQOT: a method for cDNA microarray spot quality control	claim
209	101	PALSSE: A program to delineate linear secondary structural elements from protein structures	claim
210	101	TmaDB: a repository for tissue microarray data	claim
211	100	Speeding disease gene discovery by sequence based candidate prioritization	claim
212	100	EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments	claim
213	100	Evolutionary models for insertions and deletions in a probabilistic modeling framework	claim
214	100	Scoredist: A simple and robust protein sequence distance estimator	claim
215	99	maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination	claim
216	99	Effective ambiguity checking in biosequence analysis	claim
217	99	CGH-Profiler: Data mining based on genomic aberration profiles	claim
218	99	Super paramagnetic clustering of protein sequences	claim
219	98	Iterative approach to model identification of biological networks	claim
220	98	The effects of normalization on the correlation structure of microarray data	claim
221	98	DCD - a novel plant specific domain in proteins involved in development and programmed cell death	claim
222	98	InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data	claim
223	97	Clustering the annotation space of proteins	claim
224	97	The yeast kinome displays scale free topology with functional hub clusters	claim
225	97	Sequence variation in ligand binding sites in proteins	claim
226	97	Evolutionary distance estimation and fidelity of pair wise sequence alignment	claim
227	97	Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data	claim
228	97	Modelling the correlation between the activities of adjacent genes in drosophila	claim
229	97	Comparative mapping of sequence-based and structure-based protein domains	claim
230	97	-In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1	claim
231	96	GeneNotes - A novel information management software for biologists	claim
232	96	Evaluating eukaryotic secreted protein prediction	claim
233	96	Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity	claim
234	96	Overview of BioCreAtIvE task 1B: normalized gene lists	claim
235	95	Oligomeric protein structure networks: insights into protein-protein interactions	claim
236	95	'PACLIMS': A component LIM system for high-throughput functional genomic analysis	claim
237	95	Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast	claim
238	94	Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator	claim
239	94	Measuring similarities between transcription factor binding sites	claim
240	94	Computational identification of strain-, species- and genus-specific proteins	claim
241	94	T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory	claim
242	94	Visualization-based discovery and analysis of genomic aberrations in microarray data	claim
243	94	YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities	claim
244	94	A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage	claim
245	94	Reproducible Clusters from Microarray Research: Whither?	claim
246	93	SPdb - a signal peptide database	claim
247	93	Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software)	claim
248	93	Computing expectation values for RNA motifs using discrete convolutions	claim
249	93	Two-part permutation tests for DNA methylation and microarray data	claim
250	93	Multiple sequence alignment accuracy and evolutionary distance estimation	claim
251	93	Identifying gene and protein mentions in text using conditional random fields	claim
252	92	Predicting functional sites with an automated algorithm suitable for heterogeneous datasets	claim
253	92	A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators	claim
254	92	FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform	claim
255	92	A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles	claim
256	92	Filtering high-throughput protein-protein interaction data using a combination of genomic features	claim
257	92	Browsing Isolated Population Data	claim
258	91	Providing visualisation support for the analysis of anatomy ontology data	claim
259	91	COPASAAR - A database for proteomic analysis of single amino acid repeats	claim
260	91	HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data	claim
261	90	TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins	claim
262	90	An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions	claim
263	90	DSD - An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities	claim
264	90	Text Detective: a rule-based system for gene annotation in biomedical texts	claim
265	89	Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes	claim
266	89	An empirical analysis of training protocols for probabilistic gene finders	claim
267	89	Theme discovery from gene lists for identification and viewing of multiple functional groups	claim
268	89	MILANO - custom annotation of microarray results using automatic literature searches	claim
269	89	Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society	claim
270	88	BMC Bioinformatics comes of age	claim
271	88	Analysis of concordance of different haplotype block partitioning algorithms	claim
272	88	Using large-scale perturbations in gene network reconstruction	claim
273	87	Assessing local structural perturbations in proteins	claim
274	87	Efficient decoding algorithms for generalized hidden Markov model gene finders	claim
275	87	ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins	claim
276	87	BioCreAtIvE Task 1A: gene mention finding evaluation	claim
277	86	Confirmation of human protein interaction data by human expression data	claim
278	86	Chromosomal clustering of a human transcriptome reveals regulatory background	claim
279	86	Generalizations of Markov model to characterize biological sequences	claim
280	86	WebArray: an online platform for microarray data analysis	claim
281	85	Prediction of twin-arginine signal peptides	claim
282	85	Processing methods for differential analysis of LC/MS profile data	claim
283	84	Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates	claim
284	84	A method of precise mRNA/DNA homology-based gene structure prediction	claim
285	84	A note on generalized Genome Scan Meta-Analysis statistics	claim
286	84	Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential	claim
287	83	Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis	claim
288	82	A novel method for prokaryotic promoter prediction based on DNA stability	claim
289	82	Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases	claim
290	82	Sources of variation in Affymetrix microarray experiments	claim
291	81	Evolutionary sequence analysis of complete eukaryote genomes	claim
292	81	CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes	claim
293	81	Improved prediction of critical residues for protein function based on network and phylogenetic analyses	claim
294	81	Metabolic Network Analysis: Implication And Application	claim
295	80	htSNPer1.0: software for haplotype block partition and htSNPs selection	claim
296	80	Gene finding in the chicken genome	claim
297	80	Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm	claim
298	79	Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes	claim
299	79	Mathematical design of prokaryotic clone-based microarrays	claim
300	79	Data preparation and interannotator agreement: BioCreAtIvE Task 1B	claim
301	78	PREP-Mt: predictive RNA editor for plant mitochondrial genes	claim
302	78	Correlation test to assess low-level processing of high-density oligonucleotide microarray data	claim
303	78	Automatically annotating documents with normalized gene lists	claim
304	77	Ontological visualization of protein-protein interactions	claim
305	77	Combining Affymetrix microarray results	claim
306	77	The Gene Set Builder: collation, curation, and distribution of sets of genes	claim
307	77	Structural comparison of metabolic networks in selected single cell organisms	claim
308	75	Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes	claim
309	75	Phylogenetic detection of conserved gene clusters in microbial genomes	claim
310	74	wFleaBase: the Daphnia genome database	claim
311	74	Versatile and declarative dynamic programming using pair algebras	claim
312	73	Using hexamers to predict cis-regulatory motifs in Drosophila	claim
313	73	An analysis of extensible modelling for functional genomics data	claim
314	73	Empirical codon substitution matrix	claim
315	73	Evaluation of Glycine max mRNA clusters	claim
316	73	Exploring the boundaries: gene and protein identification in biomedical text	claim
317	72	A Taxonomic Search Engine: Federating taxonomic databases using web services	claim
318	72	Shortest triplet clustering: reconstructing large phylogenies using representative sets	claim
319	70	Integrating alternative splicing detection into gene prediction	claim
320	70	AVID: An integrative framework for discovering functional relationships among proteins	claim
321	70	Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals	claim
322	69	Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts	claim
323	69	PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords	claim
324	67	Selecting additional tag SNPs for tolerating missing data in genotyping	claim
325	67	Sequence signature analysis of chromosome identity in three Drosophila species	claim
326	66	Recognition of protein/gene names from text using an ensemble of classifiers	claim
327	65	Overview of BioCreAtIvE: critical assessment of information extraction for biology	claim
328	64	EXPANDER - an integrative program suite for microarray data analysis	claim
329	64	Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software	claim
330	63	Tandem machine learning for the identification of genes regulated by transcription factors	claim
331	63	Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences	claim
332	63	Communication and re-use of chemical information in bioscience	claim
333	62	Differences in codon bias cannot explain differences in translational power among microbes	claim
334	62	Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality	claim
335	61	Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison	claim
336	61	SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures	claim
337	61	MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution	claim
338	61	Large scale hierarchical clustering of protein sequences	claim
339	61	Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family	claim
340	60	PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information	claim
341	57	Satellog: A database for the identification and prioritization of satellite repeats in disease association studies	claim
342	57	SNP-VISTA: An interactive SNP visualization tool	claim
343	56	Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data	claim
344	52	Identification of significant periodic genes in microarray gene expression data	claim

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