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BMCBI
2008

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A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

14 years 18 days ago

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Background: Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tan...

Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbe...

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Id	Views	Title	Status

1	323	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data	claim
2	259	DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites	claim
3	256	TrypanoCyc - a metabolic pathway database for Trypanosoma brucei	claim
4	244	RNAalifold: improved consensus structure prediction for RNA alignments	claim
5	242	annot8r: GO, EC and KEGG annotation of EST datasets	claim
6	242	New time-scale criteria for model simplification of bio-reaction systems	claim
7	228	Adaptive diffusion kernel learning from biological networks for protein function prediction	claim
8	226	ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining	claim
9	222	TOBFAC: the database of tobacco transcription factors	claim
10	220	Gene prediction in metagenomic fragments: A large scale machine learning approach	claim
11	219	Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles	claim
12	218	LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method	claim
13	214	Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research	claim
14	214	Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations	claim
15	211	CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies	claim
16	211	CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment	claim
17	208	GraphFind: enhancing graph searching by low support data mining techniques	claim
18	204	EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration	claim
19	202	Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data	claim
20	201	A copula method for modeling directional dependence of genes	claim
21	200	Defining functional distances over Gene Ontology	claim
22	195	Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies	claim
23	193	Missing value imputation for microarray gene expression data using histone acetylation information	claim
24	191	BatchPrimer3: A high throughput web application for PCR and sequencing primer design	claim
25	190	Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes	claim
26	189	AnEnPi: identification and annotation of analogous enzymes	claim
27	188	anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data	claim
28	187	PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes	claim
29	186	Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases	claim
30	185	Mining clinical relationships from patient narratives	claim
31	184	Integrating protein-protein interactions and text mining for protein function prediction	claim
32	184	"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition	claim
33	182	MiMiR - an integrated platform for microarray data sharing, mining and analysis	claim
34	181	Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples	claim
35	179	Building pathway clusters from Random Forests classification using class votes	claim
36	179	Bayesian modeling of recombination events in bacterial populations	claim
37	179	Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists	claim
38	178	Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization	claim
39	178	A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis	claim
40	177	Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis	claim
41	176	H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments	claim
42	175	Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces	claim
43	175	Synonym set extraction from the biomedical literature by lexical pattern discovery	claim
44	174	Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset	claim
45	173	Extraction of semantic biomedical relations from text using conditional random fields	claim
46	173	Improved machine learning method for analysis of gas phase chemistry of peptides	claim
47	173	Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments	claim
48	172	Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method	claim
49	172	Compo: composite motif discovery using discrete models	claim
50	171	Fuzzy association rules for biological data analysis: A case study on yeast	claim
51	171	A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations	claim
52	171	Comparative analysis of five protein-protein interaction corpora	claim
53	170	Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory	claim
54	170	A genetic approach for building different alphabets for peptide and protein classification	claim
55	170	Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data	claim
56	169	CompMoby: Comparative MobyDick for detection of cis-regulatory motifs	claim
57	169	MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects	claim
58	169	A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification	claim
59	168	Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements	claim
60	167	Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments	claim
61	167	Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification	claim
62	166	Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information	claim
63	166	Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies	claim
64	166	QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR	claim
65	165	Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics	claim
66	165	SWS: accessing SRS sites contents through Web Services	claim
67	164	MeInfoText: associated gene methylation and cancer information from text mining	claim
68	164	Word correlation matrices for protein sequence analysis and remote homology detection	claim
69	163	ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family	claim
70	163	Gene Ontology term overlap as a measure of gene functional similarity	claim
71	163	The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology	claim
72	163	Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling	claim
73	163	i-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology	claim
74	162	Improved identification of conserved cassette exons using Bayesian networks	claim
75	162	Background correction using dinucleotide affinities improves the performance of GCRMA	claim
76	161	Inferring gene expression dynamics via functional regression analysis	claim
77	160	A method for analyzing censored survival phenotype with gene expression data	claim
78	160	VariVis: a visualisation toolkit for variation databases	claim
79	160	Feature selection environment for genomic applications	claim
80	160	Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'	claim
81	160	A comparison of four clustering methods for brain expression microarray data	claim
82	160	Predicting cancer involvement of genes from heterogeneous data	claim
83	160	Dynamic sensitivity analysis of biological systems	claim
84	159	Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models	claim
85	159	Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments	claim
86	158	LC-MSsim - a simulation software for liquid chromatography mass spectrometry data	claim
87	158	Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis	claim
88	158	Discovering gene annotations in biomedical text databases	claim
89	158	Metrics for GO based protein semantic similarity: a systematic evaluation	claim
90	158	Real value prediction of protein solvent accessibility using enhanced PSSM features	claim
91	158	Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics	claim
92	158	VarDetect: a nucleotide sequence variation exploratory tool	claim
93	157	Dimension reduction with redundant gene elimination for tumor classification	claim
94	156	Chromhome: A rich internet application for accessing comparative chromosome homology maps	claim
95	156	ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses	claim
96	156	The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays	claim
97	155	Prediction of regulatory elements in mammalian genomes using chromatin signatures	claim
98	155	AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening	claim
99	155	ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts	claim
100	155	Extending pathways based on gene lists using InterPro domain signatures	claim
101	154	Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration	claim
102	154	GeNESiS: gene network evolution simulation software	claim
103	154	GenomeMatcher: A graphical user interface for DNA sequence comparison	claim
104	154	Extension of the COG and arCOG databases by amino acid and nucleotide sequences	claim
105	154	Sequence based residue depth prediction using evolutionary information and predicted secondary structure	claim
106	153	AWclust: point-and-click software for non-parametric population structure analysis	claim
107	153	2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments	claim
108	153	Estimating the size of the solution space of metabolic networks	claim
109	153	GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique	claim
110	153	Version VI of the ESTree db: an improved tool for peach transcriptome analysis	claim
111	153	Improved general regression network for protein domain boundary prediction	claim
112	153	How to make the most of NE dictionaries in statistical NER	claim
113	152	Predicting biological system objectives de novo from internal state measurements	claim
114	152	JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes	claim
115	151	Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs	claim
116	151	CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge	claim
117	151	An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases	claim
118	150	BibGlimpse: The case for a light-weight reprint manager in distributed literature research	claim
119	150	MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level	claim
120	150	Natural Language Processing in aid of FlyBase curators	claim
121	150	13C labeling experiments at metabolic nonstationary conditions: An exploratory study	claim
122	149	Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence	claim
123	149	Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores	claim
124	149	Accelerating the annotation of sparse named entities by dynamic sentence selection	claim
125	149	All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning	claim
126	149	MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data	claim
127	148	Automating dChip: toward reproducible sharing of microarray data analysis	claim
128	148	StAR: a simple tool for the statistical comparison of ROC curves	claim
129	148	BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments	claim
130	148	Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements	claim
131	148	Discovering biclusters in gene expression data based on high-dimensional linear geometries	claim
132	147	Simple integrative preprocessing preserves what is shared in data sources	claim
133	147	Transmembrane helix prediction using amino acid property features and latent semantic analysis	claim
134	147	Assessment of disease named entity recognition on a corpus of annotated sentences	claim
135	146	EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries	claim
136	146	nGASP - the nematode genome annotation assessment project	claim
137	146	A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data	claim
138	146	Rank-based edge reconstruction for scale-free genetic regulatory networks	claim
139	146	Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?	claim
140	146	ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization	claim
141	145	Directed acyclic graph kernels for structural RNA analysis	claim
142	145	The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction	claim
143	145	Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis	claim
144	145	A computational and analysis tool for proteomics research	claim
145	144	Local conservation scores without a priori assumptions on neutral substitution rates	claim
146	144	WGCNA: an R package for weighted correlation network analysis	claim
147	144	Automatically extracting functionally equivalent proteins from SwissProt	claim
148	144	Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis	claim
149	144	PDTD: a web-accessible protein database for drug target identification	claim
150	144	Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses	claim
151	143	Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering	claim
152	143	Automatic detection of exonic splicing enhancers (ESEs) using SVMs	claim
153	143	catmap: Case-control And TDT Meta-Analysis Package	claim
154	142	Genetic weighted k-means algorithm for clustering large-scale gene expression data	claim
155	142	Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification	claim
156	142	RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database	claim
157	142	Strategies for measuring evolutionary conservation of RNA secondary structures	claim
158	142	Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures	claim
159	142	Optimal neighborhood indexing for protein similarity search	claim
160	141	EzArray: A web-based highly automated Affymetrix expression array data management and analysis system	claim
161	141	Discovering functional interaction patterns in protein-protein interaction networks	claim
162	141	Functional discrimination of membrane proteins using machine learning techniques	claim
163	141	The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation	claim
164	141	Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction	claim
165	141	Ontology-guided data preparation for discovering genotype-phenotype relationships	claim
166	141	MiRTif: a support vector machine-based microRNA target interaction filter	claim
167	140	FUNYBASE: a FUNgal phYlogenomic dataBASE	claim
168	140	Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework	claim
169	140	Corpus annotation for mining biomedical events from literature	claim
170	140	SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences	claim
171	140	GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations	claim
172	139	Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats	claim
173	139	The C1C2: A framework for simultaneous model selection and assessment	claim
174	139	Abbreviation definition identification based on automatic precision estimates	claim
175	139	A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining	claim
176	139	New challenges for text mining: mapping between text and manually curated pathways	claim
177	138	Systematic identification of yeast cell cycle transcription factors using multiple data sources	claim
178	138	Combining transcriptional datasets using the generalized singular value decomposition	claim
179	138	Information transfer in signaling pathways: A study using coupled simulated and experimental data	claim
180	138	CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions	claim
181	138	Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions	claim
182	138	Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics	claim
183	138	Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles	claim
184	138	M-BISON: Microarray-based integration of data sources using networks	claim
185	138	Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction	claim
186	138	Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection	claim
187	138	SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803	claim
188	138	Comparative analyses of bidirectional promoters in vertebrates	claim
189	138	Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data	claim
190	137	A dynamic Bayesian network approach to protein secondary structure prediction	claim
191	137	VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays	claim
192	137	Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data	claim
193	136	LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens	claim
194	136	A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model	claim
195	136	Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models	claim
196	136	GPAT: Retrieval of genomic annotation from large genomic position datasets	claim
197	136	An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions	claim
198	135	Inferring the role of transcription factors in regulatory networks	claim
199	135	Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles	claim
200	135	Knowledge-guided multi-scale independent component analysis for biomarker identification	claim
201	135	Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data	claim
202	135	Fregene: Simulation of realistic sequence-level data in populations and ascertained samples	claim
203	135	Functional site prediction selects correct protein models	claim
204	135	Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies	claim
205	135	Facilitating the development of controlled vocabularies for metabolomics technologies with text mining	claim
206	134	Stability analysis of mixtures of mutagenetic trees	claim
207	134	Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites	claim
208	134	Prediction of protein-protein binding site by using core interface residue and support vector machine	claim
209	134	Clustering cancer gene expression data: a comparative study	claim
210	134	PEPOP: Computational design of immunogenic peptides	claim
211	134	Identification of transcription factor contexts in literature using machine learning approaches	claim
212	133	LocateP: Genome-scale subcellular-location predictor for bacterial proteins	claim
213	133	ElliPro: a new structure-based tool for the prediction of antibody epitopes	claim
214	133	SPIKE - a database, visualization and analysis tool of cellular signaling pathways	claim
215	133	MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening	claim
216	133	CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes	claim
217	133	A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data	claim
218	133	Towards ontology-driven navigation of the lipid bibliosphere	claim
219	132	Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer	claim
220	132	Exon level integration of proteomics and microarray data	claim
221	132	The Average Mutual Information Profile as a Genomic Signature	claim
222	132	SCOWLP classification: Structural comparison and analysis of protein binding regions	claim
223	132	Mixture models for analysis of melting temperature data	claim
224	132	Clustering ionic flow blockade toggles with a Mixture of HMMs	claim
225	132	Very Important Pool (VIP) genes - an application for microarray-based molecular signatures	claim
226	132	The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage	claim
227	131	Major copy proportion analysis of tumor samples using SNP arrays	claim
228	131	Modifying the DPClus algorithm for identifying protein complexes based on new topological structures	claim
229	131	K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space	claim
230	131	CoCoNUT: an efficient system for the comparison and analysis of genomes	claim
231	130	A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins	claim
232	130	IDEA: Interactive Display for Evolutionary Analyses	claim
233	130	Function approximation approach to the inference of reduced NGnet models of genetic networks	claim
234	130	A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm	claim
235	130	An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories	claim
236	130	Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases	claim
237	130	FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects	claim
238	130	Structural descriptor database: a new tool for sequence-based functional site prediction	claim
239	129	Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes	claim
240	129	EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management	claim
241	129	A unified approach to false discovery rate estimation	claim
242	129	Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses	claim
243	129	An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments	claim
244	129	Mining phenotypes for gene function prediction	claim
245	129	Gene set enrichment analysis for non-monotone association and multiple experimental categories	claim
246	129	Motif-directed network component analysis for regulatory network inference	claim
247	128	Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes	claim
248	128	Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions	claim
249	128	Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation	claim
250	128	Efficient computation of absent words in genomic sequences	claim
251	128	Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure	claim
252	128	Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites	claim
253	128	SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics	claim
254	128	HAPSIMU: a genetic simulation platform for population-based association studies	claim
255	128	An efficient visualization tool for the analysis of protein mutation matrices	claim
256	128	Validation of an NSP-based (negative selection pattern) gene family identification strategy	claim
257	128	In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches	claim
258	127	Gene and pathway identification with Lp penalized Bayesian logistic regression	claim
259	127	MetaMine - A tool to detect and analyse gene patterns in their environmental context	claim
260	127	Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides	claim
261	127	AMMO-Prot: amine system project 3D-model finder	claim
262	126	Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution	claim
263	126	NITPICK: peak identification for mass spectrometry data	claim
264	126	GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed	claim
265	126	FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification	claim
266	126	Relating gene expression data on two-component systems to functional annotations in Escherichia coli	claim
267	126	c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression	claim
268	126	Methods for evaluating gene expression from Affymetrix microarray datasets	claim
269	126	Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems	claim
270	126	Automatic inference of indexing rules for MEDLINE	claim
271	126	ISOL@: an Italian SOLAnaceae genomics resource	claim
272	125	XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data	claim
273	125	MAID : An effect size based model for microarray data integration across laboratories and platforms	claim
274	125	A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions	claim
275	125	SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes	claim
276	125	Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain	claim
277	125	SNPLims: a data management system for genome wide association studies	claim
278	125	Competition between protein aggregation and protein complex formation	claim
279	125	Disambiguation of biomedical text using diverse sources of information	claim
280	125	Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors	claim
281	125	Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation	claim
282	124	A relation based measure of semantic similarity for Gene Ontology annotations	claim
283	124	Inferring modules of functionally interacting proteins using the Bond Energy Algorithm	claim
284	124	Computational identification of ubiquitylation sites from protein sequences	claim
285	124	A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays	claim
286	124	Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease	claim
287	124	Alignment of protein structures in the presence of domain motions	claim
288	124	RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays	claim
289	124	Ontology-based, Tissue MicroArray oriented, image centered tissue bank	claim
290	123	Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes	claim
291	123	Shape based indexing for faster search of RNA family databases	claim
292	123	PocketMatch: A new algorithm to compare binding sites in protein structures	claim
293	123	Statistical methodology for the analysis of dye-switch microarray experiments	claim
294	123	Validation of protein models by a neural network approach	claim
295	123	Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach	claim
296	123	A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences	claim
297	123	Functional module detection by functional flow pattern mining in protein interaction networks	claim
298	122	Generating samples for association studies based on HapMap data	claim
299	122	Grammar-based distance in progressive multiple sequence alignment	claim
300	122	ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins	claim
301	122	High-throughput bioinformatics with the Cyrille2 pipeline system	claim
302	122	Effects of dependence in high-dimensional multiple testing problems	claim
303	122	Determining gene expression on a single pair of microarrays	claim
304	122	OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expres	claim
305	122	Reconstructing networks of pathways via significance analysis of their intersections	claim
306	122	A practical comparison of two K-Means clustering algorithms	claim
307	121	BioSAVE: Display of scored annotation within a sequence context	claim
308	121	iRefIndex: A consolidated protein interaction database with provenance	claim
309	121	GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments	claim
310	121	Modularization of biochemical networks based on classification of Petri net t-invariants	claim
311	121	Microarray data mining using landmark gene-guided clustering	claim
312	121	OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology	claim
313	121	A simple and fast heuristic for protein structure comparison	claim
314	121	Stability of gene contributions and identification of outliers in multivariate analysis of microarray data	claim
315	121	ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences	claim
316	120	E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)	claim
317	120	DBMLoc: a Database of proteins with multiple subcellular localizations	claim
318	120	Statistical issues in the analysis of Illumina data	claim
319	120	Shape-IT: new rapid and accurate algorithm for haplotype inference	claim
320	120	A protein interaction based model for schizophrenia study	claim
321	119	Snagger: A user-friendly program for incorporating additional information for tagSNP selection	claim
322	119	A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics	claim
323	119	Integrated multi-level quality control for proteomic profiling studies using mass spectrometry	claim
324	119	Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction	claim
325	119	On deducing causality in metabolic networks	claim
326	118	MetWAMer: eukaryotic translation initiation site prediction	claim
327	118	Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution	claim
328	118	DOVIS: an implementation for high-throughput virtual screening using AutoDock	claim
329	118	PseudoGeneQuest - Service for identification of different pseudogene types in the human genome	claim
330	118	Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling	claim
331	118	Kismeth: Analyzer of plant methylation states through bisulfite sequencing	claim
332	118	Virtual screening of GPCRs: An in silico chemogenomics approach	claim
333	118	Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation	claim
334	117	RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure	claim
335	117	New resampling method for evaluating stability of clusters	claim
336	117	A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge	claim
337	117	Using a logical model to predict the growth of yeast	claim
338	117	CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments	claim
339	117	An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks	claim
340	117	Cascaded classifiers for confidence-based chemical named entity recognition	claim
341	116	GBParsy: A GenBank flatfile parser library with high speed	claim
342	116	A novel representation of RNA secondary structure based on element-contact graphs	claim
343	116	Algorithm of OMA for large-scale orthology inference	claim
344	116	IgTM: An algorithm to predict transmembrane domains and topology in proteins	claim
345	116	The combination approach of SVM and ECOC for powerful identification and classification of transcription factor	claim
346	116	Clustering exact matches of pairwise sequence alignments by weighted linear regression	claim
347	116	MScanner: a classifier for retrieving Medline citations	claim
348	116	Impact of residue accessible surface area on the prediction of protein secondary structures	claim
349	116	Gene Ontology annotations: what they mean and where they come from	claim
350	116	Structuring an event ontology for disease outbreak detection	claim
351	115	Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient	claim
352	115	Systems biology driven software design for the research enterprise	claim
353	115	Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data	claim
354	115	Probe signal correction for differential methylation hybridization experiments	claim
355	115	Improving peptide-MHC class I binding prediction for unbalanced datasets	claim
356	115	BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment	claim
357	115	PARPST: a PARallel algorithm to find peptide sequence tags	claim
358	115	Quantitative systems-level determinants of drug targets	claim
359	114	TiGER: A database for tissue-specific gene expression and regulation	claim
360	114	Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping	claim
361	114	Visualizing and clustering high throughput sub-cellular localization imaging	claim
362	114	Combining classifiers for improved classification of proteins from sequence or structure	claim
363	114	The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks	claim
364	114	A visual analytics approach for understanding biclustering results from microarray data	claim
365	114	Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation	claim
366	114	Dinucleotide controlled null models for comparative RNA gene prediction	claim
367	114	Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design	claim
368	114	Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins	claim
369	114	Partial mixture model for tight clustering of gene expression time-course	claim
370	114	WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding	claim
371	113	SNPFile - A software library and file format for large scale association mapping and population genetics studies	claim
372	113	Investigating selection on viruses: a statistical alignment approach	claim
373	113	SynBlast: Assisting the analysis of conserved synteny information	claim
374	113	A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data	claim
375	112	GlycomeDB - integration of open-access carbohydrate structure databases	claim
376	112	Normalization for triple-target microarray experiments	claim
377	112	Evaluation of genomic island predictors using a comparative genomics approach	claim
378	112	Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service	claim
379	112	A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics	claim
380	112	A simplified approach to disulfide connectivity prediction from protein sequences	claim
381	112	Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies	claim
382	111	Comparative optimism in models involving both classical clinical and gene expression information	claim
383	111	SciDBMaker: new software for computer-aided design of specialized biological databases	claim
384	111	VisualRepbase: an interface for the study of occurrences of transposable element families	claim
385	111	Protein contact order prediction from primary sequences	claim
386	111	SimHap GUI: An intuitive graphical user interface for genetic association analysis	claim
387	111	Aspects of coverage in medical DNA sequencing	claim
388	111	Information-based methods for predicting gene function from systematic gene knock-downs	claim
389	111	GENOMEPOP: A program to simulate genomes in populations	claim
390	111	Probabilistic base calling of Solexa sequencing data	claim
391	111	CBESW: Sequence Alignment on the Playstation 3	claim
392	111	A perl package and an alignment tool for phylogenetic networks	claim
393	111	Distinguishing the species of biomedical named entities for term identification	claim
394	111	MLIP: using multiple processors to compute the posterior probability of linkage	claim
395	111	Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry	claim
396	110	Determining significance of pairwise co-occurrences of events in bursty sequences	claim
397	110	Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands	claim
398	110	Highly sensitive feature detection for high resolution LC/MS	claim
399	110	Assessment of composite motif discovery methods	claim
400	110	Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites	claim
401	110	Enhancing the prediction of protein pairings between interacting families using orthology information	claim
402	110	Finding microRNA regulatory modules in human genome using rule induction	claim
403	110	Testing for treatment effects on gene ontology	claim
404	109	MetaFIND: A feature analysis tool for metabolomics data	claim
405	109	ConStruct: Improved construction of RNA consensus structures	claim
406	109	LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons	claim
407	109	Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis	claim
408	109	The meaning of alignment: lessons from structural diversity	claim
409	108	Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures	claim
410	108	A nonparametric model for quality control of database search results in shotgun proteomics	claim
411	108	An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance	claim
412	108	New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background	claim
413	108	Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks	claim
414	108	Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons	claim
415	108	SPRINT: A new parallel framework for R	claim
416	107	A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data	claim
417	107	Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission	claim
418	107	Extended Newick: it is time for a standard representation of phylogenetic networks	claim
419	107	A mixture model approach to sample size estimation in two-sample comparative microarray experiments	claim
420	107	Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)	claim
421	107	GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors	claim
422	107	RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences	claim
423	107	RDFScape: Semantic Web meets Systems Biology	claim
424	107	Comparative analysis of non-classically secreted proteins in Botrytis cinerea and symbiotic fungus Laccaria bicolor	claim
425	106	Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data	claim
426	106	Identification of hot-spot residues in protein-protein interactions by computational docking	claim
427	106	SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies	claim
428	106	A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification	claim
429	106	Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities	claim
430	106	A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips	claim
431	106	An Integrated Korean Biodiversity and Genetic Information Retrieval System	claim
432	106	Integrating biological data - the Distributed Annotation System	claim
433	106	Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology	claim
434	105	Using the longest significance run to estimate region-specific p-values in genetic association mapping studies	claim
435	105	Novel computational methods for increasing PCR primer design effectiveness in directed sequencing	claim
436	105	Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols	claim
437	105	Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania	claim
438	105	A gene pattern mining algorithm using interchangeable gene sets for prokaryotes	claim
439	105	A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards	claim
440	105	SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes	claim
441	105	Predicting RNA-binding sites of proteins using support vector machines and evolutionary information	claim
442	104	Barcodes for genomes and applications	claim
443	104	Missing value imputation improves clustering and interpretation of gene expression microarray data	claim
444	104	Evolutionary Pareto-optimization of stably folding peptides	claim
445	104	ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)	claim
446	104	ExonMiner: Web service for analysis of GeneChip Exon array data	claim
447	104	Comparison of methods for estimating the nucleotide substitution matrix	claim
448	104	Analyzing the simplicial decomposition of spatial protein structures	claim
449	104	InteroPORC: an automated tool to predict highly conserved protein interaction networks	claim
450	104	Robust consensus computation	claim
451	103	TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model	claim
452	103	Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network	claim
453	103	The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences	claim
454	103	Parameter estimation for robust HMM analysis of ChIP-chip data	claim
455	103	Detection of protein catalytic residues at high precision using local network properties	claim
456	103	Discovering multi-level structures in bio-molecular data through the Bernstein inequality	claim
457	102	Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations	claim
458	102	Significance analysis of microarray for relative quantitation of LC/MS data in proteomics	claim
459	102	Response projected clustering for direct association with physiological and clinical response data	claim
460	102	Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs	claim
461	102	PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships	claim
462	102	Improving protein function prediction methods with integrated literature data	claim
463	102	mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences	claim
464	102	Stability of the core domain of p53: insights from computer simulations	claim
465	102	Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability	claim
466	102	Fast splice site detection using information content and feature reduction	claim
467	101	Prediction of glycosylation sites using random forests	claim
468	101	A comparison of common programming languages used in bioinformatics	claim
469	101	Reranking candidate gene models with cross-species comparison for improved gene prediction	claim
470	101	Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species	claim
471	101	Compressing DNA sequence databases with coil	claim
472	101	Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster	claim
473	101	Model of visual attention for video sequences	claim
474	100	easyExon - A Java-based GUI tool for processing and visualization of Affymetrix exon array data	claim
475	100	Semantic role labeling for protein transport predicates	claim
476	100	High-precision high-coverage functional inference from integrated data sources	claim
477	100	PatternLab for proteomics: a tool for differential shotgun proteomics	claim
478	100	Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations	claim
479	100	Extracting transcription factor binding sites from unaligned gene sequences with statistical models	claim
480	100	Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes	claim
481	99	A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition	claim
482	99	Designing multiple degenerate primers via consecutive pairwise alignments	claim
483	99	Towards a lightweight generic computational grid framework for biological research	claim
484	99	Binning sequences using very sparse labels within a metagenome	claim
485	99	miRNAminer: A tool for homologous microRNA gene search	claim
486	99	NestedMICA as an ab initio protein motif discovery tool	claim
487	99	Multiple organism algorithm for finding ultraconserved elements	claim
488	99	Ranking analysis of F-statistics for microarray data	claim
489	99	CWRML: representing crop wild relative conservation and use data in XML	claim
490	99	Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment	claim
491	99	Exhaustive prediction of disease susceptibility to coding base changes in the human genome	claim
492	99	Highlights from the Fourth International Society for Computational Biology Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biolo	claim
493	98	Empirical Bayes models for multiple probe type microarrays at the probe level	claim
494	98	GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach	claim
495	98	Assessing probe-specific dye and slide biases in two-color microarray data	claim
496	98	Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction	claim
497	98	The strength of co-authorship in gene name disambiguation	claim
498	98	PredGPI: a GPI-anchor predictor	claim
499	98	Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios	claim
500	98	MTAP: The Motif Tool Assessment Platform	claim
501	97	A Population Proportion approach for ranking differentially expressed genes	claim
502	97	SODa: An Mn/Fe superoxide dismutase prediction and design server	claim
503	97	Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'	claim
504	97	Interrogating domain-domain interactions with parsimony based approaches	claim
505	97	SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles	claim
506	97	Large-scale directional relationship extraction and resolution	claim
507	97	MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways	claim
508	97	Quantitative analysis of numerical solvers for oscillatory biomolecular system models	claim
509	96	SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool	claim
510	96	Use of normalization methods for analysis of microarrays containing a high degree of gene effects	claim
511	96	A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information	claim
512	96	Novel methodology for construction and pruning of quasi-median networks	claim
513	96	MSDmotif: exploring protein sites and motifs	claim
514	96	Mapping proteins to disease terminologies: from UniProt to MeSH	claim
515	96	The value of position-specific scoring matrices for assessment of protein allegenicity	claim
516	95	Methodology capture: discriminating between the "best" and the rest of community practice	claim
517	95	PURE: A webserver for the prediction of domains in unassigned regions in proteins	claim
518	95	Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method	claim
519	95	Identification and correction of abnormal, incomplete and mispredicted proteins in public databases	claim
520	95	Mining protein networks for synthetic genetic interactions	claim
521	95	Gene set analyses for interpreting microarray experiments on prokaryotic organisms	claim
522	95	Universal seeds for cDNA-to-genome comparison	claim
523	95	CMA - a comprehensive Bioconductor package for supervised classification with high dimensional data	claim
524	95	Protein structural class prediction based on an improved statistical strategy	claim
525	95	Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008	claim
526	94	Conserved co-expression for candidate disease gene prioritization	claim
527	94	Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles	claim
528	94	Structural assembly of two-domain proteins by rigid-body docking	claim
529	94	A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods	claim
530	93	VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens	claim
531	93	MPDA: Microarray pooled DNA analyzer	claim
532	93	Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence	claim
533	93	SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis	claim
534	93	Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens	claim
535	93	A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation	claim
536	93	Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations	claim
537	93	Ranking single nucleotide polymorphisms by potential deleterious effects	claim
538	93	Hybrid MM/SVM structural sensors for stochastic sequential data	claim
539	92	Proteochemometric modeling of HIV protease susceptibility	claim
540	92	OpenMS - An open-source software framework for mass spectrometry	claim
541	92	A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles	claim
542	92	Testing gene set enrichment for subset of genes: Sub-GSE	claim
543	91	PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval	claim
544	91	t2prhd: a tool to study the patterns of repeat evolution	claim
545	91	SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis	claim
546	91	Presenting and exploring biological pathways with PathVisio	claim
547	91	The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes	claim
548	90	Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation	claim
549	90	Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge	claim
550	90	A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time	claim
551	90	Ortholog-based protein-protein interaction prediction and its application to inter-species interactions	claim
552	89	R/parallel - speeding up bioinformatics analysis with R	claim
553	89	An incremental approach to automated protein localisation	claim
554	89	Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy	claim
555	88	Large-scale identification of polymorphic microsatellites using an in silico approach	claim
556	88	Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable	claim
557	88	Data capture in bioinformatics: requirements and experiences with Pedro	claim
558	88	Microarray-based gene set analysis: a comparison of current methods	claim
559	87	Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information	claim
560	87	Protein structure search and local structure characterization	claim
561	87	Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data	claim
562	87	Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces	claim
563	87	Evaluation of two methods for computational HLA haplotypes inference using a real dataset	claim
564	86	Predicting protein linkages in bacteria: Which method is best depends on task	claim
565	86	Piecewise multivariate modelling of sequential metabolic profiling data	claim
566	86	Subfamily specific conservation profiles for proteins based on n-gram patterns	claim
567	86	Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets	claim
568	85	Merging microarray data from separate breast cancer studies provides a robust prognostic test	claim
569	85	SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access	claim
570	85	Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score	claim
571	85	Comprehensive analysis of circadian periodic pattern in plant transcriptome	claim
572	85	Normalizing biomedical terms by minimizing ambiguity and variability	claim
573	85	Predicted mouse peroxisome-targeted proteins and their actual subcellular locations	claim
574	85	Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate	claim
575	84	DNAAlignEditor: DNA alignment editor tool	claim
576	84	poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening	claim
577	84	The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem	claim
578	84	Prediction of specificity-determining residues for small-molecule kinase inhibitors	claim
579	84	Revealing sequence variation patterns in rice with machine learning methods	claim
580	83	SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase	claim
581	83	An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast	claim
582	83	Prioritization of gene regulatory interactions from large-scale modules in yeast	claim
583	83	Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells	claim
584	83	Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes	claim
585	83	A Java-based tool for the design of classification microarrays	claim
586	83	Terminologies for text-mining; an experiment in the lipoprotein metabolism domain	claim
587	83	CellExcite: an efficient simulation environment for excitable cells	claim
588	82	Studying the functional conservation of cis-regulatory modules and their transcriptional output	claim
589	82	Standardized high-throughput evaluation of cell-based compound screens	claim
590	82	AMYPdb: A database dedicated to amyloid precursor proteins	claim
591	82	Envelope: interactive software for modeling and fitting complex isotope distributions	claim
592	82	Protein evolution driven by symmetric structural repeats	claim
593	82	Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation	claim
594	81	Position dependent mismatch discrimination on DNA microarrays - experiments and model	claim
595	81	A perspective for biomedical data integration: Design of databases for flow cytometry	claim
596	80	The XBabelPhish MAGE-ML and XML Translator	claim
597	80	Computational evaluation of TIS annotation for prokaryotic genomes	claim
598	80	Towards an automatic classification of protein structural domains based on structural similarity	claim
599	80	GeneFisher-P: variations of GeneFisher as processes in Bio-jETI	claim
600	79	Pathological rate matrices: from primates to pathogens	claim
601	79	Gene function prediction using labeled and unlabeled data	claim
602	79	A high-throughput pipeline for designing microarray-based pathogen diagnostic assays	claim
603	79	In silico docking of urokinase plasminogen activator and integrins	claim
604	79	Semi-automatic conversion of BioProp semantic annotation to PASBio annotation	claim
605	78	A new protein linear motif benchmark for multiple sequence alignment software	claim
606	78	Evaluation of time profile reconstruction from complex two-color microarray designs	claim
607	78	Deducing topology of protein-protein interaction networks from experimentally measured sub-networks	claim
608	78	Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features	claim
609	78	Exploiting and integrating rich features for biological literature classification	claim
610	77	A simple and robust method for connecting small-molecule drugs using gene-expression signatures	claim
611	77	SeqAn An efficient, generic C++ library for sequence analysis	claim
612	77	I-TASSER server for protein 3D structure prediction	claim
613	77	Genomic analysis of gene regulation complexity	claim
614	77	Stochastic models for the in silico simulation of synaptic processes	claim
615	76	Empirical Bayes analysis of single nucleotide polymorphisms	claim
616	76	Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors	claim
617	75	Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07)	claim
618	75	Re-searcher: a system for recurrent detection of homologous protein sequences	claim
619	75	A three-state prediction of single point mutations on protein stability changes	claim
620	75	Discovering relationships among dispersed repeats using spatial association rule mining	claim
621	75	Flanking signal and mature peptide residues influence signal peptide cleavage	claim
622	75	Bioinformatics research in the Asia Pacific: a 2007 update	claim
623	74	Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast	claim
624	74	MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids	claim
625	74	Conditional variable importance for random forests	claim
626	74	Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs	claim
627	73	Conditional clustering of temporal expression profiles	claim
628	73	PhySIC_IST: cleaning source trees to infer more informative supertrees	claim
629	73	Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies	claim
630	72	HECTAR: A method to predict subcellular targeting in heterokonts	claim
631	72	Using a literature-based NMF model for discovering gene functional relationships	claim
632	71	Prediction of TF target sites based on atomistic models of protein-DNA complexes	claim
633	71	Examining the significance of fingerprint-based classifiers	claim
634	71	A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins	claim
635	71	An improved string composition method for sequence comparison	claim
636	71	Microarray analysis of gene expression during auditory hair cell regeneration in zebrafish (Danio rerio)	claim
637	70	Assessment of protein set coherence using functional annotations	claim
638	70	Neutral network sizes of biological RNA molecules can be computed and are not atypically small	claim
639	70	Optimizations for the EcoPod field identification tool	claim
640	70	Fast NJ-like algorithms to deal with incomplete distance matrices	claim
641	70	The MoVIN server for the analysis of protein interaction networks	claim
642	68	NullHap - a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles	claim
643	68	OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature	claim
644	68	GraphCrunch: A tool for large network analyses	claim
645	68	Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles	claim
646	68	Automatic construction of rule-based ICD-9-CM coding systems	claim
647	67	Multi-label literature classification based on the Gene Ontology graph	claim
648	67	Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions	claim
649	67	Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage	claim
650	67	Functional analysis of novel SNPs and mutations in human and mouse genomes	claim
651	67	Proteome discovery pipeline for mass spectrometry-based proteomics	claim
652	66	Identifying differential correlation in gene/pathway combinations	claim
653	66	Modelling the structures of G protein-coupled receptors aided by three-dimensional validation	claim
654	66	FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures	claim
655	65	Supervised inference of gene-regulatory networks	claim
656	65	An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis	claim
657	64	Modeling mis-folded lysozyme aggregates	claim
658	63	Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks	claim
659	63	Using quality scores and longer reads improves accuracy of Solexa read mapping	claim
660	63	Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes	claim
661	63	SQUAT: A web tool to mine human, murine and avian SAGE data	claim
662	63	Recognizing speculative language in biomedical research articles: a linguistically motivated perspective	claim
663	62	A statistical toolbox for metagenomics: assessing functional diversity in microbial communities	claim
664	62	Flexible boosting of accelerated failure time models	claim
665	62	A fast structural multiple alignment method for long RNA sequences	claim
666	62	Scientific Laboratory Information Management System: Tissue Bank	claim
667	62	SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions	claim
668	62	Filtering of false positive microRNA candidates by a clustering-based approach	claim
669	61	PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data	claim
670	60	Evaluation of pooled allelotyping versus individual genotyping for genome-wide association analysis of complex disease	claim
671	60	A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data	claim
672	58	Discrimination of outer membrane proteins with improved performance	claim
673	58	Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking	claim
674	58	Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools	claim
675	58	Integration of relational and hierarchical network information for protein function prediction	claim
676	57	A novel method for high accuracy sumoylation site prediction from protein sequences	claim
677	57	Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci	claim
678	57	Precise detection of rearrangement breakpoints in mammalian chromosomes	claim
679	56	Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research	claim
680	53	minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information	claim
681	51	ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use	claim
682	50	Using a kernel density estimation based classifier to predict species-specific microRNA precursors	claim
683	46	uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts	claim

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