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BMCBI
2010

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PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms

13 years 11 months ago

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Background: Several tools have been developed to explore and search Gene Ontology (GO) databases allowing efficient GO enrichment analysis and GO tree visualization. Nevertheless,...

Marc Bruckskotten, Mario Looso, Franz Cemic, Anne ...

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Id	Views	Title	Status

1	277	PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms	claim
2	268	A high-level 3D visualization API for Java and ImageJ	claim
3	259	Rule-based spatial modeling with diffusing, geometrically constrained molecules	claim
4	243	Comparative study of unsupervised dimension reduction techniques for the visualization of microarray gene expression data	claim
5	240	TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs	claim
6	240	CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse	claim
7	233	Odefy -- From discrete to continuous models	claim
8	232	LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB	claim
9	229	Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks	claim
10	227	Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage	claim
11	224	An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data	claim
12	223	MetNetGE: interactive views of biological networks and ontologies	claim
13	219	BiologicalNetworks 2.0 - an integrative view of genome biology data	claim
14	218	Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets	claim
15	218	A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D	claim
16	216	Bayesian Inference of the Number of Factors in Gene-Expression Analysis: Application to Human Virus Challenge Studies	claim
17	214	AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number	claim
18	208	Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo	claim
19	208	A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data	claim
20	208	Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models	claim
21	205	A fast indexing approach for protein structure comparison	claim
22	202	NeMo: Network Module identification in Cytoscape	claim
23	201	Analysis of X-ray Structures of Matrix Metalloproteinases via Chaotic Map Clustering	claim
24	201	IntelliGO: a new vector-based semantic similarity measure including annotation origin	claim
25	198	ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment	claim
26	196	Content-based microarray search using differential expression profiles	claim
27	195	MBAT: A scalable informatics system for unifying digital atlasing workflows	claim
28	193	Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements	claim
29	193	caGrid Workflow Toolkit: A Taverna based workflow tool for cancer Grid	claim
30	193	MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data	claim
31	193	Mayday - integrative analytics for expression data	claim
32	191	Colonyzer: automated quantification of micro-organism growth characteristics on solid agar	claim
33	191	BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions	claim
34	191	Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2	claim
35	190	APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility	claim
36	190	A parallel and incremental algorithm for efficient unique signature discovery on DNA databases	claim
37	190	Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms	claim
38	189	High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH	claim
39	189	Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs	claim
40	189	solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database	claim
41	188	CDK-Taverna: an open workflow environment for cheminformatics	claim
42	187	PathEx: a novel multi factors based datasets selector web tool	claim
43	186	Knowledge-based biomedical word sense disambiguation: comparison of approaches	claim
44	185	ABCtoolbox: a versatile toolkit for approximate Bayesian computations	claim
45	185	MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics	claim
46	183	SING: Subgraph search In Non-homogeneous Graphs	claim
47	183	SOPRA: Scaffolding algorithm for paired reads via statistical optimization	claim
48	183	Active learning for human protein-protein interaction prediction	claim
49	183	The complexity of gene expression dynamics revealed by permutation entropy	claim
50	182	L2-norm multiple kernel learning and its application to biomedical data fusion	claim
51	182	Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images	claim
52	181	Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes	claim
53	179	A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network	claim
54	179	Circadian signatures in rat liver: from gene expression to pathways	claim
55	178	Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests	claim
56	178	CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics	claim
57	178	Applications of a formal approach to decipher discrete genetic networks	claim
58	178	An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology	claim
59	177	Modular composition predicts kinase/substrate interactions	claim
60	177	Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets	claim
61	176	Bayesian statistical modelling of human protein interaction network incorporating protein disorder information	claim
62	176	TargetSpy: a supervised machine learning approach for microRNA target prediction	claim
63	176	Reverse engineering gene regulatory network from microarray data using linear time-variant model	claim
64	176	Haplotype association analyses in resources of mixed structure using Monte Carlo testing	claim
65	175	Calibur: a tool for clustering large numbers of protein decoys	claim
66	175	Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base	claim
67	175	The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services	claim
68	175	Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective	claim
69	175	Global parameter estimation methods for stochastic biochemical systems	claim
70	174	The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data	claim
71	173	The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images	claim
72	172	Accessing the SEED genome databases via Web services API: tools for programmers	claim
73	172	Comparison of evolutionary algorithms in gene regulatory network model inference	claim
74	172	Inferring gene regression networks with model trees	claim
75	172	Nonparametric identification of regulatory interactions from spatial and temporal gene expression data	claim
76	171	PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data	claim
77	170	Integrative analysis of gene expression and copy number alterations using canonical correlation analysis	claim
78	170	Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks	claim
79	169	eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies	claim
80	167	Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach	claim
81	167	BisoGenet: a new tool for gene network building, visualization and analysis	claim
82	167	Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies	claim
83	167	Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome	claim
84	166	Accurate peak list extraction from proteomic mass spectra for identification and profiling studies	claim
85	165	Bayesian integrated modeling of expression data: a case study on RhoG	claim
86	165	MTar: a computational microRNA target prediction architecture for human transcriptome	claim
87	165	Multivariate meta-analysis of proteomics data from human prostate and colon tumours	claim
88	165	Filtering, FDR and power	claim
89	164	Gene regulatory networks modelling using a dynamic evolutionary hybrid	claim
90	164	Flexible network reconstruction from relational databases with Cytoscape and CytoSQL	claim
91	164	Investigating the validity of current network analysis on static conglomerate networks by protein network stratification	claim
92	164	Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions	claim
93	164	Merged consensus clustering to assess and improve class discovery with microarray data	claim
94	163	Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity	claim
95	163	Integration of open access literature into the RCSB Protein Data Bank using BioLit	claim
96	163	DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data	claim
97	163	RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in clo	claim
98	162	Moara: a Java library for extracting and normalizing gene and protein mentions	claim
99	162	SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping	claim
100	162	SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels	claim
101	161	GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms	claim
102	161	GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs	claim
103	161	CGHpower: exploring sample size calculations for chromosomal copy number experiments	claim
104	161	FRASS: the web-server for RNA structural comparison	claim
105	161	BPDA - A Bayesian peptide detection algorithm for mass spectrometry	claim
106	161	Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns	claim
107	161	Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers	claim
108	161	LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes	claim
109	160	Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53	claim
110	160	Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data	claim
111	160	Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins	claim
112	160	Extracting consistent knowledge from highly inconsistent cancer gene data sources	claim
113	160	eHive: An Artificial Intelligence workflow system for genomic analysis	claim
114	159	Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines	claim
115	158	Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing	claim
116	158	A Bayesian network approach to feature selection in mass spectrometry data	claim
117	157	SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read	claim
118	156	Global screening of potential Candida albicans biofilm-related transcription factors via network comparison	claim
119	156	Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments	claim
120	156	Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions	claim
121	156	Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes	claim
122	156	Mathematical model for empirically optimizing large scale production of soluble protein domains	claim
123	156	Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways	claim
124	156	Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape	claim
125	156	Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images	claim
126	156	PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci	claim
127	155	FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases	claim
128	155	BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences	claim
129	155	A flexible R package for nonnegative matrix factorization	claim
130	155	A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer	claim
131	155	BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation	claim
132	154	LINNAEUS: A species name identification system for biomedical literature	claim
133	154	Fine-tuning structural RNA alignments in the twilight zone	claim
134	154	Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data	claim
135	154	Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble	claim
136	154	An eScience-Bayes strategy for analyzing omics data	claim
137	154	EnvMine: A text-mining system for the automatic extraction of contextual information	claim
138	154	An algorithm for automated closure during assembly	claim
139	154	Candidate gene prioritization by network analysis of differential expression using machine learning approaches	claim
140	154	Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation	claim
141	153	MimoSA: a system for minimotif annotation	claim
142	153	GOAL: A software tool for assessing biological significance of genes groups	claim
143	153	VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences	claim
144	153	Metamotifs - a generative model for building families of nucleotide position weight matrices	claim
145	153	Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction	claim
146	153	Automatic symptom name normalization in clinical records of traditional Chinese medicine	claim
147	153	Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data	claim
148	153	PPLook: an automated data mining tool for protein-protein interaction	claim
149	153	Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering	claim
150	153	Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing	claim
151	153	DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules	claim
152	152	Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis	claim
153	152	A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry	claim
154	152	Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks	claim
155	152	Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks	claim
156	152	FITBAR: a web tool for the robust prediction of prokaryotic regulons	claim
157	151	BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets	claim
158	151	Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm	claim
159	151	Misty Mountain clustering: application to fast unsupervised flow cytometry gating	claim
160	151	TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base	claim
161	151	CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies	claim
162	151	Data reduction for spectral clustering to analyze high throughput flow cytometry data	claim
163	151	Using diffusion distances for flexible molecular shape comparison	claim
164	150	AMS 3.0: prediction of post-translational modifications	claim
165	150	Evolutionary rates at codon sites may be used to align sequences and infer protein domain function	claim
166	150	Systematic calibration of a cell signaling network model	claim
167	150	MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure	claim
168	150	Automatic structure classification of small proteins using random forest	claim
169	150	DeltaProt: a software toolbox for comparative genomics	claim
170	150	Kernel based methods for accelerated failure time model with ultra-high dimensional data	claim
171	149	Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes	claim
172	149	KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes	claim
173	149	A multifactorial analysis of obesity as CVD risk factor: Use of neural network based methods in a nutrigenetics context	claim
174	149	S3DB core: a framework for RDF generation and management in bioinformatics infrastructures	claim
175	149	RuleMonkey: software for stochastic simulation of rule-based models	claim
176	148	Calling SNPs without a reference sequence	claim
177	148	Applying unmixing to gene expression data for tumor phylogeny inference	claim
178	148	Analysis of interactions between ribosomal proteins and RNA structural motifs	claim
179	148	Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs	claim
180	148	SKPDB: a structural database of shikimate pathway enzymes	claim
181	147	Indirect two-sided relative ranking: a robust similarity measure for gene expression data	claim
182	147	CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays	claim
183	147	Learning biological network using mutual information and conditional independence	claim
184	147	Automatic detection of anchor points for multiple sequence alignment	claim
185	147	baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data	claim
186	146	A pairwise residue contact area-based mean force potential for discrimination of native protein structure	claim
187	146	Revealing and avoiding bias in semantic similarity scores for protein pairs	claim
188	146	Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery	claim
189	146	On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference	claim
190	146	Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers	claim
191	146	Booly: a new data integration platform	claim
192	145	JCoDA: a tool for detecting evolutionary selection	claim
193	145	WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis	claim
194	145	Clustering metagenomic sequences with interpolated Markov models	claim
195	145	Directionality in protein fold prediction	claim
196	144	Super-sparse principal component analyses for high-throughput genomic data	claim
197	144	Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model	claim
198	144	Finding sRNA generative locales from high-throughput sequencing data with NiBLS	claim
199	144	Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data	claim
200	144	Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data	claim
201	143	Shape based kinetic outlier detection in real-time PCR	claim
202	143	ETE: a python Environment for Tree Exploration	claim
203	143	An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information	claim
204	143	Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images	claim
205	143	Learning gene regulatory networks from only positive and unlabeled data	claim
206	143	A genome alignment algorithm based on compression	claim
207	142	Classification of protein sequences by means of irredundant patterns	claim
208	142	Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity	claim
209	142	pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree	claim
210	142	Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis	claim
211	141	BioPhysConnectoR: Connecting Sequence Information and Biophysical Models	claim
212	141	Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles	claim
213	141	Computing and visually analyzing mutual information in molecular co-evolution	claim
214	141	CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies	claim
215	140	Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection	claim
216	140	An improved machine learning protocol for the identification of correct Sequest search results	claim
217	139	RNAstructure: software for RNA secondary structure prediction and analysis	claim
218	139	PoGO: Prediction of Gene Ontology terms for fungal proteins	claim
219	139	A highly efficient multi-core algorithm for clustering extremely large datasets	claim
220	139	MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains	claim
221	139	A global optimization algorithm for protein surface alignment	claim
222	139	TOPSAN: a collaborative annotation environment for structural genomics	claim
223	139	CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation	claim
224	138	A database and API for variation, dense genotyping and resequencing data	claim
225	138	UFFizi: a generic platform for ranking informative features	claim
226	138	A model-independent approach to infer hierarchical codon substitution dynamics	claim
227	138	Amino acid classification based spectrum kernel fusion for protein subnuclear localization	claim
228	138	Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model	claim
229	137	BS Seeker: precise mapping for bisulfite sequencing	claim
230	137	Biana: a software framework for compiling biological interactions and analyzing networks	claim
231	137	TassDB2 - A comprehensive database of subtle alternative splicing events	claim
232	137	TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses	claim
233	137	Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments	claim
234	137	The ancient history of the structure of ribonuclease P and the early origins of Archaea	claim
235	136	An integrated Bayesian analysis of LOH and copy number data	claim
236	136	Bias correction and Bayesian analysis of aggregate counts in SAGE libraries	claim
237	136	SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale	claim
238	136	The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays	claim
239	136	A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles	claim
240	136	Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces	claim
241	135	HDAPD: a web tool for searching the disease-associated protein structures	claim
242	135	Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization	claim
243	135	Lists2Networks: Integrated analysis of gene/protein lists	claim
244	135	Detecting disease associated modules and prioritizing active genes based on high throughput data	claim
245	135	GIGA: a simple, efficient algorithm for gene tree inference in the genomic age	claim
246	135	Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models	claim
247	135	MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees	claim
248	135	Simple and flexible classification of gene expression microarrays via Swirls and Ripples	claim
249	135	A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis	claim
250	135	Integration and visualization of systems biology data in context of the genome	claim
251	135	Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data	claim
252	134	ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data	claim
253	134	Semi-automated screening of biomedical citations for systematic reviews	claim
254	134	BayesMotif: de novo protein sorting motif discovery from impure datasets	claim
255	134	R-Gada: a fast and flexible pipeline for copy number analysis in association studies	claim
256	134	Localizing triplet periodicity in DNA and cDNA sequences	claim
257	133	Data analysis issues for allele-specific expression using Illumina's GoldenGate assay	claim
258	133	Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis	claim
259	133	New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data	claim
260	133	Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction	claim
261	133	Translog, a web browser for studying the expression divergence of homologous genes	claim
262	133	Learning an enriched representation from unlabeled data for protein-protein interaction extraction	claim
263	133	Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis	claim
264	133	Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins	claim
265	133	Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines	claim
266	133	Initial steps towards a production platform for DNA sequence analysis on the grid	claim
267	132	Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation	claim
268	132	dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment	claim
269	132	Error margin analysis for feature gene extraction	claim
270	132	An interaction-motif-based scoring function for protein-ligand docking	claim
271	132	New statistical potential for quality assessment of protein models and a survey of energy functions	claim
272	132	Consistency, comprehensiveness, and compatibility of pathway databases	claim
273	132	Next generation tools for genomic data generation, distribution, and visualization	claim
274	132	Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection	claim
275	132	Parallel multiplicity and error discovery rate (EDR) in microarray experiments	claim
276	132	Data structures and compression algorithms for high-throughput sequencing technologies	claim
277	131	JISTIC: Identification of Significant Targets in Cancer	claim
278	131	Prediction of epigenetically regulated genes in breast cancer cell lines	claim
279	131	A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems	claim
280	131	FACT: Functional annotation transfer between proteins with similar feature architectures	claim
281	131	A two-step site and mRNA-level model for predicting microRNA targets	claim
282	131	Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity	claim
283	130	The behaviour of random forest permutation-based variable importance measures under predictor correlation	claim
284	130	Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors	claim
285	130	MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification	claim
286	130	Analysis of DNA strand-specific differential expression with high density tiling microarrays	claim
287	130	Knowledge-guided gene ranking by coordinative component analysis	claim
288	130	A statistical approach to finding overlooked genetic associations	claim
289	129	Automatic prediction of catalytic residues by modeling residue structural neighborhood	claim
290	129	LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships	claim
291	129	A temporal precedence based clustering method for gene expression microarray data	claim
292	129	Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison	claim
293	129	Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks	claim
294	129	Geoseq: a tool for dissecting deep-sequencing datasets	claim
295	129	The LabelHash Algorithm for Substructure Matching	claim
296	128	MPprimer: a program for reliable multiplex PCR primer design	claim
297	128	VIGOR, an annotation program for small viral genomes	claim
298	128	Conserved residue clusters at protein-protein interfaces and their use in binding site identification	claim
299	127	SplicerAV: a tool for mining microarray expression data for changes in RNA processing	claim
300	127	Computational prediction of type III secreted proteins from gram-negative bacteria	claim
301	127	PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes	claim
302	127	Deriving enzymatic and taxonomic signatures of metagenomes from short read data	claim
303	126	Cgaln: fast and space-efficient whole-genome alignment	claim
304	126	Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data	claim
305	126	A boosting method for maximizing the partial area under the ROC curve	claim
306	126	Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway	claim
307	126	GeneBrowser 2: an application to explore and identify common biological traits in a set of genes	claim
308	126	Systematic integration of experimental data and models in systems biology	claim
309	126	PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling	claim
310	125	A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins	claim
311	125	Haplotype allelic classes for detecting ongoing positive selection	claim
312	125	In-silico prediction of blood-secretory human proteins using a ranking algorithm	claim
313	125	NeatMap - non-clustering heat map alternatives in R	claim
314	125	Large-scale prediction of protein-protein interactions from structures	claim
315	125	Active machine learning for transmembrane helix prediction	claim
316	125	Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing	claim
317	125	Compartmentalization of the Edinburgh Human Metabolic Network	claim
318	125	Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types	claim
319	125	SNPlotz: a generic genome plot tool to aid the SNP association studies	claim
320	125	ProbFAST: Probabilistic Functional Analysis System Tool	claim
321	124	Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins	claim
322	124	The value of position-specific priors in motif discovery using MEME	claim
323	124	A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra	claim
324	124	GPFrontend and GPGraphics: graphical analysis tools for genetic association studies	claim
325	124	Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures	claim
326	124	A factor model to analyze heterogeneity in gene expression	claim
327	124	Estimating time since infection in early homogeneous HIV-1 samples using a poisson model	claim
328	123	A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction	claim
329	123	Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context	claim
330	123	Decoding HMMs using the k best paths: algorithms and applications	claim
331	123	eGIFT: Mining Gene Information from the Literature	claim
332	123	Computationally efficient flux variability analysis	claim
333	123	An improved classification of G-protein-coupled receptors using sequence-derived features	claim
334	123	Predicting conserved protein motifs with Sub-HMMs	claim
335	122	Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data	claim
336	122	An overview of the CellML API and its implementation	claim
337	122	An automated framework for understanding structural variations in the binding grooves of MHC class II molecules	claim
338	122	Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome	claim
339	122	Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes	claim
340	122	Fast and accurate protein substructure searching with simulated annealing and GPUs	claim
341	122	Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP	claim
342	121	Reconstructing genome trees of prokaryotes using overlapping genes	claim
343	121	A Markov blanket-based method for detecting causal SNPs in GWAS	claim
344	121	Knowledge-based annotation of small molecule binding sites in proteins	claim
345	121	MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences	claim
346	121	Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites	claim
347	121	A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences	claim
348	121	G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration	claim
349	120	Modeling expression quantitative trait loci in data combining ethnic populations	claim
350	120	KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials	claim
351	120	Optimal contact definition for reconstruction of Contact Maps	claim
352	120	Short clones or long clones? A simulation study on the use of paired reads in metagenomics	claim
353	120	AntiBP2: improved version of antibacterial peptide prediction	claim
354	120	Estimating true evolutionary distances under rearrangements, duplications, and losses	claim
355	120	Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology	claim
356	119	Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates	claim
357	119	Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study	claim
358	119	Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics	claim
359	119	A comparison of internal validation techniques for multifactor dimensionality reduction	claim
360	119	The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses	claim
361	118	Testing for mean and correlation changes in microarray experiments: an application for pathway analysis	claim
362	118	Predicting nucleosome positioning using a duration Hidden Markov Model	claim
363	118	Identifying differentially regulated subnetworks from phosphoproteomic data	claim
364	118	Towards realistic benchmarks for multiple alignments of non-coding sequences	claim
365	118	Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests	claim
366	118	From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification	claim
367	118	svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification	claim
368	118	Walk-weighted subsequence kernels for protein-protein interaction extraction	claim
369	118	Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry	claim
370	118	Bacillus anthracis genome organization in light of whole transcriptome sequencing	claim
371	118	Computing H/D-Exchange rates of single residues from data of proteolytic fragments	claim
372	117	Extracting causal relations on HIV drug resistance from literature	claim
373	117	Using jackknife to assess the quality of gene order phylogenies	claim
374	117	Identification of NAD interacting residues in proteins	claim
375	117	Properties and identification of antibiotic drug targets	claim
376	117	Beyond rotamers: a generative, probabilistic model of side chains in proteins	claim
377	117	New decoding algorithms for Hidden Markov Models using distance measures on labellings	claim
378	117	Better score function for peptide identification with ETD MS/MS spectra	claim
379	117	Automatic, context-specific generation of Gene Ontology slims	claim
380	117	MetAssimulo: Simulation of Realistic NMR Metabolic Profiles	claim
381	117	Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities	claim
382	116	permGPU: Using graphics processing units in RNA microarray association studies	claim
383	116	FiGS: a filter-based gene selection workbench for microarray data	claim
384	116	Optimization algorithms for functional deimmunization of therapeutic proteins	claim
385	116	A hybrid approach to protein folding problem integrating constraint programming with local search	claim
386	116	Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences	claim
387	116	SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments	claim
388	115	CONAN: copy number variation analysis software for genome-wide association studies	claim
389	115	Multiconstrained gene clustering based on generalized projections	claim
390	115	Machine learning methods for metabolic pathway prediction	claim
391	115	Integration of multiple data sources to prioritize candidate genes using discounted rating system	claim
392	115	Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver	claim
393	115	Non-coding RNA detection methods combined to improve usability, reproducibility and precision	claim
394	115	Assessment and optimisation of normalisation methods for dual-colour antibody microarrays	claim
395	115	Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data	claim
396	114	Detection of gene orthology from gene co-expression and protein interaction networks	claim
397	114	An integrative modular approach to systematically predict gene-phenotype associations	claim
398	114	Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development	claim
399	113	ProbABEL package for genome-wide association analysis of imputed data	claim
400	113	Gene prioritization and clustering by multi-view text mining	claim
401	113	A classification model for distinguishing copy number variants from cancer-related alterations	claim
402	113	Unifying generative and discriminative learning principles	claim
403	113	Statistical method on nonrandom clustering with application to somatic mutations in cancer	claim
404	113	Efficient protein alignment algorithm for protein search	claim
405	113	Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information	claim
406	113	Improving performance of mammalian microRNA target prediction	claim
407	113	Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse	claim
408	113	Class prediction for high-dimensional class-imbalanced data	claim
409	113	Probabilistic Principal Component Analysis for Metabolomic Data	claim
410	113	SIDEKICK: Genomic data driven analysis and decision-making framework	claim
411	112	Computational identification of rare codons of Escherichia coli based on codon pairs preference	claim
412	112	Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design	claim
413	112	PhenoFam-gene set enrichment analysis through protein structural information	claim
414	112	In silico fragmentation for computer assisted identification of metabolite mass spectra	claim
415	112	TabSQL: a MySQL tool to facilitate mapping user data to public databases	claim
416	112	A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy	claim
417	112	A parameter-adaptive dynamic programming approach for inferring cophylogenies	claim
418	112	Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships	claim
419	112	The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets	claim
420	112	SeqAnt: A web service to rapidly identify and annotate DNA sequence variations	claim
421	111	Comparative performances of DNA barcoding across insect orders	claim
422	111	Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays	claim
423	111	Protein sequences classification by means of feature extraction with substitution matrices	claim
424	111	Cloud computing for comparative genomics	claim
425	111	Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets	claim
426	110	Missing value imputation for epistatic MAPs	claim
427	110	Discovering local patterns of co - evolution: computational aspects and biological examples	claim
428	110	A random effect multiplicative heteroscedastic model for bacterial growth	claim
429	110	On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence	claim
430	110	OLS Dialog: An open-source front end to the Ontology Lookup Service	claim
431	110	Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data	claim
432	110	Concept-based query expansion for retrieving gene related publications from MEDLINE	claim
433	110	TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach	claim
434	110	MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes	claim
435	110	GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing	claim
436	110	Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays	claim
437	109	FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods	claim
438	109	Structural alphabets derived from attractors in conformational space	claim
439	109	Predicting gene function using hierarchical multi-label decision tree ensembles	claim
440	109	Free energy estimation of short DNA duplex hybridizations	claim
441	109	ParallABEL: an R library for generalized parallelization of genome-wide association studies	claim
442	109	Pripper: prediction of caspase cleavage sites from whole proteomes	claim
443	109	Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model	claim
444	109	Functional characterization and topological modularity of molecular interaction networks	claim
445	109	Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression	claim
446	109	Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment	claim
447	108	Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes	claim
448	108	Assembly complexity of prokaryotic genomes using short reads	claim
449	108	Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays	claim
450	108	A genetic ensemble approach for gene-gene interaction identification	claim
451	108	Predicting changes in protein thermostability brought about by single- or multi-site mutations	claim
452	108	An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs	claim
453	108	Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm	claim
454	108	iGTP: A software package for large-scale gene tree parsimony analysis	claim
455	108	BIGSdb: Scalable analysis of bacterial genome variation at the population level	claim
456	108	Prediction of RNA secondary structure by maximizing pseudo-expected accuracy	claim
457	108	Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset	claim
458	107	Semantic annotation of morphological descriptions: an overall strategy	claim
459	107	TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets	claim
460	107	Conditional random pattern model for copy number aberration detection	claim
461	107	Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network	claim
462	107	Interaction prediction and classification of PDZ domains	claim
463	106	A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes	claim
464	106	Multiple structure alignment and consensus identification for proteins	claim
465	106	Selection of optimal reference genes for normalization in quantitative RT-PCR	claim
466	106	TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays	claim
467	106	Predicting MHC class I epitopes in large datasets	claim
468	106	A novel approach for haplotype-based association analysis using family data	claim
469	106	Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data	claim
470	105	GWAMA: software for genome-wide association meta-analysis	claim
471	105	Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach	claim
472	105	Effects of scanning sensitivity and multiple scan algorithms on microarray data quality	claim
473	105	A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction	claim
474	105	Comparison of PGH2 binding site in prostaglandin synthases	claim
475	105	Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement	claim
476	105	Predicting phenotypic traits of prokaryotes from protein domain frequencies	claim
477	105	The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems	claim
478	104	Parameters for accurate genome alignment	claim
479	104	Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections	claim
480	104	A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants	claim
481	104	Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies	claim
482	104	A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization	claim
483	104	Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes	claim
484	104	Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy	claim
485	104	Bidirectional best hit r-window gene clusters	claim
486	104	FragViz: visualization of fragmented networks	claim
487	104	A method for automatically extracting infectious disease-related primers and probes from the literature	claim
488	104	A systematic study of genome context methods: calibration, normalization and combination	claim
489	103	A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements	claim
490	103	Nonparametric methods for the analysis of single-color pathogen microarrays	claim
491	103	Detecting internally symmetric protein structures	claim
492	103	Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information	claim
493	103	MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues	claim
494	103	Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis	claim
495	103	PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship	claim
496	103	Predicting the protein-protein interactions using primary structures with predicted protein surface	claim
497	102	Alignment and clustering of phylogenetic markers - implications for microbial diversity studies	claim
498	102	Identification of recurrent regions of copy-number variants across multiple individuals	claim
499	102	Missing genes in the annotation of prokaryotic genomes	claim
500	102	SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes	claim
501	102	Quantized correlation coefficient for measuring reproducibility of ChIP-chip data	claim
502	102	Peptide binding predictions for HLA DR, DP and DQ molecules	claim
503	102	Predicting protein-protein interactions in unbalanced data using the primary structure of proteins	claim
504	101	Enrichment of homologs in insignificant BLAST hits by co-complex network alignment	claim
505	101	Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks	claim
506	101	Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model	claim
507	101	Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots	claim
508	101	Hidden Markov model speed heuristic and iterative HMM search procedure	claim
509	100	Scaffold filling, contig fusion and comparative gene order inference	claim
510	100	Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays	claim
511	100	MapMi: automated mapping of microRNA loci	claim
512	100	Partitioning of copy-number genotypes in pedigrees	claim
513	100	A robust method for estimating gene expression states using Affymetrix microarray probe level data	claim
514	100	Trimming of mammalian transcriptional networks using network component analysis	claim
515	100	Using genomic signatures for HIV-1 sub-typing	claim
516	100	Efficiency clustering for low-density microarrays and its application to QPCR	claim
517	100	New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size	claim
518	99	Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates	claim
519	99	Shared probe design and existing microarray reanalysis using PICKY	claim
520	99	Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays	claim
521	99	A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling	claim
522	99	Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)	claim
523	98	miRMaid: a unified programming interface for microRNA data resources	claim
524	98	An optimized TOPS+ comparison method for enhanced TOPS models	claim
525	98	Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents	claim
526	98	Learning to predict expression efficacy of vectors in recombinant protein production	claim
527	98	Prediction of protein structural classes for low-homology sequences based on predicted secondary structure	claim
528	98	A semi-nonparametric mixture model for selecting functionally consistent proteins	claim
529	97	Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques	claim
530	97	Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach	claim
531	97	SeqRate: sequence-based protein folding type classification and rates prediction	claim
532	97	Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster	claim
533	97	Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins	claim
534	97	Preprocessing of gene expression data by optimally robust estimators	claim
535	97	A semi-parametric Bayesian model for unsupervised differential co-expression analysis	claim
536	96	A statistical framework for differential network analysis from microarray data	claim
537	96	Incorporating gene co-expression network in identification of cancer prognosis markers	claim
538	96	sdef: an R package to synthesize lists of significant features in related experiments	claim
539	96	The Protein-DNA Interface database	claim
540	96	FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data	claim
541	96	ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data	claim
542	96	ModuleOrganizer: detecting modules in families of transposable elements	claim
543	96	QTLminer: identifying genes regulating quantitative traits	claim
544	96	OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data	claim
545	96	Growth hormone induces proliferation in the zebrafish inner ear	claim
546	95	An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data	claim
547	95	Quantifying the relationship between sequence and three-dimensional structure conservation in RNA	claim
548	95	Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets	claim
549	95	Spatio-structural granularity of biological material entities	claim
550	95	Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso	claim
551	95	Heuristics for the inversion median problem	claim
552	95	Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions	claim
553	95	EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results	claim
554	94	MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement	claim
555	94	A high-throughput pipeline for the design of real-time PCR signatures	claim
556	94	Physicochemical property distributions for accurate and rapid pairwise protein homology detection	claim
557	94	A comparative study of conservation and variation scores	claim
558	94	Comparison study of microarray meta-analysis methods	claim
559	93	Hybridization thermodynamics of NimbleGen Microarrays	claim
560	93	JunctionViewer: customizable annotation software for repeat-rich genomic regions	claim
561	93	HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data	claim
562	93	webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser	claim
563	92	Integrating gene expression and GO classification for PCA by preclustering	claim
564	92	YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast	claim
565	92	HORI: a web server to compute Higher Order Residue Interactions in protein structures	claim
566	91	Algorithm-driven Artifacts in median polish summarization of Microarray data	claim
567	91	Ranked retrieval of Computational Biology models	claim
568	91	Coverage statistics for sequence census methods	claim
569	91	Washing scaling of GeneChip microarray expression	claim
570	90	Local alignment of generalized k-base encoded DNA sequence	claim
571	90	Using caching and optimization techniques to improve performance of the Ensembl website	claim
572	90	PuTmiR: A database for extracting neighboring transcription factors of human microRNAs	claim
573	89	Detection of gene pathways with predictive power for breast cancer prognosis	claim
574	89	Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets	claim
575	89	Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays	claim
576	89	Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS)	claim
577	89	Leukocyte Nucleus Segmentation and Nucleus Lobe Counting	claim
578	89	Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study	claim
579	88	MetaBar - a tool for consistent contextual data acquisition and standards compliant submission	claim
580	88	FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium	claim
581	88	Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information	claim
582	88	Robust probabilistic superposition and comparison of protein structures	claim
583	88	Proteome scanning to predict PDZ domain interactions using support vector machines	claim
584	88	Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010	claim
585	88	Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection	claim
586	88	The UofL Microarray Facility: merger and new location	claim
587	87	poolMC: Smart pooling of mRNA samples in microarray experiments	claim
588	87	Prodigal: prokaryotic gene recognition and translation initiation site identification	claim
589	87	Relations as patterns: bridging the gap between OBO and OWL	claim
590	87	Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model	claim
591	87	A fast and robust hepatocyte quantification algorithm including vein processing	claim
592	86	Mining protein loops using a structural alphabet and statistical exceptionality	claim
593	86	ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite	claim
594	86	A novel approach to simulate gene-environment interactions in complex diseases	claim
595	86	Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective	claim
596	86	An automatic method for identifying surface proteins in bacteria: SLEP	claim
597	86	Fast motif recognition via application of statistical thresholds	claim
598	86	Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism	claim
599	86	An exploratory data analysis method to reveal modular latent structures in high-throughput data	claim
600	86	The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand	claim
601	86	Identifying potential drugs that induce QT prolongation using electronic medical records	claim
602	85	Robust test method for time-course microarray experiments	claim
603	84	A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis	claim
604	84	Word add-in for ontology recognition: semantic enrichment of scientific literature	claim
605	84	Artificial and natural duplicates in pyrosequencing reads of metagenomic data	claim
606	84	Testing the additional predictive value of high-dimensional molecular data	claim
607	84	An integrated analysis of molecular aberrations in NCI-60 cell lines	claim
608	84	Subsystems-based servers for rapid annotation of genomes and metagenomes	claim
609	83	An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking	claim
610	83	Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins	claim
611	82	Detecting microRNA activity from gene expression data	claim
612	82	Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data	claim
613	82	SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system	claim
614	82	Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition	claim
615	82	SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data	claim
616	82	TESTLoc: protein subcellular localization prediction from EST data	claim
617	81	Discrete wavelet transform de-noising in eukaryotic gene splicing	claim
618	81	Hit integration for identifying optimal spaced seeds	claim
619	81	Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling without Replicates	claim
620	80	A benchmark for statistical microarray data analysis that preserves actual biological and technical variance	claim
621	80	Power and sample size estimation in microarray studies	claim
622	80	An ontology-based search engine for protein-protein interactions	claim
623	80	A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages	claim
624	80	Sampling the conformation of protein surface residues for flexible protein docking	claim
625	79	Gene bi-targeting by viral and human miRNAs	claim
626	79	Characterization of phylogenetic networks with NetTest	claim
627	79	Structure prediction for the helical skeletons detected from the low resolution protein density map	claim
628	79	A comparison of probe-level and probeset models for small-sample gene expression data	claim
629	78	The curvHDR method for gating flow cytometry samples	claim
630	78	Extending pathways and processes using molecular interaction networks to analyse cancer genome data	claim
631	77	web cellHTS2: A web-application for the analysis of high-throughput screening data	claim
632	77	rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data	claim
633	76	Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems	claim
634	76	Validation and characterization of DNA microarray gene expression data distribution and associated moments	claim
635	75	Context dependent substitution biases vary within the human genome	claim
636	74	vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments	claim
637	74	Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry	claim
638	74	A weighted q-gram method for glycan structure classification	claim
639	72	Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies	claim
640	72	Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials	claim
641	71	Genome rearrangements with duplications	claim
642	71	Enabling proteomics-based identification of human cancer variations	claim
643	71	High-throughput sequencing of the DBA/2J mouse genome	claim
644	70	The Text-mining based PubChem Bioassay neighboring analysis	claim
645	69	BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server	claim
646	69	OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs	claim
647	69	Extracting the abstraction pyramid from complex networks	claim
648	69	Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency	claim
649	68	Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration	claim
650	66	miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature	claim
651	66	BALL - biochemical algorithms library 1.3	claim
652	65	VIPR: A probabilistic algorithm for analysis of microbial detection microarrays	claim
653	64	State of the art: refinement of multiple sequence alignments	claim
654	64	HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data	claim
655	64	Multivariate Hawkes process models of the occurrence of regulatory elements	claim
656	63	*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants	claim
657	62	Forward-time simulation of realistic samples for genome-wide association studies	claim
658	62	Speeding up tandem mass spectrometry-based database searching by longest common prefix	claim
659	60	Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome	claim
660	58	Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)	claim
661	58	Efficient Bayesian approach for multilocus association mapping including gene-gene interactions	claim
662	57	Predicting Bevirimat resistance of HIV-1 from genotype	claim
663	56	Enhanced CellClassifier: a multi-class classification tool for microscopy images	claim
664	55	Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline	claim
665	55	Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm	claim
666	55	The structural and content aspects of abstracts versus bodies of full text journal articles are different	claim
667	55	Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development	claim
668	54	Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique	claim
669	53	SFSSClass: an integrated approach for miRNA based tumor classification	claim
670	53	Predicting protein functions by relaxation labelling protein interaction network	claim
671	50	Scanner calibration revisited	claim
672	48	Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information	claim
673	47	The identification of informative genes from multiple datasets with increasing complexity	claim

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