BIOINFORMATICS 2007

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BIOINFORMATICS
2007

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Context-dependent clustering for dynamic cellular state modeling of microarray gene expression

14 years 17 days ago

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Motivation: High-throughput expression profiling allows researchers to study gene activities globally. Genes with similar expression profiles are likely to encode proteins that ma...

Shinsheng Yuan, Ker-Chau Li

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Id	Views	Title	Status

1	195	Context-dependent clustering for dynamic cellular state modeling of microarray gene expression	claim
2	190	Towards clustering of incomplete microarray data without the use of imputation	claim
3	161	Functional evaluation of domain-domain interactions and human protein interaction networks	claim
4	151	A new protein-protein docking scoring function based on interface residue properties	claim
5	137	Annotation-based distance measures for patient subgroup discovery in clinical microarray studies	claim
6	127	De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio	claim
7	127	A review of feature selection techniques in bioinformatics	claim
8	126	A 3D pattern matching algorithm for DNA sequences	claim
9	123	A comparative genome approach to marker ordering	claim
10	117	Mining biological networks for unknown pathways	claim
11	107	SwS: a solvation web service for nucleic acids	claim
12	102	OmicBrowse: a browser of multidimensional omics annotations	claim
13	100	Boolean dynamics of genetic regulatory networks inferred from microarray time series data	claim
14	98	PIP: a database of potential intron polymorphism markers	claim
15	95	BiVisu: software tool for bicluster detection and visualization	claim
16	93	Unsupervised feature selection under perturbations: meeting the challenges of biological data	claim
17	91	Carbon-fate maps for metabolic reactions	claim
18	91	ARIA2: Automated NOE assignment and data integration in NMR structure calculation	claim
19	90	Identifying clusters of functionally related genes in genomes	claim
20	90	HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling	claim
21	89	PhylArray: phylogenetic probe design algorithm for microarray	claim
22	88	Maximum likelihood of phylogenetic networks	claim
23	88	Detecting high-order interactions of single nucleotide polymorphisms using genetic programming	claim
24	87	LFM-Pro: a tool for detecting significant local structural sites in proteins	claim
25	86	TAPPA: topological analysis of pathway phenotype association	claim
26	85	R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses	claim
27	85	A structural alignment kernel for protein structures	claim
28	83	Exploring biological network structure using exponential random graph models	claim
29	82	TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities	claim
30	81	SGN Sim, a Stochastic Genetic Networks Simulator	claim
31	79	Hierarchical tree snipping: clustering guided by prior knowledge	claim
32	78	Computing the maximum similarity bi-clusters of gene expression data	claim
33	77	AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets	claim
34	77	MSQT for choosing SNP assays from multiple DNA alignments	claim
35	76	Optimization of primer design for the detection of variable genomic lesions in cancer	claim
36	76	RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment	claim
37	75	Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat	claim
38	75	Multiple spaced seeds for homology search	claim
39	74	Simultaneous alignment and annotation of cis-regulatory regions	claim
40	73	Assortative mixing in Protein Contact Networks and protein folding kinetics	claim
41	72	The qualitative and time-dependent character of spatial relations in biomedical ontologies	claim
42	68	Estimating p-values in small microarray experiments	claim
43	68	Discovery of microRNA-mRNA modules via population-based probabilistic learning	claim
44	68	Unsupervised segmentation of continuous genomic data	claim
45	67	Co-evolving residues in membrane proteins	claim
46	66	Genomic sweeping for hypermethylated genes	claim
47	66	SNPassoc: an R package to perform whole genome association studies	claim
48	66	Gene expression network analysis and applications to immunology	claim
49	66	MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing	claim
50	65	Clustering threshold gradient descent regularization: with applications to microarray studies	claim
51	65	meta-PPISP: a meta web server for protein-protein interaction site prediction	claim
52	65	Functional profiling of microarray experiments using text-mining derived bioentities	claim
53	63	Computing exact P-values for DNA motifs	claim
54	63	SciRoKo: a new tool for whole genome microsatellite search and investigation	claim
55	62	Improving gene quantification by adjustable spot-image restoration	claim
56	62	Tools for visually exploring biological networks	claim
57	61	Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation	claim
58	61	Two-stage designs applying methods differing in costs	claim
59	61	Computational methods for diffusion-influenced biochemical reactions	claim
60	59	SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays	claim
61	59	Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects	claim
62	59	COPYCAT : cophylogenetic analysis tool	claim
63	59	Visualization-based cancer microarray data classification analysis	claim
64	58	Identifying bacterial genes and endosymbiont DNA with Glimmer	claim
65	58	Extensions to gene set enrichment	claim
66	58	IGG: A tool to integrate GeneChips for genetic studies	claim
67	58	Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study	claim
68	57	Extending assembly of short DNA sequences to handle error	claim
69	57	Bayesian modelling of shared gene function	claim
70	56	Selection and validation of normalization methods for c-DNA microarrays using within-array replications	claim
71	55	Using an alignment of fragment strings for comparing protein structures	claim
72	55	Evolutionary analysis of enzymes using Chisel	claim
73	54	The impact of function perturbations in Boolean networks	claim
74	54	The evolutionary forest algorithm	claim
75	53	Genetdes: automatic design of transcriptional networks	claim
76	53	Creating protein models from electron-density maps using particle-filtering methods	claim
77	53	Wordom: a program for efficient analysis of molecular dynamics simulations	claim
78	53	beadarray: R classes and methods for Illumina bead-based data	claim
79	53	Pepitope: epitope mapping from affinity-selected peptides	claim
80	52	PrepMS: TOF MS data graphical preprocessing tool	claim
81	52	A novel non-overlapping bi-clustering algorithm for network generation using living cell array data	claim
82	52	Annotation of selection strengths in viral genomes	claim
83	52	Four-Body Scoring Function for Mutagenesis	claim
84	52	Comparative modeling without implicit sequence alignments	claim
85	52	Bioinformatics software for biologists in the genomics era	claim
86	51	Tandem repeats over the edit distance	claim
87	50	Boltzmann probability of RNA structural neighbors and riboswitch detection	claim
88	50	Exploiting sample variability to enhance multivariate analysis of microarray data	claim
89	50	Con-Struct Map: a comparative contact map analysis tool	claim
90	49	msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots	claim
91	49	Clustal W and Clustal X version 2.0	claim
92	49	Constraint-based functional similarity of metabolic genes: going beyond network topology	claim
93	48	GENOME: a rapid coalescent-based whole genome simulator	claim
94	48	Data-based identifiability analysis of non-linear dynamical models	claim
95	47	SNPchip: R classes and methods for SNP array data	claim
96	47	I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition	claim
97	46	Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates	claim
98	45	Microarray blob-defect removal improves array analysis	claim
99	44	On the hierarchical classification of G protein-coupled receptors	claim
100	42	Multiple alignment by sequence annealing	claim
101	42	Peak selection from MALDI-TOF mass spectra using ant colony optimization	claim
102	42	STOP: searching for transcription factor motifs using gene expression	claim
103	42	Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins	claim
104	42	CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data	claim
105	42	Query-driven module discovery in microarray data	claim
106	41	Persistent voids: a new structural metric for membrane fusion	claim
107	38	Robustness analysis and tuning of synthetic gene networks	claim
108	38	Meta-analysis of gene expression data: a predictor-based approach	claim
109	38	A quantitative model for linking two disparate sets of articles in MEDLINE	claim
110	37	An error model for protein quantification	claim
111	37	Steady-state expression of self-regulated genes	claim
112	33	Murlet: a practical multiple alignment tool for structural RNA sequences	claim

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