BIOINFORMATICS 2005

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BIOINFORMATICS
2005

208views more BIOINFORMATICS 2005»

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices

13 years 5 months ago

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Dan Tsafrir, Ilan Tsafrir, Liat Ein-Dor, Or Zuk, D...

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Id	Views	Title	Status

1	208	Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices	claim
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3	152	Intervention in context-sensitive probabilistic Boolean networks	claim
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34	72	Use of within-array replicate spots for assessing differential expression in microarray experiments	claim
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38	71	Semi-supervised protein classification using cluster kernels	claim
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40	70	Genetic algorithm-based optimization of hydrophobicity tables	claim
41	69	Statistical analysis of domains in interacting protein pairs	claim
42	68	Classification of microarrays to nearest centroids	claim
43	68	GOR V server for protein secondary structure prediction	claim
44	68	Identifying genes from up-down properties of microarray expression series	claim
45	68	Divide-and-conquer approach for the exemplar breakpoint distance	claim
46	68	Efficient sorting of genomic permutations by translocation, inversion and block interchange	claim
47	66	A semantic analysis of the annotations of the human genome	claim
48	65	Predicting a set of minimal free energy RNA secondary structures common to two sequences	claim
49	65	Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction	claim
50	65	Similarity of position frequency matrices for transcription factor binding sites	claim
51	65	PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data	claim
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53	64	Association mapping and fine mapping with TreeLD	claim
54	63	DNA assembly with gaps (Dawg): simulating sequence evolution	claim
55	63	Microarray data mining with visual programming	claim
56	63	A fuzzy guided genetic algorithm for operon prediction	claim
57	63	Motif-based protein ranking by network propagation	claim
58	63	Haplotype reconstruction from SNP fragments by minimum error correction	claim
59	63	STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures	claim
60	63	LS Bound based gene selection for DNA microarray data	claim
61	63	Reconstructing biological networks using conditional correlation analysis	claim
62	62	BlastAlign: a program that uses blast to align problematic nucleotide sequences	claim
63	62	Haplotype-based linkage disequilibrium mapping via direct data mining	claim
64	62	Gene finding for the helical cytokines	claim
65	62	The Los Alamos hepatitis C sequence database	claim
66	61	Identification and measurement of neighbor-dependent nucleotide substitution processes	claim
67	61	DNA-BAR: distinguisher selection for DNA barcoding	claim
68	61	VitaPad: visualization tools for the analysis of pathway data	claim
69	61	A boosting approach for motif modeling using ChIP-chip data	claim
70	61	DPRml: distributed phylogeny reconstruction by maximum likelihood	claim
71	60	ProtTest: selection of best-fit models of protein evolution	claim
72	60	Biomarker discovery in microarray gene expression data with Gaussian processes	claim
73	60	Noise-induced cooperative behavior in a multicell system	claim
74	58	Resolving abbreviations to their senses in Medline	claim
75	58	Exploring the diversity of complex metabolic networks	claim
76	58	RDP2: recombination detection and analysis from sequence alignments	claim
77	57	A score matrix to reveal the hidden links in glycans	claim
78	57	A new measure of the robustness of biochemical networks	claim
79	57	GLAD: a system for developing and deploying large-scale bioinformatics grid	claim
80	57	Network constrained clustering for gene microarray data	claim
81	57	ProViz: protein interaction visualization and exploration	claim
82	56	DEPD: a novel database for differentially expressed proteins	claim
83	56	Integration of metabolic networks and gene expression in virtual reality	claim
84	55	GOChase: correcting errors from Gene Ontology-based annotations for gene products	claim
85	53	Pairwise alignment incorporating dipeptide covariation	claim
86	53	A periodicity analysis of transmembrane helices	claim
87	52	Statistical detection of chromosomal homology using shared-gene density alone	claim
88	52	Modeling of signal-response cascades using decision tree analysis	claim
89	52	Mapping PDB chains to UniProtKB entries	claim
90	51	The mutated subsequence problem and locating conserved genes	claim
91	51	Fold recognition by combining profile-profile alignment and support vector machine	claim
92	51	Correlation of amino acid preference and mammalian viral genome type	claim
93	51	SABmark- a benchmark for sequence alignment that covers the entire known fold space	claim
94	51	PDBML: the representation of archival macromolecular structure data in XML	claim
95	50	Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum	claim
96	49	SuperDrug: a conformational drug database	claim
97	49	MACiE: a database of enzyme reaction mechanisms	claim
98	49	Improving genome annotations using phylogenetic profile anomaly detection	claim
99	49	A friendly statistics package for microarray analysis	claim
100	49	Data pre-processing in liquid chromatography-mass spectrometry-based proteomics	claim
101	48	MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations	claim
102	48	A new progressive-iterative algorithm for multiple structure alignment	claim
103	48	Evaluation of the gene-specific dye bias in cDNA microarray experiments	claim
104	48	EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology	claim
105	47	PIBASE: a comprehensive database of structurally defined protein interfaces	claim
106	47	DIG - a system for gene annotation and functional discovery	claim
107	47	Selecton: a server for detecting evolutionary forces at a single amino-acid site	claim
108	47	Stepwise detection of recombination breakpoints in sequence alignments	claim
109	47	DisProt: a database of protein disorder	claim
110	46	Clann: investigating phylogenetic information through supertree analyses	claim
111	46	Concept-based annotation of enzyme classes	claim
112	46	A two-stage normalization method for partially degraded mRNA microarray data	claim
113	46	Non-additivity in protein-DNA binding	claim
114	46	Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap	claim
115	46	PROFcon: novel prediction of long-range contacts	claim
116	46	Pcons5: combining consensus, structural evaluation and fold recognition scores	claim
117	45	Predicting protein functions with message passing algorithms	claim
118	45	Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS	claim
119	45	MACAT - microarray chromosome analysis tool	claim
120	45	Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins	claim
121	44	Haploview: analysis and visualization of LD and haplotype maps	claim
122	44	A new algorithm for detecting low-complexity regions in protein sequences	claim
123	43	A parallel graph decomposition algorithm for DNA sequencing with nanopores	claim
124	43	MEPD: a resource for medaka gene expression patterns	claim
125	41	Protein structure alignment by deterministic annealing	claim
126	41	Structural drift: a possible path to protein fold change	claim
127	41	Dual multiple change-point model leads to more accurate recombination detection	claim
128	40	A word-oriented approach to alignment validation	claim
129	40	Weighted analysis of microarray gene expression using maximum-likelihood	claim
130	40	RBT - a tool for building refined Buneman trees	claim
131	38	DWE: Discriminating Word Enumerator	claim
132	38	Improving conformational searches by geometric screening	claim
133	37	TileMap: create chromosomal map of tiling array hybridizations	claim
134	37	HESAS: HERVs Expression and Structure Analysis System	claim
135	31	HyPhy: hypothesis testing using phylogenies	claim

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