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2011

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Clinical Synopsis Search in OMIM

12 years 11 months ago

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Background: The OMIM database is a tool used daily by geneticists. Syndrome pages include a Clinical Synopsis section containing a list of known phenotypes comprising a clinical s...

Raphael Cohen, Avitan Gefen, Michael Elhadad, Ohad...

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Id	Views	Title	Status

1	371	Clinical Synopsis Search in OMIM	claim
2	328	Detection of viral sequence fragments of HIV-1 subfamilies yet unknown	claim
3	327	VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R	claim
4	304	Phenotype Recognition with Combined Features and Random Subspace Classifier Ensemble	claim
5	296	SNPPicker: High quality tag SNP selection across multiple populations	claim
6	290	Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms	claim
7	290	Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform	claim
8	288	Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface	claim
9	287	RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis	claim
10	283	Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies	claim
11	281	SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects	claim
12	278	NeurphologyJ: an automatic neuronal morphology quantification method and its application in pharmacological discovery	claim
13	275	Meta-analysis of gene expression microarrays with missing replicates	claim
14	273	Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure	claim
15	273	Protein alignment algorithms with an efficient backtracking routine on multiple GPUs	claim
16	272	Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling	claim
17	271	PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data	claim
18	269	pROC: an open-source package for R and S+ to analyze and compare ROC curves	claim
19	268	GCOD - GeneChip Oncology Database	claim
20	268	A novel approach to the clustering of microarray data via nonparametric density estimation	claim
21	267	OrthoInspector: comprehensive orthology analysis and visual exploration	claim
22	266	MINE: Module Identification in NEtworks	claim
23	265	Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and STRUCTURE	claim
24	262	Sequential Interim Analyses of Survival Data in DNA Microarray Experiments	claim
25	262	Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data	claim
26	262	Structator: fast index-based search for RNA sequence-structure patterns	claim
27	261	Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology	claim
28	260	LabKey Server: An open source platform for scientific data integration, analysis and collaboration	claim
29	258	NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins	claim
30	256	Cell Subset Prediction for Blood Genomic Studies	claim
31	255	Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines	claim
32	255	A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis	claim
33	254	Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities	claim
34	253	Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community	claim
35	253	A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models	claim
36	253	The dChip survival analysis module for microarray data	claim
37	253	Screening synteny blocks in pairwise genome comparisons through integer programming	claim
38	252	CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes	claim
39	252	Implementation of Force Distribution Analysis for Molecular Dynamics simulations	claim
40	252	A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies	claim
41	251	CNV-WebStore: Online CNV Analysis, Storage and Interpretation	claim
42	251	Motif-guided sparse decomposition of gene expression data for regulatory module identification	claim
43	249	Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in Breast Cancer	claim
44	249	Gene set analysis for longitudinal gene expression data	claim
45	248	Learning genetic epistasis using Bayesian network scoring criteria	claim
46	248	GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models	claim
47	245	Computable visually observed phenotype ontological framework for plants	claim
48	242	Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies	claim
49	241	A Platform for Processing Expression of Short Time Series (PESTS)	claim
50	241	Bio: : Phylo - phyloinformatic analysis using Perl	claim
51	240	A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment	claim
52	239	PileLine: a toolbox to handle genome position information in next-generation sequencing studies	claim
53	239	Efficient alignment of pyrosequencing reads for re-sequencing applications	claim
54	238	N-gram analysis of 970 microbial organisms reveals presence of biological language models	claim
55	238	Appearance frequency modulated gene set enrichment testing	claim
56	237	HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods	claim
57	236	Logical Development of the Cell Ontology	claim
58	235	Identifying hypermethylated CpG islands using a quantile regression model	claim
59	235	ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry	claim
60	235	PRIN, a predicted rice interactome network	claim
61	234	SNP-based pathway enrichment analysis for genome-wide association studies	claim
62	234	Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences	claim
63	233	PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination	claim
64	233	dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation	claim
65	231	Outer membrane proteins can be simply identified using secondary structure element alignment	claim
66	231	Clustering gene expression data with a penalized graph-based metric	claim
67	231	Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation	claim
68	230	Pathway-based analysis using reduced gene subsets in genome-wide association studies	claim
69	230	DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning	claim
70	230	Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis	claim
71	229	Tiling array data analysis: a multiscale approach using wavelets	claim
72	229	DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI	claim
73	229	PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment	claim
74	229	The PathOlogist: An Automated Tool for Pathway-Centric Analysis	claim
75	228	A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping	claim
76	227	Flexible taxonomic assignment of ambiguous sequencing reads	claim
77	227	nocoRNAc: Characterization of non-coding RNAs in prokaryotes	claim
78	227	CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation	claim
79	227	To aggregate or not to aggregate high-dimensional classifiers	claim
80	226	easyDAS: Automatic creation of DAS servers	claim
81	226	SAQC: SNP array quality control	claim
82	226	The Proteogenomic Mapping Tool	claim
83	226	Evaluating methods for ranking differentially expressed genes applied to MicroArray Quality Control data	claim
84	225	Classification of viral zoonosis through receptor pattern analysis	claim
85	225	Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states	claim
86	224	Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars	claim
87	224	PeakRanger: A cloud-enabled peak caller for ChIP-seq data	claim
88	223	iPhy: an integrated phylogenetic workbench for supermatrix analyses	claim
89	223	AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS	claim
90	222	Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset	claim
91	221	Multivariate analysis of microarray data: differential expression and differential connection	claim
92	221	RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles	claim
93	221	Wavelet-based identification of DNA focal genomic aberrations from single nucleotide polymorphism arrays	claim
94	221	PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum	claim
95	221	FFCA: a feasibility-based method for flux coupling analysis of metabolic networks	claim
96	220	Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets	claim
97	219	Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library	claim
98	219	Genotype calling in tetraploid species from bi-allelic marker data using mixture models	claim
99	218	A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines	claim
100	218	Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis	claim
101	218	A mutation degree model for the identification of transcriptional regulatory elements	claim
102	217	Multiclass classification of microarray data samples with a reduced number of genes	claim
103	216	An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses	claim
104	215	Predicting functionally important SNP classes based on negative selection	claim
105	215	Gene ontology based transfer learning for protein subcellular localization	claim
106	215	AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm	claim
107	215	ENGINES: exploring single nucleotide variation in entire human genomes	claim
108	215	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data	claim
109	215	Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis	claim
110	213	Hierarchical graphs for rule-based modeling of biochemical systems	claim
111	212	Estimation of allele frequency and association mapping using next-generation sequencing data	claim
112	211	PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome	claim
113	210	A quality metric for homology modeling: the H-factor	claim
114	210	Simulated evolution applied to study the genetic code optimality using a model of codon reassignments	claim
115	209	The Biomedical Discourse Relation Bank	claim
116	208	Smith-Waterman Peak Alignment for Comprehensive Two-dimensional Gas Chromatography Mass Spectrometry	claim
117	207	MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model	claim
118	206	Context-dependent transcriptional regulations between signal transduction pathways	claim
119	206	The impact of quantitative optimization of hybridization conditions on gene expression analysis	claim
120	205	Was the Scanner Calibration Slide Used for Its Intended Purpose?	claim
121	205	Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing	claim
122	204	Network based transcription factor analysis of regenerating axolotl limbs	claim
123	204	FIND: A new software tool and development platform for enhanced multicolor flow analysis	claim
124	204	New Words in Human Mutagenesis	claim
125	203	ASPDock: protein-protein docking algorithm using atomic solvation parameters model	claim
126	202	R2R - software to speed the depiction of aesthetic consensus RNA secondary structures	claim
127	202	Tree Pruner: An efficient tool for selecting data from a biased genetic database	claim
128	202	Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?	claim
129	202	BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs	claim
130	201	A theoretical entropy score as a single value to express inhibitor selectivity	claim
131	200	Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips	claim
132	199	Bioinformatics analysis of disordered proteins in prokaryotes	claim
133	198	Empirical Bayesian models for analysing molecular serotyping microarrays	claim
134	198	Robust joint analysis allowing for model uncertainty in two-stage genetic association studies	claim
135	197	MicroSyn: A user friendly tool for detection of microsynteny in a gene family	claim
136	197	A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data	claim
137	197	Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs	claim
138	195	Systematic error detection in experimental high-throughput screening	claim
139	195	A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data	claim
140	195	Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics	claim
141	195	LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures	claim
142	194	MRCQuant- an accurate LC/MS relative isotopic quantification algorithm on TOF instruments	claim
143	194	Determinants of Antigenicity and Specificity in immune response for Protein Sequences	claim
144	193	Estimating developmental states of tumors and normal tissues using a linear time-ordered model	claim
145	193	Improving pan-genome annotation using whole genome multiple alignment	claim
146	192	A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression	claim
147	192	RegNetB: Predicting Relevant Regulator-Gene Relationships in Localized Prostate Tumor Samples	claim
148	191	Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression	claim
149	191	RAG: An Update to the RNA-As-Graphs Resource	claim
150	191	SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data	claim
151	190	GC/MS Based Metabolomics: Development of a Data Mining System for Metabolite Identification by using Soft Independent Modeling of Class Analogy (SIMCA)	claim
152	189	Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays	claim
153	188	Investigating the effect of paralogs on microarray gene-set analysis	claim
154	188	Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles	claim
155	188	Ultra-fast sequence clustering from similarity networks with SiLiX	claim
156	187	Revision history aware repositories of computational models of biological systems	claim
157	187	Detection of Lineage-Specific Evolutionary Changes among Primate Species	claim
158	186	Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions	claim
159	186	CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis	claim
160	185	A user-friendly web portal for T-Coffee on supercomputers	claim
161	185	Inference of Chromosome-Specific Copy Numbers Using Population Haplotypes	claim
162	184	MixtureTree: a program for constructing phylogeny	claim
163	182	Enhancements to the ADMIXTURE Algorithm for Individual Ancestry Estimation	claim
164	181	Shape-based peak identification for ChIP-Seq	claim
165	181	Removing Noise From Pyrosequenced Amplicons	claim
166	180	Detection of recurrent rearrangement breakpoints from copy number data	claim
167	179	CAPL: an efficient association software package using family and case-control data and accounting for population stratification	claim
168	179	In-silico prediction of disorder content using hybrid sequence representation	claim
169	177	Taxon ordering in phylogenetic trees: a workbench test	claim
170	176	Combining gene prediction methods to improve metagenomic gene annotation	claim
171	175	ChIPseqR: Analysis of ChIP-seq Experiments	claim
172	175	Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure	claim
173	174	FASIMU: flexible software for flux-balance computation series in large metabolic networks	claim
174	173	compomics-utilities: an open-source Java library for computational proteomics	claim
175	165	Using context to improve protein domain identification	claim
176	151	TreeRipper web application: towards a fully automated optical tree recognition software	claim

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