NAR 2006 - PDF Preprint Papers

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NAR
2006

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BiologicalNetworks: visualization and analysis tool for systems biology

14 years 11 days ago

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Systemslevelinvestigationofgenomicscaleinformation requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properti...

Michael Baitaluk, Mayya Sedova, Animesh Ray, Amarn...

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Id	Views	Title	Status

1	188	BiologicalNetworks: visualization and analysis tool for systems biology	claim
2	177	PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways	claim
3	170	The UCSC Genome Browser Database: update 2006	claim
4	164	FISH - family identification of sequence homologues using structure anchored hidden Markov models	claim
5	156	VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees	claim
6	142	miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes	claim
7	134	The MPI Bioinformatics Toolkit for protein sequence analysis	claim
8	129	AliWABA: alignment on the web through an A-Bruijn approach	claim
9	128	Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee	claim
10	125	Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions	claim
11	120	SuperNatural: a searchable database of available natural compounds	claim
12	120	TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure	claim
13	119	HHsenser: exhaustive transitive profile search using HMM-HMM comparison	claim
14	119	ChloroplastDB: the Chloroplast Genome Database	claim
15	113	ASD: a bioinformatics resource on alternative splicing	claim
16	110	EMAGE: a spatial database of gene expression patterns during mouse embryo development	claim
17	108	GLIDA: GPCR-ligand database for chemical genomic drug discovery	claim
18	107	CorGen - measuring and generating long-range correlations for DNA sequence analysis	claim
19	101	Epitome: database of structure-inferred antigenic epitopes	claim
20	100	The LIFEdb database in 2006	claim
21	100	StellaBase: The Nematostella vectensis Genomics Database	claim
22	99	DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification	claim
23	98	dbPTM: an information repository of protein post-translational modification	claim
24	98	oGNM: online computation of structural dynamics using the Gaussian Network Model	claim
25	97	CTGA: the database for genetic disorders in Arab populations	claim
26	96	mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences	claim
27	91	TreeFam: a curated database of phylogenetic trees of animal gene families	claim
28	91	YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms	claim
29	89	New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate	claim
30	89	AlgPred: prediction of allergenic proteins and mapping of IgE epitopes	claim
31	88	RMD: a rice mutant database for functional analysis of the rice genome	claim
32	88	PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes	claim
33	87	From genomics to chemical genomics: new developments in KEGG	claim
34	86	ISfinder: the reference centre for bacterial insertion sequences	claim
35	86	MODBASE: a database of annotated comparative protein structure models and associated resources	claim
36	85	WormBase: better software, richer content	claim
37	84	Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases	claim
38	84	PHEPS: web-based pH-dependent Protein Electrostatics Server	claim
39	83	KOBAS server: a web-based platform for automated annotation and pathway identification	claim
40	82	The RCSB PDB information portal for structural genomics	claim
41	82	PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins	claim
42	81	WEGO: a web tool for plotting GO annotations	claim
43	81	Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser	claim
44	79	The Database of Macromolecular Motions: new features added at the decade mark	claim
45	78	CrossLink: visualization and exploration of sequence relationships between (micro) RNAs	claim
46	77	SMART 5: domains in the context of genomes and networks	claim
47	76	CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments	claim
48	75	OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups	claim
49	75	DrugBank: a comprehensive resource for in silico drug discovery and exploration	claim
50	74	NOPdb: Nucleolar Proteome Database	claim
51	74	FlyRNAi: the Drosophila RNAi screening center database	claim
52	74	HHrep: de novo protein repeat detection and the origin of TIM barrels	claim
53	71	sgTarget: a target selection resource for structural genomics	claim
54	71	TSEMA: interactive prediction of protein pairings between interacting families	claim
55	70	GEPS: the Gene Expression Pattern Scanner	claim
56	68	Panzea: a database and resource for molecular and functional diversity in the maize genome	claim
57	66	MetaCyc: a multiorganism database of metabolic pathways and enzymes	claim
58	64	The PeptideAtlas project	claim
59	62	siVirus: web-based antiviral siRNA design software for highly divergent viral sequences	claim
60	61	E-MSD: improving data deposition and structure quality	claim
61	61	MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments	claim
62	61	NPInter: the noncoding RNAs and protein related biomacromolecules interaction database	claim
63	59	GenDecoder: genetic code prediction for metazoan mitochondria	claim
64	58	TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB	claim
65	57	SCOPPI: a structural classification of protein-protein interfaces	claim
66	53	MEME: discovering and analyzing DNA and protein sequence motifs	claim

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