Revision as of 18:53, 3 May 2016

Tools portals

below is a list of more tool portals that the lab has developed.

Tool Name	Release Date	Description
Genecensus	1998	we proposed a number of novel trees based on the occurrence of specific features, either folds or orthologs, throughout the whole genome. We call thesegenomic trees or whole-genome trees.

Tool Name	Release Date	Description
partslist	1995	a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

Tool Name	Release Date	Description
genometech	1995	A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.

Tool Name	Release Date	Description
HUB	2001	A tool for leveraging the structure of the semantic web to enhance information retrieval for proteomics. This tool helps Proteomics researchers to be able to quickly retrieve relevant information from the web and the biomedical literature.
Yeasthub	1997	A semantic web-based application which demonstrates how a life sciences data warehouse can be built using a native Resource Description Framework (RDF) data store. This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats.

Tool Name	Release Date	Description
ProCAT	2006	A data analysis approach for protein microarrays. ProCAT corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.
Tilescope	2007	An online analysis pipeline for high-density tiling microarray data. Tilescope normalizes signals between channels and across arrays, combines replicate experiments, score each array element, and identifies genomic features. The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis.
Tiling	NA	A platform with all our tilling array analysis tools.

Tool Name	Release Date	Description
Local Clustering	2001	A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.
OrthoClust	2014	A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.

Tool Name	Release Date	Description
BoCaTFBS	2006	A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments.
ExpressYourself	2003	An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
LESSeq Github repo	2014	Local Event-based analysis of alternative Splicing using RNA-Seq
SPINE	2001	A laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download.

@@ Line 59: / Line 59: @@
 |style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/expression/cluster '''Local Clustering''']||style="width:7%; text-align:center;"|2001||A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.
 |-style="height: 100px;"
 |style="width:15%; text-align:center;"|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style="width:7%; text-align:center;"|2014||A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.
 |}