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http://amp.pharm.mssm.edu/LJP/

Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.

Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy   

•   Source: SciCrunch Registry

https://gotrack.msl.ubc.ca/

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Proper citation: GOTrack (RRID:SCR_016399) Copy   

•   Source: SciCrunch Registry

https://github.com/Sung-Huan/ANNOgesic

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

Proper citation: ANNOgesic (RRID:SCR_016326) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services

Supplier of mice for research purposes.

Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy   

•   Source: SciCrunch Registry

https://www.modelorg.com/

Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding.

Proper citation: Shanghai Model Organisms Center (RRID:SCR_016407) Copy   

•   Source: SciCrunch Registry

http://www.nrcmm.cn/

Supplier of mice for research purposes.

Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) Copy   

•   Source: SciCrunch Registry

https://www.taconic.com/

Supplier of mice for research purposes.

Proper citation: Taconic Biosciences (RRID:SCR_016410) Copy   

•   Source: SciCrunch Registry

https://www.genomics.agilent.com/article.jsp?pageId=2100

Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MxPro QPCR (RRID:SCR_016375) Copy   

•   Source: SciCrunch Registry

https://github.com/sblanck/smagexp

Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.

Proper citation: SMAGEXP (RRID:SCR_016360) Copy   

•   Source: SciCrunch Registry

http://www.flybrain.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure.

Proper citation: FlyBrain (RRID:SCR_000706) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/esb/PiNGO/

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: PiNGO (RRID:SCR_000692) Copy   

•   Source: SciCrunch Registry

http://franklin.imgen.bcm.tmc.edu/

The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.

Proper citation: Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) Copy   

•   Source: SciCrunch Registry

http://gdm.fmrp.usp.br/

Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.

Proper citation: USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000

Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.

Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy   

•   Source: SciCrunch Registry

http://www.yandell-lab.org/software/index.html

Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. MAKER 2 (updated 01-16-2012) MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. RepeatRunner RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc...). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF - a program designed to identify novel repeats - and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes. CGL CGL is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation; we call it CGL, an acronym for Comparitive Genomics Library, and pronounce it Seagull. The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.

Proper citation: Yandell Lab Portal (RRID:SCR_000807) Copy   

•   Source: SciCrunch Registry

http://www.rostlab.org/cms/

A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.

Proper citation: ROSTLAB (RRID:SCR_000792) Copy   

•   Source: SciCrunch Registry

http://fantom.gsc.riken.jp/

International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.

Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy   

•   Source: SciCrunch Registry

http://www.genome.jp/kegg/expression/

Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/sim4cc/

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

Proper citation: sim4cc (RRID:SCR_001204) Copy   

•   Source: SciCrunch Registry

http://www.omixon.com/data-analysis-and-pro/

Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.

Proper citation: Omixon Target Data Analysis (RRID:SCR_001207) Copy   

•   Source: SciCrunch Registry