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http://edwardslab.bmcb.georgetown.edu/

The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.

Proper citation: Edwards Lab (RRID:SCR_008860) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ABA-AMB

Allen Brain Atlas P56 Mouse Ontology

Proper citation: ABA Adult Mouse Brain Ontology (RRID:SCR_010286) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry

http://targetscan.org/

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

Proper citation: TargetScan (RRID:SCR_010845) Copy   

•   Source: SciCrunch Registry

http://adacgh.bioinfo.cnio.es/

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

Proper citation: ADaCGH (RRID:SCR_010916) Copy   

•   Source: SciCrunch Registry

http://tvmouse.compmed.ucdavis.edu/

Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.

Proper citation: Visible Mouse Project (RRID:SCR_002393) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/SNP/

General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

Proper citation: dbSNP (RRID:SCR_002338) Copy   

•   Source: SciCrunch Registry

http://connectomes.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.

Proper citation: Connectomes.org (RRID:SCR_002243) Copy   

•   Source: SciCrunch Registry

https://www.genevestigator.com/gv/

A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.

Proper citation: Genevestigator (RRID:SCR_002358) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/igentbio

A commercial facility handling induced pluripotent stem cell (iPSC) generation, cellular characterization, teratoma formation, karyotyping, and KO-mouse generation.

Proper citation: iGentBio (RRID:SCR_002722) Copy   

•   Source: SciCrunch Registry

http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MBAT

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/bmap/resources/resources.htm

As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com

Proper citation: BMAP cDNA Resources (RRID:SCR_002973) Copy   

•   Source: SciCrunch Registry

http://cellfinder.de/about/ontology/

Structured vocabulary to organize cell-associated data and to place these data in clearly defined semantic relations to other biological facts. It describes cell types, their properties and origin and links this information to other existing ontologies like the Cell Ontology (CL), Foundational Model of Anatomy (FMA), Gene Ontology (GO), Mouse Anatomy and others using the top-level ontology BioTop.

Proper citation: CELDA Ontology (RRID:SCR_001601) Copy   

•   Source: SciCrunch Registry

http://tvmouse.ucdavis.edu/anatomy/

Access to Quicktime movies of histologic mouse anatomy including heart / lung, kidney, mammary gland, lymph node, prostate, spleen, liver, salivary glands, and 3-D wire model based on MRI sections; a Quicktime mouse radiographic atlas of skeletal anatomy containing a series of radiographic images with color overlays and labels; and a table containing a comparison between mouse and human anatomy. Special topics include the virtual necroscopy. Anatomic systems cover the central nervous system, male genital-urinary tract, female genital-urinary tract, mammary, kidney, skeletal, cardiovascular, gastrointestinal, and respiratory systems. The pathology and imaging section includes anatomy, histology, comparative imaging, physiology, pathology, comparative mammary, comparative prostate, GEM, and an image archive. These pages were put together as a pilot demonstration by Dr. Robert Cardiff, UCD Center for Comparative Medicine with the collaboration of Dr. Michael Paulus, Oak Ridge National Laboratories,MicroCat Group, Dr. Allan Johnson, Duke University Center for In Vivo Microscopy, and Drs. Steve Griffey, Gary Henderson and Tom Jue, University of California, Davis. This is a work in progress and for demonstration purposes.

Proper citation: Visible Mouse Anatomy (RRID:SCR_001603) Copy   

•   Source: SciCrunch Registry

http://kesm.cs.tamu.edu

A web-based, light-weight 3D volume viewer that serves large volumes (typically the whole brain) of high-resolution mouse brain images (~1.5 TB per brain, ~1 um resolution) from the Knife-Edge Scanning Microscope (KESM), invented by Bruce H. McCormick. Currently, KESMBA serves the following data sets: * Mouse: Whole-brain-scale Golgi (acquired 2008 spring): neuronal morphology: Choe et al. (2009) * Mouse: Whole-brain India Ink (acquired 2008 spring): vascular network: Choe et al. (2009); Mayerich et al. (2011); * Mouse: Whole-brain Golgi (acquired 2011 summer): neuronal morphology: Choe et al. (2011); Chung et al. (2011); * Mouse: Whole-brain Nissl (acquired 2009-2010 winter): somata (Choe et al. 2010) (Coming soon) They will ship you the full data set on a hard drive if you provide them with the hard drive and shipping cost.

Proper citation: KESM brain atlas (RRID:SCR_001559) Copy   

•   Source: SciCrunch Registry

https://www.cmtk.org/

A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application.

Proper citation: Connectome Mapping Toolkit (RRID:SCR_001644) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/resources/

Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J

Proper citation: Genes to Cognition - Biological Resources (RRID:SCR_001675) Copy   

•   Source: SciCrunch Registry