Curator Dashboard

The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks.

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• SciCrunch
• 15 years ago - by Anonymous

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.

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• SciCrunch
• 16 years ago - by Anonymous

Software repository of custom extensions to the GForge collaborative environment.

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• SciCrunch
• 14 years ago - by Anonymous

Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included.

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• SciCrunch
• 17 years ago - by Anonymous

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

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• SciCrunch
• 13 years ago - by Anonymous

Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

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• SciCrunch
• 17 years ago - by Anonymous

Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

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• SciCrunch
• 17 years ago - by Anonymous

http://www.thecommunityguide.org/uses/funding.html

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• SciCrunch
• 13 years ago - submitted by Timothy Tsui

The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools.

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• Consortia-pedia, a FasterCures Project
• 12 years ago - submitted by Taylor Cronin

Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.

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• SciCrunch
• 13 years ago - by Anonymous

CFC International holds the world''s largest collection of blood and tissue from people affected by CFC and their immediate relatives. It is the only centralized repository in the world. The CFC BioBank provides medical researchers with genetic and biological material from CFC patients and their families, so that research on CFC and other related syndromes can be performed. CFC International joined the Genetic Alliance BioBank in 2004 to make certain that your privacy and confidentiality are protected and your samples are available to any approved research project. The bank serves as a resource for researchers around the world who are willing to search to find the gene(s) responsible for the Cardio-Facio-Cutaneous Syndrome. As you know, Cardio-Facio-Cutaneous Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of CFC''s mission is to stimulate interest in CFC research, there is an increased need for cell lines. The CFC BioBank will ensure that need is met! The goals of The CFC BioBank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for CFC Syndrome * Discoveries leading to new treatments for children with CFC Syndrome If you are interested in donating to the CFC BioBank please call 607-772-9666, or e-mail us at bconger_at_cfcsyndrome.org and indicate your interest. Researchers with an interest in either donating CFC Syndrome cell lines or in applying to use material from the bank should also call or write.

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• SciCrunch
• 16 years ago - by Anonymous

Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.

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• SciCrunch
• 12 years ago - submitted by Monique Surles-Zeigler

Software providing a graphical front end for computational chemistry programs.

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• SciCrunch
• 12 years ago - by Anonymous

A virtual database currently indexing multiple podcast resources including: The Brain Science Podcast, Nature Podcast, NeuroPod, Science Podcast, The American Journal of Psychiatry Podcast, 60-Second Mind, and Science Talk.

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• SciCrunch
• 14 years ago - by Anonymous

A web application which stores and organizes scholarly papers and references. Papers of interest identified from the web can be added to the users' personal library and the associated references will be automatically extracted.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Provides histological services as well as technical support. Equipped with ventilated working areas and equipment to prepare, process and stain frozen or paraffin embedded specimens. Instrumentation include VIP Tissue Processor, BIOCARE NxGen Decloaking Chamber, Rotary Microtome, Staining Center, Leica Cryostat, Zeiss Axio Microscope/Camera Software, Leica Bond-Max Immunostainer, Leica Autostainer XL, General Data Laser Cassette Marker.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Extension to PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Preferred reporting items for systematic reviews and meta analyses literature search extension. Complements PRISMA Statement and its extensions by providing checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of search is completely reported and therefore reproducible.

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• RRID
• 3 years ago - by Anonymous