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Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.

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• SciCrunch
• 13 years ago - by Anonymous

STCDB is a database of signal transduction pathways and classifications. Signal transduction classifications are listed in signal transduction number order. Each entry provides a link to details of that signal transduction. Alternatively, if looking for a specific signal transduction used in the classification of the broad outline defined by the first two numbers are given as a tree representation. Each of these subclass entries is linked to a location where the category is subdivided to sub-subclasses. These in turn are linked to a list of recommended names for each signal transduction in the sub-subclass. The links are to a list of sub-subclasses which in turn list the signal transductions linked to separate files for each signal transduction.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The UMKC Neuroscience Brain Tissue Bank and Research Laboratory has been established to obtain, process, and distribute human brain tissue to qualified scientists and clinicians dedicated to neuroscience research. No other living organ approaches the human brain in complexity or capacity. Healthy, it astounds and inspires miracles. Diseased, it confounds and diminishes hope. The use of human brain tissue for research will provide insight into the anatomical and neurochemical aspects of diseased and non-diseased brains. While animal models are helpful and necessary in understanding disease, certain disorders can be more efficiently studied using human brain tissue. Also, modern research techniques are often best applied to human tissue. We also need samples of brain tissue that have not been affected by disease. They help us to compare a 'normal' brain with a diseased one. Also, we have a critical need for brain donations from relatives who have genetically inherited disorders. Tissue preparation consists of fresh quick-frozen tissue blocks or coronal slices (nitrogen vapor frozen; custom dissection of specific anatomic regions) or formalin-fixed coronal slices (custom dissection of specific anatomic regions).

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• SciCrunch
• 15 years ago - by Anonymous

Videos of Knight ADRC related events for educational and informational purposes. A link to additional Center produced media is provided to access the Knight ADRC YouTube Channel. Videos are in HTML5 mp4 format and are available in 1080p or 4K resolution.

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• SciCrunch
• 15 years ago - by Anonymous

SSToSS is a database that provides sequence-structural templates of single member protein domain superfamilies. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies. The templates are mapped on the sequence using different color code. Sequence-structural templates can be visualized within the three dimensional structure of the superfamily member by using molecular graphics program like CHIME or RASMOL Spatial orientation of the templates in terms of distance and angle is provided for each set of templates. Templates are also presented in a Dendrogram based on the inter motif spatial distances using PHYLIP. The sequences of the sequence-structural motif regions are also provided.In the SSToSS database we incorporated related sequence search option based on multiple-pattern matching combined with a search for statistically significant sequence similarity. The specificity of the search engine is increased by utilizing the inter-motif spacing and pair wise global alignment of the query and hits. SSToSS database also utilizes an alignment algorithm to provide multiple alignment of the similar sequences identified by multiple-motif based database search. It allows the user to obtain a control over the alignment by providing sequence-structure template regions as input to the alignment program to achieve a more structurally relevant and functionally useful alignment of protein sequences. The algorithm employs local conserved regions of the sequences to be fixed and aligns the rest based on normal progressive alignment. The chances of global misalignment are thereby reduced and the possibility of obtaining overall better alignment is increased. We also provide three dimensional model structures of the similar sequences identified by multiple-motif based similarity search as potential member of each SSToSS superfamily. 3D models are built using the program MODELLER based on the structure of superfamily member protein Currently, this database contains structural motifs for 613 single member superfamilies of PASS2 database.

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• SciCrunch
• 17 years ago - by Anonymous

Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page.

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• SciCrunch
• 13 years ago - by Anonymous

Non-profit organization providing the latest information about Restless Legs Syndrome (RLS). Its goals are to increase awareness, improve treatments, and through research, find a cure for RLS, a condition which severely affects the lives of millions of individuals. By educating healthcare providers about RLS symptoms, diagnosis, and treatment, the RLS Foundation helps patients receive the quality care they both need and deserve. In recent years the Foundation has provided information to healthcare providers at many exhibit meetings, including the American Academy of Neurology, the American College of Obstetricians and Gynecologists, and the American Academy of Nurse Practitioners. The Foundation continually strives to be the most reputable source of information on RLS. Their renowned Medical Advisory Board, composed of leading RLS experts from all over the world, has written several publications on the diagnosis and treatment of RLS. These include our comprehensive RLS Medical Bulletin, their patient brochure, and their brochures on special topics including concerns for surgery, depression, pregnancy, and children. The Foundation has taken giant strides to further RLS research, funding grants for 27 research projects. Among the most distinguished research projects the Foundation has put its resources behind is the ongoing Stanford Epidemiology Project. Although it is still underway, the Foundation recognizes that the highly anticipated results of the Stanford Epidemiology Project, including the creation of a world standard questionnaire used to accurately diagnose RLS, could be spectacular. Eventually this questionnaire may help researchers understand the health consequences of RLS and identify other conditions and diseases that are associated with or exacerbated by RLS. In addition, the RLS Foundation helped fund a study led by Dr. David Rye and deCODE Genetics in Iceland which recently announced the discovery of a gene for RLS.

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• SciCrunch
• 15 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

It provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. SRPDB assists the study of structure and function of signal recognition particles (SRP), and provides annotated SRP, RNA, and SRP protein sequences phylogenetically ordered and aligned. Included are representative RNA secondary structure diagrams where each base pair is proven by comparative sequence analysis, information about other proteins that play a role in SRP-mediated protein translocation, as well as structural information about components of SRP. Where possible, links to primary sources were established.

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• SciCrunch
• 17 years ago - by Anonymous

An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Distinctive Voices highlights innovations, discoveries, and emerging issues in an exciting and engaging public forum. Do you wonder how things work? What the future holds? If you are curious about the science and technology behind today''s hot topics, Distinctive Voices is for you! Spend an evening gaining insights on significant advances in medicine, biotechnology, energy, the environment, space exploration, and more. Learn from some of the best minds in the world including members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicinein presentations geared to the general public. Events are held in Irvine, California and Woods Hole, Massachusetts, with videos of past Distinctive Voices events available on our YouTube channel. Distinctive Voices was created in 2006 as a program of the National Academy of Sciences Communication Initiative to increase science literacy. The live programming hosted at the Beckman Center in Irvine, California received major funding from the Arnold and Mabel Beckman Fund of the National Academy of Sciences and National Academy of Engineering. Additional support is provided by The Edward Lifesciences Fund and Pacific Life Foundation. The program at the Jonsson Center in Woods Hole, Massachusetts is supported by the Frank Press Fund of the National Academy of Sciences, the Thomas Lincoln Casey Fund of the National Academy of Sciences, the Arthur L. Day Fund of the National Academy of Sciences, and the Kellogg Fund of the Institute of Medicine.

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• SciCrunch
• 15 years ago - by Anonymous

A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.

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• SciCrunch
• 13 years ago - by Anonymous

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.

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• SciCrunch
• 15 years ago - by Anonymous

Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences.

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• SciCrunch
• 13 years ago - by Anonymous

A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death.

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• SciCrunch
• 15 years ago - by Anonymous

A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).

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• SciCrunch
• 13 years ago - by Anonymous