Curator Dashboard

An integrated application software tool for miRNA identification from RNA sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.

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• SciCrunch
• 13 years ago - by Anonymous

An international team that works on a fee-for-service basis with policy makers and clinicians around the world to promote evidence-based decision making in healthcare.

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• SciCrunch
• 13 years ago - by Anonymous

NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.

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• SciCrunch
• 17 years ago - by Anonymous

Database for molecular typing and microbial genome diversity.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

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• SciCrunch
• 13 years ago - by Anonymous

Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.

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• SciCrunch
• 16 years ago - by Anonymous

This resource provides detailed information about the major research themes in the Institute of Neuroscience at the New Castle University. The major research themes of this department include: * Behavior, Psychology and Cognitive Neurosciences * Developmental Neuroscience, Aging and Neurodegeneration * Neural Circuits and Neuroimaging * Neurology, Neurosurgery, and Motor Control * Neuropharmacology and Neurotechnology * Psychiatric Neurosciences * Visual, Auditory and Sensory Neuroscience

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• SciCrunch
• 17 years ago - by Anonymous

A multi-center and multi-disciplinary study designed to dramatically increase understanding of chronic traumatic encephalopathy (CTE) and other late effects of traumatic brain injury (TBI). Overlapping clinical features, postmortem pathologies and patterns of involvement exist in TBI, CTE, and Alzheimer''s disease pose challenges to accurate diagnosis. Premortem diagnosis of CTE is currently impossible. The neuropathological consequences of single mild or moderate-severe TBI and its relationship with CTE and known dementias are unclear. The proposed project will leverage extensive resources from an ongoing population-based prospective cohort study of brain aging (Adult Changes in Thought; ACT, n=2,305) which includes excellent medical, behavioral, and genetic characterization of a cohort (20% of whom have a history of mild-moderate TBI) in addition to state-of-the-art neuropathology workup upon death. Neuropathological study of TBI effects can begin immediately in the existing ACT autopsy sample (n=489, 20% with TBI exposure). Additional cohorts of TBI- exposed individuals will come from the Brain Injury Research Center at Mount Sinai (n=150 individuals with moderate-severe TBI), the University of Texas Southwestern (n=50 retired boxers with repetitive TBI exposure), and the National Football League (n=76 retired players with repetitive TBI exposure). All participants in the proposed study (ACT and other sites) will undergo uniform harmonized neurobehavioral assessment (chosen to maximize correspondence with existing large-scale TBI and dementia studies), MRI scan, and genomic analysis. Those individuals who expire during the course of the study will undergo ex-vivo neuroimaging and extensive neuropathological exam using state-of-the-art techniques (such as Histelide) designed to quantify tau and A�� in whole brain specimens. Only by examining postmortem pathology in a sample of individuals with varying levels of TBI exposure who are well characterized during life (as proposed herein) can postmortem pathology facilitate identification of in-vivo biomarkers that can act as diagnostic tools. This project represents the most systematic and scientifically rigorous effort to date to develop a more complete understanding of the long-term clinical and neuropathological sequelae of single and multiple TBI.

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• SciCrunch
• 13 years ago - by Anonymous

A list of major inbred mouse strains from the Jackson laboratories. This list is not being actively maintained (found on Nov 27, 2013).

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• SciCrunch
• 14 years ago - by Anonymous

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

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• SciCrunch
• 13 years ago - by Anonymous

A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature.

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• SciCrunch
• 13 years ago - by Anonymous

Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

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• SciCrunch
• 13 years ago - by Anonymous

German research awards. Central self governing research funding organisation in Germany. Serves sciences and humanities and promotes research at universities and non-university research institutions. The focus is on funding projects developed by academic community.

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• SciCrunch
• 13 years ago - by Anonymous

An agency of the United States Department of Health and Human Services, one of the United States federal executive departments that is responsible for protecting and promoting public health through the regulation and supervision of food safety, tobacco products, dietary supplements, prescription and over-the-counter pharmaceutical drugs (medications), vaccines, biopharmaceuticals, blood transfusions, medical devices, electromagnetic radiation emitting devices (ERED), cosmetics and veterinary products. The FDA also enforces other laws, notably Section 361 of the Public Health Service Act and associated regulations, many of which are not directly related to food or drugs. These include sanitation requirements on interstate travel and control of disease on products ranging from certain household pets to sperm donation for assisted reproduction. (Wikipedia)

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Physiome.jp has been established to provide building blocks useful to develop in silico human. The blocks will include mathematical models and experimental data representing physiological functions. Physiome.jp is a part of the Worldwide Integrative Biomedical Research Cooperation to promote Physiome and Systems Biology. The building blocks (modules, models, biological data) representing biological functions and structure are databased and served as elements in the catalogue of human knowledge. They can be reused for deeper understanding of human physiology, eventually contributing to establishment of in silico medicine and predictive medicine. The databases (insilicoDB) at www.physiome.jp currently include a Model Database and a Morphology Database. The Model Database stores a number of modules representing biological/physiological functions. Those models are formulated by mathematical equations to describe dynamic changes of states, i.e., specific biological functions. All models in the database are written in an XML format called insilicoML. The Morphology Database provides datasets representing morphometric models of biological organs. The morphometric data are provided in several data-types including surface data such as STL and VRML and volume/voxel data. The database contents are in the public domain and aim to provide valuable models to the scientific community for model sharing/reuse, simulation, model validation, visualization of biological structure, and morphology-based dynamic simulation of biological functions. These can be accomplished by combining insilicoML models with appropriate morphology datasets. Models and related data in the insilicoDB may be freely downloaded and reused for non-profit scientific purposes. When using the models in the Model Database, we ask the users to respect the effort spent in arranging/serving the mathematical models as well as the original model construction. For any reuse of the morphology data, we also ask the users to respect the intellectual property of those who provided the original data. This should be done by acknowledging insilicoDB@physiome.jp for model reuse and by including appropriate attribution information for any reuse of the morphology data. The insilicoDB owners will not be held responsible for misuse of the Morphology Database and/or Model Database, or damage caused by use of the data and models contained therein.

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• SciCrunch
• 17 years ago - by Anonymous

We are a vibrant community of educators, students, scientists, clinicians and others working side-by-side to heal, teach, discover and serve. We support 1,750 faculty, 1,200 students and 750 residents and fellows in 27 departments and 17 centers and institutes. We offer doctorates in medicine and philosophy, masters in science, public health and physician assistant studies and combined degrees. Our faculty is dedicated to preparing physicians for the medical, ethical and humanistic responsibilities of their calling, while also providing outstanding care to patients from Oregon and elsewhere. Along with the art of teaching and healing comes the responsibility for discovery. The School of Medicine faculty is widely recognized nationally and internationally for the pursuit of new knowledge in a breadth of investigative areas ranging from molecular biology and cancer to heart disease, behavioral science and issues of public health.

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

Biomedical research institute in Germany that investigates the mechanisms of cancer and works to identify cancer risk factors. They provide the foundations for developing novel approaches in the prevention, diagnosis, and treatment of cancer and are a member of the Helmholtz Association of National Research Centers. Professor Harald zur Hausen was awarded the Nobel Prize for Medicine for his outstanding scientific contribution to the study of human papillomaviruses (HPV). In addition, the staff of the Cancer Information Service (KID) offers information about the widespread disease of cancer for patients, their families, and the general public. The Center is funded by the German Federal Ministry of Education and Research (90%) and the State of Baden-Württemberg (10%).

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page. Replication timing data were obtained by hybridizing early and late replication intermediates to Nimblegen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. After unbiased amplification of recovered DNA, the samples are differentially labeled with Cy3 and Cy5 and hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH). Raw data from two independent biological replicates in which the early and late replicating DNA were labeled reciprocally with Cy3 and Cy 5 (dye switch) are loess-normalized and scaled to have the same median-absolute deviation using the limma package (R/Bioconductor) and then averaged. Finally, the data are smoothed with a weighted moving average (loess: local polynomial smoothing).

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• SciCrunch
• 17 years ago - by Anonymous