Curator Dashboard

R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.

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• SciCrunch
• 13 years ago - by Anonymous

The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution.

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• SciCrunch
• 15 years ago - by Anonymous

A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.

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• SciCrunch
• 15 years ago - by Anonymous

A software plugin for 3D Slicer that matches morphological signatures of medical images automatically. HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002) - an elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008).

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• SciCrunch
• 15 years ago - by Anonymous

A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond.

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• SciCrunch
• 15 years ago - by Anonymous

Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy.

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• SciCrunch
• 17 years ago - by Anonymous

A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.

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• SciCrunch
• 15 years ago - by Anonymous

A tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. RPER is also more efficient than fixed-interval event related (FIER) because more stimuli can be presented within a given scanning interval at the cost of assuming that the overlap in the hemodynamic responses will be linear. In SPM parlance, RPER is referred to as ''stochastic design''. This is a subproject of the Center for Functional Neuroimaging Techniques (http://www.nitrc.org/projects/cfnt/)

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• SciCrunch
• 15 years ago - by Anonymous

EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants. The resting-state fMRI images were collected on several occasions: # the first resting-state scan in a scan session # 5-11 months after the first resting-state scan # about 30 (< 45) minutes after 2. Each scan occasion is released as a new version release of the resource. ---Caution: Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets.

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• SciCrunch
• 15 years ago - by Anonymous

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.

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• SciCrunch
• 15 years ago - by Anonymous

One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.

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• SciCrunch
• 15 years ago - by Anonymous

A virtual database currently indexing clinical trials databases including EU Clinical Trials Register and Clinicaltrials.gov.

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• SciCrunch
• 14 years ago - by Anonymous

Software program that allows researchers to perform citation analysis and calculate various impact metrics. It uses Google Scholar to obtain the raw citations, then analyzes these and presents the following statistics: * Total number of papers * Total number of citations * Average number of citations per paper * Average number of citations per author * Average number of papers per author * Average number of citations per year * Hirsch''s h-index and related parameters * Egghe''s g-index * The contemporary h-index * The age-weighted citation rate * Two variations of individual h-indices * An analysis of the number of authors per paper. The results are available on-screen and can also be copied to the Windows clipboard (for pasting into other applications) or saved to a variety of output formats (for future reference or further analysis). The Publish or Perish software is a Microsoft Windows application that can also be installed and used on Apple Mac OS X and GNU/Linux computers, with the aid of a suitable emulator such as Wine or CrossOver Mac.

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• SciCrunch
• 15 years ago - by Anonymous

On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)

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• SciCrunch
• 15 years ago - by Anonymous

Longitudinal twin study to understand individual differences in aging with corresponding data and biological samples. The twin design and the inclusion of twins reared apart makes it possible to study the importance of genetic and environmental factors that may underlie differing aging outcomes. Further, the broad spectrum of biological, psychological, and social domains assessed across the life span makes it possible to study patterns of change within and across domains and how these predict health and diseases of aging. The study is comprised of several longitudinal components including, a comprehensive questionnaire that was sent to all twins in the Swedish Twin Registry who were separated at an early age and reared apart and a control sample of twins reared together. The questionnaires include items concerning rearing, family, adult, and working environment, health status, health related behaviors (e.g. alcohol, tobacco, and dietary habits) as well as relationships, and personality measures. The questionnaires were sent again at 3 year intervals in 1987, 1990, 1993 and after a break again in 2004, 2007, and 2010. Thus far more than 2,000 twins have responded to at least one of the seven questionnaire assessments conducted between 1984 and 2010. Additionally there is information about midlife life style factors from the Swedish Twin Registry that were collected about twenty years before SATSA started. In the second component a subsample of 861 individuals have participated in at least one wave of in-person testing (IPT). The first IPT started in 1986 and since then eight IPTs have been collected and the last wave will be collected during 2012-2013. The IPT includes a health examination, structured interviews, tests of functional capacity, and memory and thinking abilities. To date, over 76% of the sample has participated in 3 or more measurement waves. At IPT9 a third component was added to SATSA, a measure of day-to-day fluctuations in memory and thinking abilities, and emotions. Information about social interactions is also collected. After the visit by the research nurses the twins fill out the day-to-day booklet during the next five days. This procedure will be repeated in IPT10. This will add information about small and short-term changes and more changes are supposed to indicate the beginning of poor health. Data from SATSA can be used to study various aspects of aging. For example, the relative importance of genetic and environmental factors for individual differences in aging especially in cognitive and physical domains has been studied. A further main focus is to study changes within and across domains and which genetic and life style factors predict these changes. Given the wide spectrum of data from measured genes to social relationships collected over more than two decades they dare to say that SATSA is a unique study, with the possibility to answer many questions within gerontology and geriatrics. Types of samples * Serum * DNA Number of sample donors: 674 (June 2010)

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• SciCrunch
• 15 years ago - by Anonymous

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free.

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• SciCrunch
• 15 years ago - by Anonymous

On line textbook of basic clinical and functional neuroscience, developed by Rand S. Swenson, D.C., M.D., Ph.D., Dartmouth Medical School Chapter Index * Introduction * Cellular organization * Peripheral nervous system * Development * Spinal cord * Brain stem organization * Sensory systems * Motor systems * Limbic system * Thalamic organization * Cerebral cortical organization * Nutrition of the brain * Conclusions

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• SciCrunch
• 15 years ago - by Anonymous