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Transmissible cancers are clonal lineages that spread through populations via contagious cancer cells. Although rare in nature, two facial tumor clones affect Tasmanian devils. Here we perform comparative genetic and functional characterization of these lineages. The two cancers have similar patterns of mutation and show no evidence of exposure to exogenous mutagens or viruses. Genes encoding PDGF receptors have copy number gains and are present on extrachromosomal double minutes. Drug screening indicates causative roles for receptor tyrosine kinases and sensitivity to inhibitors of DNA repair. Y chromosome loss from a male clone infecting a female host suggests immunoediting. These results imply that Tasmanian devils may have inherent susceptibility to transmissible cancers and present a suite of therapeutic compounds for use in conservation.
Pubmed ID: 29634948 RIS Download
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A commercial antibody supplier and provider of various services.
View all literature mentionsNEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. NEURON has benefited from judicious revision and selective enhancement, guided by feedback from the growing number of neuroscientists who have used it to incorporate empirically-based modeling into their research strategies. NEURON's computational engine employs special algorithms that achieve high efficiency by exploiting the structure of the equations that describe neuronal properties. It has functions that are tailored for conveniently controlling simulations, and presenting the results of real neurophysiological problems graphically in ways that are quickly and intuitively grasped. Instead of forcing users to reformulate their conceptual models to fit the requirements of a general purpose simulator, NEURON is designed to let them deal directly with familiar neuroscience concepts. Consequently, users can think in terms of the biophysical properties of membrane and cytoplasm, the branched architecture of neurons, and the effects of synaptic communication between cells. * helps users focus on important biological issues rather than purely computational concerns * has a convenient user interface * has a user-extendable library of biophysical mechanisms * has many enhancements for efficient network modeling * offers customizable initialization and simulation flow control * is widely used in neuroscience research by experimentalists and theoreticians * is well-documented and actively supported * is free, open source, and runs on (almost) everything
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsData analysis service to predict the functional consequences of known and unknown variants.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds.
View all literature mentionsSoftware for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
View all literature mentionsA genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs.
View all literature mentionsA generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
View all literature mentionsA web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsSoftware package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.
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Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.
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.
View all literature mentionsSoftware that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.
View all literature mentionsSoftware designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
View all literature mentionsAn Antibody supplier; Dako was purchased by Agilent in 2012 and several years later the websites began to reflect the Dako products as part of the Agilent catalog.
View all literature mentionsCell line PC-9 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line A-549 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsThis unknown targets TAZ
View all literature mentionsThis polyclonal targets S100 isolated from cow brain.
View all literature mentionsThis unknown targets PRX
View all literature mentionsThis polyclonal targets PDGF Receptor alpha antibody
View all literature mentionsThis recombinant monoclonal targets PDGF Receptor beta
View all literature mentionsThis monoclonal targets YAP1 antibody produced in mouse
View all literature mentionsThis monoclonal targets vimentin
View all literature mentionsThis monoclonal targets Smooth Muscle Actin
View all literature mentionsThis monoclonal targets ENO2
View all literature mentionsThis monoclonal targets Muscle Specific Actin
View all literature mentionsThis monoclonal targets Human epidermal callus1
View all literature mentionsA stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsA high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
View all literature mentionsThis unknown targets TAZ
View all literature mentionsThis polyclonal targets S100 isolated from cow brain.
View all literature mentionsThis unknown targets PRX
View all literature mentionsThis polyclonal targets PDGF Receptor alpha antibody
View all literature mentionsThis recombinant monoclonal targets PDGF Receptor beta
View all literature mentionsThis monoclonal targets YAP1 antibody produced in mouse
View all literature mentionsThis monoclonal targets vimentin
View all literature mentionsThis monoclonal targets Smooth Muscle Actin
View all literature mentionsThis monoclonal targets ENO2
View all literature mentionsThis monoclonal targets Muscle Specific Actin
View all literature mentionsThis monoclonal targets Human epidermal callus1
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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