Curator Dashboard

A web tool using the Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM''s classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A web tool using the consensus prediction method for identifying possible amyloidogenic regions in protein sequences. This tool uses an assortment of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils. The consensus of these methods is defined as the the hit overlap of at least two out of five methods and it is the primary output of the program. However, the individual predictions of these methods are also made available in the form of a text file, maintained on the server for 1 (one) day. Consequently, the tool predicts probable amyloidogenic determinants for a given amino acid sequence of a peptide or protein.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Created in 1997, Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET) is a professional network of field epidemiology training programs (FETPs) located in 53 countries around the world. TEPHINET aims to strengthen international public health capacity by training field epidemiologists through an applied apprenticeship program. Trainees of FETPs master a set of core competencies that are vital to the practice of public health, while providing a valuable public health service to their countries and regions.

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• SciCrunch
• 15 years ago - by Anonymous

A Parkinson's research foundation dedicated to finding a cure for Parkinson's disease and to ensuring the development of improved therapies. Pipeline Programs fund investigator-initiated proposals focused on the following critical points along the translational pathway to new therapies for Parkinson's disease.

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• SciCrunch
• 15 years ago - by Anonymous

Database containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jsp

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A web tool for prediction of signal peptides in archaea. Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Laboratory focuses on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas. In particular, original research is carried out along two main axes: # Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. # Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle. More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects. Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens. At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Consortium of 12 Biomedical sciences research infrastructure (BMS RI) partners to develop a shared e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains (providing a complex knowledge environment comprising standards, ontologies, data and services) and thus strengthen biomedical resources in Europe. The BMS RIs are on the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI). Connecting several European research infrastructures brings a diversity of ethical, legal and security concerns including data security requirements for participating e-Infrastructures that are storing or processing patient-related data (or biosamples): EATRIS, ECRIN, BBMRI, EuroBioImaging and EMBL-EBI. In addition, INSTRUCT is interested in secure sample transport and in intellectual property rights; Infrafrontier stores high-throughput data from mice. BBMRI with its focus on the availability of biomaterials is currently emphasizing aspects like k-anonymity and metadata management for its data. Sharing of imaging data by Euro-BioImaging poses challenges with respect to anonymisation and intellectual property. Therefore, an ethical, regulatory and security framework for international data sharing that covers these diverse areas and different types of data (e.g. clinical trials data, mouse data, and human genotype and DNA sequence data) is of crucial importance. The outcomes will lead to real and sustained improvement in the services the biomedical sciences research infrastructures offer to the research community. Data curation and sample description will be improved by the adoption of best practices and agreed standards. Many improvements will emerge from new interactions between RIs created by data linkage and networking. Ensuring access to relevant information for all life science researchers across all BMS RIs will enable scientists to conduct and share cutting-edge research.

• Organization
• Consortia-pedia, a FasterCures Project
• 14 years ago - by Anonymous

Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Web service that returns International Federation of Digital Seismograph Networks (FDSN) station metadata in FDSN StationXML format or as delimited text. Results are available at multiple levels of granularity: network, station, channel and response. Metadata may be selected based on channel descriptors, time ranges, geographic regions, and more. This service is an implementation of the FDSN web service specification version 1.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus.

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• SciCrunch
• 15 years ago - by Anonymous

Provides information and tools to help consumers stay healthy including resources on a wide range of health topics selected from over 1,600 government and non-profit organizations to provide the best, most reliable health information possible.

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• SciCrunch
• 15 years ago - by Anonymous

A web utility providing a direct interface to perform SQL queries directly on the GO database, allowing users to run custom queries without having to install a copy of the GO database locally. GOOSE includes many sample queries to aid novice users and allows results to be retrieved as a web page or as tab-delimited text. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD).

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 10th,2023. Commercial provider of cognitive assessments, including their proprietary database, the Brain Resource International Database (BRID) that allows users to quantify individual differences in brain function, compare individual performance against peers, and provide a robust frame of reference for clinical assessment and treatment decisions. Database provides evidence for brain behavior connection so important to reliably enabling optimal solutions for mental health and wellbeing. It powers all Brain Resource products.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible.

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• SciCrunch
• 15 years ago - by Anonymous

Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P.

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• SciCrunch
• 15 years ago - by Anonymous

Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.

• Resource
• SciCrunch
• 15 years ago - by Anonymous