• This Symposium will cover real-world use cases across many areas, including drug discovery and design, R&D, molecular modeling, next-generation sequencing, and bioinformatics. (globus.org)
  • Genes and Tissue Culture Technology - Next Generation Sequencing - Applicatio. (slideshare.net)
  • General understanding of possibilities and limitations of Next Generation Sequencing (NGS) data, with an emphasis on RNA and whole genome/exome sequencing. (uib.no)
  • Familiarity with next-generation sequencing and a basic understanding of molecular biology and/or genetics are desirable. (uib.no)
  • Clinical trials--Data processing Bioinformatics United States. (columbia.edu)
  • The talk will discuss, also from historical and paradigmatic perspective, some computational problems, algorithmic techniques and future goals of bioinformatics, ranging from the genome reconstruction and sequence indexing to the analysis of gene regulation. (helsinki.fi)
  • The main objective of this course is to provide the candidates with the knowledge central for successful application of bioinformatics and data analysis in clinical research on human tissue. (uib.no)
  • This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)
  • Adding Genbank sequences, we inferred systematic relationships among 1,114 plumularioids, corresponding to 123 nominal species and 17 novel morphospecies in five families of Plumularioidea. (nature.com)
  • Descripciones de secuencias específicas de aminoácidos, carbohidratos o nucleótidos que han aparecido en publicaciones o están incluidas y actualizadas en bancos de datos como el GENBANK, el Laboratorio Europeo de Biología Molecular (EMBL), la Fundación Nacional de Investigación Biomédica (NBRF) u otros archivos de secuencias. (bvsalud.org)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK , European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (bvsalud.org)
  • We compared the sequences of two housekeeping genes ( hspA and glmM ) from these clones with those of 131 unrelated strains from patients living in different geographic regions. (cdc.gov)
  • Clonal descent has been demonstrated by comparing alleles of genes such as vacA , flaA , and flaB of isolates infecting members of the same family ( 10 - 12 ) and by sequencing three housekeeping genes ( ureI , atpA , and ahpC ) ( 13 ). (cdc.gov)
  • Analysis of the sequences of housekeeping genes ( atpD , scoB , glnA and recA ) showed that strains cluster according to their geographic origins ( 15 , 20 ). (cdc.gov)
  • To assess the genetic diversity and relationships between the isolates, we sequenced two housekeeping genes ( glmM and hspA ). (cdc.gov)
  • TARGET investigators sequenced and analyzed microRNA to identify dysregulated genes and assess the utility of microRNA signature for improved outcome prediction. (cancer.gov)
  • A relatively obvious approach to phylogenetic analysis of whole genomes is to extract as many genes as possible from the genome sequences, create a multiple sequence alignment from each of the genes and to concatenate all alignments. (biomedcentral.com)
  • Difficulties with this approach may arise if orthologous genes cannot be identified with certainty or if the combined sequence length is still too small to give well-resolved trees. (biomedcentral.com)
  • Tissues and clinical data used for the TARGET AML project were obtained from patients enrolled on biology studies and clinical trials managed through COG. (cancer.gov)
  • Such data is abundant due to modern molecular biology measurement techniques like high-throughput sequencing. (helsinki.fi)
  • With the advent of high-throughput sequencing the amount of sequence data has exploded, making molecular biology research totally dependent on efficient computation. (helsinki.fi)
  • The science of figuring out these trees, known as systematics, has progressed significantly in the last two decades largely due to advances in computation, genetics and molecular biology. (scienceagogo.com)
  • Vector NTI Advance is a desktop sequence analysis and molecular biology data management system. (va.gov)
  • Hypothesizing common ancestry of each group of taxa in a hierarchic ordering, taxonomists seek diagnostic morphological (but also physiological and molecular) homologous characters for each cluster, and name the resulting assemblages. (nature.com)
  • Impatiens longiaristata (Balsaminaceae), a new species from western Sichuan Province in China, is described and illustrated here based on morphological and molecular data. (researchgate.net)
  • The objective of this study was to combine new and existing genetic data, along with reanalysis of morphological characters, to test the distinctiveness of V . coatlicue . (scielo.br)
  • The synthesis of molecular and morphological data supports the recognition of V . coatlicue as a junior synonym of V . zonata . (scielo.br)
  • A new species of the genus Microhyla is described from Jamun Khadi, Jhapa district of eastern Nepal, based on molecular and morphological comparisons. (mapress.com)
  • Dutta, A.K., Paloi, S., Pradhan, P. & Acharya, K. (2015) A new species of Russula (Russulaceae) from India based on morphological and molecular (ITS sequence) data. (mapress.com)
  • This web-based application performed pairwise comparisons of HIV-1 protease and partial reverse transcriptase to measure sequence relatedness and identify sequences that were highly genetically similar at a genetic distance of ≤0.015 substitutions per site ( 6 , 7 ). (cdc.gov)
  • The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) AML projects elucidate comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of high-risk or hard-to-treat childhood cancers. (cancer.gov)
  • A Custom Hepatitis A Virus Assay for Whole-Genome Sequencing. (cdc.gov)
  • Unlike most data in natural sciences, the biological sequence data such as DNA and amino acid sequences is discrete rather than continuous by nature. (helsinki.fi)
  • An alignment is the first analytical step, after raw molecular data (typically, DNA sequences converted to amino acid sequences) are obtained. (uncommondescent.com)
  • Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of molecular sequence data--some surprises. (pensoft.net)
  • Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
  • David L. Swofford and Gary J. Olsen, chapter on Phylogeny Reconstruction, in Molecular Systematics (Sinauer, 1990, eds. (uncommondescent.com)
  • Thus, a couple of years later, when I heard Scott Lanyon (at the time, on the staff at the Field Museum in Chicago) state, "The first thing I ask myself, when I see a published molecular phylogeny is, 'How much of this should I believe? (uncommondescent.com)
  • Before a tree, or phylogeny, can be determined, DNA and protein sequence data must be organized. (scienceagogo.com)
  • This species is the sister taxon of Microhyla ornata and can be distinguished by a unique vocalization, morphology and molecular phylogeny. (mapress.com)
  • Determination of Molecular Descriptors from Analysis of Sequence and Genome Data. (forskningsradet.no)
  • We develop algorithms and data structures for the analysis of genome-scale data. (helsinki.fi)
  • Tracing Foodborne Botulism Events Caused by Clostridium botulinum in Xinjiang Province, China, Using a Core Genome Sequence Typing Scheme. (cdc.gov)
  • Vector NTI uses a proprietary local database to provide storage and organization functions for molecules and other objects used in cloning strategies, molecule manipulation and analysis, and sequence analysis. (va.gov)
  • Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. (biomedcentral.com)
  • Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
  • Molecular phylogenetic analysis based on nuclear ITS and plastid atpB-rbcL sequences shows that the two new species belong to I. sect. (researchgate.net)
  • This, however, led to the discovery that almost half the severe cases of haemophilia A or a fifth of all cases are due to frequently occurring inversions caused by homologous intra-chromosome (-chromatid) recombination between repeated sequences 9.5 kb long. (nih.gov)
  • The Genomics & Sequencing Data Integration, Analysis and Visualization Symposium is a part of the Molecular Medicine Tri-Conference. (globus.org)
  • Please join us for a talk by Ravi Madduri on the subject "Integrated Research Data Management and Analysis in NGS Using Globus Genomics. (globus.org)
  • Globus Genomics is a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing Analysis using Galaxy, Globus Online and Amazon Web Services. (globus.org)
  • Analysis of HIV sequence data is a useful tool for characterizing transmission patterns not immediately apparent using traditional public health interview data, even in a state with lower HIV morbidity. (cdc.gov)
  • Furthermore, phylogenetic analysis based on molecular data also support the recognization of this new species. (researchgate.net)
  • Molecular analysis confirmed its placement in sect. (researchgate.net)
  • The Informatics Division , where informatics tools for genomic sequence analysis, sequencing project management, and biological databases are developed and implemented. (umontreal.ca)
  • Since the invention of DNA sequencing in the 1970's, the analysis of molecular biological sequences has been an inspiring source of computational problems, and even a computing machine using DNA molecules has been proposed. (helsinki.fi)
  • Hence biological sequence analysis is, in addition to fields like text processing and information retrieval, another natural application area of combinatorial algorithms for strings (stringology). (helsinki.fi)
  • Alignment is probably the most difficult and least understood component of a phylogenetic analysis from sequence data. (uncommondescent.com)
  • When regions of the sequences are so divergent that a reasonable alignment cannot be attained by manual methods using a sequence editor ("by eye"), those regions should probably be eliminated from the analysis. (uncommondescent.com)
  • This technology offers comprehensive data analysis and provides data management, integration, and scalability. (va.gov)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • Big data analysis and dimensionality reduction. (uib.no)
  • Specimens were collected from 9 provinces during 2 seasonal activities in 2001-2002, identified morphologically and subjected to PCR assay and direct sequencing. (who.int)
  • Exposure of endothelial cells (EC) to hypoxia results in the increased expression of a distinct set of proteins with molecular masses of 56, 47, 39, 36, and 34 kDa. (nih.gov)
  • To understand the mechanism(s) and significance of the up-regulation of these proteins we have identified the 36-kDa protein by limited amino-terminal amino acid sequencing. (nih.gov)
  • Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
  • Those who live and work with molecular systematics don't need any introduction to the alignment nightmare. (uncommondescent.com)
  • H. pylori is one of the most genetically diverse bacterial species, displaying from 2.7% to 8.0% of DNA sequence polymorphism ( 14 - 16 ). (cdc.gov)
  • ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)
  • The molecular data and relative distribution of these species in relation to their vectorial capacity and the epidemiology of malaria in the region are discussed. (who.int)
  • It will enable the creation of much more accurate trees, especially for the Tree of Life, which deals with hundreds of thousands of gene sequences from the millions of species on Earth. (scienceagogo.com)
  • Our results showed that a total of 13 polychaetes species identified in this study exhibited high levels of interspecific variation among 31 analyzed sequences. (scielo.cl)
  • Benchmarking second and third-generation sequencing platforms for microbial metagenomics. (cdc.gov)
  • 2019) based on molecular sequence data. (wikipedia.org)
  • Graph generated 31 August 2019 using data from PubMed using criteria . (cancerindex.org)
  • GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. (biomedcentral.com)
  • Strain relationships within the family were determined by analyzing allelic variation at both loci and building phylogenetic trees and by using multilocus sequence typing. (cdc.gov)
  • Public Health Approach to Big Data in the Age of Genomics: How Can we Separate Signal from Noise? (cdc.gov)
  • But now, after the accumulation of literally tens of thousands of molecular phylogenies - a vast literature groaning on library shelves - a larger audience is waking up to the fact that something may be very amiss in the house of molecular evolution. (uncommondescent.com)
  • Our process is novel because it rapidly and simultaneously aligns sequences and looks for the best phylogenies," says Linder. (scienceagogo.com)
  • To provide a quantum leap in this field, computer scientist Tandy Warnow, biologist Randy Linder and their graduate students, have created an automated computing method, called SATé, that can analyze these molecular data from thousands of organisms, simultaneously figuring out how the sequences should be organized and computing their evolutionary relatedness in as little as 24 hours. (scienceagogo.com)
  • Observational data are useful because we don't understand the pathogenesis of the disease in humans yet. (medscape.com)
  • The overwhelming lesson I brought home from the workshop, aside from the pricey beauty of that part of Cape Cod, was the utterly seat-of-the-pants, lost-in-space nature of molecular sequence alignment methods. (uncommondescent.com)
  • Actually, the sequences don't tell one that (for reasons I'll explore in part 2): for most investigators, an alignment software package such as Clustal-W or Muscle does the job. (uncommondescent.com)
  • El objetivo de este estudio fue utilizar datos moleculares nuevos con datos moleculares previamente publicados en combinación con una reanálisis de los caracteres morfológicos para testear la validez taxonómica de la especie V . coatlicue . (scielo.br)
  • Nuestra síntesis de datos moleculares y morfológicos provee evidencia para reconocer a V. coatlicue como una sinónima mas reciente de V . zonata . (scielo.br)
  • Data quality control: removal of low quality samples, detection of sample outliers and data filtering, identification of mislabeled samples. (uib.no)
  • It is vitally important to get some clinical data from these outbreaks," he told Medscape Medical News . (medscape.com)
  • These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. (mdpi.com)
  • Epidemiology and Molecular Characteristics of mcr-9 in Citrobacter spp. (cdc.gov)
  • Evaluating the health impact of large scale biological, social, and environmental data is an emerging challenge. (cdc.gov)
  • Twenty years ago, as a 2nd-year graduate student, I attended the first Molecular Evolution Workshop at the Marine Biological Laboratory-Woods Hole. (uncommondescent.com)
  • For their paper, published in Science , Warnow, the researchers tested SATé using computer-generated data and real biological data. (scienceagogo.com)
  • The biological data had been previously aligned manually by other experts. (scienceagogo.com)
  • Many life science organizations and research labs use internal and external informatics resources to store sequencing data. (globus.org)
  • Among named partner linkages where both persons had an HIV sequence available, 33.8% also had a molecular linkage and were deemed plausible transmission partners. (cdc.gov)
  • Of course, selectively eliminating regions opens the door to the criticism that the researcher is arbitrarily "throwing away data. (uncommondescent.com)
  • BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. (biomedcentral.com)
  • The Wisconsin Division of Public Health (DPH) analyzed HIV sequence data generated from provider-ordered drug resistance testing and collected through routine HIV surveillance to identify molecular clusters and describe demographic and transmission risk characteristics among pairs of persons whose sequences were highly genetically similar (i.e., molecular linkages). (cdc.gov)
  • The term Big Data is used to describe massive volumes of both structured and unstructured data that is so large and complex it is difficult to process and analyze. (cdc.gov)
  • In addition, SATé can accurately analyze DNA sequences that are rapidly evolving. (scienceagogo.com)
  • The 21-amino acid sequence from the bovine protein exhibited 90.5% identity with the human sequence of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). (nih.gov)
  • Figuring out these relationships requires analyzing large amounts of molecular data, such as DNA and protein sequences. (scienceagogo.com)
  • HIV sequence data, generated from provider-ordered drug resistance testing, can be used to understand characteristics of molecular clusters, a group of sequences for which each sequence is highly similar (linked) to all other sequences, and assess whether named partners are plausible HIV transmission partners. (cdc.gov)
  • HIV sequence data derived from standard drug resistance testing are reportable by laboratories to the Wisconsin DPH and are maintained in a secure surveillance database. (cdc.gov)
  • PCP is an important cause of pneumonia in patients newly-diagnosed with HIV in Uganda, is associated with high mortality, and putative molecular evidence of drug resistance is prevalent. (plos.org)
  • HIV-1 sequence data reported in Wisconsin during 2014-2017 for persons with HIV infection diagnosed through August 15, 2017, were analyzed using Secure HIV-TRACE (Secure HIV TRAnsmission Cluster Engine). (cdc.gov)
  • We would counter this argument with the rebuttal that the researcher has already discarded data, in a sense, by choosing to sequence one molecule rather than another because the latter did not evolve at an appropriate rate for the problem of interest. (uncommondescent.com)
  • These sequences have been previously avoided due to concern that the resulting trees would be poor. (scienceagogo.com)