Bioinformatics sequence analysis dna. Medical search. Frequent questions

The company, which has about 15 employees but shares additional staff members and resources with its parent firm, currently offers a variety of genomic services, including next-generation sequencing on the Roche/454 GS FLX and GS Junior platforms. (genomeweb.com)
In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
Single-cell sequencing is a high-throughput technique that enables detection of genomic, transcriptomic, and epigenomic information at the individual cell level, offering significant advantages in detecting cellular heterogeneity, precise cell classification, and identifying rare subpopulations. (frontiersin.org)
Under SBIR funding by the National Science Foundation, Natural Selection, Inc. developed evolved classifiers to predict the locations of microRNA genes in genomic DNA. (natural-selection.com)
We begin with an introduction to bioinformatics and omics data analysis, and conclude with the walkthrough of a simple bioinformatics workflow for aligning transcriptomic sequences with genomic data. (r-bloggers.com)
we accept a wide range of biological and clinical samples including genomic DNA, cells, tissues, formalin-fixed and paraffin-embedded samples. (creativebiomart.net)
A volume of 5 ml of peripheral blood was drawn from each participant for genomic DNA isolation. (molvis.org)
Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. (lu.se)
We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. (lu.se)

If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist," says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the 'Center for Medical Systems Biology' (CMSB), a center of the Netherlands Genomics Initiative. (eurekalert.org)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
These data are used for a wide variety of important biological analyzes, including genome sequencing, comparative genomics, transcriptome analysis, and personalized medicine but are complicated by the volume and complexity of the data involved. (umd.edu)
Nov 2013-present: Senior Lecturer in Genomics and Bioinformatics, School of BABS, UNSW, Australia. (edu.au)
DNA Subway can make high-level DNA analysis available to faculty and students by simplifying annotation and comparative genomics workflows. (constantcontact.com)
The University of Auckland Centre for Genomics and Proteomics is a hub for research and teaching of Genomics, Proteomics and Bioinformatics. (auckland.ac.nz)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
Today, scientists working in the field of genomics have an array of sequencing methods at their disposal, each with unique strengths and limitations. (integra-biosciences.com)
Dr. Oakeson is a bioinformatics and genomics research analyst with the Utah Department of Health. (cdc.gov)
Genome structure, comparative genomics, and bioinformatics. (lu.se)
Presently, systematic and prospective analyses of breast cancer are ongoing to evaluate genomics in blood-based monitoring of residual disease of treatment effect. (lu.se)

Projects include annotating genomes and/or specific gene families, developing bioinformatics tools/workflows for assessing and tidying genome assemblies, and identifying/characterising ultraconserved elements. (edu.au)
Integrated Meta-Analysis of Prostate Cancer Genomes," E01 W81XWH2210247. (uclahealth.org)
The ability of single genes vs full genomes to resolve time and space in outbreak analysis. (cdc.gov)
Mobile DNA elements and the dynamics of genomes. (lu.se)
As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
NARST accomplishes these goals for surveillance on sporadic cases, outbreaks of illness, and special studies by conducting susceptibility testing and sequencing whole pathogen genomes. (cdc.gov)

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. (mpg.de)
Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. (elifesciences.org)
We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. (elifesciences.org)
Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor. (elifesciences.org)
This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. (elifesciences.org)
The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. (elifesciences.org)
DNA methylation, particularly 5-methylcytosine (5mC) at CpG sequences, is widely conserved in eukaryotes. (elifesciences.org)
it remains unclear if there is any common process or event that leads to the loss of DNA methylation systems in certain evolutionary lineages. (elifesciences.org)
Could the emergence or loss of a specific nucleosome regulator affect the evolution of DNA methylation as an epigenetic mechanism? (elifesciences.org)
Maintenance DNMTs (directly or indirectly) recognize hemimethylated CpGs and restore symmetric methylation at these sites to prevent the passive loss of 5mC upon DNA replication. (elifesciences.org)
Conversely, methylation by de novo DNMTs does not require methylated DNA templates. (elifesciences.org)
QIAseq Targeted Methyl Panels deliver high mapping efficiency (figure QIAseq Targeted Methyl Panel: mapping efficiency Input >1 ng – gDNA – FFPE – ccfDNA Results show high mapping on primer and high unique mapping. "> QIAseq Targeted Methyl Panel: mapping efficiency ), high reproducibility (figure QIAseq Targeted Methyl Panel: methylation degree reproducibility To test methylation degree accuracy and reproducibility, 40 ng control DNA with 0%, 50% and 100% methylation were processed using the QIAseq Targeted Methyl Panel, which consisted of 749 primers. Samples were sequenced on MiSeq and methylation degree of CpG covered by >30 UMI was evaluated, resulting in accurate and highly reproducible methylation calling. "> QIAseq Targeted Methyl Panel: methylation degree reproducibility ) and high correlation with established methods (figures QIAseq Targeted Methyl Panel - high correlation with established methods To test correlation with established methods, the QIAseq Targeted Methyl Panel was used with 40 ng input gDNA from hepatocytes. The panel consisted of 102 primers, covering 71 CpGs. Compared to the Supplier I array, methylation degree resulted in high correlation. "> QIAseq Targeted Methyl Panel - high correlation with established methods and QIAseq Targeted Methyl Panel: methylation status of FFPE DNA: methylation degree To test methylation status of FFPE DNA, the QIAseq Targeted Methyl Panel was used with 40 ng input FFPE DNA. The panel consisting of 93 primers covered 566 CpG sites. The evaluated methylation degree of 7 CpG sites of the MGMT gene highly correlates to the methylation degree that was previously validated with Pyrosequencing. "> QIAseq Targeted Methyl Panel: methylation status of FFPE DNA: methylation degree ). (qiagen.com)
In addition to RNA-associated silencing and histone modification, a major epigenetic mechanism in higher-order eukaryotes is DNA methylation. (qiagen.com)
DNA methylation occurs on cytosine residues, especially in CpG islands, which are GC-rich regions. (qiagen.com)
QIAseq Targeted Methyl Panels enable Sample to Insight, targeted next-generation sequencing (NGS) to interrogate DNA methylation degree. (qiagen.com)
Bisulfite sequencing is recognized as the "gold standard" for DNA methylation sequencing. (creativebiomart.net)
EGE investigated the consequences of early-life exposure to aflatoxin at the epigenome (DNA methylation [DNAm]) level. (who.int)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
The basics of DNA, RNA and protein sequences. (aber.ac.uk)
It encompasses every aspect of computational biology, from DNA sequence analysis to protein structure analysis and prediction. (uniba.it)
After my PhD, I moved into full-time bioinformatics, with a focus on protein. (edu.au)
During my second postdoc, I coined the term "Short Linear Motif" (SLiM) for a specific type of protein interaction motif and was instrumental in developing SLiMDisc and SLiMFinder, two of the first algorithms for successfully predicting SLiMs from protein sequences. (edu.au)
My lab employs sequence analysis techniques to interrogate protein and DNA sequences for the signals left behind by evolution. (edu.au)
This course is an interdisciplinary introduction to computational methods used to solve important problems in DNA and protein sequence analysis. (jhu.edu)
Real-time quantitative PCR (RT-qPCR) analysis and sfGFP (superfolder green fluorescent protein) analysis reveal that AmtR directly and negatively regulates the transcription and expression of crn A, cre T, csh A, and hyu B. A growth test shows that C. glutamicum ATCC 14067 can use creatine or creatinine as a sole nitrogen source. (frontiersin.org)
This commonly includes DNA, RNA, or protein sequence data. (r-bloggers.com)
Tet-assisted bisulfite sequencing (TAB-Seq) utilizes the activity of the Ten-Eleven Translocation (TET) family protein to gradually oxidize the 5mC and eventually demethylation. (creativebiomart.net)
Bioinformatic analyses of DNA- and protein sequences. (lu.se)

In this course, students learn the techniques required for the characterization of fossil DNA (DNA extraction, preparation of DNA libraries for high-throughput sequencing, quantification of DNA libraries) in the laboratory. (uni-tuebingen.de)
The project would suit a student with an interest in evolutionary and molecular ecology and with some previous experience of R. Ideally, the student will have some molecular lab experience and will carry out DNA extractions and preparation of sequencing libraries. (lu.se)
We also offer expertise, consultation, and discussion around the design of experiments, the construction of sequencing libraries as well as support in data processing and bioinformatic strategies. (lu.se)

The following graphic depicts a typical workflow for preparing, analyzing, and visualizing results from transcriptomic RNA sequencing data. (r-bloggers.com)
A great benefit of developing a common bioinformatics workflow is the ability to create a pipeline, in which the necessary outputs from the previous steps are passed on as inputs to subsequent steps. (r-bloggers.com)

Data analysis was performed by Gene Mapper 1.4. (intechopen.com)
1. Describe the current algorithms and data structures used in bioinformatic sequence analysis. (aber.ac.uk)
3. Demonstrate an understanding of the potential sources of error in this type of data and subsequent analyses. (aber.ac.uk)
Data analysis skills, algorithm and data structure skills. (aber.ac.uk)
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. (mpg.de)
However, the vast amount of biological data available and the demand for increasingly complex cations for their analysis offer vast opportunities for the systematic application of a wide range of techniques from computer science, including those based on computational logics. (uniba.it)
Students are also introduced to bioinformatics and analysis of high-throughput sequencing data. (uni-tuebingen.de)
We are a bioinformatics lab but like to incorporate bench data through collaboration wherever possible. (edu.au)
The first aims to centralize prostate cancer DNA sequencing data from around the country, then use bioinformatics computing pipelines developed by Dr. Boutros's lab to identify which genes are mutated repeatedly in prostate cancer to create biomarkers and ultimately optimize patient treatment. (uclahealth.org)
DNA Subway is a collaborative workspace to generate DNA sequence annotations, conduct phylogenetic analyses, and analyze Next-Generation Sequencing data. (constantcontact.com)
A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. (doe.gov)
Prior to graduate studies at UMD, Keith spent close to five years working on visualization and data analysis problems in the solar physics division at NASA Goddard Space Flight Center in Greenbelt, MD. (iscb.org)
In this tutorial participants will learn about biological data analysis with R and Unix/Linux tools. (r-bloggers.com)
Be able to use bioinformatics software tools to prepare omics data for analysis. (r-bloggers.com)
It is a computational field that involves the analysis of complex omics data. (r-bloggers.com)
Bioinformatics data is generated through various omics technologies used to analyze different types of biological molecules. (r-bloggers.com)
In this lesson you will gain experience in performing omics data analysis by working through part of a bioinformatics pipeline for analyzing gene expression data. (r-bloggers.com)
As a first step, we will begin with collecting some data for analysis. (r-bloggers.com)
3 On the other hand, Sanger sequencing remains popular for sequencing a short region in a small number of samples, because it can accurately read up to 1,000 base pairs without requiring complex data analysis. (integra-biosciences.com)
The simpler data analysis of Sanger sequencing, in combination with longer reads - Illumina sequencing typically only generates reads up to 300 bp - is especially useful for sequences with repeats. (integra-biosciences.com)
Comparing this data with untreated DNA sequencing data can identify methylated sites. (creativebiomart.net)
During the depth sequencing, unmethylated cytosines and 5mC are read as T, while 5hmC is still C. Combining this data with data generated from standard bisulfite sequencing yields a genome-wide 5hmC profiling at single-base resolution. (creativebiomart.net)
customers only need to provide samples, and we will complete full TAB-Seq experiment from sonication, adaptor ligation, glucosylation, TET oxidation, bisulfite treatment, PCR amplification, on-machine sequencing to data analysis. (creativebiomart.net)
we provide you with both standard data analyses and customized bioinformatics analyses. (creativebiomart.net)
Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (cdc.gov)
Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (cdc.gov)
Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)
So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)
Bioinformatics is an interdisciplinary field where methods and software tools for understanding biological data are developed. (lu.se)
Scientific discovery now relies heavily on efficient handling and analysis of the enormous amount of data generated from wet lab experiments. (lu.se)
Bioinformatics combines biology, computer science and statistics to analyse this kind of data. (lu.se)
The Bioinformatics programme trains students, from different fields, in the computational analysis of biological data. (lu.se)
All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)
Typically when data are presented, the fluor- escent intensity from the tissue is pseudo-colored red and the intensity from the reference green, and the logarithmic ratio of background corrected red and green intensities for each gene (spot) is subject to analysis (see Fig. 1 ). (lu.se)
CTG uses secure LSENS servers hosted by LUNARC, center for scientific and technical computing at Lund University facility, for internal data management and analysis. (lu.se)
During my Ph.D. studies, my focus has been analyzing sequencing data in relation to transposable elements. (lu.se)
I have been mainly involved in the data analysis and interpretation of this data, working closely with biologists who conduct experiments in the lab. (lu.se)
The student will employ bioinformatics approaches to process the sequence data and carry out multivariate analyses in R. (lu.se)

And I take care of all of the bioinformatic analyses, as well here. (cdc.gov)
Kelly Oakeson] The purpose of our perspective in EID was really to help public health laboratories around the country understand sort of basics of typical bioinformatic pipelines and analyses, right? (cdc.gov)

The initiator element (Inr) is the most common sequence found at the transcription start site of eukaryotic genes. (wikipedia.org)
Though the Inr element is not fully understood it has been recognized as the most frequently occurring sequence at the start site of genes in multiple species. (wikipedia.org)
We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
Using DNA sequencing followed by extensive bioinformatics analyses, researchers identified 34 mutations in 17 CH-driver genes. (spaceref.com)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
Thirty-four known candidate genes for congenital cataracts were analyzed in the probands of 21 families with targeted next-generation sequencing (NGS). (molvis.org)
Previous studies regarding gene mutations in congenital cataracts have used Sanger sequencing in known disease-causing genes. (molvis.org)
Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)

Phylogenetic analyses indicate regional dissemi- pendix Table 1). (cdc.gov)
The primer and probe sets in the HA gene were checked for mismatches, and phylogenetic analyses were performed to determine the molecular epidemiology of these viruses. (who.int)

As the virus circulates and spreads, it accumulates mutations that are used to name new virus sequences so that researchers, health care providers, and public health authorities have a common language to describe genetic sequence mutations. (fda.gov)
The impact of mutations on a test's performance is influenced by several factors, including the sequence of the variant, the design of the test, and the prevalence of the variant in the population. (fda.gov)
They discovered DNA mutations, known as somatic mutations, in the blood-forming system (hematopoietic stem cells) in all 14 astronauts studied. (spaceref.com)

High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
The emergence of high-throughput sequencing technologies (HTS) has been a significant step forward in recent years, greatly reducing both the cost and the labor required for biodiversity studies (Bohmann et al. (springer.com)
So far, we have not ventured into ultra high-throughput sequencing, for two main reasons. (genomeweb.com)
2,3 Because Sanger sequencing can only sequence a single fragment at a time, Illumina's NGS technology - which can sequence millions of DNA molecules simultaneously - is preferred for high throughput applications. (integra-biosciences.com)
Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)

However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
From the pioneering work of Sanger sequencing to the cutting-edge advancements in next generation sequencing (NGS) technologies, we have come a long way in our ability to decipher the genetic code. (integra-biosciences.com)
To help you choose the right one for your application, we will compare Sanger sequencing with NGS techniques in this blog, before discussing the differences between Illumina, PacBio and Nanopore sequencing. (integra-biosciences.com)
What is Sanger sequencing used for? (integra-biosciences.com)
Sanger sequencing was invented in 1977 and, despite the development of several NGS methods - such as Illumina, PacBio and Nanopore sequencing - since that time, it is still being used in laboratories today. (integra-biosciences.com)
For example, clinical laboratories often rely on Sanger sequencing to validate gene variants that have been identified by NGS using Illumina platforms, primarily due to the method's unparalleled accuracy of 99.99 percent. (integra-biosciences.com)
3 These repeats can be determined more easily with Sanger sequencing, because the Illumina technique requires many short overlapping sequences to be linked together, a task that can be difficult, especially when the repeat sequence is longer than the read sequence. (integra-biosciences.com)
7 On the other hand, the cost of sequencing 1,000 bases is considerably higher on a Sanger sequencer than on an Illumina instrument, 8 so throughput will ultimately determine what makes financial sense for long term investment. (integra-biosciences.com)
We've just seen that Sanger sequencing is preferred over Illumina sequencing when dealing with repeats. (integra-biosciences.com)
However, the two long-read NGS methods - PacBio and Nanopore sequencing - are even better suited for this, 9 as their read lengths outperform Sanger sequencing. (integra-biosciences.com)
An advantage that all three NGS methods have over Sanger sequencing is higher sensitivity. (integra-biosciences.com)
With Sanger sequencing, one chromatogram is generated for all the molecules being sequenced. (integra-biosciences.com)
Sanger sequencing was used to perform the cosegregation analysis. (molvis.org)
Compared with traditional Sanger sequencing, targeted NGS for genetic testing of congenital cataracts markedly increases the mutation detection rate and is cost-effective. (molvis.org)
One unit for Next-Generation Sequencing (NGS) and a second unit for more traditional Sanger DNA sequencing. (lu.se)
Our unit has instruments and resources for traditional Sanger Sequencing (ABI 3500) but also for the so-called Next-Generation Sequencing (NGS) based on the Illumina MiSeq platform. (lu.se)

Bioinformatics is a truly interdisciplinary field at the boundary between biology and computer science. (uniba.it)
Bioinformatics is an interdisciplinary field that combines techniques and knowledge from both computer science and biology. (r-bloggers.com)

Bioinformatics is a multidisciplinary field that combines biology with quantitative methods to help understand biological processes, such as disease progression. (edu.au)
The emphasis will be on the computational algorithms that allow us to discover information from biological sequence. (aber.ac.uk)
Most of the tools routinely used in bioinformatics have been developed by scientists with a background in biological sciences. (uniba.it)
My research interests stem from a fascination with the molecular basis of evolutionary change and how we can harness genetic sequence patterns to make useful predictions about biological systems. (edu.au)
2011-2013: Lecturer (Bioinformatics and Molecular Evolution), Centre for Biological Sciences, University of Southampton, UK. (edu.au)
2007-2011: Senior Research Fellow (Bioinformatics), Centre for Biological Sciences, University of Southampton, UK. (edu.au)

I am now involved in multiple de novo whole genome sequencing and assembly projects, using short read (Illumina), long read (PacBio & Nanopore) and linked read (10x Chromium) sequencing. (edu.au)
We are using the latest generation of sequencing, assembly and scaffolding technologies (10x Chromium "linked reads", PacBio, Oxford Nanopore, HiC) to assemble multiple species including venomous snakes, the cane toad, marsupials, dog breeds, and Australian flora. (edu.au)
Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples. (cdc.gov)

Since starting my own research group in 2007, I have expanded my collaborative activities, developing and applying sequence analysis pipelines for a number of different projects under the broad general umbrella of adaptation and response to climate change. (edu.au)
Their focus is creating pipelines to enhance and automate analyses. (folkhalsomyndigheten.se)

Emerging single-cell sequencing technologies will undoubtedly enhance our understanding of the complex biology of pancreatic cancer and pave the way for new directions in its clinical diagnosis and treatment. (frontiersin.org)
Our live panel discussion will talk about the paths of our panel members, students and professionals, in Bioinformatics and Computational Biology. (iscb.org)
I am broadly interested in population genetics, bioinformatics, and molecular biology and evolution related to infectious diseases, forensic science, and Monarch butterflies. (iscb.org)

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
The solid evolutionary analyses form a strong basis for experimental follow-up studies. (elifesciences.org)
These predictions led to many novel microRNA sequences that were later confirmed by experimental analysis and deep sequencing. (natural-selection.com)
The core offers state-of-the art next generation sequencing technology for experimental and preclinical studies with particular expertise in transcriptome analysis. (lu.se)
Our facility staff have expertise in most aspects of DNA sequence analyses and can offer help and advice on experimental design, library constructions, analyses and bioinformatics and provides assistance to both beginners and experienced users. (lu.se)
The course covers the basics, principles and limitations for the most common methods for multivariate statistics (analysis of variance, principal component analysis and partial least squares regression), experimental design (super-saturated and factorial designs) and method validation with a focus on practical use. (lu.se)

Cloacal samples for microbiome analysis have been collected from adult and nestling tawny owls from a nestbox-breeding population close to Lund between 2020 and 2023. (lu.se)

In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)

We undertake DNA sequencing, genotyping and gene expression analysis, as well as a full range of proteomic and mass spectrometric services including 2-D electrophoresis, HPLC, small molecule elucidation peptide mass fingerprinting, sequencing and quantitative proteomics. (auckland.ac.nz)

Power Quant System (Promega, USA) was used for DNA quantification of the samples. (intechopen.com)
This is performed by quantification of cell-free tumor DNA in plasma, which has shown very promising result. (lu.se)

Methods for analysis of gene expression: microarray, hybridisation, promoter analyses. (lu.se)

Moreover, the meeting could also be a chance to bring together researchers that work in the Bioinformatics application domain using approaches that fall into different areas of Artificial Intelligence, with the aim of identifying possibilities of cooperation and synergies between the respective areas of interest. (uniba.it)
EGE also develops epigenomic methodologies, profiling strategies, and bioinformatics tools, applicable to population-based cohorts and molecular epidemiology studies coordinated by IARC researchers and external collaborators. (who.int)

SARS-CoV-2 genetic sequences are identified and named using the Phylogenetic Assignment of Named Global Outbreak (PANGO) nomenclature referred to as the PANGO lineage. (fda.gov)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

3 NGS methods have a much lower detection limit, because they analyze the nucleotide sequence of each molecule individually. (integra-biosciences.com)
7 With Illumina sequencing, for example, the detection limit is 1 percent. (integra-biosciences.com)
Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. (cdc.gov)
The CDC's Office of Advanced Molecular Detection is doing a great job of helping educate people on what bioinformatics is and how it's being applied. (cdc.gov)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)
The team also provides bioinformatics analyses for bacterial outbreak detection, public health laboratory support, and development of new bioinformatics tools. (cdc.gov)

Infectious Disease Metagenomics: Error Mitigation and Best Practices for the Clinical Routine Use of Metagenomic Sequencing. (cdc.gov)
The Bioinformatics and Metagenomics Team (BIOME) provides bioinformatics support and research for foodborne pathogen surveillance and outbreak investigation. (cdc.gov)

Here, we analysed the urinary microbiota of healthy men and women and compared it with that of women during BV and after antibiotic treatment using next-generation sequencing of the 16S rRNA gene V1-V2 regions. (biomedcentral.com)
Molecular sampling at logarithmic rates for next-generation sequencing. (cdc.gov)
Sarah Gregory] And following on that, what is Next Generation Sequencing? (cdc.gov)
The MultiPark next generation sequencing (NGS) facility is located at the BMC in Lund. (lu.se)
The Public Health Agency's Next Generation Sequencing (NGS) platform performs massive parallel sequencing of DNA and RNA. (folkhalsomyndigheten.se)
NBL also uses next-generation sequencing methods to characterize and subtype Clostridium botulinum and related organisms, including a national molecular surveillance database for comparing genetic relatedness among strains across the United States and identifying trends among botulism cases. (cdc.gov)

A mutation (also referred to as viral mutation or genetic mutation) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is a change in the genetic sequence of the SARS-CoV-2 virus when compared with a reference sequence such as Wuhan-Hu1 (the first genetic sequence identified) or USA-WA1/2020 (the first identified in the United States). (fda.gov)

Methods for gene identification and analysis of gene structure: cloning, PCR, restriction mapping, in situ hybridisation, DNA sequencing. (lu.se)

Multivariate statistical analysis of epigenetic regulation with application to the analysis of human embryonic stem cells. (mpg.de)

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics. (cdc.gov)
Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)

Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)
These studies show that maternal novel method that enables sensitive and assessed in plasma taken at 1-16 weeks exposure and diet during the early stages targeted deep DNAm analysis in minute of pregnancy, and global DNAm of of pregnancy is associated with changes amounts of DNA present in body fluids white blood cel s from their infants was in epigenome patterns of infants. (who.int)

However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
Read alignment maps short DNA sequences to a reference genome to discover conserved and polymorphic regions of the genome. (umd.edu)

The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

Sequence similarity, alignment and k-mer algorithms. (aber.ac.uk)

Although Inr element varies between promoters, the sequence is highly conserved between humans and yeast. (wikipedia.org)
While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. (elifesciences.org)

Creative BioMart provides Tet-assisted bisulfite sequencing (TAB-Seq), which is based on bisulfite sequencing and identifies 5hmC at a single-base resolution and determines its abundance at each modified site. (creativebiomart.net)
What Is Tet-Assisted Bisulfite Sequencing? (creativebiomart.net)
Treatment of DNA with sodium bisulfite converts unmethylated cytosine (C) to uracil (U), which is eventually shown as thymine (T) in the DNA sequencing reaction. (creativebiomart.net)
However, standard bisulfite sequencing cannot distinguish 5hmC from 5mC because both of them are resistant to bisulfite treatment. (creativebiomart.net)
Finally, the DNA is treated with bisulfite. (creativebiomart.net)
The main advantage of TAB-Seq over oxidative bisulfite sequencing (oxBS-Seq) is that it actually measures 5hmC and does not infer it. (creativebiomart.net)

We are able to develop complete assays from scratch, so customers can come to us and say, 'we want targeted resequencing done on gene X', and we develop everything necessary, either using amplicon enrichment or in-solution enrichment, for example the Agilent SureSelect system, and then we perform the sequencing. (genomeweb.com)

In this chapter we will present the usefulness of genetic DNA testing of skeletonized remains for human identification, by using automate DNA extraction from three different human bone types: tooth, femur and petrous pyramid. (intechopen.com)
The DNA extraction from bone samples was performed on the automate Maxwell RSC 48 Instrument (Promega, USA), using the Maxwell FSC DNA IQ Casework Kit (Promega, USA). (intechopen.com)
Considering that these cases involved DNA extraction from teeth, bones and old human remains, automate system was felt to be the best option to reduce handling errors and increase the possibilities of obtaining good quality DNA. (intechopen.com)

Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
This workshop aims at collecting contributes, and at bringing together scientists and practitioners, whose research interests lie across the areas of Logics (along various possible representation formalisms, inference strategies and approaches) and Bioinformatics. (uniba.it)
Hence, the twofold attempt of the workshop: stimulating application of Logic approaches in Bioinformatics, and searching for new challenges posed by Bioinformatics that can be successfully tackled by Logic-based approaches. (uniba.it)
His current research efforts are focused on the development of novel approaches for the integrative analysis of large-scale drug screen and molecular profiling datasets, in order to detect biomarkers related to patient response to drug treatment. (iscb.org)

Transposable elements refer to DNA sequences capable of moving from one part of the genome to another. (lu.se)

In animals, 5mC is maintained during DNA replication by DNMT1 together with UHRF1, which directly recognizes hemimethylated cytosine via the SRA domain and stimulates activity of DNMT1 in a manner dependent on its ubiquitin-ligase activity ( Nishiyama and Nakanishi, 2021 ). (elifesciences.org)

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. (mpg.de)

In the last two decades, DNA barcoding, the sequencing of short species-specific amplicons, has considerably simplified community analyses (Hebert et al. (springer.com)
The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)

Topics covered include the analysis of ancient DNA, phylogenetics, evolutionary genetics, and population genetic methods. (uni-tuebingen.de)

The DNA Sequencing Facility is a cross-faculty facility for DNA and cDNA (RNA-Seq) sequencing and is primarily intended for academic research groups based at Lund University. (lu.se)
We offer services for DNA and cDNA (RNA-Seq) sequencing. (lu.se)

16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)

The FDA will update this page when significant new information becomes available, including when the FDA's analyses identify tests for which performance may be impacted for known SARS-CoV-2 variants. (fda.gov)
7 This makes analysis easy, but variants are only detected when they occur in about 15 to 20 percent of the sequences. (integra-biosciences.com)
Bioinformatics analysis of the sequence variants was performed through computational predictive programs. (molvis.org)

The DNA is that of dr Marjolein Kriek, a clinical geneticist at LUMC. (eurekalert.org)
BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology. (cdc.gov)
Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)
In addition, clinical trials, including the BRCA diagnostic laboratory as well as the unique prospective south Sweden Cancerome Analysis Network in Breast cancer (SCAN-B) has been successfully established in Lund. (lu.se)

In addition to the diagnostic DNA sequences, Chamberlainium capense sp. (degruyter.com)
The American College of Obstetricians and Gynecologists (ACOG) has recommended that serum screening, cell-free DNA screening, and diagnostic tests, such as chorionic villus sampling (CVS) and amniocentesis , be discussed with and offered to all women early in pregnancy, regardless of their age. (medscape.com)

Moreover, single-cell sequencing provides unique insights into the mechanisms of pancreatic cancer metastasis and cachexia, paving the way for developing novel preventive strategies. (frontiersin.org)

The DNA samples were amplified on a Pro Flex PCR System (Thermo Fischer, USA), using the Global Filer PCR Amplification Kit (Applied Biosystems, USA). (intechopen.com)
DNA extracts of these samples were amplified by PCR and genotyped by spoligotyping. (who.int)

The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. (nature.com)
Epigenetic Analysis of Human Embryonic Stem Cells: Basics, Computational Methods, Applications. (mpg.de)
From the paleogenetics group, this includes a review of genetic methods used to reconstruct human past from both extant populations and ancient DNA. (uni-tuebingen.de)
Shifting our attention to NGS methods, we will now examine Illumina and PacBio sequencing side by side. (integra-biosciences.com)

Anatomy2

Organisms8

Diseases1

Chemicals and Drugs38

Analytical, Diagnostic and Therapeutic Techniques and Equipment47

Phenomena and Processes95

Disciplines and Occupations18

Anthropology, Education, Sociology and Social Phenomena6

Technology, Industry, Agriculture3

Humanities2

Information Science52

Health Care12

Geographicals1

Genomic9

Genomics11

Genomes6

Methylation17

Protein18

Libraries3

Workflow2

Data43

Bioinformatic2

Genes8

Phylogenetic analyses2

Mutations3

High-throughput5

Sanger16

Interdisciplinary field2

Biological6

Nanopore3

Pipelines2

Biology3

Experimental6

20231

Massively parallel1

Proteomics1

Quantification2

Microarray1

Researchers2

Genetic sequences2

Detection6

Metagenomics2

Next-generation6

20201

Situ1

Multivariate1

Pathogen2

Enables2

Reference genome2

RRNA gene1

Similarity1

Highly conserved2

Bisulfite6

Enrichment1

Extraction3

Approaches4

Transposable elements1

20211

Epigenomic1

Amplicons2

Evolutionary1

CDNA2

Bacterial3

Variants3

Clinical5

Diagnostic2

Insights1

Samples were amplified2

Methods4