The Experts below are selected from a list of 92574 Experts worldwide ranked by ideXlab platform
Michael Snyder - One of the best experts on this subject based on the ideXlab platform.
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High Throughput Sequencing and Assessing Disease Risk
Cold Spring Harbor perspectives in medicine, 2019Co-Authors: Shannon Rego, Michael SnyderAbstract:High-Throughput Sequencing has dramatically improved our ability to determine and diagnose the underlying causes of human disease. The use of whole-genome and whole-exome Sequencing has facilitated faster and more cost-effective identification of new genes implicated in Mendelian disease. It has also improved our ability to identify disease-causing mutations for Mendelian diseases whose associated genes are already known. These benefits apply not only in cases in which the objective is to assess genetic disease risk in adults and children, but also for prenatal genetic testing and embryonic testing. High-Throughput Sequencing has also impacted our ability to assess risk for complex diseases and will likely continue to influence this area of disease research as more and more individuals undergo Sequencing and we better understand the significance of variation, both rare and common, across the genome. Through these activities, High-Throughput Sequencing has the potential to revolutionize medicine.
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High-Throughput Sequencing Technologies
Molecular cell, 2015Co-Authors: Jason A. Reuter, Damek V. Spacek, Michael SnyderAbstract:The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA Sequencing technologies over the past 10 years. Here, we discuss commonly used High-Throughput Sequencing platforms, the growing array of Sequencing assays developed around them, as well as the challenges facing current Sequencing platforms and their clinical application.
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Overview of High Throughput Sequencing Technologies to Elucidate Molecular Pathways in Cardiovascular Diseases
Circulation research, 2013Co-Authors: Jared M. Churko, Gary L. Mantalas, Michael SnyderAbstract:High Throughput Sequencing technologies have become essential in studies on genomics, epigenomics, and transcriptomics. Although Sequencing information has traditionally been elucidated using a low Throughput technique called Sanger Sequencing, High Throughput Sequencing technologies are capable of Sequencing multiple DNA molecules in parallel, enabling hundreds of millions of DNA molecules to be sequenced at a time. This advantage allows High Throughput Sequencing to be used to create large data sets, generating more comprehensive insights into the cellular genomic and transcriptomic signatures of various diseases and developmental stages. Within High Throughput Sequencing technologies, whole exome Sequencing can be used to identify novel variants and other mutations that may underlie many genetic cardiac disorders, whereas RNA Sequencing can be used to analyze how the transcriptome changes. Chromatin immunoprecipitation Sequencing and methylation Sequencing can be used to identify epigenetic changes, whereas ribosome Sequencing can be used to determine which mRNA transcripts are actively being translated. In this review, we will outline the differences in various Sequencing modalities and examine the main Sequencing platforms on the market in terms of their relative read depths, speeds, and costs. Finally, we will discuss the development of future Sequencing platforms and how these new technologies may improve on current Sequencing platforms. Ultimately, these Sequencing technologies will be instrumental in further delineating how the cardiovascular system develops and how perturbations in DNA and RNA can lead to cardiovascular disease.
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High‐Throughput Sequencing for biology and medicine
Molecular systems biology, 2013Co-Authors: Wendy Weijia Soon, Manoj Hariharan, Michael SnyderAbstract:Advances in genome Sequencing have progressed at a rapid pace, with increased Throughput accompanied by plunging costs. But these advances go far beyond faster and cheaper. High-Throughput Sequencing technologies are now routinely being applied to a wide range of important topics in biology and medicine, often allowing researchers to address important biological questions that were not possible before. In this review, we discuss these innovative new approaches—including ever finer analyses of transcriptome dynamics, genome structure and genomic variation—and provide an overview of the new insights into complex biological systems catalyzed by these technologies. We also assess the impact of genotyping, genome Sequencing and personal omics profiling on medical applications, including diagnosis and disease monitoring. Finally, we review recent developments in single-cell Sequencing, and conclude with a discussion of possible future advances and obstacles for Sequencing in biology and health.
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High Throughput Sequencing for biology and medicine
Molecular Systems Biology, 2013Co-Authors: Wendy Weijia Soon, Manoj Hariharan, Michael SnyderAbstract:Advances in genome Sequencing have progressed at a rapid pace, with increased Throughput accompanied by plunging costs. But these advances go far beyond faster and cheaper. High-Throughput Sequencing technologies are now routinely being applied to a wide range of important topics in biology and medicine, often allowing researchers to address important biological questions that were not possible before. In this review, we discuss these innovative new approaches—including ever finer analyses of transcriptome dynamics, genome structure and genomic variation—and provide an overview of the new insights into complex biological systems catalyzed by these technologies. We also assess the impact of genotyping, genome Sequencing and personal omics profiling on medical applications, including diagnosis and disease monitoring. Finally, we review recent developments in single-cell Sequencing, and conclude with a discussion of possible future advances and obstacles for Sequencing in biology and health.
Fredrik Söderbom - One of the best experts on this subject based on the ideXlab platform.
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Identification and verification of microRNAs by High-Throughput Sequencing.
Methods in molecular biology (Clifton N.J.), 2013Co-Authors: Jimmie Hällman, Lotta Avesson, Johan Reimegård, Max Käller, Fredrik SöderbomAbstract:High-Throughput Sequencing methods have become invaluable for detection and analysis of small RNAs. The results are millions of sequences that need to be carefully analyzed by computational methods and preferentially verified by different experimental techniques. Here we describe how to use High-Throughput Sequencing followed by bioinformatics and northern blot to identify one particular class of small RNA, microRNAs.
Yongqin Yin - One of the best experts on this subject based on the ideXlab platform.
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Verification of miRNAs in ginseng decoction by High-Throughput Sequencing and quantitative real-time PCR.
Heliyon, 2019Co-Authors: Yingfang Wang, Mengyuan Peng, Wenjuan Wang, Yanlin Chen, Jingjing Cao, Zhiyun Lin, Zemin Yang, Mengjuan Gong, Yongqin YinAbstract:Abstract Panax ginseng C. A. Meyer is a precious traditional Chinese medicine that has been clinically used for over thousands of years. In general, ginseng needs to be prepared to ginseng decoction before taking it. MicroRNAs are a class of small (18–24 nt), single-stranded molecules that regulate gene expression at the post-transcriptional level. Considering that ginseng miRNAs may be bioactive compounds, we used Illumina High-Throughput Sequencing and quantitative real-time PCR (qRT-PCR) to validate the existence of miRNAs in fresh ginseng decoction which have been boiled at High temperature. Our previous studies have demonstrated that there are several miRNAs in fresh ginseng. The roots of fresh Panax ginseng were prepared according to routine methods, from which miRNAs were extracted and sequenced. A total of 43 miRNAs were identified from water decoction by Illumina High-Throughput Sequencing, belonging to 71 miRNA families. The target genes of these miRNAs were predicted by Sequencing, and were annotated by GO, KEGG and Nr databases. The functions of these target genes mainly included plant hormone signal transduction, transcription regulation, macromolecular metabolism and auxin signaling. Nine Highly expressed miRNAs (miR159, miR167, miR396, miR166, miR168, miR156, miR165, miR162 and miR394) were verified by qRT-PCR, and the results of Illumina High-Throughput Sequencing and qRT-PCR were consistent. Results from this study indicate that miRNAs remained stable in P. ginseng after High-temperature boiling. Additionally, Illumina High-Throughput Sequencing was superior in the acquisition of Higher amount of small RNAs.
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Verification of miRNAs in ginseng decoction by High-Throughput Sequencing and quantitative real-time PCR
Elsevier, 2019Co-Authors: Yingfang Wang, Mengyuan Peng, Wenjuan Wang, Yanlin Chen, Jingjing Cao, Zhiyun Lin, Zemin Yang, Mengjuan Gong, Yongqin YinAbstract:Panax ginseng C. A. Meyer is a precious traditional Chinese medicine that has been clinically used for over thousands of years. In general, ginseng needs to be prepared to ginseng decoction before taking it. MicroRNAs are a class of small (18–24 nt), single-stranded molecules that regulate gene expression at the post-transcriptional level. Considering that ginseng miRNAs may be bioactive compounds, we used Illumina High-Throughput Sequencing and quantitative real-time PCR (qRT-PCR) to validate the existence of miRNAs in fresh ginseng decoction which have been boiled at High temperature. Our previous studies have demonstrated that there are several miRNAs in fresh ginseng. The roots of fresh Panax ginseng were prepared according to routine methods, from which miRNAs were extracted and sequenced. A total of 43 miRNAs were identified from water decoction by Illumina High-Throughput Sequencing, belonging to 71 miRNA families. The target genes of these miRNAs were predicted by Sequencing, and were annotated by GO, KEGG and Nr databases. The functions of these target genes mainly included plant hormone signal transduction, transcription regulation, macromolecular metabolism and auxin signaling. Nine Highly expressed miRNAs (miR159, miR167, miR396, miR166, miR168, miR156, miR165, miR162 and miR394) were verified by qRT-PCR, and the results of Illumina High-Throughput Sequencing and qRT-PCR were consistent. Results from this study indicate that miRNAs remained stable in P. ginseng after High-temperature boiling. Additionally, Illumina High-Throughput Sequencing was superior in the acquisition of Higher amount of small RNAs. Keywords: Bioinformatics, Molecular biolog
Karen B Avraham - One of the best experts on this subject based on the ideXlab platform.
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High-Throughput Sequencing to decipher the genetic heterogeneity of deafness
Genome Biology, 2012Co-Authors: Zippora Brownstein, Yoni Bhonker, Karen B AvrahamAbstract:Identifying genes causing non-syndromic hearing loss has been challenging using traditional approaches. We describe the impact that High-Throughput Sequencing approaches are having in discovery of genes related to hearing loss and the implications for clinical diagnosis.
Alberto Carbonell - One of the best experts on this subject based on the ideXlab platform.
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Immunoprecipitation and High-Throughput Sequencing of ARGONAUTE-Bound Target RNAs from Plants.
Methods in molecular biology (Clifton N.J.), 2017Co-Authors: Alberto CarbonellAbstract:ARGONAUTE (AGO) proteins function in small RNA (sRNA)-based RNA silencing pathways to regulate gene expression and control invading nucleic acids. In posttranscriptional RNA silencing pathways, plant AGOs associate with sRNAs to interact with Highly sequence-complementary target RNAs. Once the AGO-sRNA-target RNA ternary complex is formed, target RNA is typically repressed through AGO-mediated cleavage or through other cleavage-independent mechanisms. The universe of sRNAs associating with diverse plant AGOs has been determined though AGO immunoprecipitation (IP) and High-Throughput Sequencing of co-immunoprecipitated sRNAs. To better understand the biological functions of AGO-sRNA complexes, it is crucial to identify the repertoire of target RNAs they regulate. Here I present a detailed AGO-RNA IP followed by High-Throughput Sequencing (AGO RIP-Seq) methodology for the isolation of AGO ternary complexes from plant tissues and the High-Throughput Sequencing of AGO-bound target RNAs. In particular, the protocol describes the IP of slicer-deficient hemagglutinin (HA)-tagged AGO proteins expressed in plant tissues, the isolation of AGO-bound RNAs, and the generation of target RNA libraries for High-Throughput Sequencing.