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Search Results: 1 - 10 of 303440 matches for " Scott J Emrich "
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Hot RAD: A Tool for Analysis of Next-Gen RAD Tag Data
Lauren A. Assour,Nicholas LaRosa,Scott J. Emrich
Quantitative Biology , 2015,
Abstract: Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be applied to a non-model organism without a reference genome, though this creates the problem of how to begin data analysis on unmapped and unannotated reads. Our program, Hot RAD, presents a straightforward and easy-to-use method to take raw Illumina data that has been RAD tagged and produce consensus contigs or sequence stacks using a distributed framework, creating a basis on which to begin analyzing an organism's DNA. The GUI (graphical user interface) element of our tool makes it easy for those not familiar with the command line to take raw sequence files and produce usable data in a timely manner.
A statistical approach to finding overlooked genetic associations
Andrew K Rider, Geoffrey Siwo, Nitesh V Chawla, Michael Ferdig, Scott J Emrich
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-526
Abstract: We propose an alternative method to identify eQTLs that builds on traditional approaches. In contrast to genome-wide techniques, our method determines the significance of an association between an expression trait and a locus with respect to the set of all associations to the expression trait. The use of this specific information facilitates identification of expression traits that have an expression profile that is characterized by a single exceptional association to a locus.Our approach identifies expression traits that have exceptional associations regardless of the genome-wide significance of those associations. This property facilitates the identification of possible false negatives for genome-wide significance. Further, our approach has the property of prioritizing expression traits that are affected by few strong associations. Expression traits identified by this method may warrant additional study because their expression level may be affected by targeting genes near a single locus.We demonstrate our method by identifying eQTL hotspots in Plasmodium falciparum (malaria) and Saccharomyces cerevisiae (yeast). We demonstrate the prioritization of traits with few strong genetic effects through Gene Ontology (GO) analysis of Yeast. Our results are strongly consistent with results gathered using genome-wide methods and identify additional hotspots and eQTLs.New eQTLs and hotspots found with this method may represent regions of the genome or biological processes that are controlled through few relatively strong genetic interactions. These points of interest warrant experimental investigation.eQTL studies use gene expression data and genetic variation between individuals to calculate the association between expression traits and genotypes. In the context of eQTL studies an 'expression trait' refers to the quantity of labeled (c)DNA hybridizing to a single probe on a microarray. An eQTL is a strong association between one locus in the genome and one expression trait.
Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon
Shawn T O'Neil, Jason DK Dzurisin, Rory D Carmichael, Neil F Lobo, Scott J Emrich, Jessica J Hellmann
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-310
Abstract: Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments.Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5.Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).Although the costs of genome sequencing have declined dramatically, full genome sequencing efforts are still impractical for many nonmodel species. In such cases, transc
High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
Upeka Samarakoon, Allison Regier, Asako Tan, Brian A Desany, Brendan Collins, John C Tan, Scott J Emrich, Michael T Ferdig
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-116
Abstract: We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.Advances in genotyping technology led to an explosion of studies to identify genes of interest using classical genetic approaches [1]. Such studies facilitate the discovery of genetic factors related to disease, drug resistance and environmental response. Different approaches evolved rapidly with improvements in sequencing technology. Additional advances in molecular biology techniques have greatly increased the speed and throughput of discovery and analysis. For example, microarray-based marker discovery has been applied to model organisms such as yeast [2], Arabidopsis [3,4], rice [5-7], and non model organisms including the human malaria parasite Plasmodium falciparum [8-11]; however, this platform can be susceptible to poor hybridization efficiency of low complexity regions and difficulties in reproducibility. Such problems are magnified in organisms with high nucleotide bias, particularl
Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion
Neil F Lobo, Djibril M Sangaré, Allison A Regier, Kyanne R Reidenbach, David A Bretz, Maria V Sharakhova, Scott J Emrich, Sekou F Traore, Carlo Costantini, Nora J Besansky, Frank H Collins
Malaria Journal , 2010, DOI: 10.1186/1475-2875-9-293
Abstract: Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon.The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations.The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.Anopheles gambiae sensu stricto, the most important vector of human malaria in Africa, is the nominal member of a group of at least seven morphologically indistinguishable and closely related mosquito species [1,2]. Polytene chromosome analysis of this group, the An. gambiae complex, revealed an abundance of paracentric inversions [1,3], characterized by the breakage and 180 degree rearrangement of chromosome segments excluding the centromere. More than 130 paracentric inversions have been detected across the group as a whole, with 10 i
力学与实践 , 1981,
Abstract: 流体动力学作为物理学的一个独立的领域,并具有自己的一系列问题,这主要是由于二次大战中所积累的经验的结果.在那时以前,流体中发生的各种现象通常是作为数学问题或工程问题考虑的.然而,在
力学与实践 , 1981, DOI: 10.6052/1000-0992-1981-069
Abstract: 流体动力学作为物理学的一个独立的领域,并具有自己的一系列问题,这主要是由于二次大战中所积累的经验的结果.在那时以前,流体中发生的各种现象通常是作为数学问题或工程问题考虑的.然而,在...
Genetic Characterization of a Novel Iflavirus Associated with Vomiting Disease in the Chinese Oak Silkmoth Antheraea pernyi
Peng Geng, Wenli Li, Lan Lin, Joachim R. de Miranda, Scott Emrich, Lijia An, Olle Terenius
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092107
Abstract: Larvae of the Chinese oak silkmoth (Antheraea pernyi) are often affected by AVD (A. pernyi vomiting disease), whose causative agent has long been suspected to be a virus. In an unrelated project we discovered a novel positive sense single-stranded RNA virus that could reproduce AVD symptoms upon injection into healthy A. pernyi larvae. The genome of this virus is 10,163 nucleotides long, has a natural poly-A tail, and contains a single, large open reading frame flanked at the 5′ and 3′ ends by untranslated regions containing putative structural elements for replication and translation of the virus genome. The open reading frame is predicted to encode a 3036 amino acid polyprotein with four viral structural proteins (VP1-VP4) located in the N-terminal end and the non-structural proteins, including a helicase, RNA-dependent RNA polymerase and 3C-protease, located in the C-terminal end of the polyprotein. Putative 3C-protease and autolytic cleavage sites were identified for processing the polyprotein into functional units. The genome organization, amino acid sequence and phylogenetic analyses suggest that the virus is a novel species of the genus Iflavirus, with the proposed name of Antheraea pernyi Iflavirus (ApIV).
Hat die Psychiatrie Aufgaben in der Diagnostik gesellschaftlicher Befindlichkeiten und Problemlagen?
Emrich HM
Journal für Neurologie, Neurochirurgie und Psychiatrie , 2009,
Abstract: Hinsichtlich der Frage nach gesellschaftlichen Befindlichkeiten und Problemlagen erscheint es sinnvoll, die verschiedenen soziologischen Reflexionsebenen zu unterscheiden: die mikrosoziale Ebene, den Mesobereich und die Makroebene der Politik. Die gesellschaftlichen Problemlagen und emotionalen Situationen werden dabei in der Gegenwart sehr stark durch die Konzepte der "postmodernen Hyperflexibilit t" (Lyotard) gepr gt, wobei insbesondere auch die Medien eine zentrale Funktion einnehmen. Hierbei zeigt sich, dass es eine neue Form von Inszenierungen und Selbstdarstellungen gibt, die man als "Hysterie als Lebensform" charakterisieren kann.
Standardized Metadata for Human Pathogen/Vector Genomic Sequences
Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Ruchi M. Newman, Brett E. Pickett, Lynn M. Schriml, Timothy B. Stockwell, Christian J. Stoeckert, Dan E. Sullivan, Indresh Singh, Doyle V. Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M. Bruno, Elizabet Caler, Sinéad Chapman, Frank H. Collins, Christina A. Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W. Florian Fricke, Maria Giovanni, Matthew R. Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C. Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F. Mongodin, Cheryl I. Murphy, Garry Myers, Daniel E. Neafsey, Karen E. Nelson, William C. Nierman, Julia Puzak, David Rasko, David S. Roos, Lisa Sadzewicz, Joana C. Silva, Bruno Sobral, R. Burke Squires, Rick L. Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, Richard H. Scheuermann
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099979
Abstract: High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.
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