keyword
MENU ▼
Read by QxMD icon Read
search

Genome annotation

keyword
https://www.readbyqxmd.com/read/29029205/transcriptome-analysis-of-the-triatoma-infestans-hemiptera-reduviidae-integument
#1
Gustavo M Calderón-Fernández, Débora E Moriconi, Andrea B Dulbecco, M Patricia Juárez
The insect integument, formed by the cuticle and the underlying epidermis, is essential for insect fitness, regulation of lipid biosynthesis and storage, insect growth and feeding, together with development progress. Its participation in insecticide resistance has also been outlined. Triatoma infestans Klug (Hemiptera: Reduviidae) is one of the major vectors of Chagas disease in South America; however, genomic data are scarce. In this study, we performed a transcriptome analysis of the nymph integument in order to identify which genes are expressed and their putative role...
September 27, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29028988/quasar-mpra-accurate-allele-specific-analysis-for-massively-parallel-reporter-assays
#2
Cynthia A Kalita, Gregory A Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi
Motivation: The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRA), have been used to functionally validate non-coding variants...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028909/the-systematic-analysis-of-ultraconserved-genomic-regions-in-the-budding-yeast
#3
Zhi-Kai Yang, Feng Gao
Motivation: In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028889/segway-2-0-gaussian-mixture-models-and-minibatch-training
#4
Rachel C W Chan, Maxwell W Libbrecht, Eric G Roberts, Jeffrey A Bilmes, William Stafford Noble, Michael M Hoffman
Summary: Segway performs semi-automated genome annotation, discovering joint patterns across multiple genomic signal datasets. We discuss a major new version of Segway and highlight its ability to model data with substantially greater accuracy. Major enhancements in Segway 2.0 include the ability to model data with a mixture of Gaussians, enabling capture of arbitrarily complex signal distributions, and minibatch training, leading to better learned parameters. Availability and Implementation: Segway and its source code are freely available for download at http://segway...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028836/affected-pathways-and-transcriptional-regulators-in-gene-expression-response-to-an-ultra-marathon-trail-global-and-independent-activity-approaches
#5
Maria Maqueda, Emma Roca, Daniel Brotons, Jose Manuel Soria, Alexandre Perera
Gene expression (GE) analyses on blood samples from marathon and half-marathon runners have reported significant impacts on the immune and inflammatory systems. An ultra-marathon trail (UMT) represents a greater effort due to its more testing conditions. For the first time, we report the genome-wide GE profiling in a group of 16 runners participating in an 82 km UMT competition. We quantified their differential GE profile before and after the race using HuGene2.0st microarrays (Affymetrix Inc., California, US)...
2017: PloS One
https://www.readbyqxmd.com/read/29028314/heterologous-gene-expression-of-n-terminally-truncated-variants-of-lippks1-suggests-a-functionally-critical-structural-motif-in-the-n-terminus-of-modular-polyketide-synthase
#6
Satoshi Yuzawa, Constance B Bailey, Tatsuya Fujii, Renee Jocic, Jesus F Barajas, Veronica T Benites, Edward E K Baidoo, Yan Chen, Christopher J Petzold, Leonard Katz, Jay D Keasling
Streptomyces genomes have a high G + C content and typically use an ATG or GTG codon to initiate protein synthesis. Although gene-finding tools perform well in low GC genomes, it is known that the accuracy in predicting a translational start site (TSS) is much less for high GC genomes. LipPks1 is a Streptomyces-derived, well-characterized modular polyketide synthase (PKS). Using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae...
October 13, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29028265/stereogene-rapid-estimation-of-genome-wide-correlation-of-continuous-or-interval-feature-data
#7
Elena D Stavrovskaya, Tejasvi Niranjan, Elana J Fertig, Sarah J Wheelan, Alexander V Favorov, Andrey A Mironov
Motivation: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Results: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028263/epigenomic-annotation-based-interpretation-of-genomic-data-from-enrichment-analysis-to-machine-learning
#8
Mikhail G Dozmorov
Motivation: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29025942/complete-genome-sequence-of-porphyrobacter-sp-strain-caciam-03h1-a-proteobacterium-obtained-from-a-nonaxenic-culture-of-microcystis-aeruginosa
#9
Wendel de Oliveira Castro, Alex Ranieri Jerônimo Lima, Pablo Henrique Gonçalves Moraes, Andrei Santos Siqueira, Délia Cristina Figueira Aguiar, Anna Rafaella Ferreira Baraúna, Luisa Carício Martins, Hellen Thais Fuzii, Danielle Costa Carrara Couto, Regiane Silva Kawasaki Francês, Clayton Pereira Silva de Lima, João Lídio Silva Gonçalves Vianez-Júnior, Márcio Roberto Teixeira Nunes, Leonardo Teixeira Dall'Agnol, Evonnildo Costa Gonçalves
Here, we present a complete genome sequence and annotation of Porphyrobacter sp. strain CACIAM 03H1, which was obtained from a nonaxenic culture of Microcystis aeruginosa, a cyanobacterium isolated from an Amazonian freshwater environment.
October 12, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29025933/complete-genome-sequences-of-four-brucella-strains-isolated-from-china
#10
Xiaowen Yang, Xiaofang Cao, Ning Wang, Jiawei Wang, Pengfei Bie, Yanli Lyu, Qingmin Wu
Brucella spp. are facultative intracellular pathogens that cause a contagious zoonotic disease. Twelve different species are currently identified. This study presents the complete genome sequences of four Brucella strains. These complete genomes were annotated and the contents compared to those of other strains isolated from China.
October 12, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29025594/gene-expression-profiling-pathway-analysis-and-subtype-classification-reveal-molecular-heterogeneity-in-hepatocellular-carcinoma-and-suggest-subtype-specific-therapeutic-targets
#11
Rahul Agarwal, Jitendra Narayan, Amitava Bhattacharyya, Mayank Saraswat, Anil Kumar Tomar
A very low 5-year survival rate among hepatocellular carcinoma (HCC) patients is mainly due to lack of early stage diagnosis, distant metastasis and high risk of postoperative recurrence. Hence ascertaining novel biomarkers for early diagnosis and patient specific therapeutics is crucial and urgent. Here, we have performed a comprehensive analysis of the expression data of 423 HCC patients (373 tumors and 50 controls) downloaded from The Cancer Genome Atlas (TCGA) followed by pathway enrichment by gene ontology annotations, subtype classification and overall survival analysis...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29024922/isolation-and-whole-genome-analysis-of-endospore-forming-bacteria-from-heroin
#12
Jörn Kalinowski, Björn Ahrens, Arwa Al-Dilaimi, Anika Winkler, Daniel Wibberg, Uwe Schleenbecker, Christian Rückert, Roman Wölfel, Gregor Grass
Infections caused by endospore-forming bacteria have been associated with severe illness and death among persons who inject drugs. Analysis of the bacteria residing in heroin has thus been biased towards species that affect human health. Similarly, exploration of the bacterial diversity of seized street market heroin correlated with the skin microflora of recreational heroin users insofar as different Staphylococus spp. or typical environmental endospore formers including Bacillus cereus and other Bacilli outside the B...
October 4, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29023590/de-novo-assembly-and-analysis-of-the-transcriptome-of-rumex-patientia-l-during-cold-stress
#13
Jianxin Liu, Yongqing Xu, Liguo Zhang, Wei Li, Zhenxue Cai, Fei Li, Mu Peng, Fenglan Li, Baozhong Hu
BACKGROUND: Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. patientia under normal and cold conditions to evaluate how it responds to cold stress. RESULTS: After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/29022581/the-impact-of-rare-variation-on-gene-expression-across-tissues
#14
Xin Li, Yungil Kim, Emily K Tsang, Joe R Davis, Farhan N Damani, Colby Chiang, Gaelen T Hess, Zachary Zappala, Benjamin J Strober, Alexandra J Scott, Amy Li, Andrea Ganna, Michael C Bassik, Jason D Merker, Ira M Hall, Alexis Battle, Stephen B Montgomery
Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022135/pcal_1311-an-alcohol-dehydrogenase-homologue-from-pyrobaculum-calidifontis-displays-nadh-dependent-high-aldehyde-reductase-activity
#15
Raza Ashraf, Naeem Rashid, Tamotsu Kanai, Tadayuki Imanaka, Muhammad Akhtar
Genome sequence of Pyrobaculum calidifontis, a hyperthermophilic archaeon, harbors three open-reading frames annotated as alcohol dehydrogenases. One of them, Pcal_1311, does not display a significantly high homology with any of the characterized alcohol dehydrogenases. Highest homology of 38% was found with the characterized counterpart from Geobacillus stearothermophilus. To examine the biochemical properties of Pcal_1311, we have cloned and functionally expressed the gene in Escherichia coli. Purified recombinant Pcal_1311 catalyzed the NAD(H)-dependent oxidation of various alcohols and reduction of aldehydes, with a marked preference for substrates with functional group at the terminal carbon...
October 11, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29022094/transcriptomic-changes-in-echinochloa-colona-in-response-to-treatment-with-the-herbicide-imazamox
#16
Alice A Wright, Rajkumar Sasidharan, Liisa Koski, Marianela Rodriguez-Carres, Daniel G Peterson, Vijay K Nandula, Jeffery D Ray, Jason A Bond, David R Shaw
Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide. Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. In this study, changes in gene expression in response to herbicide exposure in imazamox-sensitive (S) and- resistant (R) junglerice (Echinochloa colona L...
October 11, 2017: Planta
https://www.readbyqxmd.com/read/29021818/algorithms-for-matching-partially-labelled-sequence-graphs
#17
William R Taylor
BACKGROUND: In order to find correlated pairs of positions between proteins, which are useful in predicting interactions, it is necessary to concatenate two large multiple sequence alignments such that the sequences that are joined together belong to those that interact in their species of origin. When each protein is unique then the species name is sufficient to guide this match, however, when there are multiple related sequences (paralogs) in each species then the pairing is more difficult...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/29021802/genome-wide-identification-of-circular-rnas-in-arabidopsis-thaliana
#18
Gang Chen, Jiawen Cui, Li Wang, Yingfang Zhu, Zhaogeng Lu, Biao Jin
Circular RNAs (circRNAs) are a family of transcripts with covalently closed circular structures and still largely unknown functions. Large numbers of circRNAs have been found in various biological processes in humans and animals, but fewer circRNAs have been identified in plants. We performed a genome-wide analysis of circRNAs in Arabidopsis thaliana via deep sequencing. We constructed 14 strand-specific libraries from 13 samples of plants from four developmental stages, four stress treatments, and five organs and a mixed sample across the lifespan...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29021218/transcriptomic-analysis-of-octanoic-acid-response-in-drosophila-sechellia%C3%A2-using-rna-sequencing
#19
Stephen M Lanno, Sara M Gregory, Serena J Shimshak, Maximilian K Alverson, Kenneth Chiu, Arden L Feil, Morgan G Findley, Taylor E Forman, Julia T Gordon, Josephine Ho, Joanna L Krupp, Ivy Lam, Josh Lane, Samuel C Linde, Ashley E Morse, Serena Rusk, Robie Ryan, Avva Saniee, Ruchi B Sheth, Jennifer J Siranosian, Lalitpatr Sirichantaropart, Sonya R Sternlieb, Christina M Zaccardi, Joseph D Coolon
The dietary specialist fruit fly Drosophila sechellia has evolved to specialize on the toxic fruit of its host plant Morinda citrifolia Toxicity of Morinda fruit is primarily due to high levels of octanoic acid (OA). Using RNA interference (RNAi), prior work found that knockdown of Osiris family genes Osiris 6 (Osi6), Osi7, and Osi8 led to increased susceptibility to OA in adult D. melanogaster flies, likely representing genes underlying a Quantitative Trait Locus (QTL) for OA resistance in D. sechellia While genes in this major effect locus are beginning to be revealed, prior work has shown at least five regions of the genome contribute to OA resistance...
October 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29021151/rapid-nanopore-sequencing-of-plasmids-and-resistance-gene-detection-in-clinical-isolates
#20
Jamie K Lemon, Pavel P Khil, Karen M Frank, John P Dekker
Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. Here, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection...
October 11, 2017: Journal of Clinical Microbiology
keyword
keyword
83321
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"