keyword
MENU ▼
Read by QxMD icon Read
search

Genome annotation

keyword
https://www.readbyqxmd.com/read/28829774/a-large-scale-plasmodium-vivax-saimiri-boliviensis-trophozoite-schizont-transition-proteome
#1
D C Anderson, Stacey A Lapp, John W Barnwell, Mary R Galinski
Plasmodium vivax is a complex protozoan parasite with over 6,500 genes and stage-specific differential expression. Much of the unique biology of this pathogen remains unknown, including how it modifies and restructures the host reticulocyte. Using a recently published P. vivax reference genome, we report the proteome from two biological replicates of infected Saimiri boliviensis host reticulocytes undergoing transition from the late trophozoite to early schizont stages. Using five database search engines, we identified a total of 2000 P...
2017: PloS One
https://www.readbyqxmd.com/read/28829439/an-integrated-expression-atlas-of-mirnas-and-their-promoters-in-human-and-mouse
#2
Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Michiel J L de Hoon
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species...
August 21, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28828235/rna-sequencing-rna-seq-of-lymph-node-spleen-and-thymus-transcriptome-from-wild-peninsular-malaysian-cynomolgus-macaque-macaca-fascicularis
#3
Joey Ee Uli, Christina Seok Yien Yong, Swee Keong Yeap, Jeffrine J Rovie-Ryan, Nurulfiza Mat Isa, Soon Guan Tan, Noorjahan Banu Alitheen
The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology...
2017: PeerJ
https://www.readbyqxmd.com/read/28827531/field-based-species-identification-of-closely-related-plants-using-real-time-nanopore-sequencing
#4
Joe Parker, Andrew J Helmstetter, Dion Devey, Tim Wilkinson, Alexander S T Papadopulos
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28827396/genetic-diagnosis-of-polycystic-kidney-disease-alport-syndrome-and-thalassemia-minor-in-a-large-chinese-family
#5
Yun Miao, Jun Xiong, Xuelian Zhang, Huajie Huang, Lixin Yu, Jianfan Chen, Wenfeng Deng, Huiling Xu, Rumin Liu, Xiangmin Xu, Chenglin Xiang, Fu Xiong
Background : Polycystic kidney disease (PKD) and Alport syndrome (AS) are serious inherited disorders associated with renal disease, and thalassemia is a hereditary blood disease with a high prevalence in south China. Here, we report an exceptional PKD coincidence of thalassemia minor and AS (diagnosed genetically) in a large Chinese family. Methods : Whole genome next-generation sequencing (NGS) was performed on the proband and all family members underwent clinical evaluations. Sanger sequencing was used to validate the mutations distinguished by NGS...
August 21, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28822795/strategies-for-analyzing-bisulfite-sequencing-data
#6
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#7
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28819820/genome-wide-characterization-of-the-wrky-gene-family-in-radish-raphanus-sativus-l-reveals-its-critical-functions-under-different-abiotic-stresses
#8
Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Xianwen Zhu, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M'mbone Muleke, Liwang Liu
The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative...
August 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28819158/discovering-condition-specific-gene-co-expression-patterns-using-gaussian-mixture-models-a-cancer-case-study
#9
Stephen P Ficklin, Leland J Dunwoodie, William L Poehlman, Christopher Watson, Kimberly E Roche, F Alex Feltus
A gene co-expression network (GCN) describes associations between genes and points to genetic coordination of biochemical pathways. However, genetic correlations in a GCN are only detectable if they are present in the sampled conditions. With the increasing quantity of gene expression samples available in public repositories, there is greater potential for discovery of genetic correlations from a variety of biologically interesting conditions. However, even if gene correlations are present, their discovery can be masked by noise...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819148/analysis-and-comparative-genomics-of-r997-the-first-sxt-r391-integrative-and-conjugative-element-ice-of-the-indian-sub-continent
#10
Michael P Ryan, Patricia Armshaw, John A O'Halloran, J Tony Pembroke
The aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818895/genome-sequence-of-the-thermophilic-biomass-degrading-fungus-malbranchea-cinnamomea-fch-10-5
#11
Zoraide Granchi, Sake van Pelt, Vu Nguyen Thanh, Lisbeth Olsson, Silvia Hüttner
We report here the annotated draft genome sequence of the thermophilic biomass-degrading fungus Malbranchea cinnamomea strain FCH 10.5, isolated from compost at a waste treatment plant in Vietnam. The genome sequence contains 24.96 Mb with an overall GC content of 49.79% and comprises 9,437 protein-coding genes.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818891/complete-genome-sequence-of-pseudoalteromonas-piscicida-strain-de2-b-a-bacterium-with-broad-inhibitory-activity-toward-human-and-fish-pathogens
#12
Gary P Richards, David S Needleman, Michael A Watson
Pseudoalteromonas piscicida strain DE2-B is a halophilic bacterium which has broad inhibitory activity toward vibrios and other human and fish pathogens. We report the first closed genome sequence for this species, which consists of two chromosomes (4,128,210 and 1,188,838 bp). Annotation revealed multiple genes encoding proteases with potential antibacterial properties.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818737/genome-wide-dna-methylation-profiling-of-articular-cartilage-reveals-significant-epigenetic-alterations-in-kashin-beck-disease-and-osteoarthritis
#13
Wenyu Wang, Yan Yu, Jingcan Hao, Yan Wen, Jing Han, Weikun Hou, Ruiyu Liu, Bo Zhao, Awen He, Ping Li, Qianrui Fan, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo, Feng Zhang
OBJECTIVE: To determine genome-wide DNA methylation profiles of knee cartilage from patients with Kashin-Beck disease (KBD) and osteoarthritis (OA). METHOD: Knee cartilage was collected from 14 grade III KBD patients, 5 primary OA patients and 13 healthy subjects. The genome-wide methylation profiles of 5 KBD cartilage, 5 OA cartilage and 5 normal cartilage were determined by Illumina HumanMethylation450 array. Illumina Methylation Analyzer package was employed for identifying differentially methylated CpG sites...
August 14, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28815912/assembly-and-rna-free-annotation-of-highly-heterozygous-genomes-the-case-of-the-thick-billed-murre-uria-lomvia
#14
Anna Tigano, Timothy B Sackton, Vicki L Friesen
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats, and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird...
August 16, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28815542/long-noncoding-rnas-in-pluripotency-of-stem-cells-and-cell-fate-specification
#15
Debosree Pal, M R S Rao
Since the annotation of the mouse genome (FANTOM project) [Kawai J et al (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409(6821):685-690] or the human genome [An integrated encyclopedia of DNA elements in the human genome. (2012) Nature 489(7414):57-74; Harrow J et al (2012) GENCODE: the reference human genome annotation for the ENCODE project. Genome Res 22(9):1760-1774], the roles of long noncoding RNAs in coordinating specific signaling pathways have been established in a wide variety of model systems...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814988/the-draft-genome-of-the-hyperthermophilic-archaeon-pyrodictium-delaneyi-strain-hulk-an-iron-and-nitrate-reducer-reveals-the-capacity-for-sulfate-reduction
#16
Lucas M Demey, Caitlin R Miller, Michael P Manzella, Rachel R Spurbeck, Sukhinder K Sandhu, Gemma Reguera, Kazem Kashefi
Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06(T), which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28814974/time-resolved-transcriptome-analysis-and-lipid-pathway-reconstruction-of-the-oleaginous-green-microalga-monoraphidium-neglectum-reveal-a-model-for-triacylglycerol-and-lipid-hyperaccumulation
#17
Daniel Jaeger, Anika Winkler, Jan H Mussgnug, Jörn Kalinowski, Alexander Goesmann, Olaf Kruse
BACKGROUND: Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS: An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28814946/protein-signatures-of-molecular-pathways-in-non-small-cell-lung-carcinoma-nsclc-comparison-of-glycoproteomics-and-global-proteomics
#18
Shuang Yang, Lijun Chen, Daniel W Chan, Qing Kay Li, Hui Zhang
BACKGROUND: Non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are substantially different between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in different subtypes of NSCLC using advanced proteomic approaches has not yet been conducted...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28814272/identification-of-new-protein-coding-genes-with-a-potential-role-in-the-virulence-of-the-plant-pathogen-xanthomonas-euvesicatoria
#19
Ulrike Abendroth, Norman Adlung, Andreas Otto, Benjamin Grüneisen, Dörte Becher, Ulla Bonas
BACKGROUND: Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequenced Xanthomonas genomes increases rapidly, however, accurate annotation of these genomes is difficult, because it relies on gene prediction programs. In this study, we used a mass-spectrometry (MS)-based approach to identify the proteome of Xanthomonas euvesicatoria (Xe) strain 85-10 also known as X...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28814265/a-genome-wide-transcriptome-map-of-pistachio-pistacia-vera-l-provides-novel-insights-into-salinity-related-genes-and-marker-discovery
#20
Maryam Moazzzam Jazi, Seyed Mahdi Seyedi, Esmaeil Ebrahimie, Mansour Ebrahimi, Gianluca De Moro, Christopher Botanga
BACKGROUND: Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress...
August 17, 2017: BMC Genomics
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"