journal
MENU ▼
Read by QxMD icon Read
search

Genomics

journal
https://www.readbyqxmd.com/read/27974244/a-new-method-to-analyze-protein-sequence-similarity-using-dynamic-time-warping
#1
Hou Wenbing, Pan Qiuhui, Peng Qianying, He Mingfeng
Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same length to calculate the distance between different sequences by DTW...
December 11, 2016: Genomics
https://www.readbyqxmd.com/read/27989800/next-generation-sequencing-identifies-abnormal-y-chromosome-and-candidate-causal-variants-in-premature-ovarian-failure-patients
#2
Yujung Lee, Changshin Kim, YoungJoon Park, Jung-A Pyun, KyuBum Kwack
Premature ovarian failure (POF) is characterized by heterogeneous genetic causes such as chromosomal abnormalities and variants in causal genes. Recently, development of techniques made next generation sequencing (NGS) possible to detect genome wide variants including chromosomal abnormalities. Among 37 Korean POF patients, XY karyotype with distal part deletions of Y chromosome, Yp11.32-31 and Yp12 end part, was observed in two patients through NGS. Six deleterious variants in POF genes were also detected which might explain the pathogenesis of POF with abnormalities in the sex chromosomes...
October 29, 2016: Genomics
https://www.readbyqxmd.com/read/27940149/close-genetic-relationships-between-a-spousal-pair-with-autism-affected-children-and-high-minor-allele-content-in-cases-in-autism-associated-snps
#3
Zuobin Zhu, Xitong Lu, Dejian Yuan, Shi Huang
Parents of children affected with autism spectrum disorders (ASD) often have mild forms of autistic-like characteristics. Past studies have focused on searching for individual genetic risk loci of ASD. Here we studied the overall properties of the genomes of ASD trios by using previously published genome-wide data for common SNPs. The pairwise genetic distance (PGD) between a spousal pair with ASD-affected children was found smaller than that of a random pair selected among the spouses in the ASD trios, and spousal relatedness correlated with severe forms of ASD...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#4
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species' reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double-stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#5
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#6
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
January 2017: Genomics
https://www.readbyqxmd.com/read/27867104/identification-of-transcripts-involved-in-digestion-detoxification-and-immune-response-from-transcriptome-of-empoasca-vitis-hemiptera-cicadellidae-nymphs
#7
En-Si Shao, Gui-Fang Lin, Sijun Liu, Xiao-Li Ma, Ming-Feng Chen, Li Lin, Song-Qing Wu, Li Sha, Zhao-Xia Liu, Xiao-Hua Hu, Xiong Guan, Ling-Ling Zhang
Tea production has been significantly impacted by the false-eye leafhopper, Empoasca vitis (Göthe), around Asia. To identify the key genes which are responsible for nutrition absorption, xenobiotic metabolism and immune response, the transcriptome of either alimentary tracts or bodies minus alimentary tract of E. vitis was sequenced and analyzed. Over 31 million reads were obtained from Illumina sequencing. De novo sequence assembly resulted in 52,182 unigenes with a mean size of 848nt. The assembled unigenes were then annotated using various databases...
January 2017: Genomics
https://www.readbyqxmd.com/read/27856224/tid-standalone-software-for-mining-putative-drug-targets-from-bacterial-proteome
#8
Reena Gupta, Dibyabhaba Pradhan, Arun Kumar Jain, Chandra Shekhar Rai
TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application...
January 2017: Genomics
https://www.readbyqxmd.com/read/27851990/genetic-variants-associated-with-primary-open-angle-glaucoma-in-indian-population
#9
REVIEW
Sunil Kumar, Manzoor Ahmad Malik, Sooraj K, Ramanjit Sihota, Jasbir Kaur
Glaucoma is a very common disorder of the eye wherein the disturbance of the structural or functional integrity of the optic nerve causes characteristic atrophic changes in the optic nerve, which may lead to specific visual field defects over time. Primary open angle glaucoma (POAG) is most frequent among the three principle glaucoma subtypes. With well-established role of genes like Myocilin (MYOC), Optineurin (OPTN) and WD repeat Domain 36, (WDR36), at least 29 genetic loci have been found till date to be linked to POAG...
January 2017: Genomics
https://www.readbyqxmd.com/read/27816578/distinctive-gene-expression-profile-in-women-with-history-of-postpartum-depression
#10
Anna Landsman, Rafael Aidelman, Yoav Smith, Matthew Boyko, Chaya Greenberger
Postpartum depression (PPD) is a disease which incorporates a variety of depressive states differing in nature and severity. To assist in the understanding of the pathogenesis of the disease, we aimed to ascertain a molecular mechanism underlying PPD development. We applied microarray technology to characterize gene expression of euthymic women with a history of PPD and compared the results with healthy controls. Our study demonstrated that women who considered euthymic on a clinical level, in fact, had an altered molecular profile when compared to participants with no PPD history...
January 2017: Genomics
https://www.readbyqxmd.com/read/27856225/correlations-of-vdr-and-vdbp-genetic-polymorphisms-with-susceptibility-to-adolescent-idiopathic-scoliosis-and-efficacy-of-brace-treatment
#11
Yu Wang, Zhi-Qiang Cui, Tian-Bao Luo, Long Liu
OBJECTIVE: This paper aimed to elucidate the correlations of VDR and VDBP polymorphisms with susceptibility to adolescent idiopathic scoliosis (AIS) and efficacy of brace treatment. METHODS: AIS patients and healthy controls were enrolled. Lumbar spine bone mineral density (LSBMD) and femoral neck bone mineral density (FNBMD) were detected by dual energy X-ray absorptiometry. VDR and VDBP polymorphisms were detected by PCR-RFLP. Efficacy of brace treatment was evaluated by Cobb measurement...
December 2016: Genomics
https://www.readbyqxmd.com/read/27829169/slc44a2-single-nucleotide-polymorphisms-isoforms-and-expression-association-with-severity-of-meniere-s-disease
#12
Thankam S Nair, Pavan K Kommareddi, Maria M Galano, Danielle M Miller, Bala Naveen Kakaraparthi, Steven A Telian, H Alex Arts, Hussam El-Kashlan, Alyse Kilijanczyk, Amy Anne D Lassig, Martin P Graham, Susan G Fisher, Stefan W Stoll, Rajan P Nair, James T Elder, Thomas E Carey
SLC44A2 was discovered as the target of an antibody that causes hearing loss. Knockout mice develop age related hearing loss, loss of sensory cells and spiral ganglion neurons. SLC44A2 has polymorphic sites implicated in human disease. Transfusion related acute lung injury (TRALI) is linked to rs2288904 and genome wide association studies link rs2288904 and rs9797861 to venous thromboembolism (VTE), coronary artery disease and stroke. Here we report linkage disequilibrium of rs2288904 with rs3087969 and the association of these SLC44A2 SNPs with Meniere's disease severity...
December 2016: Genomics
https://www.readbyqxmd.com/read/27826049/methylation-status-of-homeobox-genes-in-common-human-cancers
#13
REVIEW
Maria Fernanda Setúbal Destro Rodrigues, Carina Magalhães Esteves, Flávia Caló Aquino Xavier, Fabio Daumas Nunes
Approximately 300 homeobox loci were identified in the euchromatic regions of the human genome, of which 235 are probable functional genes and 65 are likely pseudogenes. Many of these genes play important roles in embryonic development and cell differentiation. Dysregulation of homeobox gene expression is a frequent occurrence in cancer. Accumulating evidence suggests that as genetics disorders, epigenetic modifications alter the expression of oncogenes and tumor suppressor genes driving tumorigenesis and perhaps play a more central role in the evolution and progression of this disease...
December 2016: Genomics
https://www.readbyqxmd.com/read/27810268/identification-and-characterization-of-micrornas-in-maize-endosperm-response-to-exogenous-sucrose-using-small-rna-sequencing
#14
Huanhuan Huang, Jiao Long, Lanjie Zheng, Yangping Li, Yufeng Hu, Guowu Yu, Hanmei Liu, Yinghong Liu, Zhi Huang, Junjie Zhang, Yubi Huang
Sucrose acts as a signaling molecule for genes critical to starch biosynthesis in maize endosperm. Previously, we showed that sucrose could regulate starch biosynthesis in maize via transcription factors. To better understand the complex regulation of starch biosynthesis, the 10days after pollination endosperm from Zea mays L. B73 inbred line was collected and treated with sucrose for small RNA sequencing. The sequencing results revealed that 24 known miRNAs and 190 novel miRNAs were significantly differentially expressed in response to sucrose...
December 2016: Genomics
https://www.readbyqxmd.com/read/27789319/genome-wide-regulatory-dynamics-of-g-quadruplexes-in-human-malaria-parasite-plasmodium-falciparum
#15
Deeksha Bhartiya, Vandna Chawla, Sourav Ghosh, Ravi Shankar, Niti Kumar
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from other Plasmodium species. A distinct predominance of quadruplexes was observed in nuclear and organellar genes that participate in antigenic variation, pathogenesis, DNA/RNA regulation, metabolic and protein quality control processes...
December 2016: Genomics
https://www.readbyqxmd.com/read/27732888/tissue-specific-transcriptome-characterization-for-developing-tadpoles-of-the-northern-leopard-frog-lithobates-pipiens
#16
Jeffrey R Row, Michael E Donaldson, Jessica N Longhi, Barry J Saville, Dennis L Murray
A potential cause of amphibian population declines are the impacts of environmental degradation on tadpole development. We conducted RNA sequencing on developing northern leopard frog tadpoles and through de novo transcriptome assembly we annotated a large number of open reading frames comparable in number and extent to genes identified in Xenopus. Using our transcriptome, we found transcript level changes between early (Gosner 26-31) and late (Gosner 36-41) stage tadpoles were the greatest in the tail, which is reabsorbed throughout development...
December 2016: Genomics
https://www.readbyqxmd.com/read/27746014/a-pubmed-wide-study-of-endometriosis
#17
Ji-Long Liu, Miao Zhao
Endometriosis affects 5-10% of women in reproductive age, leading to dysmenorrhea, pelvic pain and infertility; however, our understanding on the pathogenesis of this disease remains incomplete. In the present study, we performed a systematic analysis of endometriosis-related genes using text mining. Taking text mining results as input, we subsequently generated a filtered gene set by computing the likelihood of finding more than expected occurrences for every gene across the disease-centered subset of the PubMed database...
October 13, 2016: Genomics
https://www.readbyqxmd.com/read/27720826/the-ciona-intestinalis-cleavage-clock-is-independent-of-dna-methylation
#18
Miho M Suzuki, Tomoko Mori, Noriyuki Satoh
The initiation of embryonic gene expression in ascidian embryos appears to be tightly regulated by the number of DNA replication cycles. DNA methylation is thought to contribute to the clock mechanism that counts the rounds of DNA replication. We used mass spectrometry and whole genome bisulfite sequencing to characterize DNA methylation changes that occur in early developmental stages of the ascidian, Ciona intestinalis. We found that global DNA methylation in early Ciona development was static, and a base-wise comparison between the genomes of consecutive developmental stages found no DNA demethylation that was related to zygotic gene activation...
October 5, 2016: Genomics
https://www.readbyqxmd.com/read/27702613/insights-in-human-epigenomic-dynamics-through-comparative-primate-analysis
#19
Christopher G Bell
Epigenomic analysis gives a molecular insight into cell-specific genomic activity. It provides a detailed functional plan to dissect an organism, tissue by tissue. Therefore comparative epigenomics may increase understanding of human-acquired traits, by revealing regulatory changes in systems such as the neurological, musculoskeletal, and immunological. Enhancer loci evolve fast by hijacking elements from other tissues or rewiring and amplifying existing units for human-specific function. Promoters by contrast often require a CpG dense genetic infrastructure...
October 1, 2016: Genomics
https://www.readbyqxmd.com/read/27524493/diet-induced-weight-loss-leads-to-a-switch-in-gene-regulatory-network-control-in-the-rectal-mucosa
#20
Ashley J Vargas, John Quackenbush, Kimberly Glass
BACKGROUND: Weight loss may decrease risk of colorectal cancer in obese individuals, yet its effect in the colorectum is not well understood. We used integrative network modeling, Passing Attributes between Networks for Data Assimilation, to estimate transcriptional regulatory network models from mRNA expression levels from rectal mucosa biopsies measured pre- and post-weight loss in 10 obese, pre-menopausal women. RESULTS: We identified significantly greater regulatory targeting of glucose transport pathways in the post-weight loss regulatory network, including "regulation of glucose transport" (FDR=0...
October 2016: Genomics
journal
journal
29719
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"