26 results match your criteria Genomics Insights [Journal]

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Corrigendum.

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Genomics Insights 2018 6;11:1178631018801448. Epub 2018 Sep 6.

[This corrects the article DOI: 10.4137/GEI.S32477. Read More

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http://dx.doi.org/10.1177/1178631018801448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6128074PMC
September 2018
2 Reads

Expression Levels of Candidate Circulating microRNAs in Early-Onset Neonatal Sepsis Compared With Healthy Newborns.

Genomics Insights 2018 2;11:1178631018797079. Epub 2018 Sep 2.

Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.

The high mortality rate of neonatal sepsis is directly connected with time-consuming diagnostic methods that have low sensitivity and specificity. The need of the hour is to develop novel diagnostic techniques that are rapid and more specific. In this study, we estimated the expression levels of circulating microRNAs (miRNAs) that are involved in regulating immune response genes and underlying inflammatory responses, which may be used for sepsis diagnosis. Read More

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http://dx.doi.org/10.1177/1178631018797079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6122238PMC
September 2018
4 Reads

Application of the GRADE Approach in the Development of Guidelines and Recommendations in Genomic Medicine.

Genomics Insights 2018 30;11:1178631017753360. Epub 2018 Jan 30.

Section of Hygiene, Institute of Public Health, Faculty of Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.

A great deal of ambiguity exists in the development of guidelines for genomic applications used in clinical practice. The GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach has the potential to be applied in the guidelines and recommendations development process in genomics. Here, we discuss whether and how GRADE can be applied to address the challenges posed by the evidence-based guidelines and recommendations development process in genomics. Read More

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http://dx.doi.org/10.1177/1178631017753360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794043PMC
January 2018
2 Reads

Insights Into Upland Cotton ( L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents.

Genomics Insights 2017 21;10:1178631017735104. Epub 2017 Dec 21.

USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, USA.

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. Read More

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http://dx.doi.org/10.1177/1178631017735104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751910PMC
December 2017
17 Reads

Exon Mapping in Long Noncoding RNAs Using Digital Filters.

Genomics Insights 2017 29;10:1178631017732029. Epub 2017 Sep 29.

Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, India.

Long noncoding RNAs (lncRNAs) which were initially dismissed as "transcriptional noise" have become a vital area of study after their roles in biological regulation were discovered. Long noncoding RNAs have been implicated in various developmental processes and diseases. Here, we perform exon mapping of human lncRNA sequences (taken from National Center for Biotechnology Information GenBank) using digital filters. Read More

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http://dx.doi.org/10.1177/1178631017732029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624354PMC
September 2017
3 Reads

Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies.

Authors:
Kevin H M Kuo

Genomics Insights 2017 1;10:1178631017721178. Epub 2017 Aug 1.

Departments of Medical Oncology and Hematology and Medicine, University Health Network, Toronto, ON, Canada.

The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. Read More

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http://dx.doi.org/10.1177/1178631017721178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542087PMC
August 2017
7 Reads

SNP Marker Discovery in Pima Cotton ( L.) Leaf Transcriptomes.

Genomics Insights 2016 2;9:51-60. Epub 2016 Oct 2.

USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA.

The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton ( L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. Read More

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http://dx.doi.org/10.4137/GEI.S40377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049682PMC
October 2016
3 Reads

Novel Approach to Analyzing MFE of Noncoding RNA Sequences.

Genomics Insights 2016 18;9:41-49. Epub 2016 Sep 18.

Professor, Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, Kerala, India.

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029481PMC
http://dx.doi.org/10.4137/GEI.S39995DOI Listing
September 2016
3 Reads

MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner.

Genomics Insights 2016 28;9:29-39. Epub 2016 Mar 28.

Department of Biochemistry, University of California at Riverside, Riverside, CA, USA.

In mammals, extracellular miRNAs circulate in biofluids as stable entities that are secreted by normal and diseased tissues, and can enter cells and regulate gene expression. Drosophila melanogaster is a proven system for the study of human diseases. They have an open circulatory system in which hemolymph (HL) circulates in direct contact with all internal organs, in a manner analogous to vertebrate blood plasma. Read More

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http://dx.doi.org/10.4137/GEI.S38147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811268PMC
April 2016
25 Reads

Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis.

Genomics Insights 2016 16;9:1-16. Epub 2016 Feb 16.

Discipline of Nutrition and Dietetics, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.

Ganoderma lucidum (lingzhi) has been used for the general promotion of health in Asia for many centuries. The common method of consumption is to boil lingzhi in water and then drink the liquid. In this study, we examined the potential anticancer activities of G. Read More

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http://dx.doi.org/10.4137/GEI.S32477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778854PMC
March 2016
16 Reads

Inferring Orthologs: Open Questions and Perspectives.

Authors:
Fredj Tekaia

Genomics Insights 2016 25;9:17-28. Epub 2016 Feb 25.

Institut Pasteur, Unit of Structural Microbiology, CNRS URA 3528 and University Paris Diderot, Sorbonne Paris Cité, Paris, France.

With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. Read More

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http://dx.doi.org/10.4137/GEI.S37925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778853PMC
March 2016
3 Reads
6 Citations

Applying Side-chain Flexibility in Motifs for Protein Docking.

Genomics Insights 2015 15;8:1-10. Epub 2015 Oct 15.

School of Electronics and Information Engineering, Hebei University, Baoding, Hebei, China.

Conventional rigid docking algorithms have been unsatisfactory in their computational results, largely due to the fact that protein structures are flexible in live environments. In response, we propose to introduce the side-chain flexibility in protein motif into the docking. First, the Morse theory is applied to curvature labeling and surface region growing, for segmentation of the protein surface into smaller patches. Read More

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http://journals.sagepub.com/doi/10.4137/GEI.S29821
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http://dx.doi.org/10.4137/GEI.S29821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610727PMC
October 2015
6 Reads

Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid.

Genomics Insights 2014 3;7:13-22. Epub 2014 Sep 3.

Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil. ; Graduate Program in Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil.

Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the parental species genomes. Read More

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http://dx.doi.org/10.4137/GEI.S15522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504075PMC
July 2015
14 Reads

Application of Machine Learning to Development of Copy Number Variation-based Prediction of Cancer Risk.

Genomics Insights 2014 26;7:1-11. Epub 2014 Jun 26.

Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.

In the present study, recurrent copy number variations (CNVs) from non-tumor blood cell DNAs of Caucasian non-cancer subjects and glioma, myeloma, and colorectal cancer-patients, and Korean non-cancer subjects and hepatocellular carcinoma, gastric cancer, and colorectal cancer patients, were found to reveal for each of the two ethnic cohorts highly significant differences between cancer patients and controls with respect to the number of CN-losses and size-distribution of CN-gains, suggesting the existence of recurrent constitutional CNV-features useful for prediction of predisposition to cancer. Upon identification by machine learning, such CNV-features could extensively discriminate between cancer-patient and control DNAs. When the CNV-features selected from a learning-group of Caucasian or Korean mixed DNAs consisting of both cancer-patient and control DNAs were employed to make predictions on the cancer predisposition of an unseen test group of mixed DNAs, the average prediction accuracy was 93. Read More

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http://dx.doi.org/10.4137/GEI.S15002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504076PMC
July 2015
9 Reads

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology.

Genomics Insights 2013 18;6:25-36. Epub 2013 Aug 18.

Department of Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, India.

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Read More

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http://journals.sagepub.com/doi/10.4137/GEI.S12732
Publisher Site
http://dx.doi.org/10.4137/GEI.S12732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510601PMC
July 2015
6 Reads

Inter-Laboratory Variability in Array-Based RNA Quantification Methods.

Genomics Insights 2013 6;6:13-24. Epub 2013 May 6.

University of New Haven, West Haven, CT 06516, USA.

Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. Read More

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http://dx.doi.org/10.4137/GEI.S11909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510603PMC
July 2015
4 Reads

The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology.

Genomics Insights 2013 4;6:1-12. Epub 2013 Mar 4.

Telos-Philosophische Praxis, Buermoos, Austria.

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. Read More

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http://dx.doi.org/10.4137/GEI.S11490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510605PMC
July 2015
4 Reads

Transcriptional Changes of Blood Eosinophils After Methacholine Inhalation Challenge in Asthmatics.

Genomics Insights 2012 30;5:1-12. Epub 2012 Jan 30.

Institute for HEART+LUNG Health, Vancouver, BC, Canada. ; Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada. ; Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, BC, Canada.

Background: Methacholine challenge is commonly used within the asthma diagnostic algorithm. Methacholine challenge has recently been shown to induce airway remodelling in asthma via bronchoconstriction, without additional airway inflammation. We evaluated the effect of methacholine-induced bronchoconstriction on the peripheral whole-blood transcriptome. Read More

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http://dx.doi.org/10.4137/GEI.S9125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510604PMC
July 2015
4 Reads

Cloning and Initial Functional Characterization of Mlk4α and Mlk4β.

Genomics Insights 2011 22;4:1-12. Epub 2011 Mar 22.

Department of Microbiology, Tumor and Cell Biology, Department of Clinical Science and Education, Södersjukhuset, Karolinska Institute, Stockholm, 17177, Sweden. ; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.

We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, MLK4α (580 aa) and MLK4β (1036 aa), have been identified and mapped to chromosomal band 1q42. MLK4 shows high amino acid homology to the kinase catalytic domain of MLK3 (72%), MLK1 (71%) and MLK2 (69%). Read More

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http://dx.doi.org/10.4137/GEI.S6092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510602PMC
July 2015
22 Reads

Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.

Genomics Insights 2009 Jul;2009(2):23-48

Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA.

More than half a century after the discovery of the molecular basis of Sickle Cell Disease (SCD), the causes of the phenotypic heterogeneity of the disease remain unclear. This heterogeneity manifests with different clinical outcomes such as stroke, vaso-occlusive episodes, acute chest syndrome, avascular necrosis, leg ulcers, priapism and retinopathy. These outcomes cannot be explained by the single mutation in the beta-globin gene alone but may be attributed to genetic modifiers and environmental effects. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855197PMC
July 2009
3 Reads

Design, Construction and Validation of Targeted BAC Array-Based CGH Test for Detecting the Most Commons Chromosomal Abnormalities.

Genomics Insights 2010 11;3:9-21. Epub 2010 Mar 11.

Department of Biopathology, Tor Vergata University, Rome, Italy. ; Azienda Ospedaliera Universitaria Policlinico Tor Vergata, Rome, Italy. ; Fondazione Livio Patrizi, Rome, Italy.

We designed a targeted-array called GOLD (Gain or Loss Detection) Chip consisting of 900 FISH-mapped non-overlapping BAC clones spanning the whole genome to enhance the coverage of 66 unique human genomic regions involved in well known microdeletion/microduplication syndromes. The array has a 10 Mb backbone to guarantee the detection of the aneuploidies, and has an implemented resolution for telomeres, and for regions involved in common genomic diseases. In order to evaluate clinical diagnostic applicability of GOLDChip, analytical validity was carried-out via retrospective analysis of DNA isolated from a series of cytogenetically normal amniocytes and cytogenetically abnormal DNA obtained from cultured amniocytes, peripheral blood and/or cell lines. Read More

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http://journals.sagepub.com/doi/10.4137/GEI.S3683
Publisher Site
http://dx.doi.org/10.4137/GEI.S3683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510597PMC
August 2015
14 Reads

Single Nucleotide Polymorphisms Caused by Assembly Errors.

Genomics Insights 2010 4;3:1-8. Epub 2010 Feb 4.

Stanford University Biomedical Informatics, Stanford, California, USA.

We compare the results of three different assembler programs, Celera, Phrap and Mira2, for the same set of about a hundred thousand Sanger reads derived from an unknown bacterial genome. In difference to previous assembly comparisons we do not focus on speed of computation and numbers of assembled contigs but on how the different sequence assemblies agree by content. Threefold consistently assembled genome regions are identified in order to estimate a lower bound of erroneously identified single nucleotide polymorphisms (SNP) caused by nothing but the process of mathematical sequence assembly. Read More

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http://dx.doi.org/10.4137/GEI.S3653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510600PMC
August 2015
5 Reads

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

Genomics Insights 2010 28;3:29-56. Epub 2010 Oct 28.

Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética. Laboratório de Genômica e Proteômica, Ilhéus, Bahia, Brazil. ; Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brazil.

We report here on the characterization of a cDNA library from seeds of Jatropha curcas L. at three stages of fruit maturation before yellowing. We sequenced a total of 2200 clones and obtained a set of 931 non-redundant sequences (unigenes) after trimming and quality control, ie, 140 contigs and 791 singlets with PHRED quality ≥10. Read More

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http://dx.doi.org/10.4137/GEI.S4340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510598PMC
July 2015
10 Reads

Molecular Cloning of a Novel Bradykinin-Related Peptide from the Skin of Indian Bronzed Frog Hylarana Temporalis.

Genomics Insights 2010 18;3:23-8. Epub 2010 Oct 18.

Chemical Biology Group, Molecular Medicine Division, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram-695014, Kerala, India.

Bradykinin-related peptides (BRPs) constitute one of the most studied groups of bioactive peptides in amphibian skin secretions. The present study describes the successful isolation of a novel BRP (hylaranakinin TE) from the skin secretion of the Indian bronzed frog Hylarana temporalis. The deduced open reading frame consisted of 115 amino acid residues with a putative signal peptide of 22 amino acid residues, followed by a spacer region and mature peptide regions that encode for two BRPs: a canonical bradykinin R-9-R with a C-terminal extension of FVPASSL and Thr6-BK. Read More

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http://dx.doi.org/10.4137/GEI.S5409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510599PMC
July 2015
4 Reads

Gene Expression Analysis of Four Radiation-resistant Bacteria.

Genomics Insights 2009 16;2:11-22. Epub 2009 Jun 16.

Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, School of Life Sciences, Shandong University of Technology, Zibo 255049, P.R. China.

To investigate the general radiation-resistant mechanisms of bacteria, bioinformatic method was employed to predict highly expressed genes for four radiation-resistant bacteria, i.e. Deinococcus geothermalis (D. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510606PMC
August 2015
4 Reads

Low Serum Alpha-Antitrypsin Associated with Anti-PR-3 ANCA in Autistic Children with GI Disease.

Genomics Insights 2009 4;2:1-9. Epub 2009 Jun 4.

Thoughtful House Center for Children, 3001 Bee Caves Road, Austin, Texas, 78746.

Aim: To assess the possible relationship between serum alpha-1 antitrypsin (AAT) levels and anti-neutrophil cytoplasmic antibodies (ANCA) in autistic children with severe GI disease and to test the hypothesis that there is an association between low serum AAT levels, the presence of ANCA and inflammatory GI disease seen in some autistic children.

Subjects And Methods: Serum from 40 autistic children with chronic digestive disease (many with ileo-colonic lymphoid nodular hyperplasia (LNH) and inflammation of the colorectum, small bowel and/or stomach), and 41 controls (21 age matched autistic children with no GI disease and 20 age matched children without autism or GI disease) were tested using ELISAs designed to quantitate ANCA (anti-PR3), AAT and PR3 levels.

Results: We found that a significant number of autistic children with chronic digestive disease had anti-PR3 ANCA, high serum PR3 and high severity of disease when compared to controls. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510608PMC
August 2015
3 Reads
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