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https://www.readbyqxmd.com/read/28212312/genome-wide-prediction-of-dna-methylation-using-dna-composition-and-sequence-complexity-in-human
#1
Chengchao Wu, Shixin Yao, Xinghao Li, Chujia Chen, Xuehai Hu
DNA methylation plays a significant role in transcriptional regulation by repressing activity. Change of the DNA methylation level is an important factor affecting the expression of target genes and downstream phenotypes. Because current experimental technologies can only assay a small proportion of CpG sites in the human genome, it is urgent to develop reliable computational models for predicting genome-wide DNA methylation. Here, we proposed a novel algorithm that accurately extracted sequence complexity features (seven features) and developed a support-vector-machine-based prediction model with integration of the reported DNA composition features (trinucleotide frequency and GC content, 65 features) by utilizing the methylation profiles of embryonic stem cells in human...
February 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28212192/genetic-control-of-erythropoiesis
#2
Laxminath Tumburu, Swee Lay Thein
PURPOSE OF REVIEW: The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait. RECENT FINDINGS: Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1)...
February 15, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28209158/gene-regulatory-network-underlying-the-immortalization-of-epithelial-cells
#3
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28209135/marv-a-tool-for-genome-wide-multi-phenotype-analysis-of-rare-variants
#4
Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P Morris, Inga Prokopenko
BACKGROUND: Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and recent advances in technology to produce high-dimensional data cost-effectively have led to method development beyond standard common variant analysis, including single-phenotype rare variant and multi-phenotype common variant analysis, with the latter increasing power for locus discovery and providing suggestions of pleiotropic effects...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28207848/resolving-host-pathogen-interactions-by-dual-rna-seq
#5
REVIEW
Alexander J Westermann, Lars Barquist, Jörg Vogel
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#6
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28204942/molecular-modeling-in-the-age-of-clinical-genomics-the-enterprise-of-the-next-generation
#7
Jeremy W Prokop, Jozef Lazar, Gabrielle Crapitto, D Casey Smith, Elizabeth A Worthey, Howard J Jacob
Protein modeling and molecular dynamics hold a unique toolset to aide in the characterization of clinical variants that may result in disease. Not only do these techniques offer the ability to study under characterized proteins, but they do this with the speed that is needed for time-sensitive clinical cases. In this paper we retrospectively study a clinical variant in the XIAP protein, C203Y, while addressing additional variants seen in patients with similar gastrointestinal phenotypes as the C203Y mutation...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28198669/ulfasqtl-an-ultra-fast-method-of-composite-splicing-qtl-analysis
#8
Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
BACKGROUND: Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197719/regulatory-crosstalk-between-micrornas-and-hormone-signalling-cascades-controls-the-variation-on-seed-dormancy-phenotype-at-arabidopsis-thaliana-seed-set
#9
Yang Liu, Yousry A El-Kassaby
We employed an Illumina sequencing approach to identify candidate microRNA cohorts that may greatly contribute to seed dormancy modulation and to construct a microRNA-gene regulatory network in hormone signalling cascades. MicroRNAs (miRNAs) are important signalling molecules and regulate many developmental programs of plants. Some miRNAs have been integrated into gene regulatory networks (GRNs) and coordinate developmental plasticity, but few study systematically investigated how phenotypical variations are regulated through differential expression of miRNA tags in GRNs during seed set...
February 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28196892/modeling-the-two-way-feedback-between-contractility-and-matrix-realignment-reveals-a-nonlinear-mode-of-cancer-cell-invasion
#10
Hossein Ahmadzadeh, Marie R Webster, Reeti Behera, Angela M Jimenez Valencia, Denis Wirtz, Ashani T Weeraratna, Vivek B Shenoy
Cancer cell invasion from primary tumors is mediated by a complex interplay between cellular adhesions, actomyosin-driven contractility, and the physical characteristics of the extracellular matrix (ECM). Here, we incorporate a mechanochemical free-energy-based approach to elucidate how the two-way feedback loop between cell contractility (induced by the activity of chemomechanical interactions such as Ca(2+) and Rho signaling pathways) and matrix fiber realignment and strain stiffening enables the cells to polarize and develop contractile forces to break free from the tumor spheroids and invade into the ECM...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193509/pilot-study-analyzing-automated-ecg-screening-of-hypertrophic-cardiomyopathy
#11
Matthew Campbell, Xuefu Zhou, Chia Han, Hedayat Abrishami, Gregory Webster, Christina Y Miyake, Christopher T Sower, Jeffery B Anderson, Timothy K Knilans, Richard J Czosek
BACKGROUND: Hypertrophic cardiomyopathy (HCM) is one of the leading causes of sudden cardiac death in athletes. However, pre-participation ECG screening has often been criticized for failing to meet cost-effectiveness thresholds, in part because of high false-positive rates and the cost of ECG screening itself. OBJECTIVES: To assess the testing characteristics of an automated ECG algorithm designed to screen for HCM in a multi-institutional pediatric cohort. METHODS: ECGs from patients with HCM aged 12 - 20 years from 3 pediatric institutions were screened for ECG criteria for HCM using a previously described automated computer algorithm developed specifically for HCM ECG screening...
February 10, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28191785/impact-of-the-secretome-of-human-mesenchymal-stem-cells-on-brain-structure-and-animal-behavior-in-a-rat-model-of-parkinson-s-disease
#12
Fábio G Teixeira, Miguel M Carvalho, Krishna M Panchalingam, Ana J Rodrigues, Bárbara Mendes-Pinheiro, Sandra Anjo, Bruno Manadas, Leo A Behie, Nuno Sousa, António J Salgado
Research in the last decade strongly suggests that mesenchymal stem cell (MSC)-mediated therapeutic benefits are mainly due to their secretome, which has been proposed as a possible therapeutic tool for the treatment of Parkinson's disease (PD). Indeed, it has been shown that the MSC secretome increases neurogenesis and cell survival, and has numerous neuroprotective actions under different conditions. Additionally, using dynamic culturing conditions (through computer-controlled bioreactors) can further modulate the MSC secretome, thereby generating a more potent neurotrophic factor cocktail (i...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28187811/determinants-of-prognosis-in-neurocatastrophes
#13
K Sharma, R D Stevens
A neurocatastrophe or severe brain injury (SBI) is a central nervous system insult associated with a high likelihood of death or severe disability. While many etiologic processes may lead to SBI, the most common and best-studied clinical paradigms are traumatic brain injury and anoxic-ischemic encephalopathy following cardiac arrest. Clinical phenotypes following SBI include acute and chronic disorders of consciousness as well as a range of cognitive and behavioral impairments. A fundamental task for medical teams working in the acute phase is to estimate SBI recovery probabilities with the highest degree of accuracy possible...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/28187409/pgminer-reloaded-fully-automated-proteogenomic-annotation-tool-linking-genomes-to-proteomes
#14
Canan Has, Sergey A Lashin, Alexey V Kochetov, Jens Allmer
Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28185277/three-dimensional-parametric-modeling-of-bicuspid-aortopathy-and-comparison-with-computational-flow-predictions
#15
Salvatore Pasta, Giovanni Gentile, Giuseppe M Raffa, Francesco Scardulla, Diego Bellavia, Angelo Luca, Michele Pilato, Cesare Scardulla
Bicuspid aortic valve (BAV)-associated ascending aneurysmal aortopathy (namely "bicuspid aortopathy") is a heterogeneous disease making surgeon predictions particularly challenging. Computational flow analysis can be used to evaluate the BAV-related hemodynamic disturbances, which likely lead to aneurysm enlargement and progression. However, the anatomic reconstruction process is time consuming so that predicting hemodynamic and structural evolution by computational modeling is unfeasible in routine clinical practice...
February 10, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28183533/chronic-embolic-pulmonary-hypertension-caused-by-pulmonary-embolism-and-vascular-endothelial-growth-factor-inhibition
#16
Evandro M Neto-Neves, Mary Beth Brown, Maria V Zaretskaia, Samin Rezania, Adam G Goodwill, Brian P McCarthy, Scott A Persohn, Paul R Territo, Jeffrey A Kline
Our understanding of the pathophysiological basis of chronic thromboembolic pulmonary hypertension (CTEPH) will be accelerated by an animal model that replicates the phenotype of human CTEPH. Sprague-Dawley rats were administered a combination of a single dose each of plastic microspheres and vascular endothelial growth factor receptor antagonist in polystyrene microspheres (PE) + tyrosine kinase inhibitor SU5416 (SU) group. Shams received volume-matched saline; PE and SU groups received only microspheres or SU5416, respectively...
February 6, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28183364/growth-of-total-fat-and-lean-and-of-primal-cuts-is-affected-by-the-sex-type
#17
A Carabús, R D Sainz, J W Oltjen, M Gispert, M Font-I-Furnols
Knowledge of tissue and cuts growth depending on the sex could be used to improve performance and efficiency. Computed tomography (CT) is a non-invasive technology that enables the study of the body composition of live animals during growth. The aims of the present study were (1) to evaluate variation in the body composition of four sex types (SEX) of pigs (castrated males (CM), immunocastrated males (IM), entire males (EM) and females (FE)) at the live weight of 30, 70, 100 and 120 kg, assessed using CT; (2) to model the growth of the main tissues and cuts; and (3) to predict the mature BW (MBW) of the four SEX and establish the relationships between the growth models and the MBW...
February 10, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28179518/computational-biomechanics-changes-our-view-on-insect-head-evolution
#18
Alexander Blanke, Peter J Watson, Richard Holbrey, Michael J Fagan
Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to objectively identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships...
February 8, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28179480/transient-voltage-activated-k-currents-in-central-antennal-lobe-neurons-cell-type-specific-functional-properties
#19
Lars Paeger, Viktor Bardos, Peter Kloppenburg
Here we analyzed transient voltage-activated K(+) currents (IA) of projection neurons and local interneurons in the antennal lobe (AL) of the cockroach Periplaneta americana. The AL is the first synaptic processing station for olfactory information in insects. Local interneurons are crucial for computing olfactory information and form local synaptic connections exclusively in the AL, while a primary task of the projection neurons is the transfer of preprocessed olfactory information from the AL to the protocerebrum...
February 8, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28177654/phenotype-analysis-method-for-identification-of-gene-functions-involved-in-asymmetric-division-of-caenorhabditis-elegans
#20
Sihai Yang, Xianhua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa, Yenwei Chen
In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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