keyword
MENU ▼
Read by QxMD icon Read
search

Genetics cross validation

keyword
https://www.readbyqxmd.com/read/28711280/unsupervised-extraction-of-stable-expression-signatures-from-public-compendia-with-an-ensemble-of-neural-networks
#1
Jie Tan, Georgia Doing, Kimberley A Lewis, Courtney E Price, Kathleen M Chen, Kyle C Cady, Barret Perchuk, Michael T Laub, Deborah A Hogan, Casey S Greene
Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models...
July 11, 2017: Cell Systems
https://www.readbyqxmd.com/read/28710898/projected-climate-changes-threaten-ancient-refugia-of-kelp-forests-in-the-north-atlantic
#2
Jorge Assis, Miguel B Araújo, Ester A Serrão
Intra-specific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial-interglacial cycles. We use ecological niche modeling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm-temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid-Holocene (6,000 YBP) and the present...
July 15, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28710504/mapping-novel-aphid-resistance-qtl-from-wild-soybean-glycine-soja-85-32
#3
Shichen Zhang, Zhongnan Zhang, Carmille Bales, Cuihua Gu, Chris DiFonzo, Ming Li, Qijian Song, Perry Cregan, Zhenyu Yang, Dechun Wang
Two novel QTLs conferring aphid resistance were mapped and validated on soybean chromosomes 8 and 16, respectively. Closely linked markers were developed to assist breeding for aphid resistance. Soybean aphid, Aphis glycines Matsumura, is a highly destructive pest for soybean production. E08934, a soybean advanced breeding line derived from the wild soybean Glycine soja 85-32, has shown strong resistance to aphids. To dissect the genetic basis of aphid resistance in E08934, a mapping population (070020) consisting of 140 F3-derived lines was developed by crossing E08934 with an aphid-susceptible line E00003...
July 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28707250/genomic-prediction-of-starch-content-and-chipping-quality-in-tetraploid-potato-using-genotyping-by-sequencing
#4
Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre L Nielsen
Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development...
July 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28702565/identifying-the-common-genetic-networks-of-adr-adverse-drug-reaction-clusters-and-developing-an-adr-classification-model
#5
Youhyeon Hwang, Min Oh, Giup Jang, Taekeon Lee, Chihyun Park, Jaegyoon Ahn, Youngmi Yoon
Adverse drug reactions (ADRs) are one of the major concerns threatening public health and have resulted in failures in drug development. Thus, predicting ADRs and discovering the mechanisms underlying ADRs have become important tasks in pharmacovigilance. Identification of potential ADRs by computational approaches in the early stages would be advantageous in drug development. Here we propose a computational method that elucidates the action mechanisms of ADRs and predicts potential ADRs by utilizing ADR genes, drug features, and protein-protein interaction (PPI) networks...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28697783/validation-of-qtl-mapping-and-transcriptome-profiling-for-identification-of-candidate-genes-associated-with-nitrogen-stress-tolerance-in-sorghum
#6
Malleswari Gelli, Anji Reddy Konda, Kan Liu, Chi Zhang, Thomas E Clemente, David R Holding, Ismail M Dweikat
BACKGROUND: Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations...
July 11, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28697758/identification-of-qtls-controlling-grain-protein-concentration-using-a-high-density-snp-and-ssr-linkage-map-in-barley-hordeum-vulgare-l
#7
Chaofeng Fan, Huijie Zhai, Huifang Wang, Yafei Yue, Minghu Zhang, Jinghui Li, Shaozhe Wen, Ganggang Guo, Yawen Zeng, Zhongfu Ni, Mingshan You
BACKGROUND: Grain protein concentration (GPC) is a major determinant of quality in barley (Hordeum vulgare L.). Breeding barley cultivars with high GPC has practical value for feed and food properties. The aim of the present study was to identify quantitative trait loci (QTLs) for GPC that could be detected under multiple environments. RESULTS: A population of 190 recombinant inbred lines (RILs) deriving from a cross between Chinese landrace ZGMLEL with high GPC (> 20%) and Australian cultivar Schooner was used for linkage and QTL analyses...
July 11, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28696921/aspsirna-a-resource-of-asp-sirnas-having-therapeutic-potential-for-human-genetic-disorders-and-algorithm-for-prediction-of-their-inhibitory-efficacy
#8
Isha Monga, Abid Qureshi, Nishant Thakur, Amit Kumar Gupta, Manoj Kumar
Allele-specific siRNAs (ASP-siRNAs) have emerged as promising therapeutic molecules owing to their selectivity to inhibit the mutant allele or associated single nucleotide polymorphisms (SNPs) sparing the expression of the wild-type counterpart. Thus, a dedicated bioinformatics platform encompassing updated ASP-siRNAs and an algorithm for the prediction of their inhibitory efficacy will be helpful in tackling currently intractable genetic disorders. In the present study, we have developed the ASPsiRNA resource (http://crdd...
July 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28696432/cross-disorder-risk-gene-cacna1c-differentially-modulates-susceptibility-to-psychiatric-disorders-during-development-and-adulthood
#9
N Dedic, M L Pöhlmann, J S Richter, D Mehta, D Czamara, M W Metzger, J Dine, B T Bedenk, J Hartmann, K V Wagner, A Jurik, L M Almli, A Lori, S Moosmang, F Hofmann, C T Wotjak, G Rammes, M Eder, A Chen, K J Ressler, W Wurst, M V Schmidt, E B Binder, J M Deussing
Single-nucleotide polymorphisms (SNPs) in CACNA1C, the α1C subunit of the voltage-gated L-type calcium channel Cav1.2, rank among the most consistent and replicable genetics findings in psychiatry and have been associated with schizophrenia, bipolar disorder and major depression. However, genetic variants of complex diseases often only confer a marginal increase in disease risk, which is additionally influenced by the environment. Here we show that embryonic deletion of Cacna1c in forebrain glutamatergic neurons promotes the manifestation of endophenotypes related to psychiatric disorders including cognitive decline, impaired synaptic plasticity, reduced sociability, hyperactivity and increased anxiety...
July 11, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28687792/maldi-tof-ms-as-a-novel-tool-for-the-estimation-of-postmortem-interval-in-liver-tissue-samples
#10
Chengzhi Li, Zhengdong Li, Ya Tuo, Dong Ma, Yan Shi, Qinghua Zhang, Xianyi Zhuo, Kaifei Deng, Yijiu Chen, Zhenyuan Wang, Ping Huang
Estimation of the postmortem interval (PMI) is a complicated task in forensic medicine, especially during homicide and unwitnessed death investigations. Many biological, chemical, and physical indicators can be used to determine the postmortem interval, but most are not accurate. Here, we present a novel matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method that can be used for the estimation of PMI using molecular images and multivariate analyses. In this study, we demonstrate that both rat and human liver tissues of various PMIs (0, 2, 4, and 6days) can be discriminated using MALDI imaging and principal component analysis (PCA)...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28674662/bmi-prediction-within-a-korean-population
#11
Jin Sol Lee, Hyun Sub Cheong, Hyoung-Doo Shin
BACKGROUND: Body Mass Index (BMI) is widely regarded as an important clinical trait for obesity and other diseases such as Type 2 diabetes, coronary heart disease, and osteoarthritis. METHODS: This study uses 6,011 samples of genotype data from ethnic Korean subjects. The data was retrieved from the Korea Association Resource. To identify the BMI-related markers within the Korean population, we collected genome-wide association study (GWAS) markers using a GWAS catalog and also obtained other markers from nearby regions...
2017: PeerJ
https://www.readbyqxmd.com/read/28673486/quantifying-dimensional-severity-of-obsessive-compulsive-disorder-for-neurobiological-research
#12
Roseli G Shavitt, Guaraci Requena, Pino Alonso, Gwyneth Zai, Daniel L C Costa, Carlos Alberto de Bragança Pereira, Maria Conceição do Rosário, Ivanil Morais, Leonardo Fontenelle, Carolina Cappi, James Kennedy, Jose M Menchon, Euripedes Miguel, Peggy M A Richter
Current research to explore genetic susceptibility factors in obsessive-compulsive disorder (OCD) has resulted in the tentative identification of a small number of genes. However, findings have not been readily replicated. It is now broadly accepted that a major limitation to this work is the heterogeneous nature of this disorder, and that an approach incorporating OCD symptom dimensions in a quantitative manner may be more successful in identifying both common as well as dimension-specific vulnerability genetic factors...
July 1, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28668296/igg-glycan-patterns-are-associated-with-type-2-diabetes-in-independent-european-populations
#13
Roosmarijn F H Lemmers, Marija Vilaj, Daniel Urda, Felix Agakov, Mirna Šimurina, Lucija Klaric, Igor Rudan, Harry Campbell, Caroline Hayward, Jim F Wilson, Aloysius G Lieverse, Olga Gornik, Eric J G Sijbrands, Gordan Lauc, Mandy van Hoek
BACKGROUND: Type 2 diabetes results from interplay between genetic and acquired factors. Glycans on proteins reflect genetic, metabolic and environmental factors. However, associations of IgG glycans with type 2 diabetes have not been described. We compared IgG N-glycan patterns in type 2 diabetes with healthy subjects. METHODS: In the DiaGene study, a population-based case-control study, (1886 cases and 854 controls) 58 IgG glycan traits were analyzed. Findings were replicated in the population-based CROATIA-Korcula-CROATIA-Vis-ORCADES studies (162 cases and 3162 controls), and meta-analyzed...
June 28, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28667666/translating-advances-in-the-molecular-basis-of-schizophrenia-into-novel-cognitive-treatment-strategies
#14
REVIEW
Colm M P Oapos Tuathaigh, Paula M Moran, Xuechu C Zhen, John L Waddington
The presence and severity of cognitive symptoms, including working memory, executive dysfunction and attentional impairment, contributes materially to functional impairment in schizophrenia. Cognitive symptoms have proven resistant to both first- and second-generation antipsychotic drugs. Efforts to develop a consensus set of cognitive domains that are both disrupted in schizophrenia and are amenable to cross-species validation (e.g. the NIMH CNTRICS and RDoC initiatives) are an important step towards standardisation of outcome measures that can used in preclinical testing of new drugs...
June 30, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28666484/prediction-of-new-hsp90-inhibitors-based-on-3-4-isoxazolediamide-scaffold-using-qsar-study-molecular-docking-and-molecular-dynamic-simulation
#15
Maryam Abbasi, Hojjat Sadeghi-Aliabadi, Massoud Amanlou
BACKGROUND: Heat shock protein90 (Hsp90) are overexpressed in tumor cells, so the inhibition of the Hsp90 ATPase activity would be a significantly effective strategy in cancer therapy. METHODS: In the current study, 3,4-isoxazolediamide derivatives were suggested as an Hsp90 inhibitor for anti-cancer therapy. Multiple linear regression (MLR) and genetic algorithm of partial least square (GA-PLS) methods were performed to build models to predict the inhibitory activity of Hsp90...
June 30, 2017: Daru: Journal of Faculty of Pharmacy, Tehran University of Medical Sciences
https://www.readbyqxmd.com/read/28661468/study-on-the-association-among-mycotoxins-and-other-variables-in-children-with-autism
#16
Barbara De Santis, Maria Elisabetta Raggi, Giorgio Moretti, Francesco Facchiano, Alessandra Mezzelani, Laura Villa, Arianna Bonfanti, Alessandra Campioni, Stefania Rossi, Serena Camposeo, Sabina Soricelli, Gabriele Moracci, Francesca Debegnach, Emanuela Gregori, Francesca Ciceri, Luciano Milanesi, Anna Marabotti, Carlo Brera
Environmental factors and genetic susceptibility are implicated in the increased risk of autism spectrum disorder (ASD). Mycotoxins are agricultural contaminants of fungal origin that represent real risk factors for human health and especially for children. Thus, the main hypothesis of this work is that the deterioration of the clinical manifestation of autism in children may result from the exposure to mycotoxins through the consumption of contaminated food. Within a cross-sectional study, a group of autistic children (n = 172) and a group of controls (n = 61) (siblings and non-parental) were recruited in North and South Italy...
June 29, 2017: Toxins
https://www.readbyqxmd.com/read/28649752/investigating-dna-rna-and-protein-based-features-as-a-means-to-discriminate-pathogenic-synonymous-variants
#17
Mark Livingstone, Lukas Folkman, Yuedong Yang, Ping Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Bela Stantic, Yaoqi Zhou
Synonymous single nucleotide variants (SNVs), although they do not alter the encoded protein sequences, have been implicated in many genetic diseases. Experimental studies indicate that synonymous SNVs can lead to changes in the secondary and tertiary structures of DNA and RNA, thereby impacting translational efficiency, co-translational protein folding as well as the binding of DNA/RNA-binding proteins. However, the importance of these various features in disease phenotypes is not clearly understood. Here we have built a support vector machine model (termed DDIG-SN) as a means to discriminate disease-causing synonymous variants...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#18
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#19
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633685/cross-validation-analysis-for-genetic-evaluation-models-for-ranking-in-endurance-horses
#20
S García-Ballesteros, L Varona, M Valera, J P Gutiérrez, I Cervantes
Ranking trait was used as a selection criterion for competition horses to estimate racing performance. In the literature the most common approaches to estimate breeding values are the linear or threshold statistical models. However, recent studies have shown that a Thurstonian approach was able to fix the race effect (competitive level of the horses that participate in the same race), thus suggesting a better prediction accuracy of breeding values for ranking trait. The aim of this study was to compare the predictability of linear, threshold and Thurstonian approaches for genetic evaluation of ranking in endurance horses...
June 21, 2017: Animal: An International Journal of Animal Bioscience
keyword
keyword
101054
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"