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BMC Medical Genomics

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https://www.readbyqxmd.com/read/29329538/peripheral-blood-gene-expression-signatures-which-reflect-smoking-and-aspirin-exposure-are-associated-with-cardiovascular-events
#1
James A Wingrove, Karen Fitch, Brian Rhees, Steven Rosenberg, Deepak Voora
BACKGROUND: Cardiovascular disease and its sequelae are major causes of global mortality, and better methods are needed to identify patients at risk for future cardiovascular events. Gene expression analysis can inform on the molecular underpinnings of risk factors for cardiovascular events. Smoking and aspirin have known opposing effects on platelet reactivity and MACE, however their effects on each other and on MACE are not well described. METHODS: We measured peripheral blood gene expression levels of ITGA2B, which is upregulated by aspirin and correlates with platelet reactivity on aspirin, and a 5 gene validated smoking gene expression score (sGES) where higher expression correlates with smoking status, in participants from the previously reported PREDICT trial (NCT 00500617)...
January 12, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297383/predicting-drug-disease-interactions-by-semi-supervised-graph-cut-algorithm-and-three-layer-data-integration
#2
Guangsheng Wu, Juan Liu, Caihua Wang
BACKGROUND: Prediction of drug-disease interactions is promising for either drug repositioning or disease treatment fields. The discovery of novel drug-disease interactions, on one hand can help to find novel indictions for the approved drugs; on the other hand can provide new therapeutic approaches for the diseases. Recently, computational methods for finding drug-disease interactions have attracted lots of attention because of their far more higher efficiency and lower cost than the traditional wet experiment methods...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297370/reverse-engineering-of-gene-networks-for-regulating-early-blood-development-from-single-cell-measurements
#3
Jiangyong Wei, Xiaohua Hu, Xiufen Zou, Tianhai Tian
BACKGROUND: Recent advances in omics technologies have raised great opportunities to study large-scale regulatory networks inside the cell. In addition, single-cell experiments have measured the gene and protein activities in a large number of cells under the same experimental conditions. However, a significant challenge in computational biology and bioinformatics is how to derive quantitative information from the single-cell observations and how to develop sophisticated mathematical models to describe the dynamic properties of regulatory networks using the derived quantitative information...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297367/disease-named-entity-recognition-from-biomedical-literature-using-a-novel-convolutional-neural-network
#4
Zhehuan Zhao, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang
BACKGROUND: Automatic disease named entity recognition (DNER) is of utmost importance for development of more sophisticated BioNLP tools. However, most conventional CRF based DNER systems rely on well-designed features whose selection is labor intensive and time-consuming. Though most deep learning methods can solve NER problems with little feature engineering, they employ additional CRF layer to capture the correlation information between labels in neighborhoods which makes them much complicated...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297358/stable-solution-to-l-2-1-based-robust-inductive-matrix-completion-and-its-application-in-linking-long-noncoding-rnas-to-human-diseases
#5
Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, Chris Ding, Jean X Gao
BACKGROUNDS: A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links between the two entities through biological experiments are expensive. However, a plethora lincRNA-data are available now, thanks to the High Throughput Sequencing (HTS) platforms, Genome Wide Association Studies (GWAS), etc, which opens the opportunity for cutting-edge machine learning and data mining approaches to extract meaningful relationships among lincRNAs and diseases...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297351/probability-based-collaborative-filtering-model-for-predicting-gene-disease-associations
#6
Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodríguez-Patón, Quan Zou
BACKGROUND: Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene-disease data verified by biological experiments, we can apply computational methods to perform accurate predictions with reduced time and expenses. METHODS: We propose a probability-based collaborative filtering model (PCFM) to predict pathogenic human genes. Several kinds of data sets, containing data of humans and data of other nonhuman species, are integrated in our model...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297344/ioptics-gso-for-identifying-protein-complexes-from-dynamic-ppi-networks
#7
Xiujuan Lei, Huan Li, Aidong Zhang, Fang-Xiang Wu
BACKGROUND: Identifying protein complexes plays an important role for understanding cellular organization and functional mechanisms. As plenty of evidences have indicated that dense sub-networks in dynamic protein-protein interaction network (DPIN) usually correspond to protein complexes, identifying protein complexes is formulated as density-based clustering. METHODS: In this paper, a new approach named iOPTICS-GSO is developed, which is the improved Ordering Points to Identify the Clustering Structure (OPTICS) algorithm with Glowworm swarm optimization algorithm (GSO) to optimize the parameters in OPTICS when finding dense sub-networks...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297338/measuring-disease-similarity-and-predicting-disease-related-ncrnas-by-a-novel-method
#8
Yang Hu, Meng Zhou, Hongbo Shi, Hong Ju, Qinghua Jiang, Liang Cheng
BACKGROUND: Similar diseases are always caused by similar molecular origins, such as diasease-related protein-coding genes (PCGs). And the molecular associations reflect their similarity. Therefore, current methods for calculating disease similarity often utilized functional interactions of PCGs. Besides, the existing methods have neglected a fact that genes could also be associated in the gene functional network (GFN) based on intermediate nodes. METHODS: Here we presented a novel method, InfDisSim, to deduce the similarity of diseases...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29284484/platform-independent-gene-expression-signature-differentiates-sessile-serrated-adenomas-polyps-and-hyperplastic-polyps-of-the-colon
#9
Yasir Rahmatallah, Magomed Khaidakov, Keith K Lai, Hannah E Goyne, Laura W Lamps, Curt H Hagedorn, Galina Glazko
BACKGROUND: Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps can have overlapping morphological features resulting in sessile serrated polyps diagnosed as hyperplastic. While sessile serrated polyps can progress into colon cancer, hyperplastic polyps have virtually no risk for colon cancer. Objective measures, differentiating these types of polyps would improve cancer prevention and treatment outcome...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322937/predicting-binary-discrete-and-continued-lncrna-disease-associations-via-a-unified-framework-based-on-graph-regression
#10
Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Yu-Xi Long, Siu-Ming Yiu
BACKGROUND: In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322935/classifying-cancer-genome-aberrations-by-their-mutually-exclusive-effects-on-transcription
#11
Jonathan B Dayton, Stephen R Piccolo
BACKGROUND: Malignant tumors are typically caused by a conglomeration of genomic aberrations-including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. One way to address this problem is to examine the downstream, transcriptional effects of genomic aberrations and to identify characteristic patterns...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322932/identification-of-prognostic-signature-in-cancer-based-on-dna-methylation-interaction-network
#12
Wei-Lin Hu, Xiong-Hui Zhou
BACKGROUND: The identification of prognostic biomarkers for cancer patients is essential for cancer research. These days, DNA methylation has been proved to be associated with cancer prognosis. However, there are few methods which identify the prognostic markers based on DNA methylation data systematically, especially considering the interaction among DNA methylation sites. METHODS: In this paper, we first evaluated the stabilities of microRNA, mRNA, and DNA methylation data in prognosis of cancer...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322931/differential-responses-of-innate-immunity-triggered-by-different-subtypes-of-influenza-a-viruses-in-human-and-avian-hosts
#13
Yingying Cao, Yaowei Huang, Ke Xu, Yuanhua Liu, Xuan Li, Ye Xu, Wu Zhong, Pei Hao
BACKGROUND: Innate immunity provides first line of defense against viral infections. The interactions between hosts and influenza A virus and the response of host innate immunity to viral infection are critical determinants for the pathogenicity or virulence of influenza A viruses. This study was designed to investigate global changes of gene expression and detailed responses of innate immune systems in human and avian hosts during the course of infection with various subtypes of influenza A viruses, using collected and self-generated transcriptome sequencing data from human bronchial epithelial (HBE), human tracheobronchial epithelial (HTBE), and A549 cells infected with influenza A virus subtypes, namely H1N1, H3N2, H5N1 HALo mutant, and H7N9, and from ileum and lung of chicken and quail infected with H5N1, or H5N2...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322925/subtype-identification-from-heterogeneous-tcga-datasets-on-a-genomic-scale-by-multi-view-clustering-with-enhanced-consensus
#14
Menglan Cai, Limin Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. The problem is challenging when different data types show poor agreement of clustering structure...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322922/analysis-of-viral-diversity-for-vaccine-target-discovery
#15
Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August
BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322921/tensor-decomposition-based-unsupervised-feature-extraction-identifies-candidate-genes-that-induce-post-traumatic-stress-disorder-mediated-heart-diseases
#16
Y-H Taguchi
BACKGROUND: Although post-traumatic stress disorder (PTSD) is primarily a mental disorder, it can cause additional symptoms that do not seem to be directly related to the central nervous system, which PTSD is assumed to directly affect. PTSD-mediated heart diseases are some of such secondary disorders. In spite of the significant correlations between PTSD and heart diseases, spatial separation between the heart and brain (where PTSD is primarily active) prevents researchers from elucidating the mechanisms that bridge the two disorders...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29212506/chromosome-9p-copy-number-gains-involving-pd-l1-are-associated-with-a-specific-proliferation-and-immune-modulating-gene-expression-program-active-across-major-cancer-types
#17
Jan Budczies, Carsten Denkert, Balázs Győrffy, Peter Schirmacher, Albrecht Stenzinger
BACKGROUND: Inhibition of the PD-L1/PD-1 immune checkpoint axis represents one of the most promising approaches of immunotherapy for various cancer types. However, immune checkpoint inhibition is successful only in subpopulations of patients emphasizing the need for powerful biomarkers that adequately reflect the complex interaction between the tumor and the immune system. Recently, recurrent copy number gains (CNG) in chromosome 9p involving PD-L1 were detected in many cancer types including lung cancer, melanoma, bladder cancer, head and neck cancer, cervical cancer, soft tissue sarcoma, prostate cancer, gastric cancer, ovarian cancer, and triple-negative breast cancer...
December 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29187224/correction-to-flags-frequently-mutated-genes-in-public-exomes
#18
Casper Shyr, Maja Tarailo-Graovac, Michael Gottlieb, Jessica Jy Lee, Clara van Karnebeek, Wyeth W Wasserman
Unfortunately, the original article [1] contained an error. The additional files were included incorrectly. The correct additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14 are published in this correction.
November 29, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29179725/high-resolution-chromosomal-microarray-analysis-in-paediatric-obsessive-compulsive-disorder
#19
Edna Grünblatt, Beatrice Oneda, Arif B Ekici, Juliane Ball, Julia Geissler, Steffen Uebe, Marcel Romanos, Anita Rauch, Susanne Walitza
BACKGROUND: Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range...
November 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29141684/bioinformatics-prediction-of-mir-30a-targets-and-its-inhibition-of-cell-proliferation-of-osteosarcoma-by-up-regulating-the-expression-of-pten
#20
Biao Zhong, Shang Guo, Wei Zhang, Chi Zhang, Yukai Wang, Changqing Zhang
BACKGROUND: MiRNAs are frequently abnormally expressed in the progression of human osteosarcoma. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is one of the tumor suppressors in various types of human cancer. In the present study, we detected how hsa-miR-30a-3p regulated PTEN and further tested the role of hsa-miR-30a-3p in the cell proliferation of osteosarcoma cells. METHODS: The levels of miR-30a were determined by real time PCR. The expression of PTEN was tested by western blotting analysis...
November 15, 2017: BMC Medical Genomics
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