BMC Medical Genomics
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation
Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional...BMC Medical Genomics 2020 13:6Identification of biomarkers and drug repurposing candidates based on an immune-, inflammation- and membranous glomerulonephritis-associated triplets network for membranous glomerulonephritis
Membranous glomerulonephritis (MGN) is a common kidney disease. Despite many evidences support that many immune and inflammation-related genes could serve as effective biomarkers and treatment targets for MGN ...BMC Medical Genomics 2020 13:5Genome-wide analysis reveals the association between alternative splicing and DNA methylation across human solid tumors
Dysregulation of alternative splicing (AS) is a critical signature of cancer. However, the regulatory mechanisms of cancer-specific AS events, especially the impact of DNA methylation, are poorly understood.BMC Medical Genomics 2020 13:4MiR-182-5p and its target HOXA9 in non-small cell lung cancer: a clinical and in-silico exploration with the combination of RT-qPCR, miRNA-seq and miRNA-chip
MiR-182-5p, a cancer-related microRNA (miRNA), modulates tumorigenesis and patient outcomes in various human malignances. This study interroted the clinicopathological significance and molecular mechanisms of ...BMC Medical Genomics 2020 13:312q14 microduplication: a new clinical entity reciprocal to the microdeletion syndrome?
12q14 microdeletion syndrome is characterized by low birth weight and failure to thrive, proportionate short stature and developmental delay. The opposite syndrome (microduplication) has not yet been character...BMC Medical Genomics 2020 13:2Genome-wide analysis of aberrant methylation of enhancer DNA in human osteoarthritis
Osteoarthritis is a chronic musculoskeletal disease characterized by age-related gradual thinning and a high risk in females. Recent studies have shown that DNA methylation plays important roles in osteoarthri...BMC Medical Genomics 2020 13:1MEG3 promotes proliferation and inhibits apoptosis in osteoarthritis chondrocytes by miR-361-5p/FOXO1 axis
This study aimed to investigate the role of long non-coding RNA (lncRNA) maternally expressed 3 (MEG3) and related molecular mechanisms, in osteoarthritis (OA).BMC Medical Genomics 2019 12:201Genome analysis and knowledge-driven variant interpretation with TGex
The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant gene...BMC Medical Genomics 2019 12:200Identifying driver genes involving gene dysregulated expression, tissue-specific expression and gene-gene network
Cancer as a kind of genomic alteration disease each year deprives many people’s life. The biggest challenge to overcome cancer is to identify driver genes that promote the cancer development from a huge amount...BMC Medical Genomics 2019 12(Suppl 7):168This article is part of a Supplement: Volume 12 Supplement 7Prediction of comorbid diseases using weighted geometric embedding of human interactome
Comorbidity is the phenomenon of two or more diseases occurring simultaneously not by random chance and presents great challenges to accurate diagnosis and treatment. As an effort toward better understanding t...BMC Medical Genomics 2019 12(Suppl 7):161This article is part of a Supplement: Volume 12 Supplement 7A network view of microRNA and gene interactions in different pathological stages of colon cancer
Colon cancer is one of the common cancers in human. Although the number of annual cases has decreased drastically, prognostic screening and translational methods can be improved. Hence, it is critical to under...BMC Medical Genomics 2019 12(Suppl 7):158This article is part of a Supplement: Volume 12 Supplement 7A new method for mining information of co-expression network based on multi-cancers integrated data
Gene co-expression network is a favorable method to reveal the nature of disease. With the development of cancer, the way to build gene co-expression networks based on cancer data has been become a hot spot. H...BMC Medical Genomics 2019 12(Suppl 7):155This article is part of a Supplement: Volume 12 Supplement 7A network clustering based feature selection strategy for classifying autism spectrum disorder
Advanced non-invasive neuroimaging techniques offer new approaches to study functions and structures of human brains. Whole-brain functional networks obtained from resting state functional magnetic resonance i...BMC Medical Genomics 2019 12(Suppl 7):153This article is part of a Supplement: Volume 12 Supplement 7MECoRank: cancer driver genes discovery simultaneously evaluating the impact of SNVs and differential expression on transcriptional networks
Although there are huge volumes of genomic data, how to decipher them and identify driver events is still a challenge. The current methods based on network typically use the relationship between genomic events...BMC Medical Genomics 2019 12(Suppl 7):140This article is part of a Supplement: Volume 12 Supplement 7HiSSI: high-order SNP-SNP interactions detection based on efficient significant pattern and differential evolution
Detecting single nucleotide polymorphism (SNP) interactions is an important and challenging task in genome-wide association studies (GWAS). Various efforts have been devoted to detect SNP interactions. However...BMC Medical Genomics 2019 12(Suppl 7):139This article is part of a Supplement: Volume 12 Supplement 7Region-based interaction detection in genome-wide case-control studies
In genome-wide association study (GWAS), conventional interaction detection methods such as BOOST are mostly based on SNP-SNP interactions. Although single nucleotides are the building blocks of human genome, ...BMC Medical Genomics 2019 12(Suppl 7):133This article is part of a Supplement: Volume 12 Supplement 7Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs
Most statistical methods used to identify cancer driver genes are either biased due to choice of assumed parametric models or insensitive to directional relationships important for causal inference. To overcom...BMC Medical Genomics 2019 12(Suppl 7):129This article is part of a Supplement: Volume 12 Supplement 7Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis
Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been e...BMC Medical Genomics 2019 12:199Integrative subspace clustering by common and specific decomposition for applications on cancer subtype identification
Recent high throughput technologies have been applied for collecting heterogeneous biomedical omics datasets. Computational analysis of the multi-omics datasets could potentially reveal deep insights for a giv...BMC Medical Genomics 2019 12(Suppl 9):191This article is part of a Supplement: Volume 12 Supplement 9Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data
The application of next-generation sequencing in cancer has revealed the genomic landscape of many tumour types and is nowadays routinely used in research and clinical settings. Multiple algorithms have been d...BMC Medical Genomics 2019 12(Suppl 9):181This article is part of a Supplement: Volume 12 Supplement 9wtest: an integrated R package for genetic epistasis testing
With the increasing amount of high-throughput genomic sequencing data, there is a growing demand for a robust and flexible tool to perform interaction analysis. The identification of SNP-SNP, SNP-CpG, and high...BMC Medical Genomics 2019 12(Suppl 9):180This article is part of a Supplement: Volume 12 Supplement 9CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis
Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality. However, besides known changes in the PAX3/7-FOXO1 fusion gene in alveolar RMS, the molecular me...BMC Medical Genomics 2019 12:198Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data
Understanding the complex biological mechanisms of cancer patient survival using genomic and clinical data is vital, not only to develop new treatments for patients, but also to improve survival prediction. Ho...BMC Medical Genomics 2019 12(Suppl 10):189This article is part of a Supplement: Volume 12 Supplement 10A network embedding model for pathogenic genes prediction by multi-path random walking on heterogeneous network
Prediction of pathogenic genes is crucial for disease prevention, diagnosis, and treatment. But traditional genetic localization methods are often technique-difficulty and time-consuming. With the development ...BMC Medical Genomics 2019 12(Suppl 10):188This article is part of a Supplement: Volume 12 Supplement 10HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks
As a standardized vocabulary of phenotypic abnormalities associated with human diseases, the Human Phenotype Ontology (HPO) has been widely used by researchers to annotate phenotypes of genes/proteins. For sav...BMC Medical Genomics 2019 12(Suppl 10):187This article is part of a Supplement: Volume 12 Supplement 10Heterogeneous network embedding enabling accurate disease association predictions
It is significant to identificate complex biological mechanisms of various diseases in biomedical research. Recently, the growing generation of tremendous amount of data in genomics, epigenomics, metagenomics,...BMC Medical Genomics 2019 12(Suppl 10):186This article is part of a Supplement: Volume 12 Supplement 10MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation
Studies have shown that miRNAs are functionally associated with the development of many human diseases, but the roles of miRNAs in diseases and their underlying molecular mechanisms have not been fully underst...BMC Medical Genomics 2019 12(Suppl 10):185This article is part of a Supplement: Volume 12 Supplement 10Parameter, noise, and tree topology effects in tumor phylogeny inference
Accurate inference of the evolutionary history of a tumor has important implications for understanding and potentially treating the disease. While a number of methods have been proposed to reconstruct the evol...BMC Medical Genomics 2019 12(Suppl 10):184This article is part of a Supplement: Volume 12 Supplement 10Karyotyping and prenatal diagnosis of 47,XX,+ 8[67]/46,XX [13] Mosaicism: case report and literature review
Trisomy 8 mosaicism has a wide phenotypic variability, ranging from mild dysmorphic features to severe malformations. This report concluded a female pregnant woman with trisomy 8 mosaicism, and carefully cytog...BMC Medical Genomics 2019 12:197GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining
An important task in the interpretation of sequencing data is to highlight pathogenic genes (or detrimental variants) in the field of Mendelian diseases. It is still challenging despite the recent rapid develo...BMC Medical Genomics 2019 12(Suppl 8):193This article is part of a Supplement: Volume 12 Supplement 8Identification of lung cancer gene markers through kernel maximum mean discrepancy and information entropy
The early diagnosis of lung cancer has been a critical problem in clinical practice for a long time and identifying differentially expressed gene as disease marker is a promising solution. However, the most ex...BMC Medical Genomics 2019 12(Suppl 8):183This article is part of a Supplement: Volume 12 Supplement 8Finding prognostic gene pairs for cancer from patient-specific gene networks
Molecular characterization of individual cancer patients is important because cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. Many studies have been conducted...BMC Medical Genomics 2019 12(Suppl 8):179This article is part of a Supplement: Volume 12 Supplement 8A deep neural network approach to predicting clinical outcomes of neuroblastoma patients
The availability of high-throughput omics datasets from large patient cohorts has allowed the development of methods that aim at predicting patient clinical outcomes, such as survival and disease recurrence. S...BMC Medical Genomics 2019 12(Suppl 8):178This article is part of a Supplement: Volume 12 Supplement 8Differential alternative splicing regulation among hepatocellular carcinoma with different risk factors
Hepatitis B virus (HBV), hepatitis C virus (HCV), and alcohol consumption are predominant causes of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying how differently these causes are...BMC Medical Genomics 2019 12(Suppl 8):175This article is part of a Supplement: Volume 12 Supplement 8Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells
To facilitate the investigation of the pathogenic roles played by various immune cells in complex tissues such as tumors, a few computational methods for deconvoluting bulk gene expression profiles to predict ...BMC Medical Genomics 2019 12(Suppl 8):169This article is part of a Supplement: Volume 12 Supplement 8Genome-wide association study in Chinese cohort identifies one novel hypospadias risk associated locus at 12q13.13
Hypospadias risk–associated gene variants have been reported in populations of European descent using genome-wide association studies (GWASs). There is little known at present about any possible hypospadias ri...BMC Medical Genomics 2019 12:196RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery
Formalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcom...BMC Medical Genomics 2019 12:195Competitive endogenous RNA (ceRNA) regulation network of lncRNAs, miRNAs, and mRNAs in Wilms tumour
Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. However, an understanding of the ceRNA regulatory network in Wilms tumour (WT) remains limited.BMC Medical Genomics 2019 12:194Systematic computational identification of prognostic cytogenetic markers in neuroblastoma
Neuroblastoma (NB) is the most common extracranial solid tumor found in children. The frequent gain/loss of many chromosome bands in tumor cells and absence of mutations found at diagnosis suggests that NB is ...BMC Medical Genomics 2019 12:192Analysis of disease comorbidity patterns in a large-scale China population
Disease comorbidity is popular and has significant indications for disease progress and management. We aim to detect the general disease comorbidity patterns in Chinese populations using a large-scale clinical...BMC Medical Genomics 2019 12(Suppl 12):177This article is part of a Supplement: Volume 12 Supplement 12Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists
When ordering genetic testing or triaging candidate variants in exome and genome sequencing studies, it is critical to generate and test a comprehensive list of candidate genes that succinctly describe the com...BMC Medical Genomics 2019 12:190A female patient with retinoblastoma and severe intellectual disability carrying an X;13 balanced translocation without rearrangement in the RB1 gene: a case report
Female carriers of a balanced X; autosome translocation generally undergo selective inactivation of the normal X chromosome. This is because inactivation of critical genes within the autosomal region of the de...BMC Medical Genomics 2019 12:182Correction to: A functional polymorphism in the promoter of miR-17-92 cluster is associated with decreased risk of ischemic stroke
Following publication of the original article [1], it was reported that during the production process, Fig. 3b was omitted from the final article.BMC Medical Genomics 2019 12:176The original article was published in BMC Medical Genomics 2019 12:159Reinterpretation, reclassification, and its downstream effects: challenges for clinical laboratory geneticists
In recent years, the amount of genomic data produced in clinical genetics services has increased significantly due to the advent of next-generation sequencing. This influx of genomic information leads to conti...BMC Medical Genomics 2019 12:170High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome
Psoriasis is a chronic inflammatory skin disease characterized by hyperproliferation and abnormal differentiation of keratinocytes. It is one of the most prevalent chronic inflammatory skin conditions in adult...BMC Medical Genomics 2019 12:174Return of genetic and genomic research findings: experience of a pediatric biorepository
Assess process, uptake, validity and resource needs for return of actionable research findings to biobank participants.BMC Medical Genomics 2019 12:173MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration
The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential ge...BMC Medical Genomics 2019 12:172Identification and ranking of recurrent neo-epitopes in cancer
Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognitio...BMC Medical Genomics 2019 12:171Correction to: RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking
Following publication of the original article [1], the authors provided an updated accession number in the “Availability of data and materials” section of the declarations.BMC Medical Genomics 2019 12:166The original article was published in BMC Medical Genomics 2017 10:58Classification of glioma based on prognostic alternative splicing
Previously developed classifications of glioma have provided enormous advantages for the diagnosis and treatment of glioma. Although the role of alternative splicing (AS) in cancer, especially in glioma, has b...BMC Medical Genomics 2019 12:165
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