Published in BMC Medical Genomics
BackgroundGenome-wide association studies (GWAS) have been widely used to identify phenotype-related genetic variants using many statistical methods, such as logistic and linear regression. However, GWAS-identified SNPs, as identified with stringent statistical significance, explain just a small portion of the overall estimated genetic heritability...
Published in BMC Medical Genomics
BackgroundThe current understanding of the genetic basis of complex human diseases is that they are caused and affected by many common and rare genetic variants. A considerable number of the disease-associated variants have been identified by Genome Wide Association Studies, however, they can explain only a small proportion of heritability. One of ...
Published in BMC Medical Genomics
BackgroundMultidimensional data mining from an integrated environment of different data sources is frequently performed in computational system biology. The molecular mechanism from the analysis of a complex network of gene-miRNA can aid to diagnosis and treatment of associated diseases.MethodsIn this work, we mainly focus on finding inflammatory b...
Published in BMC Medical Genomics
BackgroundIn cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression of important genes including tumor suppressor genes. Mutations on the epigenetic modifiers could affect the enzyme activity, which would result in the difference in genome-wide...
Published in BMC Medical Genomics
BackgroundBreast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an important part of clinical decision-making. Although this problem has been addressed using machine learning ...
Published in BMC Medical Genomics
BackgroundCancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challenging task due largely to a high rate of false-positives.Results...
Published in BMC Medical Genomics
BackgroundMany previous clinical studies have found that accumulated sequential mutations are statistically related to tumorigenesis. However, they are limited in fully elucidating the significance of the ordered-mutation because they did not focus on the network dynamics. Therefore, there is a pressing need to investigate the dynamics characterist...
Published in BMC Medical Genomics
BackgroundSingle cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information.ResultsWe developed V...
Published in BMC Medical Genomics
BackgroundInfluenza infections produce a spectrum of disease severity, ranging from a mild respiratory illness to respiratory failure and death. The host-response pathways associated with the progression to severe influenza disease are not well understood.MethodsTo gain insight into the disease mechanisms associated with progression to severe infec...
Published in BMC Medical Genomics
BackgroundThe amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ maturation; yet, defining normal expression and splicing patterns for biomarker discovery in obstetrics requires larger heterogeneous...
