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Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predicti...
Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only...
The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene ex...
Histopathological assessment has a low potential to predict clinical outcome in patients with the same stage of colorectal cancer. More specific and sensitive biomarkers to determine patients’ survival are nee...
Genomic testing has reached the point where, technically at least, it can be cheaper to undertake panel-, exome- or whole genome testing than it is to sequence a single gene. An attribute of these approaches i...
Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a defin...
DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related...
The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, select...
Detection of disease-associated markers plays a crucial role in gene screening for biological studies. Two-sample test statistics, such as the t-statistic, are widely used to rank genes based on gene expression d...
CpG islands (CGIs) are interspersed DNA sequences that have unusually high CpG ratios and GC contents. CGIs are typically located in the promoter of protein-coding genes. They normally lack DNA methylation but...
This article is part of a Supplement: Volume 9 Supplement 1
Kawasaki disease (KD) is an autoimmune disease preferentially attacking children younger than five years worldwide. So far, the principal treatment to KD is the administration of Intravenous immunoglobulin (IV...
This article is part of a Supplement: Volume 9 Supplement 1
Sequencing technologies are generating enormous amounts of read data, however assembly of genomes and metagenomes remain among the most challenging tasks. In this paper we study the comparison of genomes and m...
This article is part of a Supplement: Volume 9 Supplement 1
Exome sequencing has been emerged as a primary method to identify detailed sequence variants associated with complex diseases including Crohn’s disease in the protein-coding regions of human genome. However, c...
This article is part of a Supplement: Volume 9 Supplement 1
Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and c...
This article is part of a Supplement: Volume 9 Supplement 1
We explored premature stop-gain variants to test the hypothesis that variants, which are likely to have a consequence on protein structure and function, will reveal important insights with respect to the pheno...
This article is part of a Supplement: Volume 9 Supplement 1
The increasing availability of multiple types of genomic profiles measured from the same cancer patients has provided numerous opportunities for investigating genomic mechanisms underlying cancer. In particula...
This article is part of a Supplement: Volume 9 Supplement 1
Pathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer’s disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rar...
This article is part of a Supplement: Volume 9 Supplement 1
Tyrosine kinase inhibitor (TKI)-based therapy is a recommended treatment for patients with chronic myeloid leukemia (CML). However, a considerable group of CML patients do not respond well to the TKI therapy. ...
This article is part of a Supplement: Volume 9 Supplement 1
Non-small cell lung cancer (NSCLC) remains a lethal disease despite many proposed treatments. Recent studies have indicated that epigenetic therapy, which targets epigenetic effects, might be a new therapeutic...
This article is part of a Supplement: Volume 9 Supplement 1
Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically...
Inferring gene regulatory networks is one of the most interesting research areas in the systems biology. Many inference methods have been developed by using a variety of computational models and approaches. Ho...
This article is part of a Supplement: Volume 9 Supplement 2
Cell segmentation is a critical step for quantification and monitoring of cell cycle progression, cell migration, and growth control to investigate cellular immune response, embryonic development, tumorigenesi...
This article is part of a Supplement: Volume 9 Supplement 2
Genomic variations are associated with the metabolism and the occurrence of adverse reactions of many therapeutic agents. The polymorphisms on over 2000 locations of cytochrome P450 enzymes (CYP) due to many f...
This article is part of a Supplement: Volume 9 Supplement 2
Development of biologically relevant models from gene expression data notably, microarray data has become a topic of great interest in the field of bioinformatics and clinical genetics and oncology. Only a sma...
This article is part of a Supplement: Volume 9 Supplement 2
Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and...
This article is part of a Supplement: Volume 9 Supplement 2
In biomedical research, events revealing complex relations between entities play an important role. Biomedical event trigger identification has become a research hotspot since its important role in biomedical ...
This article is part of a Supplement: Volume 9 Supplement 2
Measurement of various markers of single cells using flow cytometry has several biological applications. These applications include improving our understanding of behavior of cellular systems, identifying rare...
This article is part of a Supplement: Volume 9 Supplement 2
The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs—to find new uses for which they weren’t intended, and to thereby reduce the overall cost...
Based on age of presentation, celiac disease (CD) is categorised as pediatric CD and adult CD. It however remains unclear if these are genetically and/or phenotypically distinct disorders or just different spe...
Identification of prognostic gene expression markers from clinical cohorts might help to better understand disease etiology. A set of potentially important markers can be automatically selected when linking ge...
Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in sil...
The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Circulating blood cells may carry informative changes in their RNA e...
The original article was published in BMC Medical Genomics 2016 9:26
The original article was published in BMC Medical Genomics 2015 8:59
Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outc...
At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-st...
The Erratum to this article has been published in BMC Medical Genomics 2016 9:39
The use of an overall risk assessment based on genomic information is consistent with precision medicine. Despite the enthusiasm, there is a need for public engagement on the appropriate use of such emerging t...
Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs inc...
A new paradigm in disease classification, diagnosis and treatment is rapidly approaching. Known as precision medicine, this new healthcare model incorporates and integrates genetic information, microbiome data...
Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA r...
MicroRNAs (miRNAs) have been implicated in the incidence and progression of cancer. It has been proposed that single nucleotide polymorphisms (SNPs) influence cancer risk due to their position within genes inv...
Essential hypertension is a significant risk factor for cardiovascular diseases. Emerging research suggests a role of DNA methylation in blood pressure physiology. We aimed to investigate epigenetic associatio...
Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significa...
Liver cancer, of which hepatocellular carcinoma (HCC) is by far the most common type, is the second most deadly cancer (746,000 deaths in 2012). Currently, the only curative treatment for HCC is surgery to rem...
The question of whether DNA obtained from saliva is an acceptable alternative to DNA from blood is a topic of considerable interest for large genetics studies. We compared the yields, quality and performance o...
Mutation studies of pancreatic ductal adenocarcinoma (PDA) have revealed complicated heterogeneous genomic landscapes of the disease. These studies cataloged a number of genes mutated at high frequencies, but ...
Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC...
Because of the rapid development in genomics, more research findings have emerged. However, the association between society and research results remains controversial. This article examines the experiences and...
The Erratum to this article has been published in BMC Medical Genomics 2017 10:6
Diamond–Blackfan anemia (DBA) was the first ribosomopathy associated with mutations in ribosome protein (RP) genes. The clinical phenotypes of DBA include failure of erythropoiesis, congenital anomalies and ca...
The systemic information enclosed in microarray data encodes relevant clues to overcome the poorly understood combination of genetic and environmental factors in Parkinson’s disease (PD), which represents the ...
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