Articles

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals

An individual’s response to environmental exposures varies depending on their genotype, which has been termed the gene-environment interaction. The phenotype of cell exposed can also be a key determinant in th...

Authors: Andreanna Burman, Rolando Garcia-Milian and Shannon Whirledge

An investigation of genetic polymorphisms in heparan sulfate proteoglycan core proteins and key modification enzymes in an Australian Caucasian multiple sclerosis population

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease affecting the central nervous system in young adults. Heparan sulfate proteoglycans (HSPGs) are ubiquitous to the cell surface and the ex...

Authors: Rachel K. Okolicsanyi, Julia Bluhm, Cassandra Miller, Lyn R. Griffiths and Larisa M. Haupt

COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission

The recent coronavirus disease (COVID-19), caused by SARS-CoV-2, is inarguably the most challenging coronavirus outbreak relative to the previous outbreaks involving SARS-CoV and MERS-CoV. With the number of C...

Authors: Krystal J. Godri Pollitt, Jordan Peccia, Albert I. Ko, Naftali Kaminski, Charles S. Dela Cruz, Daniel W. Nebert, Juergen K.V. Reichardt, David C. Thompson and Vasilis Vasiliou

Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene

Schizophrenia is a chronic and severe mental disorder, and it has been predicted to be highly polygenic. Common SNPs located in or near BNIP3L were found to be genome-wide significantly associated with schizophre...

Authors: Juan Zhou, Chuanchuan Ma, Ke Wang, Xiuli Li, Xuemin Jian, Han Zhang, Jianmin Yuan, Jiajun Yin, Jianhua Chen and Yongyong Shi

Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?

5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an...

Authors: Tianmin Xu and Haoyue Gao

A novel method to predict essential proteins based on tensor and HITS algorithm

Essential proteins are an important part of the cell and closely related to the life activities of the cell. Hitherto, Protein-Protein Interaction (PPI) networks have been adopted by many computational methods...

Authors: Zhihong Zhang, Yingchun Luo, Sai Hu, Xueyong Li, Lei Wang and Bihai Zhao

Reply to “Is the number of DNA repair genes associated with evolution rate and size of genomes?”

Authors: Konstantinos Voskarides

Is the number of DNA repair genes associated with evolution rate and size of genomes?

Authors: Ion Udroiu

Do epigenetic changes caused by commensal microbiota contribute to development of ocular disease? A review of evidence

There is evidence that genetic polymorphisms and environmentally induced epigenetic changes play an important role in modifying disease risk. The commensal microbiota has the ability to affect the cellular env...

Authors: Ashima Nayyar, Sofya Gindina, Arturo Barron, Yan Hu and John Danias

Metabolomic profiling of metoprolol hypertension treatment reveals altered gut microbiota-derived urinary metabolites

Metoprolol succinate is a long-acting beta-blocker prescribed for the management of hypertension (HTN) and other cardiovascular diseases. Metabolomics, the study of end-stage metabolites of upstream biologic p...

Authors: Chad N. Brocker, Thomas Velenosi, Hania K. Flaten, Glenn McWilliams, Kyle McDaniel, Shelby K. Shelton, Jessica Saben, Kristopher W. Krausz, Frank J. Gonzalez and Andrew A. Monte

Hyperinsulinism associated with GLUD1 mutation: allosteric regulation and functional characterization of p.G446V glutamate dehydrogenase

Gain-of-function mutations in the GLUD1 gene, encoding for glutamate dehydrogenase (GDH), result in the hyperinsulinism/hyperammonemia HI/HA syndrome. HI/HA patients present with harmful hypoglycemia secondary to...

Authors: Karolina Luczkowska, Caroline Stekelenburg, Frédérique Sloan-Béna, Emmanuelle Ranza, Giacomo Gastaldi, Valérie Schwitzgebel and Pierre Maechler

TRPM3_miR-204: a complex locus for eye development and disease

First discovered in a light-sensitive retinal mutant of Drosophila, the transient receptor potential (TRP) superfamily of non-selective cation channels serve as polymodal cellular sensors that participate in dive...

Authors: Alan Shiels

Identification and characterization of methylation-mediated transcriptional dysregulation dictate methylation roles in preeclampsia

Preeclampsia (PE) is a heterogeneous, hypertensive disorder of pregnancy, with no robust biomarkers or effective treatments. PE increases the risk of poor outcomes for both the mother and the baby. Methylation...

Authors: Shuyu Zhao, Nan Lv, Yan Li, Tianyi Liu, Yuhong Sun and Xiaodan Chu

Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics

Genome-wide association studies (GWAS) have significantly contributed to the association of many clinical conditions and phenotypic characteristics with genomic variants. The majority of these genomic findings...

Authors: Maria Koromina, Stefania Koutsilieri and George P. Patrinos

Re-analysis of whole blastocysts after trophectoderm biopsy indicated chromosome aneuploidy

To compare the concordance between trophectoderm (TE) analysis and whole blastocyst analysis of embryos from chromosomal structural rearrangement (SR) carriers.

Authors: Zhanhui Ou, Zhiheng Chen, Minna Yin, Yu Deng, Yunhao Liang, Wenjun Wang, Yuanqing Yao and Ling Sun

Investigating diagnostic sequencing techniques for CADASIL diagnosis

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease caused by mutations in the NOTCH3 gene. Our laboratory has been undertaking ...

Authors: P. J. Dunn, N. Maksemous, R. A. Smith, H. G. Sutherland, L. M. Haupt and L. R. Griffiths

Associations between microRNA (miR-25, miR-32, miR-125, and miR-222) polymorphisms and recurrent implantation failure in Korean women

Recurrent implantation failure (RIF) is the failure of embryos to implant more than two times in a given individual. There is debate about a precise definition for RIF, but we consider more than two implantati...

Authors: Jeong Yong Lee, Eun Hee Ahn, Jung Oh Kim, Han Sung Park, Chang Soo Ryu, Ji Hyang Kim, Young Ran Kim, Woo Sik Lee and Nam Keun Kim

Downregulation of miR-542-3p promotes osteogenic transition of vascular smooth muscle cells in the aging rat by targeting BMP7

Aging is believed to have a close association with cardiovascular diseases, resulting in various pathological alterations in blood vessels, including vascular cell phenotypic shifts. In aging vessels, the micr...

Authors: Huan Liu, Hongwei Wang, Sijin Yang and Dehui Qian

The multi-faceted functioning portrait of LRF/ZBTB7A

Transcription factors (TFs) consisting of zinc fingers combined with BTB (for broad-complex, tram-track, and bric-a-brac) domain (ZBTB) are a highly conserved protein family that comprises a multifunctional an...

Authors: Caterina Constantinou, Magda Spella, Vasiliki Chondrou, George P. Patrinos, Adamantia Papachatzopoulou and Argyro Sgourou

Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease

Chronic alcohol consumption is a significant cause of liver disease worldwide. Several biochemical mechanisms have been linked to the initiation and progression of alcoholic liver disease (ALD) such as oxidati...

Authors: Mohammed A. Assiri, Hadi R. Ali, John O. Marentette, Youngho Yun, Juan Liu, Matthew D. Hirschey, Laura M. Saba, Peter S. Harris and Kristofer S. Fritz

Human genetics and genomics research in Ecuador: historical survey, current state, and future directions

In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limit...

Authors: Marlon S. Zambrano-Mila, Spiros N. Agathos and Juergen K. V. Reichardt

EFTUD2 gene deficiency disrupts osteoblast maturation and inhibits chondrocyte differentiation via activation of the p53 signaling pathway

Mandibulofacial dysostosis with microcephaly (MFDM) is characteristic of multiple skeletal anomalies comprising craniofacial anomalies/dysplasia, microcephaly, dysplastic ears, choanal atresia, and short statu...

Authors: Jing Wu, Yi Yang, You He, Qiang Li, Xu Wang, Chengjun Sun, Lishun Wang, Yu An and Feihong Luo

Factors affecting cell-free DNA fetal fraction: statistical analysis of 13,661 maternal plasmas for non-invasive prenatal screening

The identification of cell-free fetal DNA (cffDNA) facilitated non-invasive prenatal screening (NIPS) through analysis of cffDNA in maternal plasma. However, challenges regarding its clinical implementation be...

Authors: Yaping Hou, Jiexia Yang, Yiming Qi, Fangfang Guo, Haishan Peng, Dongmei Wang, Yixia Wang, Xiaohui Luo, Yi Li and Aihua Yin

Genetics and functions of the retinoic acid pathway, with special emphasis on the eye

Retinoic acid (RA) is a potent morphogen required for embryonic development. RA is formed in a multistep process from vitamin A (retinol); RA acts in a paracrine fashion to shape the developing eye and is esse...

Authors: Brian Thompson, Nicholas Katsanis, Nicholas Apostolopoulos, David C. Thompson, Daniel W. Nebert and Vasilis Vasiliou

Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features

Since the discovery of cell-free DNA (cfDNA) in maternal plasma, it has opened up new approaches for non-invasive prenatal testing. With the development of whole-genome sequencing, small subchromosomal deletio...

Authors: Yibo Chen, Qi Yu, Xiongying Mao, Wei Lei, Miaonan He and Wenbo Lu

Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms

Tobacco smoking induces immunomodulatory and pro-inflammatory effects associated with transcriptome changes in monocytes and other immune cell types. While smoking is prevalent in HIV-infected (HIV+) individua...

Authors: David R. Lorenz, Vikas Misra and Dana Gabuzda

Association between polymorphism in CDKN2B-AS1 gene and its interaction with smoking on the risk of lung cancer in a Chinese population

Long non-coding RNAs became the hot spots in the carcinogenesis of various tumors. This case-control study evaluated the association between the rs2151280 in lncRNA CDKN2B-AS1 and lung cancer risk.

Authors: Xiaoting Lv, Zhigang Cui, Hang Li, Juan Li, Zitai Yang, Yanhong Bi, Min Gao, Ziwei Zhang, Shengli Wang, Baosen Zhou and Zhihua Yin

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis

Chromosomal inversions are structural genetic variants where a chromosome segment changes its orientation. While sporadic de novo inversions are known genetic risk factors for cancer susceptibility, it is unkn...

Authors: Carlos Ruiz-Arenas, Alejandro Cáceres, Victor Moreno and Juan R. González

Genetic variants of VEGFR-1 gene promoter in acute myocardial infarction

Coronary artery disease (CAD) including acute myocardial infarction (AMI) is a common complex disease caused by atherosclerosis. Vascular epithelial growth factor receptor-1 (VEGFR-1) stimulates angiogenesis a...

Authors: Haihua Wang, Shufang Zhang, Na Wang, Jie Zhang, Mingkai Chen, Xiaohui He, Yinghua Cui, Shuchao Pang and Bo Yan

Identification of key candidate genes and molecular pathways in white fat browning: an anti-obesity drug discovery based on computational biology

Obesity—with its increased risk of obesity-associated metabolic diseases—has become one of the greatest public health epidemics of the twenty-first century in affluent countries. To date, there are no ideal dr...

Authors: Yuyan Pan, Jiaqi Liu and Fazhi Qi

Copy number of 8q24.3 drives HSF1 expression and patient outcome in cancer: an individual patient data meta-analysis

The heat-shock transcription factor 1 (HSF1) has been linked to cell proliferation and survival in cancer and has been proposed as a biomarker for poor prognosis. Here, we assessed the role of HSF1 expression in ...

Authors: Nele Brusselaers, Karl Ekwall and Mickael Durand-Dubief

Identification and functional characterization of two novel mutations in KCNJ10 and PI4KB in SeSAME syndrome without electrolyte imbalance

Dysfunction in inwardly rectifying potassium channel Kir4.1 has been implicated in SeSAME syndrome, an autosomal-recessive (AR), rare, multi-systemic disorder. However, not all neurological, intellectual disab...

Authors: Ravi K. Nadella, Anirudh Chellappa, Anand G. Subramaniam, Ravi Prabhakar More, Srividya Shetty, Suriya Prakash, Nikhil Ratna, V. P. Vandana, Meera Purushottam, Jitender Saini, Biju Viswanath, P. S. Bindu, Madhu Nagappa, Bhupesh Mehta, Sanjeev Jain and Ramakrishnan Kannan

Human mitochondrial genome compression using machine learning techniques

In recent years, with the development of high-throughput genome sequencing technologies, a large amount of genome data has been generated, which has caused widespread concern about data storage and transmissio...

Authors: Rongjie Wang, Tianyi Zang and Yadong Wang

Using Apache Spark on genome assembly for scalable overlap-graph reduction

De novo genome assembly is a technique that builds the genome of a specimen using overlaps of genomic fragments without additional work with reference sequence. Sequence fragments (called reads) are assembled ...

Authors: Alexander J. Paul, Dylan Lawrence, Myoungkyu Song, Seung-Hwan Lim, Chongle Pan and Tae-Hyuk Ahn

Prediction of microbial communities for urban metagenomics using neural network approach

Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the tr...

Authors: Guangyu Zhou, Jyun-Yu Jiang, Chelsea J.-T. Ju and Wei Wang

Robust hypergraph regularized non-negative matrix factorization for sample clustering and feature selection in multi-view gene expression data

As one of the most popular data representation methods, non-negative matrix decomposition (NMF) has been widely concerned in the tasks of clustering and feature selection. However, most of the previously propo...

Authors: Na Yu, Ying-Lian Gao, Jin-Xing Liu, Juan Wang and Junliang Shang

An embedded method for gene identification problems involving unwanted data heterogeneity

Modern applications such as bioinformatics collecting data in various ways can easily result in heterogeneous data. Traditional variable selection methods assume samples are independent and identically distrib...

Authors: Meng Lu

HMNPPID—human malignant neoplasm protein–protein interaction database

Protein–protein interaction (PPI) information extraction from biomedical literature helps unveil the molecular mechanisms of biological processes. Especially, the PPIs associated with human malignant neoplasms...

Authors: Qingqing Li, Zhihao Yang, Zhehuan Zhao, Ling Luo, Zhiheng Li, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang and Yijia Zhang

A semi-supervised machine learning framework for microRNA classification

MicroRNAs (miRNAs) are a family of short, non-coding RNAs that have been linked to critical cellular activities, most notably regulation of gene expression. The identification of miRNA is a cross-disciplinary ...

Authors: Mohsen Sheikh Hassani and James R. Green

Size matters: how sample size affects the reproducibility and specificity of gene set analysis

Gene set analysis is a well-established approach for interpretation of data from high-throughput gene expression studies. Achieving reproducible results is an essential requirement in such studies. One factor ...

Authors: Farhad Maleki, Katie Ovens, Ian McQuillan and Anthony J. Kusalik

Genomics of rare genetic diseases—experiences from India

Home to a culturally heterogeneous population, India is also a melting pot of genetic diversity. The population architecture characterized by multiple endogamous groups with specific marriage patterns, includi...

Authors: Sridhar Sivasubbu and Vinod Scaria

SLC39A8 gene encoding a metal ion transporter: discovery and bench to bedside

SLC39A8 is an evolutionarily highly conserved gene that encodes the ZIP8 metal cation transporter in all vertebrates. SLC39A8 is ubiquitously expressed, including pluripotent embryonic stem cells; SLC39A8 express...

Authors: Daniel W. Nebert and Zijuan Liu

lncRNA TUG1 modulates proliferation, apoptosis, invasion, and angiogenesis via targeting miR-29b in trophoblast cells

Pre-eclampsia (PE) is regarded as the leading cause of maternal and neonatal morbidity and mortality. Nevertheless, the potential mechanism for the regulation of trophoblast behaviors and the pathogenesis of P...

Authors: Qian Li, Jing Zhang, Dong-Mei Su, Li-Na Guan, Wei-Hong Mu, Mei Yu, Xu Ma and Rong-Juan Yang

Novel analytical methods to interpret large sequencing data from small sample sizes

Targeted therapies have greatly improved cancer patient prognosis. For instance, chronic myeloid leukemia is now well treated with imatinib, a tyrosine kinase inhibitor. Around 80% of the patients reach comple...

Authors: Florence Lichou, Sébastien Orazio, Stéphanie Dulucq, Gabriel Etienne, Michel Longy, Christophe Hubert, Alexis Groppi, Alain Monnereau, François-Xavier Mahon and Béatrice Turcq

Three miRNAs cooperate with host genes involved in human cardiovascular disease

Understanding the roles of miRNAs in cardiovascular disease remains a challenge. Genomic linkage indicates a functional relationship between intronic miRNAs and their host genes. However, few studies have show...

Authors: Yan Zhu, Jingjing Xie and Hong Sun

Translating pharmacogenomics into clinical decisions: do not let the perfect be the enemy of the good

The field of pharmacogenomics (PGx) is gradually shifting from the reactive testing of single genes toward the proactive testing of multiple genes to improve treatment outcomes, reduce adverse events, and decr...

Authors: Kristi Krebs and Lili Milani

Diversity of ATM gene variants: a population-based genome data analysis for precision medicine

Ataxia-telangiectasia (AT) is a rare autosomal recessive disorder that causes deficiency or dysfunction of the ataxia-telangiectasia mutated (ATM) protein. Not only AT patients, but also certain ATM heterozygous ...

Authors: Hisanori Fukunaga, Yasuyuki Taki and Kevin M. Prise

Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes

While genome-wide association studies (GWAS) of multiple myeloma (MM) have identified variants at 23 regions influencing risk, the genes underlying these associations are largely unknown. To identify candidate...

Authors: Molly Went, Ben Kinnersley, Amit Sud, David C. Johnson, Niels Weinhold, Asta Försti, Mark van Duin, Giulia Orlando, Jonathan S. Mitchell, Rowan Kuiper, Brian A. Walker, Walter M. Gregory, Per Hoffmann, Graham H. Jackson, Markus M. Nöthen, Miguel Inacio da Silva Filho…

Identification and potential mechanisms of a 4-lncRNA signature that predicts prognosis in patients with laryngeal cancer

This study aimed to describe the use of a novel 4-lncRNA signature to predict prognosis in patients with laryngeal cancer and to explore its possible mechanisms.

Authors: Guihai Zhang, Erxi Fan, Qiuyue Zhong, Guangyong Feng, Yu Shuai, Mingna Wu, Qiying Chen and Xiaoxia Gou

Meeting report: the Human Genome Meeting (HGM) 2019 in Seoul, Korea

Authors: Angela Solano, Giuseppe Novelli, Shruti Baghat, Piero Carnici, Gert-Jan van Ommen and Juergen K. V. Reichardt