Articles

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

Next-generation sequencing in liquid biopsy: cancer screening and early detection

In recent years, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost with improved accuracy. In the area of liquid biopsy, NGS has been ...

Authors: Ming Chen and Hongyu Zhao

Identification of a novel long non-coding RNA within RUNX1 intron 5

RUNX1 gene, a master regulator of the hematopoietic process, participates in pathological conditions as a partner for several genes in chromosomal translocations. One of the most frequent chromosomal translocatio...

Authors: Nicolás Schnake, Marcela Hinojosa and Soraya Gutiérrez

Helicobacter pylori infection, serum pepsinogens as markers of atrophic gastritis, and leukocyte telomere length: a population-based study

Persistent infections that induce prolonged inflammation might negatively affect the leukocyte telomere length (LTL); however, the role in LTL of Helicobacter pylori (H. pylori) infection, which persistently colo...

Authors: Khitam Muhsen, Ronit Sinnreich, Dafna Merom, Hisham Nassar, Dani Cohen and Jeremy D. Kark

Essential genetic findings in neurodevelopmental disorders

Neurodevelopmental disorders (NDDs) represent a growing medical challenge in modern societies. Ever-increasing sophisticated diagnostic tools have been continuously revealing a remarkably complex architecture ...

Authors: Ana R. Cardoso, Mónica Lopes-Marques, Raquel M. Silva, Catarina Serrano, António Amorim, Maria J. Prata and Luísa Azevedo

A novel knowledge-derived data potentizing method revealed unique liver cancer-associated genetic variants

Next-generation sequencing (NGS) has been advancing the progress of detection of disease-associated genetic variants and genome-wide profiling of expressed sequences over the past decade. NGS enables the analy...

Authors: Naznin Sultana, Mijanur Rahman, Sanat Myti, Jikrul Islam, Md. G. Mustafa and Kakon Nag

Correction to: Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

In the original publication of this article [1], the Figure 1 and Figure 2 were wrong. The Figure 1 “Heat map showing the quantity of DNA repair genes, from red to blue in ascending order, per species’ genome (nu...

Authors: Konstantinos Voskarides, Harsh Dweep and Charalambos Chrysostomou

Genome-wide enriched pathway analysis of acute post-radiotherapy pain in breast cancer patients: a prospective cohort study

Adjuvant radiotherapy (RT) can increase the risk of developing pain; however, the molecular mechanisms of RT-related pain remain unclear. The current study aimed to identify susceptibility loci and enriched pa...

Authors: Eunkyung Lee, Cristiane Takita, Jean L. Wright, Susan H. Slifer, Eden R. Martin, James J. Urbanic, Carl D. Langefeld, Glenn J. Lesser, Edward G. Shaw and Jennifer J. Hu

Interplay Between the Host, the Human Microbiome, and Drug Metabolism

The human microbiome is composed of four major areas including intestinal, skin, vaginal, and oral microbiomes, with each area containing unique species and unique functionalities. The human microbiome may be ...

Authors: Robert G. Nichols, Jeffrey M. Peters and Andrew D. Patterson

Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. T...

Authors: Konstantinos Voskarides, Harsh Dweep and Charalambos Chrysostomou

IFITM5 pathogenic variant causes osteogenesis imperfecta V with various phenotype severity in Ukrainian and Vietnamese patients

Osteogenesis imperfecta (OI) covers a spectrum of bone fragility disorders. OI is classified into five types; however, the genetic causes of OI might hide in pathogenic variants of 20 different genes. Often cl...

Authors: Lidiia Zhytnik, Katre Maasalu, Binh Ho Duy, Andrey Pashenko, Sergey Khmyzov, Ene Reimann, Ele Prans, Sulev Kõks and Aare Märtson

Statement on bioinformatics and capturing the benefits of genome sequencing for society

The HUGO Committee on Ethics, Law and Society (CELS) undertook a Working Group exploration of the key ethical issues arising from genome sequencing in 2013. The Imagined Futures paper the group subsequently publi...

Authors: Benjamin Capps, Ruth Chadwick, Yann Joly, Tamra Lysaght, Catherine Mills, John J. Mulvihill and Hub Zwart

What influences public views on forensic DNA testing in the criminal field? A scoping review of quantitative evidence

Forensic DNA testing is a powerful tool used to identify, convict, and exonerate individuals charged of criminal offenses, but there are different views on its benefits and risks. Knowledge about public views ...

Authors: Helena Machado and Susana Silva

Genetics of heart rate in heart failure patients (GenHRate)

Elevated resting heart rate (HR) is a risk factor and therapeutic target in patients with heart failure (HF) and reduced ejection fraction (HFrEF). Previous studies indicate a genetic contribution to HR in pop...

Authors: Kaleigh L. Evans, Heidi S. Wirtz, Jia Li, Ruicong She, Juan Maya, Hongsheng Gui, Andrew Hamer, Christophe Depre and David E. Lanfear

Genome-wide association study identifies novel loci for type 2 diabetes-attributed end-stage kidney disease in African Americans

End-stage kidney disease (ESKD) is a significant public health concern disproportionately affecting African Americans (AAs). Type 2 diabetes (T2D) is the leading cause of ESKD in the USA, and efforts to uncove...

Authors: Meijian Guan, Jacob M. Keaton, Latchezar Dimitrov, Pamela J. Hicks, Jianzhao Xu, Nicholette D. Palmer, Lijun Ma, Swapan K. Das, Yii-Der I. Chen, Josef Coresh, Myriam Fornage, Nora Franceschini, Holly Kramer, Carl D. Langefeld, Josyf C. Mychaleckyj, Rulan S. Parekh…

Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

Genome-wide association studies (GWAS) of diseases and traits have found associations to gene regions but not the functional SNP or the gene mediating the effect. Difference in gene regulatory signals can be d...

Authors: Marco Cavalli, Nicholas Baltzer, Gang Pan, José Ramón Bárcenas Walls, Karolina Smolinska Garbulowska, Chanchal Kumar, Stanko Skrtic, Jan Komorowski and Claes Wadelius

Mutations in ATP13A2 (PARK9) are associated with an amyotrophic lateral sclerosis-like phenotype, implicating this locus in further phenotypic expansion

Amyotrophic lateral sclerosis [1] is a genetically heterogeneous neurodegenerative disorder, characterized by late-onset degeneration of motor neurons leading to progressive limb and bulbar weakness, as well as o...

Authors: Rossella Spataro, Maria Kousi, Sali M. K. Farhan, Jason R. Willer, Jay P. Ross, Patrick A. Dion, Guy A. Rouleau, Mark J. Daly, Benjamin M. Neale, Vincenzo La Bella and Nicholas Katsanis

The significance of trisomy 7 mosaicism in noninvasive prenatal screening

This study was an evaluation of the role of noninvasive prenatal testing (NIPT) in the detection of trisomy 7 in prenatal diagnosis.

Authors: Yiming Qi, Jiexia Yang, Yaping Hou, Fangfang Guo, Haishan Peng, Dongmei Wang, Qianyi Du and Aihua Yin

Shared genetic underpinnings of childhood obesity and adult cardiometabolic diseases

Obesity during childhood can lead to increased risk of adverse cardiometabolic diseases such as type 2 diabetes and coronary artery disease during adult life. Evidence for strong genetic correlations between c...

Authors: Fasil Tekola-Ayele, Anthony Lee, Tsegaselassie Workalemahu and Katy Sánchez-Pozos

Correction to: The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau

Abstract

Authors: Hadi Charati, Min-Sheng Peng, Wei Chen, Xing-Yan Yang, Roghayeh Jabbari Ori, Mohsen Aghajanpour-Mir, Ali Esmailizadeh and Ya-Ping Zhang

Transcriptome-wide analysis of differentially expressed chemokine receptors, SNPs, and SSRs in the age-related macular degeneration

Age-related macular degeneration (AMD) is the most common, progressive, and polygenic cause of irreversible visual impairment in the world. The molecular pathogenesis of the primary events of AMD is poorly und...

Authors: Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Lijuan Fan, Zhengmao Hu and Hu Huang

Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies

Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the developm...

Authors: Hua Hu, Li Wang, Jiayan Wu, Peng Zhou, Jingli Fu, Jiuchen Sun, Weiyi Cai, Hailiang Liu and Ying Yang

Association of HTRA1 and ARMS2 gene polymorphisms with response to intravitreal ranibizumab among neovascular age-related macular degenerative subjects

The association of HTRA1 rs11200638 and ARMS2 rs10490924 gene polymorphisms with response to intravitreal ranibizumab therapy among neovascular AMD (nAMD) subjects in Malaysia was determined in this study, follow...

Authors: Nur Afiqah Mohamad, Vasudevan Ramachandran, Hazlita Mohd Isa, Yoke Mun Chan, Nor Fariza Ngah, Siew Mooi Ching, Fan Kee Hoo, Wan Aliaa Wan Sulaiman, Liyana Najwa Inche Mat and Mohd Hazmi Mohamed

Association of genetic ancestry with colorectal tumor location in Puerto Rican Latinos

Colorectal cancer (CRC) is the first cause of cancer deaths among Puerto Ricans. The incidence and mortality of CRC in Puerto Rico continue to be on the rise. The burden of CRC in Puerto Rico is higher than am...

Authors: Julyann Pérez-Mayoral, Marievelisse Soto-Salgado, Ebony Shah, Rick Kittles, Mariana C. Stern, Myrta I. Olivera, María Gonzalez-Pons, Segundo Rodriguez-Quilichinni, Marla Torres, Jose S. Reyes, Luis Tous, Nicolas López, Victor Carlo Chevere and Marcia Cruz-Correa

Update on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an “evolutionary bloom”

Lipocalins (LCNs) are members of a family of evolutionarily conserved genes present in all kingdoms of life. There are 19 LCN-like genes in the human genome, and 45 Lcn-like genes in the mouse genome, which inclu...

Authors: Georgia Charkoftaki, Yewei Wang, Monica McAndrews, Elspeth A. Bruford, David C. Thompson, Vasilis Vasiliou and Daniel W. Nebert

Considerations for the use of Cre recombinase for conditional gene deletion in the mouse lens

Despite a number of different transgenes that can mediate DNA deletion in the developing lens, each has unique features that can make a given transgenic line more or less appropriate for particular studies. Th...

Authors: Phuong T. Lam, Stephanie L. Padula, Thanh V. Hoang, Justin E. Poth, Lin Liu, Chun Liang, Adam S. LeFever, Lindsay M. Wallace, Ruth Ashery-Padan, Penny K. Riggs, Jordan E. Shields, Ohad Shaham, Sheldon Rowan, Nadean L. Brown, Tom Glaser and Michael L. Robinson

vi-HMM: a novel HMM-based method for sequence variant identification in short-read data

Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), plays a fundamental role in next-generation sequencing...

Authors: Man Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang and Xiaowei Wu

Toward a clinical diagnostic pipeline for SPINK1 intronic variants

The clinical significance of SPINK1 intronic variants in chronic pancreatitis has been previously assessed by various approaches including a cell culture-based full-length gene assay. A close correlation between ...

Authors: Xin-Ying Tang, Jin-Huan Lin, Wen-Bin Zou, Emmanuelle Masson, Arnaud Boulling, Shun-Jiang Deng, David N. Cooper, Zhuan Liao, Claude Férec, Zhao-Shen Li and Jian-Min Chen

The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau

The ability to digest dietary lactose is associated with lactase persistence (LP) in the intestinal lumen in human. The genetic basis of LP has been investigated in many populations in the world. Iran has a lo...

Authors: Hadi Charati, Min-Sheng Peng, Wei Chen, Xing-Yan Yang, Roghayeh Jabbari Ori, Mohsen Aghajanpour-Mir, Ali Esmailizadeh and Ya-Ping Zhang

A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts

Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist.

Authors: Anna L. Guyatt, Rebecca R. Brennan, Kimberley Burrows, Philip A. I. Guthrie, Raimondo Ascione, Susan M. Ring, Tom R. Gaunt, Angela Pyle, Heather J. Cordell, Debbie A. Lawlor, Patrick F. Chinnery, Gavin Hudson and Santiago Rodriguez

The association of functional polymorphisms in genes expressed in endothelial cells and smooth muscle cells with the myocardial infarction

The association of platelet endothelial cell adhesion molecule 1 (PECAM1), hypoxia-inducible factor 1 subunit alpha (HIF1A), and KIAA1462 in myocardial infarction (MI) was investigated. The study included 401 ...

Authors: Yilan Li, Shipeng Wang, Dandan Zhang, Xueming Xu, Bo Yu and Yao Zhang

Germline TP53 and MSH6 mutations implicated in sporadic triple-negative breast cancer (TNBC): a preliminary study

Germline BRCA1/2 prevalence is relatively low in sporadic triple-negative breast cancer (TNBC). We hypothesized that non-BRCA genes may also have significant germline contribution to Chinese sporadic TNBC, and...

Authors: Dandan Yi, Lei Xu, Jiaqi Luo, Xiaobin You, Tao Huang, Yi Zi, Xiaoting Li, Ru Wang, Zaixuan Zhong, Xiaoqiao Tang, Ang Li, Yujian Shi, Jianmei Rao, Yifen Zhang and Jianfeng Sang

Population and breast cancer patients’ analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population

Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in c...

Authors: J. C. Fernández-Lopez, S. Romero-Córdoba, R. Rebollar-Vega, L. A. Alfaro-Ruiz, S. Jiménez-Morales, F. Beltrán-Anaya, R. Arellano-Llamas, A. Cedro-Tanda, M. Rios-Romero, M. Ramirez-Florencio, V. Bautista-Piña, C. Dominguez-Reyes, F. Villegas-Carlos, A. Tenorio-Torres and A. Hidalgo-Miranda