Articles

A comparative study on the unified model based multifactor dimensionality reduction methods for identifying gene-gene interactions associated with the survival phenotype

For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely employed to reduce multi-levels of gene-gene interactions into high- or low-risk groups using a binary ...

Authors: Jung Wun Lee and Seungyeoun Lee

Performance of model-based multifactor dimensionality reduction methods for epistasis detection by controlling population structure

In genome-wide association studies the extent and impact of confounding due to population structure have been well recognized. Inadequate handling of such confounding is likely to lead to spurious associations...

Authors: Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Diane Duroux, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson and Kristel Van Steen

DASSI: differential architecture search for splice identification from DNA sequences

The data explosion caused by unprecedented advancements in the field of genomics is constantly challenging the conventional methods used in the interpretation of the human genome. The demand for robust algorit...

Authors: Shabir Moosa, Prof. Abbes Amira and Dr. Sabri Boughorbel

Gene function finding through cross-organism ensemble learning

Structured biological information about genes and proteins is a valuable resource to improve discovery and understanding of complex biological processes via machine learning algorithms. Gene Ontology (GO) cont...

Authors: Gianluca Moro and Marco Masseroli

The Matthews correlation coefficient (MCC) is more reliable than balanced accuracy, bookmaker informedness, and markedness in two-class confusion matrix evaluation

Evaluating binary classifications is a pivotal task in statistics and machine learning, because it can influence decisions in multiple areas, including for example prognosis or therapies of patients in critica...

Authors: Davide Chicco, Niklas Tötsch and Giuseppe Jurman

Data analytics and clinical feature ranking of medical records of patients with sepsis

Sepsis is a life-threatening clinical condition that happens when the patient’s body has an excessive reaction to an infection, and should be treated in one hour. Due to the urgency of sepsis, doctors and phys...

Authors: Davide Chicco and Luca Oneto

Acoustic and language analysis of speech for suicidal ideation among US veterans

Screening for suicidal ideation in high-risk groups such as U.S. veterans is crucial for early detection and suicide prevention. Currently, screening is based on clinical interviews or self-report measures. Bo...

Authors: Anas Belouali, Samir Gupta, Vaibhav Sourirajan, Jiawei Yu, Nathaniel Allen, Adil Alaoui, Mary Ann Dutton and Matthew J. Reinhard

Sparse self-attention aggregation networks for neural sequence slice interpolation

Microscopic imaging is a crucial technology for visualizing neural and tissue structures. Large-area defects inevitably occur during the imaging process of electron microscope (EM) serial slices, which lead to...

Authors: Zejin Wang, Jing Liu, Xi Chen, Guoqing Li and Hua Han

A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions

Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex diseases such as Alzheimer’s, diabetes, and cardiovascular disease. Detecting interactions r...

Authors: Alena Orlenko and Jason H. Moore

Empowering the data science scientist

Authors: Jason H. Moore

Feature selection using distributions of orthogonal PLS regression vectors in spectral data

Feature selection, which is important for successful analysis of chemometric data, aims to produce parsimonious and predictive models. Partial least squares (PLS) regression is one of the main methods in chemo...

Authors: Geonseok Lee and Kichun Lee

Privacy-preserving chi-squared test of independence for small samples

The importance of privacy protection in analyses of personal data, such as genome-wide association studies (GWAS), has grown in recent years. GWAS focuses on identifying single-nucleotide polymorphisms (SNPs) ...

Authors: Yuichi Sei and Akihiko Ohsuga

Mechanistic modeling of the SARS-CoV-2 disease map

Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral in...

Authors: Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, María Peña-Chilet and Joaquín Dopazo

COVID-TRACK: world and USA SARS-COV-2 testing and COVID-19 tracking

The COVID-19 pandemic has caused major health and socio-economic disruptions worldwide. Accurate investigation of emerging data is crucial to inform policy makers as they construct viral mitigation strategies....

Authors: Ye Emma Zohner and Jeffrey S. Morris

An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features

Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experi...

Authors: Ji-Yong An, Fan-Rong Meng and Zi-Ji Yan

LightCUD: a program for diagnosing IBD based on human gut microbiome data

The diagnosis of inflammatory bowel disease (IBD) and discrimination between the types of IBD are clinically important. IBD is associated with marked changes in the intestinal microbiota. Advances in next-gene...

Authors: Congmin Xu, Man Zhou, Zhongjie Xie, Mo Li, Xi Zhu and Huaiqiu Zhu

Identification of the active substances and mechanisms of ginger for the treatment of colon cancer based on network pharmacology and molecular docking

Colon cancer is occurring at an increasing rate and ginger (Zingiber officinale), as a commonly used herbal medicine, has been suggested as a potential agent for colon cancer. This study was aimed to identify the...

Authors: Meng-Meng Zhang, Dan Wang, Feng Lu, Rong Zhao, Xun Ye, Lin He, Li Ai and Chun-Jie Wu

Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods

Accurate identification of acute ischemic stroke (AIS) patient cohorts is essential for a wide range of clinical investigations. Automated phenotyping methods that leverage electronic health records (EHRs) rep...

Authors: Phyllis M. Thangaraj, Benjamin R. Kummer, Tal Lorberbaum, Mitchell S. V. Elkind and Nicholas P. Tatonetti

ISLAND: in-silico proteins binding affinity prediction using sequence information

Determining binding affinity in protein-protein interactions is important in the discovery and design of novel therapeutics and mutagenesis studies. Determination of binding affinity of proteins in the formati...

Authors: Wajid Arshad Abbasi, Adiba Yaseen, Fahad Ul Hassan, Saiqa Andleeb and Fayyaz Ul Amir Afsar Minhas

Exploring active ingredients and function mechanisms of Ephedra-bitter almond for prevention and treatment of Corona virus disease 2019 (COVID-19) based on network pharmacology

COVID-19 has caused a global pandemic, and there is no wonder drug for epidemic control at present. However, many clinical practices have shown that traditional Chinese medicine has played an important role in...

Authors: Kai Gao, Yan-Ping Song and Anna Song

Ten important roles for academic leaders in data science

Data science has emerged as an important discipline in the era of big data and biological and biomedical data mining. As such, we have seen a rapid increase in the number of data science departments, research ...

Authors: Jason H. Moore

Examining the effector mechanisms of Xuebijing injection on COVID-19 based on network pharmacology

Chinese medicine Xuebijing (XBJ) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases. But the bioactive compounds and potential mechanisms of XBJ for COVID-19 preventi...

Authors: Wen-jiang Zheng, Qian Yan, Yong-shi Ni, Shao-feng Zhan, Liu-liu Yang, Hong-fa Zhuang, Xiao-hong Liu and Yong Jiang

Identification of microbial interaction network: zero-inflated latent Ising model based approach

Throughout their lifespans, humans continually interact with the microbial world, including those organisms which live in and on the human body. Research in this domain has revealed the extensive links between...

Authors: Jie Zhou, Weston D. Viles, Boran Lu, Zhigang Li, Juliette C. Madan, Margaret R. Karagas, Jiang Gui and Anne G. Hoen

Therapeutic mechanism of Toujie Quwen granules in COVID-19 based on network pharmacology

Chinese medicine Toujie Quwen granule (TJQW) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases by relieving symptoms, slowing the progression of the disease, and boo...

Authors: Ying Huang, Wen-jiang Zheng, Yong-shi Ni, Mian-sha Li, Jian-kun Chen, Xiao-hong Liu, Xing-hua Tan and Ji-qiang Li

Diagnosis of thyroid nodules for ultrasonographic characteristics indicative of malignancy using random forest

Various combinations of ultrasonographic (US) characteristics are increasingly utilized to classify thyroid nodules. But they lack theories, and heavily depend on radiologists’ experience, and cannot correctly...

Authors: Dan Chen, Jun Hu, Mei Zhu, Niansheng Tang, Yang Yang and Yuran Feng

Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator

Identification of non-trivial and meaningful patterns in omics data is one of the most important biological tasks. The patterns help to better understand biological systems and interpret experimental outcomes....

Authors: František Malinka, Filip železný and Jiří Kléma

Application of network pharmacology and molecular docking to elucidate the potential mechanism of Eucommia ulmoides-Radix Achyranthis Bidentatae against osteoarthritis

Osteoarthritis is a disabling disease, which seriously affects the quality of life of patients. Increasing evidence has indicated that Chinese herbal medicine including Eucommia ulmoides (EU) and Radix Achyranthi...

Authors: Gong-hui Jian, Bing-zhu Su, Wen-jia Zhou and Hui Xiong

Network pharmacology reveals the multiple mechanisms of Xiaochaihu decoction in the treatment of non-alcoholic fatty liver disease

Non-alcoholic fatty liver (NAFLD) is a chronic disease worldwide, which poses a huge threat to human health. Xiaochaihu decoction is a well-known traditional Chinese medicine prescription. It has been proven e...

Authors: Qichao Hu, Shizhang Wei, Jianxia Wen, Wenwen Zhang, Yinxiao Jiang, Caiyan Qu, Junbao Xiang, Yanling Zhao, Xi Peng and Xiao Ma

Deep learning-based ovarian cancer subtypes identification using multi-omics data

Identifying molecular subtypes of ovarian cancer is important. Compared to identify subtypes using single omics data, the multi-omics data analysis can utilize more information. Autoencoder has been widely use...

Authors: Long-Yi Guo, Ai-Hua Wu, Yong-xia Wang, Li-ping Zhang, Hua Chai and Xue-Fang Liang

Conservation machine learning

Authors: Moshe Sipper and Jason H. Moore

Merging microarray studies to identify a common gene expression signature to several structural heart diseases

Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature dea...

Authors: Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva and José Luís Oliveira

An epistatic interaction between pre-natal smoke exposure and socioeconomic status has a significant impact on bronchodilator drug response in African American youth with asthma

Asthma is one of the leading chronic illnesses among children in the United States. Asthma prevalence is higher among African Americans (11.2%) compared to European Americans (7.7%). Bronchodilator medications...

Authors: J. Magaña, M. G. Contreras, K. L. Keys, O. Risse-Adams, P. C. Goddard, A. M. Zeiger, A. C. Y. Mak, J. R. Elhawary, L. A. Samedy-Bates, E. Lee, N. Thakur, D. Hu, C. Eng, S. Salazar, S. Huntsman, T. Hu…

Identification of therapeutic targets from genetic association studies using hierarchical component analysis

Mapping disease-associated genetic variants to complex disease pathophysiology is a major challenge in translating findings from genome-wide association studies into novel therapeutic opportunities. The diffic...

Authors: Hao-Chih Lee, Osamu Ichikawa, Benjamin S. Glicksberg, Aparna A. Divaraniya, Christine E. Becker, Pankaj Agarwal and Joel T. Dudley

Revisiting the use of graph centrality models in biological pathway analysis

The use of graph theory models is widespread in biological pathway analyses as it is often desired to evaluate the position of genes and proteins in their interaction networks of the biological systems. In thi...

Authors: Pourya Naderi Yeganeh, Chrsitine Richardson, Erik Saule, Ann Loraine and M. Taghi Mostafavi

The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

Late-onset Parkinson’s disease (LOPD) is a common neurodegenerative disorder and lacks disease-modifying treatments, attracting major attentions as the aggravating trend of aging population. There were numerou...

Authors: Shiyan Li, Hongxin Liu, Shiyu Bian, Xianzheng Sha, Yixue Li and Yin Wang

Ideas for how informaticians can get involved with COVID-19 research

The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on population health and wellbeing. Biomedical informatics is central to COVID-19 research efforts and for the delivery of healthca...

Authors: Jason H. Moore, Ian Barnett, Mary Regina Boland, Yong Chen, George Demiris, Graciela Gonzalez-Hernandez, Daniel S. Herman, Blanca E. Himes, Rebecca A. Hubbard, Dokyoon Kim, Jeffrey S. Morris, Danielle L. Mowery, Marylyn D. Ritchie, Li Shen, Ryan Urbanowicz and John H. Holmes

A network pharmacology-based study on Alzheimer disease prevention and treatment of Qiong Yu Gao

As the pathological mechanisms of AD are complex, increasing evidence have demonstrated Chinese Medicine with multi-ingredients and multi-targets may be more suitable for the treatment of diseases with complex...

Authors: Jie-shu You, Chen-yue Li, Wei Chen, Xia-lin Wu, Li-jie Huang, Ren-kai Li, Fei Gao, Ming-yue Zhang, Huan-lan Liu and Wei-ling Qu

Deep learning methods improve linear B-cell epitope prediction

B-cell epitopes play important roles in vaccine design, clinical diagnosis, and antibody production. Although some models have been developed to predict linear or conformational B-cell epitopes, their performa...

Authors: Tao Liu, Kaiwen Shi and Wuju Li

Correction to: Investigating the parameter space of evolutionary algorithms

Following publication of the original article [1], an error was reported in one of the experiments.

Authors: Moshe Sipper, Weixuan Fu, Karuna Ahuja and Jason H. Moore

SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500

The sequencing platform BGISEQ-500 is based on DNBSEQ technology and provides high throughput with low costs. This sequencer has been widely used in various areas of scientific and clinical research. A better ...

Authors: Yanqiu Zhou, Chen Liu, Rongfang Zhou, Anzhi Lu, Biao Huang, Liling Liu, Ling Chen, Bei Luo, Jin Huang and Zhijian Tian

Screening for mouse genes lost in mammals with long lifespans

Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate spe...

Authors: Lev I. Rubanov, Andrey G. Zaraisky, Gregory A. Shilovsky, Alexandr V. Seliverstov, Oleg A. Zverkov and Vassily A. Lyubetsky

Predicting metabolite-disease associations based on KATZ model

Increasing numbers of evidences have illuminated that metabolites can respond to pathological changes. However, identifying the diseases-related metabolites is a magnificent challenge in the field of biology a...

Authors: Xiujuan Lei and Cheng Zhang

Integrative analysis of genetic and epigenetic profiling of lung squamous cell carcinoma (LSCC) patients to identify smoking level relevant biomarkers

Incidence and mortality of lung cancer have dramatically decreased during the last decades, yet still approximately 160,000 deaths per year occurred in United States. Smoking intensity, duration, starting age,...

Authors: Bidong Ma, Zhiyou Huang, Qian Wang, Jizhou Zhang, Bin Zhou and Jiaohong Wu

RNSCLC-PRSP software to predict the prognostic risk and survival in patients with resected T_1-3N_0–2 M₀ non-small cell lung cancer

The clinical outcomes of patients with resected T_1-3N_0–2M₀ non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic predicti...

Authors: Yunkui Zhang, YaoChen Li, Rongsheng Zhang, Yujie Zhang and Haitao Ma

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontolog...

Authors: Aurélien Brionne, Amélie Juanchich and Christelle Hennequet-Antier

Disease associations depend on visit type: results from a visit-wide association study

Widespread adoption of Electronic Health Records (EHR) increased the number of reported disease association studies, or Phenome-Wide Association Studies (PheWAS). Traditional PheWAS studies ignore visit type (i.e...

Authors: Mary Regina Boland, Snigdha Alur-Gupta, Lisa Levine, Peter Gabriel and Graciela Gonzalez-Hernandez

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies

The principal line of investigation in Genome Wide Association Studies (GWAS) is the identification of main effects, that is individual Single Nucleotide Polymorphisms (SNPs) which are associated with the trai...

Authors: Elisabetta Manduchi, Patryk R. Orzechowski, Marylyn D. Ritchie and Jason H. Moore

On the utilization of deep and ensemble learning to detect milk adulteration

Fraudulent milk adulteration is a dangerous practice in the dairy industry that is harmful to consumers since milk is one of the most consumed food products. Milk quality can be assessed by Fourier Transformed...

Authors: Habib Asseiss Neto, Wanessa L.F. Tavares, Daniela C.S.Z. Ribeiro, Ronnie C.O. Alves, Leorges M. Fonseca and Sérgio V.A. Campos

ClickGene: an open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration

Tremendous amount of whole-genome sequencing data have been provided by large consortium projects such as TCGA (The Cancer Genome Atlas), COSMIC and so on, which creates incredible opportunities for functional...

Authors: Jia-Hao Bi, Yi-Fan Tong, Zhe-Wei Qiu, Xing-Feng Yang, John Minna, Adi F. Gazdar and Kai Song

Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies

In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag the actual causal variants. In Genome-Wide Association Interactio...

Authors: Marc Joiret, Jestinah M. Mahachie John, Elena S. Gusareva and Kristel Van Steen