Articles

A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a disease with a high incidence and a poor prognosis. Growing amounts of evidence have shown that the immune system plays a critical role in the biological processes of HCC su...

Authors: Qian Yan, Wenjiang Zheng, Boqing Wang, Baoqian Ye, Huiyan Luo, Xinqian Yang, Ping Zhang and Xiongwen Wang

A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism

Machine learning approaches for predicting disease risk from high-dimensional whole genome sequence (WGS) data often result in unstable models that can be difficult to interpret, limiting the identification of...

Authors: Maya Varma, Kelley M. Paskov, Brianna S. Chrisman, Min Woo Sun, Jae-Yoon Jung, Nate T. Stockham, Peter Y. Washington and Dennis P. Wall

Estimating sequencing error rates using families

As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care. However, sequencing platforms and variant-ca...

Authors: Kelley Paskov, Jae-Yoon Jung, Brianna Chrisman, Nate T. Stockham, Peter Washington, Maya Varma, Min Woo Sun and Dennis P. Wall

Machine learning and statistical approaches for classification of risk of coronary artery disease using plasma cytokines

As per the 2017 WHO fact sheet, Coronary Artery Disease (CAD) is the primary cause of death in the world, and accounts for 31% of total fatalities. The unprecedented 17.6 million deaths caused by CAD in 2016 u...

Authors: Seema Singh Saharan, Pankaj Nagar, Kate Townsend Creasy, Eveline O. Stock, James Feng, Mary J. Malloy and John P. Kane

Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis

Longitudinal gene expression analysis and survival modeling have been proved to add valuable biological and clinical knowledge. This study proposes a novel framework to discover gene signatures and patterns in...

Authors: Cláudia S. Constantino, Alexandra M. Carvalho and Susana Vinga

Prescreening and treatment of aortic dissection through an analysis of infinite-dimension data

Aortic dissection (AD) is one of the most catastrophic aortic diseases associated with a high mortality rate. In contrast to the advances in most cardiovascular diseases, both the incidence and in-hospital mor...

Authors: Peng Qiu, Yixuan Li, Kai Liu, Jinbao Qin, Kaichuang Ye, Tao Chen and Xinwu Lu

Prediction of short-term mortality in acute heart failure patients using minimal electronic health record data

Acute heart failure (AHF) is associated with significant morbidity and mortality. Effective patient risk stratification is essential to guiding hospitalization decisions and the clinical management of AHF. Cli...

Authors: Ashwath Radhachandran, Anurag Garikipati, Nicole S. Zelin, Emily Pellegrini, Sina Ghandian, Jacob Calvert, Jana Hoffman, Qingqing Mao and Ritankar Das

Ten important roles for academic leaders to promote equity, diversity, and inclusion in data science

Authors: Jason H. Moore, Van Q. Truong, Ashley B. Robbins, David Nicholson and Clar Lynda Williams-Devane

A multi-feature hybrid classification data mining technique for human-emotion

The ideal treatment of illnesses is the interest of every era. Data innovation in medical care has become extremely quick to analyze diverse diseases from the most recent twenty years. In such a finding, past ...

Authors: Y. Wang, Y. M. Chu, A. Thaljaoui, Y. A. Khan, W. Chammam and S. Z. Abbas

Indels in SARS-CoV-2 occur at template-switching hotspots

The evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ...

Authors: Brianna Sierra Chrisman, Kelley Paskov, Nate. Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Woo Sun, Sepideh Maleki and Dennis P. Wall

RASMA: a reverse search algorithm for mining maximal frequent subgraphs

Given a collection of coexpression networks over a set of genes, identifying subnetworks that appear frequently is an important research problem known as mining frequent subgraphs. Maximal frequent subgraphs a...

Authors: Saeed Salem, Mohammed Alokshiya and Mohammad Al Hasan

Genetic risk score for ovarian cancer based on chromosomal-scale length variation

Twin studies indicate that a substantial fraction of ovarian cancers should be predictable from genetic testing. Genetic risk scores can stratify women into different classes of risk. Higher risk women can be ...

Authors: Christopher Toh and James P. Brody

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