Articles

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

Innovative strategies for annotating the “relationSNP” between variants and molecular phenotypes

Characterizing how variation at the level of individual nucleotides contributes to traits and diseases has been an area of growing interest since the completion of sequencing the first human genome. Our unders...

Authors: Jason E. Miller, Yogasudha Veturi and Marylyn D. Ritchie

Within-sample co-methylation patterns in normal tissues

DNA methylation is an epigenetic event that may regulate gene expression. Because of this regulation role, aberrant DNA methylation is often associated with many diseases. Within-sample DNA co-methylation is t...

Authors: Lillian Sun and Shuying Sun

Characterizing human genomic coevolution in locus-gene regulatory interactions

Coevolution has been used to identify and predict interactions and functional relationships between proteins of many different organisms including humans. Current efforts in annotating the human genome increas...

Authors: Daniel Savel and Mehmet Koyutürk

Encodings and models for antimicrobial peptide classification for multi-resistant pathogens

Antimicrobial peptides (AMPs) are part of the inherent immune system. In fact, they occur in almost all organisms including, e.g., plants, animals, and humans. Remarkably, they show effectivity also against mu...

Authors: Sebastian Spänig and Dominik Heider

Testing the assumptions of parametric linear models: the need for biological data mining in disciplines such as human genetics

Authors: Jason H. Moore, Trudy F. C. Mackay and Scott M. Williams

Approximate kernel reconstruction for time-varying networks

Most existing algorithms for modeling and analyzing molecular networks assume a static or time-invariant network topology. Such view, however, does not render the temporal evolution of the underlying biologica...

Authors: Gregory Ditzler, Nidhal Bouaynaya, Roman Shterenberg and Hassan M. Fathallah-Shaykh

A biplot correlation range for group-wise metabolite selection in mass spectrometry

Analytic methods are available to acquire extensive metabolic information in a cost-effective manner for personalized medicine, yet disease risk and diagnosis mostly rely upon individual biomarkers based on st...

Authors: Youngja H Park, Taewoon Kong, James R. Roede, Dean P. Jones and Kichun Lee

Predicting opioid dependence from electronic health records with machine learning

The opioid epidemic in the United States is averaging over 100 deaths per day due to overdose. The effectiveness of opioids as pain treatments, and the drug-seeking behavior of opioid addicts, leads physicians...

Authors: Randall J. Ellis, Zichen Wang, Nicholas Genes and Avi Ma’ayan

Use case driven evaluation of open databases for pediatric cancer research

A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but a...

Authors: Fleur Jeanquartier, Claire Jean-Quartier and Andreas Holzinger

Application of an interpretable classification model on Early Folding Residues during protein folding

Machine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Mea...

Authors: Sebastian Bittrich, Marika Kaden, Christoph Leberecht, Florian Kaiser, Thomas Villmann and Dirk Labudde

Unified Cox model based multifactor dimensionality reduction method for gene-gene interaction analysis of the survival phenotype

One strategy for addressing missing heritability in genome-wide association study is gene-gene interaction analysis, which, unlike a single gene approach, involves high-dimensionality. The multifactor dimensio...

Authors: Seungyeoun Lee, Donghee Son, Yongkang Kim, Wenbao Yu and Taesung Park

Distributed retrieval engine for the development of cloud-deployed biological databases

The integration of cloud resources with federated data retrieval has the potential of improving the maintenance, accessibility and performance of specialized databases in the biomedical field. However, such an...

Authors: David Bouzaglo, Israel Chasida and Elishai Ezra Tsur

Knomics-Biota - a system for exploratory analysis of human gut microbiota data

Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experi...

Authors: Daria Efimova, Alexander Tyakht, Anna Popenko, Anatoly Vasilyev, Ilya Altukhov, Nikita Dovidchenko, Vera Odintsova, Natalya Klimenko, Robert Loshkarev, Maria Pashkova, Anna Elizarova, Viktoriya Voroshilova, Sergei Slavskii, Yury Pekov, Ekaterina Filippova, Tatiana Shashkova…

A fast forward 3D connection algorithm for mitochondria and synapse segmentations from serial EM images

It is becoming increasingly clear that the quantification of mitochondria and synapses is of great significance to understand the function of biological nervous systems. Electron microscopy (EM), with the nece...

Authors: Weifu Li, Jing Liu, Chi Xiao, Hao Deng, Qiwei Xie and Hua Han

Transition-transversion encoding and genetic relationship metric in ReliefF feature selection improves pathway enrichment in GWAS

ReliefF is a nearest-neighbor based feature selection algorithm that efficiently detects variants that are important due to statistical interactions or epistasis. For categorical predictors, like genotypes, th...

Authors: M. Arabnejad, B. A. Dawkins, W. S. Bush, B. C. White, A. R. Harkness and B. A. McKinney

Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction

In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced ac...

Authors: Eleonora Cappelli, Giovanni Felici and Emanuel Weitschek

To know the objective is not (necessarily) to know the objective function

Authors: Moshe Sipper, Ryan J. Urbanowicz and Jason H. Moore

Grasping frequent subgraph mining for bioinformatics applications

Searching for interesting common subgraphs in graph data is a well-studied problem in data mining. Subgraph mining techniques focus on the discovery of patterns in graphs that exhibit a specific network struct...

Authors: Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals and Kris Laukens

Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

The genetic architecture underlying central cornea thickness (CCT) is far from understood. Most of the CCT-associated variants are located in the non-coding regions, raising the difficulty of following functio...

Authors: Jing Zhang, Dan Wu, Yiqin Dai and Jianjiang Xu

Evolutionary methods for variable selection in the epidemiological modeling of cardiovascular diseases

The redundancy of information is becoming a critical issue for epidemiologists. High-dimensional datasets require new effective variable selection methods to be developed. This study implements an advanced evo...

Authors: Christina Brester, Jussi Kauhanen, Tomi-Pekka Tuomainen, Sari Voutilainen, Mauno Rönkkö, Kimmo Ronkainen, Eugene Semenkin and Mikko Kolehmainen

Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm

The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction ...

Authors: Cheng-Hong Yang, Kuo-Chuan Wu, Yu-Shiun Lin, Li-Yeh Chuang and Hsueh-Wei Chang

A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies

Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information abou...

Authors: Jorge Parraga-Alava, Marcio Dorn and Mario Inostroza-Ponta

TRIQ: a new method to evaluate triclusters

Triclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of tric...

Authors: David Gutiérrez-Avilés, Raúl Giráldez, Francisco Javier Gil-Cumbreras and Cristina Rubio-Escudero

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activit...

Authors: Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan and Casey S. Greene