Articles

Compositional zero-inflated network estimation for microbiome data

The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challe...

Authors: Min Jin Ha, Junghi Kim, Jessica Galloway-Peña, Kim-Anh Do and Christine B. Peterson

LDscaff: LD-based scaffolding of de novo genome assemblies

Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing...

Authors: Zicheng Zhao, Yingxiao Zhou, Shuai Wang, Xiuqing Zhang, Changfa Wang and Shuaicheng Li

Genome-wide detection of short tandem repeat expansions by long-read sequencing

Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific r...

Authors: Qian Liu, Yao Tong and Kai Wang

Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study

Although genetic risk factors and network-level neuroimaging abnormalities have shown effects on cognitive performance and brain atrophy in Alzheimer’s disease (AD), little is understood about how apolipoprote...

Authors: Jin Li, Chenyuan Bian, Dandan Chen, Xianglian Meng, Haoran Luo, Hong Liang and Li Shen

In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells

Cancer stem cells (CSCs) have features such as the ability to self-renew, differentiate into defined progenies and initiate the tumor growth. Treatments of cancer include drugs, chemotherapy and radiotherapy o...

Authors: Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik and Zhongming Zhao

Deep learning detection of informative features in tau PET for Alzheimer’s disease classification

Alzheimer’s disease (AD) is the most common type of dementia, typically characterized by memory loss followed by progressive cognitive decline and functional impairment. Many clinical trials of potential thera...

Authors: Taeho Jo, Kwangsik Nho, Shannon L. Risacher and Andrew J. Saykin

Integrative approach for detecting membrane proteins

Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools ...

Authors: Munira Alballa and Gregory Butler

ARPIR: automatic RNA-Seq pipelines with interactive report

RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different al...

Authors: Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini and Maria Paola Martelli

Predicting substitutions to modulate disorder and stability in coiled-coils

Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disorder...

Authors: Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine and Alessandra Carbone

A2A: a platform for research in biomedical literature search

Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published lit...

Authors: Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen and Cecile Paris

Inter-protein residue covariation information unravels physically interacting protein dimers

Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synth...

Authors: Sara Salmanian, Hamid Pezeshk and Mehdi Sadeghi

Inferring time-dependent population growth rates in cell cultures undergoing adaptation

The population growth rate is an important characteristic of any cell culture. During sustained experiments, the growth rate may vary due to competition or adaptation. For instance, in presence of a toxin or a...

Authors: H. Jonathan G. Lindström and Ran Friedman

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We descri...

Authors: M. Suhr, C. Lehmann, C. R. Bauer, T. Bender, C. Knopp, L. Freckmann, B. Öst Hansen, C. Henke, G. Aschenbrandt, L. K. Kühlborn, S. Rheinländer, L. Weber, B. Marzec, M. Hellkamp, P. Wieder, U. Sax…

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference

Authors:

Graph embeddings on gene ontology annotations for protein–protein interaction prediction

Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations an...

Authors: Xiaoshi Zhong and Jagath C. Rajapakse

DRACP: a novel method for identification of anticancer peptides

Millions of people are suffering from cancers, but accurate early diagnosis and effective treatment are still tough for all doctors. Common ways against cancer include surgical operation, radiotherapy and chem...

Authors: Tianyi Zhao, Yang Hu and Tianyi Zang

Filtering de novo indels in parent-offspring trios

Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches us...

Authors: Yongzhuang Liu, Jian Liu and Yadong Wang

BioRel: towards large-scale biomedical relation extraction

Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...

Authors: Rui Xing, Jie Luo and Tengwei Song

NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data

Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelin...

Authors: Ruiyu Xiao, Guoshan Lu, Wanqian Guo and Shuilin Jin

Combining sequence and network information to enhance protein–protein interaction prediction

Protein–protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to th...

Authors: Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang and Jiajie Peng

Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost

With the rapid development of medical treatment, many patients not only consider the survival time, but also care about the quality of life. Changes in physical, psychological and social functions after and du...

Authors: Huijuan Xu, Hairong Wang, Chenshan Yuan, Qinghua Zhai, Xufeng Tian, Lei Wu and Yuanyuan Mi

Predicting functions of maize proteins using graph convolutional network

Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are an...

Authors: Guangjie Zhou, Jun Wang, Xiangliang Zhang, Maozu Guo and Guoxian Yu

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion predict...

Authors: Krutika S. Gaonkar, Federico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel A. Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam C. Resnick, Konstantin Strauch, Jaclyn N. Taroni and Jo Lynne Rokita

Flora Capture: a citizen science application for collecting structured plant observations

Digital plant images are becoming increasingly important. First, given a large number of images deep learning algorithms can be trained to automatically identify plants. Second, structured image-based observat...

Authors: David Boho, Michael Rzanny, Jana Wäldchen, Fabian Nitsche, Alice Deggelmann, Hans Christian Wittich, Marco Seeland and Patrick Mäder

Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab

The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cel...

Authors: Bernhard Roither, Chris Oostenbrink and Wolfgang Schreiner

Validation of a yellow fever vaccine model using data from primary vaccination in children and adults, re-vaccination and dose-response in adults and studies with immunocompromised individuals

An effective yellow fever (YF) vaccine has been available since 1937. Nevertheless, questions regarding its use remain poorly understood, such as the ideal dose to confer immunity against the disease, the need...

Authors: Carla Rezende Barbosa Bonin, Guilherme Côrtes Fernandes, Reinaldo de Menezes Martins, Luiz Antonio Bastos Camacho, Andréa Teixeira-Carvalho, Licia Maria Henrique da Mota, Sheila Maria Barbosa de Lima, Ana Carolina Campi-Azevedo, Olindo Assis Martins-Filho, Rodrigo Weber dos Santos and Marcelo Lobosco

Computational modeling of the immune response in multiple sclerosis using epimod framework

Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS e...

Authors: Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero and Simona Rolla

Toward computational modelling on immune system function

The 3rd edition of the computational methods for the immune system function workshop has been held in San Diego, CA, in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIB...

Authors: Francesco Pappalardo, Giulia Russo and Pedro A. Reche

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform

SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgentl...

Authors: Giulia Russo, Marzio Pennisi, Epifanio Fichera, Santo Motta, Giuseppina Raciti, Marco Viceconti and Francesco Pappalardo

Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices

The aim of a recent research project was the investigation of the mechanisms involved in the onset of type 2 diabetes in the absence of familiarity. This has led to the development of a computational model tha...

Authors: Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio and Filippo Castiglione

Identification of CD8⁺ T cell epitopes through proteasome cleavage site predictions

We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model t...

Authors: Marta Gomez-Perosanz, Alvaro Ras-Carmona, Esther M. Lafuente and Pedro A. Reche

Utilizing heart rate variability to predict ICU patient outcome in traumatic brain injury

Prediction of patient outcome in medical intensive care units (ICU) may help for development and investigation of early interventional strategies. Several ICU scoring systems have been developed and are used t...

Authors: Ping Zhang, Tegan Roberts, Brent Richards and Luke J. Haseler

Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB

In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still c...

Authors: Giulia Russo, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Miguel A. Juarez, Pere-Joan Cardona, Santo Motta, Kenneth B. Walker, Epifanio Fichera, Marco Viceconti and Francesco Pappalardo

Generation of digital patients for the simulation of tuberculosis with UISS-TB

The STriTuVaD project, funded by Horizon 2020, aims to test through a Phase IIb clinical trial one of the most advanced therapeutic vaccines against tuberculosis. As part of this initiative, we have developed ...

Authors: Miguel A. Juárez, Marzio Pennisi, Giulia Russo, Dimitrios Kiagias, Cristina Curreli, Marco Viceconti and Francesco Pappalardo

PyClone-VI: scalable inference of clonal population structures using whole genome data

At diagnosis tumours are typically composed of a mixture of genomically distinct malignant cell populations. Bulk sequencing of tumour samples coupled with computational deconvolution can be used to identify t...

Authors: Sierra Gillis and Andrew Roth

ped_draw: pedigree drawing with ease

Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped fi...

Authors: Matt Velinder, Dillon Lee and Gabor Marth

iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features

Protein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-transl...

Authors: Kai-Yao Huang, Fang-Yu Hung, Hui-Ju Kao, Hui-Hsuan Lau and Shun-Long Weng

Hybrid attentional memory network for computational drug repositioning

Drug repositioning has been an important and efficient method for discovering new uses of known drugs. Researchers have been limited to one certain type of collaborative filtering (CF) models for drug repositi...

Authors: Jieyue He, Xinxing Yang, Zhuo Gong and lbrahim Zamit

ideal: an R/Bioconductor package for interactive differential expression analysis

RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still pro...

Authors: Federico Marini, Jan Linke and Harald Binder

High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status

A low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial ...

Authors: L. M. Hall and A. E. Hendricks

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data

Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some pec...

Authors: Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha and Paola Bonizzoni

Convolutional neural network for automated mass segmentation in mammography

Automatic segmentation and localization of lesions in mammogram (MG) images are challenging even with employing advanced methods such as deep learning (DL) methods. We developed a new model based on the archit...

Authors: Dina Abdelhafiz, Jinbo Bi, Reda Ammar, Clifford Yang and Sheida Nabavi

Decoy selection for protein structure prediction via extreme gradient boosting and ranking

Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and nega...

Authors: Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev and Amarda Shehu

Linear space string correction algorithm using the Damerau-Levenshtein distance

The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another...

Authors: Chunchun Zhao and Sartaj Sahni

So you think you can PLS-DA?

Partial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and classifier. In an effort to understand its strength...

Authors: Daniel Ruiz-Perez, Haibin Guan, Purnima Madhivanan, Kalai Mathee and Giri Narasimhan

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data

Gaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of different tools and algorithms have b...

Authors: Sebastian Canzler and Jörg Hackermüller

Regional registration of whole slide image stacks containing major histological artifacts

High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, howev...

Authors: Mahsa Paknezhad, Sheng Yang Michael Loh, Yukti Choudhury, Valerie Koh Cui Koh, Timothy Tay Kwang Yong, Hui Shan Tan, Ravindran Kanesvaran, Puay Hoon Tan, John Yuen Shyi Peng, Weimiao Yu, Yongcheng Benjamin Tan, Yong Zhen Loy, Min-Han Tan and Hwee Kuan Lee

Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq

Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functiona...

Authors: Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert Barber and Gang Huang

Current trend and development in bioinformatics research

This is an editorial report of the supplements to BMC Bioinformatics that includes 6 papers selected from the BIOCOMP’19—The 2019 International Conference on Bioinformatics and Computational Biology. These art...

Authors: Yuanyuan Fu, Zhougui Ling, Hamid Arabnia and Youping Deng

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the ...

Authors: Casey Cole, Caleb Parks, Julian Rachele and Homayoun Valafar