Articles

RAFTS³G: an efficient and versatile clustering software to analyses in large protein datasets

Clustering methods are essential to partitioning biological samples being useful to minimize the information complexity in large datasets. Tools in this context usually generates data with greed algorithms tha...

Authors: Bruno Thiago de Lima Nichio, Aryel Marlus Repula de Oliveira, Camilla Reginatto de Pierri, Leticia Graziela Costa Santos, Alexandre Quadros Lejambre, Ricardo Assunção Vialle, Nilson Antônio da Rocha Coimbra, Dieval Guizelini, Jeroniza Nunes Marchaukoski, Fabio de Oliveira Pedrosa and Roberto Tadeu Raittz

Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness

Asymmetry during cellular division, both in the uneven partitioning of damaged cellular components and of cell volume, is a cell biological phenomenon experienced by many unicellular organisms. Previous work b...

Authors: Ruijie Song and Murat Acar

Viral coinfection analysis using a MinHash toolkit

Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 10...

Authors: Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello and Richard Durbin

RESCUE: imputing dropout events in single-cell RNA-sequencing data

Single-cell RNA-sequencing technologies provide a powerful tool for systematic dissection of cellular heterogeneity. However, the prevalence of dropout events imposes complications during data analysis and, de...

Authors: Sam Tracy, Guo-Cheng Yuan and Ruben Dries

PEPOP 2.0: new approaches to mimic non-continuous epitopes

Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a ...

Authors: Vincent Demolombe, Alexandre G. de Brevern, Liza Felicori, Christophe NGuyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina and Violaine Moreau

Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer’s disease

Mathematical models of biological networks can provide important predictions and insights into complex disease. Constraint-based models of cellular metabolism and probabilistic models of gene regulatory networ...

Authors: Han Yu and Rachael Hageman Blair

CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB

In cancer research, robustness of a complex biochemical network is one of the most relevant properties to investigate for the development of novel targeted therapies. In cancer systems biology, biological netw...

Authors: Fortunato Bianconi, Chiara Antonini, Lorenzo Tomassoni and Paolo Valigi

Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks

Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousan...

Authors: Ryohei Eguchi, Naoaki Ono, Aki Hirai Morita, Tetsuo Katsuragi, Satoshi Nakamura, Ming Huang, Md. Altaf-Ul-Amin and Shigehiko Kanaya

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data

Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the da...

Authors: Savvas Kinalis, Finn Cilius Nielsen, Ole Winther and Frederik Otzen Bagger

Analyzing magnetic bead QuantiGene® Plex 2.0 gene expression data in high throughput mode using QGprofiler

The QuantiGene® Plex 2.0 platform (ThermoFisher Scientific) combines bDNA with the Luminex/xMAP magnetic bead capturing technology to assess differential gene expression in a compound exposure setting. This te...

Authors: Bie Verbist, Eva Adriaensen, Vikki Keersmaekers, Dea Putri, Marjolein Crabbe, Maarten Derks, Rytis Bagdziunas, Griet Laenen and Hans De Wolf

ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins

Electron transport chain is a series of protein complexes embedded in the process of cellular respiration, which is an important process to transfer electrons and other macromolecules throughout the cell. It i...

Authors: Nguyen Quoc Khanh Le, Edward Kien Yee Yapp and Hui-Yuan Yeh

Improving MetFrag with statistical learning of fragment annotations

Molecule identification is a crucial step in metabolomics and environmental sciences. Besides in silico fragmentation, as performed by MetFrag, also machine learning and statistical methods evolved, showing an...

Authors: Christoph Ruttkies, Steffen Neumann and Stefan Posch

Exploring the information transmission properties of noise-induced dynamics: application to glioma differentiation

Cells operate in an uncertain environment, where critical cell decisions must be enacted in the presence of biochemical noise. Information theory can measure the extent to which such noise perturbs normal cell...

Authors: Aditya Sai and Nan Kong

iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis

One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytica...

Authors: Teresia M. Buza, Triza Tonui, Francesca Stomeo, Christian Tiambo, Robab Katani, Megan Schilling, Beatus Lyimo, Paul Gwakisa, Isabella M. Cattadori, Joram Buza and Vivek Kapur

ENTRNA: a framework to predict RNA foldability

RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particu...

Authors: Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan and Teresa Wu

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations

Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have ...

Authors: Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal and Piero Fariselli

Analysis of common targets for circular RNAs

The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...

Authors: Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang and Kuei-Yang Hsiao

SRAssembler: Selective Recursive local Assembly of homologous genomic regions

The falling cost of next-generation sequencing technology has allowed deep sequencing across related species and of individuals within species. Whole genome assemblies from these data remain high time- and res...

Authors: Thomas W. McCarthy, Hsien-chao Chou and Volker P. Brendel

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensional...

Authors: Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera and Joaquín Dopazo

Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters

Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. ...

Authors: Sergii Domanskyi, Anthony Szedlak, Nathaniel T Hawkins, Jiayin Wang, Giovanni Paternostro and Carlo Piermarocchi

MassComp, a lossless compressor for mass spectrometry data

Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years...

Authors: Ruochen Yang, Xi Chen and Idoia Ochoa

JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles

Differential expression analysis on tumor expression profiles has always been a key issue for subsequent biological experimental validation. It is important how to select features which best discriminate betwe...

Authors: Yi Li, Yanan Liu, Yiming Wu and Xudong Zhao

Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data

Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when bui...

Authors: Ryan J. Eller, Sarath C. Janga and Susan Walsh

In silico analysis of missense mutations in exons 1–5 of the F9 gene that cause hemophilia B

Missense mutations in the first five exons of F9, which encodes factor FIX, represent 40% of all mutations that cause hemophilia B. To address the ongoing debate regarding in silico identification of disease-caus...

Authors: Lennon Meléndez-Aranda, Ana Rebeca Jaloma-Cruz, Nina Pastor and Marina María de Jesús Romero-Prado

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data

Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.

Authors: Akio Miyao, Jianyu Song Kiyomiya, Keiko Iida, Koji Doi and Hiroshi Yasue

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies...

Authors: Leandro Gabriel Roser, Fernán Agüero and Daniel Oscar Sánchez

Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison

Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast ...

Authors: Tomas Vicar, Jan Balvan, Josef Jaros, Florian Jug, Radim Kolar, Michal Masarik and Jaromir Gumulec

FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis

Gene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, resear...

Authors: Matthew L. Hale, Ishwor Thapa and Dario Ghersi

Block Forests: random forests for blocks of clinical and omics covariate data

In the last years more and more multi-omics data are becoming available, that is, data featuring measurements of several types of omics data for each patient. Using multi-omics data as covariate data in outcom...

Authors: Roman Hornung and Marvin N. Wright

A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants

C4 photosynthesis is a key domain of plant research with outcomes ranging from crop quality improvement, biofuel production and efficient use of water and nutrients. A metabolic network model of C4 “lab organi...

Authors: Rahul Shaw and C. Y. Maurice Cheung

Twiner: correlation-based regularization for identifying common cancer gene signatures

Breast and prostate cancers are typical examples of hormone-dependent cancers, showing remarkable similarities at the hormone-related signaling pathways level, and exhibiting a high tropism to bone. While the ...

Authors: Marta B. Lopes, Sandra Casimiro and Susana Vinga

An iteration method for identifying yeast essential proteins from heterogeneous network

Essential proteins are distinctly important for an organism’s survival and development and crucial to disease analysis and drug design as well. Large-scale protein-protein interaction (PPI) data sets exist in Sac...

Authors: Bihai Zhao, Yulin Zhao, Xiaoxia Zhang, Zhihong Zhang, Fan Zhang and Lei Wang

Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species

Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.

Authors: Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang and Jinxing Tu

NPCMF: Nearest Profile-based Collaborative Matrix Factorization method for predicting miRNA-disease associations

Predicting meaningful miRNA-disease associations (MDAs) is costly. Therefore, an increasing number of researchers are beginning to focus on methods to predict potential MDAs. Thus, prediction methods with impr...

Authors: Ying-Lian Gao, Zhen Cui, Jin-Xing Liu, Juan Wang and Chun-Hou Zheng

PaSS: a sequencing simulator for PacBio sequencing

Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next g...

Authors: Wenmin Zhang, Ben Jia and Chaochun Wei

DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information

Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on gra...

Authors: Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu and Guojun Li

Comparison of pathway analysis and constraint-based methods for cell factory design

Computational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factori...

Authors: Vítor Vieira, Paulo Maia, Miguel Rocha and Isabel Rocha

Testing adequacy for DNA substitution models

Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum like...

Authors: Wei Chen, Toby Kenney, Joseph Bielawski and Hong Gu

A stochastic model of size control in the budding yeast cell cycle

Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generat...

Authors: Mansooreh Ahmadian, John J. Tyson and Yang Cao

Optimal clustering with missing values

Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate th...

Authors: Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian and Edward R. Dougherty

Cross-population analysis for functional characterization of type II diabetes variants

As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Po...

Authors: Dalia Elmansy and Mehmet Koyutürk

A linear delay algorithm for enumerating all connected induced subgraphs

Real biological and social data is increasingly being represented as graphs. Pattern-mining-based graph learning and analysis techniques report meaningful biological subnetworks that elucidate important intera...

Authors: Mohammed Alokshiya, Saeed Salem and Fidaa Abed

Characterizing building blocks of resource constrained biological networks

Identification of motifs–recurrent and statistically significant patterns–in biological networks is the key to understand the design principles, and to infer governing mechanisms of biological systems. This, h...

Authors: Yuanfang Ren, Ahmet Ay, Alin Dobra and Tamer Kahveci

Recursive model for dose-time responses in pharmacological studies

Clinical studies often track dose-response curves of subjects over time. One can easily model the dose-response curve at each time point with Hill equation, but such a model fails to capture the temporal evolu...

Authors: Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh and Ranadip Pal

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Authors: Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci and Ranadip Pal

Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application

The hybrid stochastic simulation algorithm, proposed by Haseltine and Rawlings (HR), is a combination of differential equations for traditional deterministic models and Gillespie’s algorithm (SSA) for stochast...

Authors: Minghan Chen and Yang Cao

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks

Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified dif...

Authors: Chieh Lo and Radu Marculescu

Network-based prediction of polygenic disease genes involved in cell motility

Schizophrenia and autism are examples of polygenic diseases caused by a multitude of genetic variants, many of which are still poorly understood. Recently, both diseases have been associated with disrupted neu...

Authors: Miriam Bern, Alexander King, Derek A. Applewhite and Anna Ritz

DDmap: a MATLAB package for the double digest problem using multiple genetic operators

In computational biology, the physical mapping of DNA is a key problem. We know that the double digest problem (DDP) is NP-complete. Many algorithms have been proposed for solving the DDP, although it is still...

Authors: Licheng Wang, Jingwen Suo, Yun Pan and Lixiang Li

Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality

In the era of precision oncology and publicly available datasets, the amount of information available for each patient case has dramatically increased. From clinical variables and PET-CT radiomics measures to ...

Authors: Michael C. Rendleman, John M. Buatti, Terry A. Braun, Brian J. Smith, Chibuzo Nwakama, Reinhard R. Beichel, Bart Brown and Thomas L. Casavant