Articles

Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice

It was highlighted that the original article [1] contained errors in the figures and their legends and by extension the in-text figure citations. This Corrections article shows the correct figures and correct ...

Authors: Guan-Sheng Liu, Richard Ballweg, Alan Ashbaugh, Yin Zhang, Joseph Facciolo, Melanie T. Cushion and Tongli Zhang

Network-based characterization of drug-protein interaction signatures with a space-efficient approach

Characterization of drug-protein interaction networks with biological features has recently become challenging in recent pharmaceutical science toward a better understanding of polypharmacology.

Authors: Yasuo Tabei, Masaaki Kotera, Ryusuke Sawada and Yoshihiro Yamanishi

GNE: a deep learning framework for gene network inference by aggregating biological information

The topological landscape of gene interaction networks provides a rich source of information for inferring functional patterns of genes or proteins. However, it is still a challenging task to aggregate heterog...

Authors: Kishan KC, Rui Li, Feng Cui, Qi Yu and Anne R. Haake

Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks

Systematic fusion of multiple data sources for Gene Regulatory Networks (GRN) inference remains a key challenge in systems biology. We incorporate information from protein-protein interaction networks (PPIN) i...

Authors: Wenting Liu and Jagath C. Rajapakse

Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus

Major alteration in lifestyle of human population has promoted Type 2 diabetes mellitus (T2DM) to the level of an epidemic. This metabolic disorder is characterized by insulin resistance and pancreatic β-cell dys...

Authors: Pritha Dutta, Lichun Ma, Yusuf Ali, Peter M.A. Sloot and Jie Zheng

Ultrafast clustering of single-cell flow cytometry data using FlowGrid

Flow cytometry is a popular technology for quantitative single-cell profiling of cell surface markers. It enables expression measurement of tens of cell surface protein markers in millions of single cells. It ...

Authors: Xiaoxin Ye and Joshua W. K. Ho

Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO

Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and wi...

Authors: Hansheng Xue, Jiajie Peng and Xuequn Shang

Anti-TNF- αtreatment-related pathways and biomarkers revealed by transcriptome analysis in Chinese psoriasis patients

Anti-tumor necrosis factor alpha (TNF- α) therapy has made a significant impact on treating psoriasis. Despite these agents being designed to block TNF- α activity, their mechanism of action in the remission of p...

Authors: Lunfei Liu, Wenting Liu, Yuxin Zheng, Jisu Chen, Jiong Zhou, Huatuo Dai, Suiqing Cai, Jianjun Liu, Min Zheng and Yunqing Ren

A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data

Single-cell RNA sequencing (scRNAseq) data always involves various unwanted variables, which would be able to mask the true signal to identify cell-types. More efficient way of dealing with this issue is to ex...

Authors: Shiquan Sun, Yabo Chen, Yang Liu and Xuequn Shang

Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms

Identification of Hürthle cell cancers by non-operative fine-needle aspiration biopsy (FNAB) of thyroid nodules is challenging. Resultingly, non-cancerous Hürthle lesions were conventionally distinguished from...

Authors: Yangyang Hao, Quan-Yang Duh, Richard T. Kloos, Joshua Babiarz, R. Mack Harrell, S. Thomas Traweek, Su Yeon Kim, Grazyna Fedorowicz, P. Sean Walsh, Peter M. Sadow, Jing Huang and Giulia C. Kennedy

FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs

Biological experiments have confirmed the association between miRNAs and various diseases. However, such experiments are costly and time consuming. Computational methods help select potential disease-related m...

Authors: Xiaoying Li, Yaping Lin, Changlong Gu and Jialiang Yang

PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach

Numerous experimental results have indicated that microRNAs (miRNAs) play a vital role in biological processes, as well as outbreaks of diseases at the molecular level. Despite their important role in biologic...

Authors: Jihwan Ha, Chihyun Park and Sanghyun Park

Adaptive information processing of network modules to dynamic and spatial stimuli

Adaptation and homeostasis are basic features of information processing in cells and seen in a broad range of contexts. Much of the current understanding of adaptation in network modules/motifs is based on the...

Authors: J. Krishnan and Ioannis Floros

Correction to: Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

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Authors: Guillermo de Anda-Jáuregui, Kai Guo, Brett A. McGregor, Eva L. Feldman and Junguk Hur

How to schedule VEGF and PD-1 inhibitors in combination cancer therapy?

One of the questions in the design of cancer clinical trials with combination of two drugs is in which order to administer the drugs. This is an important question, especially in the case where one agent may i...

Authors: Xiulan Lai and Avner Friedman

LSM-W²: laser scanning microscopy worker for wheat leaf surface morphology

Microscopic images are widely used in plant biology as an essential source of information on morphometric characteristics of the cells and the topological characteristics of cellular tissue pattern due to mode...

Authors: Ulyana S. Zubairova, Pavel Yu. Verman, Polina A. Oshchepkova, Alina S. Elsukova and Alexey V. Doroshkov

Systems biology research at BGRS-2018

Authors: Yuriy L. Orlov, Ralf Hofestädt and Ancha V. Baranova

Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology

A cancer cell line originating from human epithelial colorectal adenocarcinoma (Caco-2 cells) serves as a high capacity model for a preclinical screening of drugs. Recent need for incorporating barrier tissue ...

Authors: Dmitry Sakharov, Diana Maltseva, Evgeny Knyazev, Sergey Nikulin, Andrey Poloznikov, Sergey Shilin, Ancha Baranova, Irina Tsypina and Alexander Tonevitsky

Urine proteome changes associated with autonomic regulation of heart rate in cosmonauts

The strategy of adaptation of the human body in microgravity is largely associated with the plasticity of cardiovascular system regulatory mechanisms. During long-term space flights the changes in the stroke v...

Authors: Lyudmila H. Pastushkova, Vasily B. Rusanov, Anna G. Goncharova, Alexander G. Brzhozovskiy, Alexey S. Kononikhin, Anna G. Chernikova, Daria N. Kashirina, Andrey M. Nosovsky, Roman M. Baevsky, Evgeny N. Nikolaev and Irina M. Larina

Effects of unpaired 1 gene overexpression on the lifespan of Drosophila melanogaster

The JAK/STAT signaling pathway is involved in many aging-related cellular functions. However, effects of overexpression of genes controlling JAK/STAT signal transduction on longevity of model organisms have no...

Authors: Alexey Moskalev, Ekaterina Proshkina, Alex Zhavoronkov and Mikhail Shaposhnikov

Mathematical modeling of movement on fitness landscapes

Movement of populations on fitness landscapes has been a problem of interest for a long time. While the subject has been extensively developed theoretically, reconciliation of the theoretical work with recent ...

Authors: Nishant Gerald, Dibyendu Dutta, R. G. Brajesh and Supreet Saini

Computational modelling of energy balance in individuals with Metabolic Syndrome

A positive energy balance is considered to be the primary cause of the development of obesity-related diseases. Treatment often consists of a combination of reducing energy intake and increasing energy expendi...

Authors: Yvonne J. W. Rozendaal, Yanan Wang, Peter A. J. Hilbers and Natal A. W. van Riel

A mathematical model of iron import and trafficking in wild-type and Mrs3/4ΔΔ yeast cells

Iron plays crucial roles in the metabolism of eukaryotic cells. Much iron is trafficked into mitochondria where it is used for iron-sulfur cluster assembly and heme biosynthesis. A yeast strain in which Mrs3/4...

Authors: Joshua D. Wofford and Paul A. Lindahl

Correction to: miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson’s disease

Abstract

Authors: Xiaoting Liu, Jinhu Chen, Tianyuan Guan, Hui Yao, Wenpei Zhang, Zhenlong Guan and Yanqin Wang

In-silico comparison of two induction regimens (7 + 3 vs 7 + 3 plus additional bone marrow evaluation) in acute myeloid leukemia treatment

Clinical integration of systems biology approaches is gaining in importance in the course of digital revolution in modern medicine. We present our results of the analysis of an extended mathematical model desc...

Authors: Jan Christoph Banck and Dennis Görlich

How to prevent viremia rebound? Evidence from a PRRSv data-supported model of immune response

Understanding what determines the between-host variability in infection dynamics is a key issue to better control the infection spread. In particular, pathogen clearance is desirable over rebounds for the heal...

Authors: Natacha Go, Suzanne Touzeau, Zeenath Islam, Catherine Belloc and Andrea Doeschl-Wilson

Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells

It was highlighted that the original article [1] contained a mistake in the grant number in the Funding section of the Declarations, and in the legend of Fig. 6. This Correction article shows the incorrect and...

Authors: Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song and Ping Han

Correction to: MISC: missing imputation for single-cell RNA sequencing data

It was highlighted that the original article [1] contained a typesetting error in the last name of Allon Canaan. This was incorrectly captured as Allon Canaann in the original article which has since been upda...

Authors: Mary Qu Yang, Sherman M. Weissman, William Yang, Jialing Zhang, Allon Canaan and Renchu Guan

A mathematical model to estimate cholesterylester transfer protein (CETP) triglycerides flux in human plasma

Cholesterylester transfer protein (CETP) modulates the composition of various lipoproteins associated with cardiovascular disease. Despite its central role in lipoprotein metabolism, its mode of action is stil...

Authors: Martin Jansen, Gerhard Puetz, Michael M. Hoffmann and Karl Winkler

Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified s...

Authors: Carolina A. Contador, Vida Rodríguez, Barbara A. Andrews and Juan A. Asenjo

miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson’s disease

Parkinson’s disease (PD) is the second most common neurodegenerative disease, and it is a multifactorial disease with no definite diagnostic index. The aim of this study is to construct a molecular network to ...

Authors: Xiaoting Liu, Jinhu Chen, Tianyuan Guan, Hui Yao, Wenpei Zhang, Zhenlong Guan and Yanqin Wang

Model-based virtual patient analysis of human liver regeneration predicts critical perioperative factors controlling the dynamic mode of response to resection

Liver has the unique ability to regenerate following injury, with a wide range of variability of the regenerative response across individuals. Existing computational models of the liver regeneration are largel...

Authors: Babita K. Verma, Pushpavanam Subramaniam and Rajanikanth Vadigepalli

Multi-omics integration reveals molecular networks and regulators of psoriasis

Psoriasis is a complex multi-factorial disease, involving both genetic susceptibilities and environmental triggers. Genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS) have bee...

Authors: Yuqi Zhao, Deepali Jhamb, Le Shu, Douglas Arneson, Deepak K. Rajpal and Xia Yang

An agent-based model of the Notch signaling pathway elucidates three levels of complexity in the determination of developmental patterning

The Notch signaling pathway is involved in cell fate decision and developmental patterning in diverse organisms. A receptor molecule, Notch (N), and a ligand molecule (in this case Delta or Dl) are the central...

Authors: Elaine R. Reynolds, Ryan Himmelwright, Christopher Sanginiti and Jeffrey O. Pfaffmann

Constructing network topologies for multiple signal-encoding functions

Cells use signaling protein networks to sense their environment and mediate specific responses. Information about environmental stress is usually encoded in the dynamics of the signaling molecules, and qualita...

Authors: Lili Wu, Hongli Wang and Qi Ouyang

Plasmodium vivax readiness to transmit: implication for malaria eradication

The lack of a continuous long-term in vitro culture system for Plasmodium vivax severely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding of P. vivax h...

Authors: Swamy Rakesh Adapa, Rachel A. Taylor, Chengqi Wang, Richard Thomson-Luque, Leah R. Johnson and Rays H. Y. Jiang

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

A recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the correspond...

Authors: Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven and Jens Nielsen

Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways

The formation of acetate by fast-growing Escherichia coli (E. coli) is a commonly observed phenomenon, often referred to as overflow metabolism. Among various studies that have been carried over decades, a recent...

Authors: Hong Zeng and Aidong Yang

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Genome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype.

Authors: Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders and Bernhard O. Palsson

Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

Aggregation of high-throughput biological data using pathway-based approaches is useful to associate molecular results to functional features related to the studied phenomenon. Biological pathways communicate ...

Authors: Guillermo de Anda-Jáuregui, Kai Guo, Brett A. McGregor, Eva L. Feldman and Junguk Hur

rPCMP: robust p-value combination by multiple partitions with applications to ATAC-seq data

Evaluating the significance for a group of genes or proteins in a pathway or biological process for a disease could help researchers understand the mechanism of the disease. For example, identifying related pa...

Authors: Menglan Cai and Limin Li

Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements

One of the important steps in the process of assembling a genome sequence from short reads is scaffolding, in which the contigs in a draft genome are ordered and oriented into scaffolds. Currently, several sca...

Authors: Kun-Tze Chen, Hsin-Ting Shen and Chin Lung Lu

Integrating node embeddings and biological annotations for genes to predict disease-gene associations

Predicting disease causative genes (or simply, disease genes) has played critical roles in understanding the genetic basis of human diseases and further providing disease treatment guidelines. While various co...

Authors: Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu and Xiao-Li Li

A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization

During the identification of potential candidates, computational prediction of drug-target interactions (DTIs) is important to subsequent expensive validation in wet-lab. DTI screening considers four scenarios...

Authors: Jian-Yu Shi, An-Qi Zhang, Shao-Wu Zhang, Kui-Tao Mao and Siu-Ming Yiu

Computational drug repositioning using meta-path-based semantic network analysis

Drug repositioning is a promising and efficient way to discover new indications for existing drugs, which holds the great potential for precision medicine in the post-genomic era. Many network-based approaches...

Authors: Zhen Tian, Zhixia Teng, Shuang Cheng and Maozu Guo

Hot spot prediction in protein-protein interactions by an ensemble system

Hot spot residues are functional sites in protein interaction interfaces. The identification of hot spot residues is time-consuming and laborious using experimental methods. In order to address the issue, many...

Authors: Quanya Liu, Peng Chen, Bing Wang, Jun Zhang and Jinyan Li

Analysis of significant protein abundance from multiple reaction-monitoring data

Discovering reliable protein biomarkers is one of the most important issues in biomedical research. The ELISA is a traditional technique for accurate quantitation of well-known proteins. Recently, the multiple...

Authors: Jongsu Jun, Jungsoo Gim, Yongkang Kim, Hyunsoo Kim, Su Jong Yu, Injun Yeo, Jiyoung Park, Jeong-Ju Yoo, Young Youn Cho, Dong Hyeon Lee, Eun Ju Cho, Jeong-Hoon Lee, Yoon Jun Kim, Seungyeoun Lee, Jung-Hwan Yoon, Youngsoo Kim…

Laplacian normalization and bi-random walks on heterogeneous networks for predicting lncRNA-disease associations

Evidences have increasingly indicated that lncRNAs (long non-coding RNAs) are deeply involved in important biological regulation processes leading to various human complex diseases. Experimental investigations...

Authors: Yaping Wen, Guosheng Han and Vo V. Anh

FMSM: a novel computational model for predicting potential miRNA biomarkers for various human diseases

MicroRNA (miRNA) plays a key role in regulation mechanism of human biological processes, including the development of disease and disorder. It is necessary to identify potential miRNA biomarkers for various hu...

Authors: Yiwen Sun, Zexuan Zhu, Zhu-Hong You, Zijie Zeng, Zhi-An Huang and Yu-An Huang

Identification of active signaling pathways by integrating gene expression and protein interaction data

Signaling pathways are the key biological mechanisms that transduce extracellular signals to affect transcription factor mediated gene regulation within cells. A number of computational methods have been devel...

Authors: Md Humayun Kabir, Ralph Patrick, Joshua W. K. Ho and Michael D. O’Connor