BMC systems biology

Keyphrases

Publications

volume 13, number 1, 2019

Benjamín J Sánchez, Feiran Li, Eduard J Kerkhoven, Jens Nielsen
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. BMC systems biology 13 (1) (2019)
Hong Zeng, Aidong Yang
Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways. BMC systems biology 13 (1) (2019)
Laurence Yang, Ali Ebrahim, Colton J Lloyd, Michael A Saunders, Bernhard O Palsson
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC systems biology 13 (1) (2019)
Elaine R Reynolds, Ryan Himmelwright, Christopher Sanginiti, Jeffrey O Pfaffmann
An agent-based model of the Notch signaling pathway elucidates three levels of complexity in the determination of developmental patterning. BMC systems biology 13 (1) (2019)
Babita K Verma, Pushpavanam Subramaniam, Rajanikanth Vadigepalli
Model-based virtual patient analysis of human liver regeneration predicts critical perioperative factors controlling the dynamic mode of response to resection. BMC systems biology 13 (1) (2019)
Qichang Yang, Jing Wu, Jian Zhao, Tianyi Xu, Zhongming Zhao, Xiaofeng Song, Ping Han
Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells. BMC systems biology 13 (1) (2019)
Mary Qu Yang, Sherman M Weissman, William Yang, Jialing Zhang, Allon Canaan, Renchu Guan
Correction to: MISC: missing imputation for single-cell RNA sequencing data. BMC systems biology 13 (1) (2019)
Nishant Gerald, Dibyendu Dutta, R G Brajesh, Supreet Saini
Mathematical modeling of movement on fitness landscapes. BMC systems biology 13 (1) (2019)
Joshua D Wofford, Paul A Lindahl
A mathematical model of iron import and trafficking in wild-type and Mrs3/4ΔΔ yeast cells. BMC systems biology 13 (1) (2019)
Natacha Go, Suzanne Touzeau, Zeenath Islam, Catherine Belloc, Andrea Doeschl-Wilson
How to prevent viremia rebound? Evidence from a PRRSv data-supported model of immune response. BMC systems biology 13 (1) (2019)
Guillermo de Anda-Jáuregui, Kai Guo, Brett A McGregor, Eva L Feldman, Junguk Hur
Correction to: Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone. BMC systems biology 13 (1) (2019)
Xiaoting Liu, Jinhu Chen, Tianyuan Guan, Hui Yao, Wenpei Zhang, Zhenlong Guan, Yanqin Wang
Correction to: miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease. BMC systems biology 13 (1) (2019)
Martin Jansen, Gerhard Puetz, Michael M Hoffmann, Karl Winkler
A mathematical model to estimate cholesterylester transfer protein (CETP) triglycerides flux in human plasma. BMC systems biology 13 (1) (2019)
Swamy Rakesh Adapa, Rachel A Taylor, Chengqi Wang, Richard Thomson-Luque, Leah R Johnson, Rays H Y Jiang
Plasmodium vivax readiness to transmit: implication for malaria eradication. BMC systems biology 13 (1) (2019)
Yuqi Zhao, Deepali Jhamb, Le Shu, Douglas Arneson, Deepak K Rajpal, Xia Yang
Multi-omics integration reveals molecular networks and regulators of psoriasis. BMC systems biology 13 (1) (2019)
Lili Wu, Hongli Wang, Qi Ouyang
Constructing network topologies for multiple signal-encoding functions. BMC systems biology 13 (1) (2019)
Guillermo de Anda-Jáuregui, Kai Guo, Brett A McGregor, Eva L Feldman, Junguk Hur
Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone. BMC systems biology 13 (1) (2019)
J Krishnan, Ioannis Floros
Adaptive information processing of network modules to dynamic and spatial stimuli. BMC systems biology 13 (1) (2019)
Xiulan Lai, Avner Friedman
How to schedule VEGF and PD-1 inhibitors in combination cancer therapy? BMC systems biology 13 (1) (2019)
Guan-Sheng Liu, Richard Ballweg, Alan Ashbaugh, Yin Zhang, Joseph Facciolo, Melanie T Cushion, Tongli Zhang
Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice. BMC systems biology 13 (1) (2019)
Carolina A Contador, Vida Rodríguez, Barbara A Andrews, Juan A Asenjo
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. BMC systems biology 13 (1) (2019)
Yvonne J W Rozendaal, Yanan Wang, Peter A J Hilbers, Natal A W van Riel
Computational modelling of energy balance in individuals with Metabolic Syndrome. BMC systems biology 13 (1) (2019)
Jan Christoph Banck, Dennis Görlich
In-silico comparison of two induction regimens (7 + 3 vs 7 + 3 plus additional bone marrow evaluation) in acute myeloid leukemia treatment. BMC systems biology 13 (1) (2019)
Jihwan Ha, Chihyun Park, Sanghyun Park
PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach. BMC systems biology 13 (1) (2019)
Xiaoting Liu, Jinhu Chen, Tianyuan Guan, Hui Yao, Wenpei Zhang, Zhenlong Guan, Yanqin Wang
miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease. BMC systems biology 13 (1) (2019)

volume 13, number Suppl 1, 2019

Alexey Moskalev, Ekaterina Proshkina, Alex Zhavoronkov, Mikhail Shaposhnikov
Effects of unpaired 1 gene overexpression on the lifespan of Drosophila melanogaster. BMC systems biology 13 (Suppl 1) (2019)
Yuriy L Orlov, Ralf Hofestädt, Ancha V Baranova
Systems biology research at BGRS-2018. BMC systems biology 13 (Suppl 1) (2019)
Dmitry Sakharov, Diana Maltseva, Evgeny Knyazev, Sergey Nikulin, Andrey Poloznikov, Sergey Shilin, Ancha Baranova, Irina Tsypina, Alexander Tonevitsky
Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology. BMC systems biology 13 (Suppl 1) (2019)
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, Irina M Larina
Urine proteome changes associated with autonomic regulation of heart rate in cosmonauts. BMC systems biology 13 (Suppl 1) (2019)
Ulyana S Zubairova, Pavel Yu Verman, Polina A Oshchepkova, Alina S Elsukova, Alexey V Doroshkov
LSM-W2: laser scanning microscopy worker for wheat leaf surface morphology. BMC systems biology 13 (Suppl 1) (2019)

volume 13, number Suppl 2, 2019

Pritha Dutta, Lichun Ma, Yusuf Ali, Peter M A Sloot, Jie Zheng
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. BMC systems biology 13 (Suppl 2) (2019)
Lunfei Liu, Wenting Liu, Yuxin Zheng, Jisu Chen, Jiong Zhou, Huatuo Dai, Suiqing Cai, Jianjun Liu, Min Zheng, Yunqing Ren
Anti-TNF- αtreatment-related pathways and biomarkers revealed by transcriptome analysis in Chinese psoriasis patients. BMC systems biology 13 (Suppl 2) (2019)
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, Giulia C Kennedy
Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms. BMC systems biology 13 (Suppl 2) (2019)
Hansheng Xue, Jiajie Peng, Xuequn Shang
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC systems biology 13 (Suppl 2) (2019)
Yasuo Tabei, Masaaki Kotera, Ryusuke Sawada, Yoshihiro Yamanishi
Network-based characterization of drug-protein interaction signatures with a space-efficient approach. BMC systems biology 13 (Suppl 2) (2019)
Wenting Liu, Jagath C Rajapakse
Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks. BMC systems biology 13 (Suppl 2) (2019)
Xiaoying Li, Yaping Lin, Changlong Gu, Jialiang Yang
FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs. BMC systems biology 13 (Suppl 2) (2019)
Xiaoxin Ye, Joshua W K Ho
Ultrafast clustering of single-cell flow cytometry data using FlowGrid. BMC systems biology 13 (Suppl 2) (2019)
Kishan Kc, Rui Li, Feng Cui, Qi Yu, Anne R Haake
GNE: a deep learning framework for gene network inference by aggregating biological information. BMC systems biology 13 (Suppl 2) (2019)
Shiquan Sun, Yabo Chen, Yang Liu, Xuequn Shang
A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data. BMC systems biology 13 (Suppl 2) (2019)

volume 12, number Suppl 9, 2018

Quanya Liu, Peng Chen, Bing Wang, Jun Zhang, Jinyan Li
Hot spot prediction in protein-protein interactions by an ensemble system. BMC systems biology 12 (Suppl 9) (2018)
Menglan Cai, Limin Li
rPCMP: robust p-value combination by multiple partitions with applications to ATAC-seq data. BMC systems biology 12 (Suppl 9) (2018)
Kun-Tze Chen, Hsin-Ting Shen, Chin Lung Lu
Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements. BMC systems biology 12 (Suppl 9) (2018)
Ke Zhang, Wei Geng, Shuqin Zhang
Network-based logistic regression integration method for biomarker identification. BMC systems biology 12 (Suppl 9) (2018)
Yaping Wen, Guosheng Han, Vo V Anh
Laplacian normalization and bi-random walks on heterogeneous networks for predicting lncRNA-disease associations. BMC systems biology 12 (Suppl 9) (2018)
Zhen Tian, Zhixia Teng, Shuang Cheng, Maozu Guo
Computational drug repositioning using meta-path-based semantic network analysis. BMC systems biology 12 (Suppl 9) (2018)
Jian-Yu Shi, An-Qi Zhang, Shao-Wu Zhang, Kui-Tao Mao, Siu-Ming Yiu
A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization. BMC systems biology 12 (Suppl 9) (2018)
Dong Wang, Jie Li, Rui Liu, Yadong Wang
Optimizing gene set annotations combining GO structure and gene expression data. BMC systems biology 12 (Suppl 9) (2018)
Yiwen Sun, Zexuan Zhu, Zhu-Hong You, Zijie Zeng, Zhi-An Huang, Yu-An Huang
FMSM: a novel computational model for predicting potential miRNA biomarkers for various human diseases. BMC systems biology 12 (Suppl 9) (2018)
Md Humayun Kabir, Ralph Patrick, Joshua W K Ho, Michael D O'Connor
Identification of active signaling pathways by integrating gene expression and protein interaction data. BMC systems biology 12 (Suppl 9) (2018)