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  1. 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
    Citation: BMC Systems Biology 2019 13:40
    Content type: Correction Published on:

    The original article was published in BMC Systems Biology 2018 12:77

  2. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):39
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  3. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  4. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):37
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  5. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  6. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):35
    Content type: Methods Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  7. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):34
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  8. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):29
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  9. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):28
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  10. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):27
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  11. 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
    Citation: BMC Systems Biology 2019 13(Suppl 2):26
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  16. 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
    Citation: BMC Systems Biology 2019 13(Suppl 1):22
    Content type: Software Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  18. 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
    Citation: BMC Systems Biology 2019 13(Suppl 1):19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  19. 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
    Citation: BMC Systems Biology 2019 13(Suppl 1):17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  20. 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
    Citation: BMC Systems Biology 2019 13(Suppl 1):16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  21. 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
    Citation: BMC Systems Biology 2019 13:25
    Content type: Research article Published on:

  22. 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
    Citation: BMC Systems Biology 2019 13:24
    Content type: Research article Published on:

  25. 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
    Citation: BMC Systems Biology 2019 13:18
    Content type: Research article Published on:

  26. 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
    Citation: BMC Systems Biology 2019 13:15
    Content type: Research article Published on:

  27. 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
    Citation: BMC Systems Biology 2019 13:14
    Content type: Correction Published on:

    The original article was published in BMC Systems Biology 2018 12:128

  28. 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
    Citation: BMC Systems Biology 2019 13:13
    Content type: Correction Published on:

    The original article was published in BMC Systems Biology 2018 12:114

  29. 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
    Citation: BMC Systems Biology 2019 13:12
    Content type: Research article Published on:

  30. 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
    Citation: BMC Systems Biology 2019 13:11
    Content type: Research article Published on:

  31. 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
    Citation: BMC Systems Biology 2019 13:10
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Systems Biology 2019 13:20

  32. 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
    Citation: BMC Systems Biology 2019 13:9
    Content type: Research article Published on:

  33. 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
    Citation: BMC Systems Biology 2019 13:8
    Content type: Research article Published on:

  34. 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
    Citation: BMC Systems Biology 2019 13:7
    Content type: Research article Published on:

  36. 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
    Citation: BMC Systems Biology 2019 13:5
    Content type: Research article Published on:

  37. 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
    Citation: BMC Systems Biology 2019 13:4
    Content type: Methodology article Published on:

  38. 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
    Citation: BMC Systems Biology 2019 13:3
    Content type: Research article Published on:

  40. 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
    Citation: BMC Systems Biology 2019 13:1
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Systems Biology 2019 13:31

  41. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):141
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  42. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):139
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  43. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):138
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  44. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):136
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  45. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):134
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  46. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):132
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  47. 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…
    Citation: BMC Systems Biology 2018 12(Suppl 9):123
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  48. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):122
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  49. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):121
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  50. 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
    Citation: BMC Systems Biology 2018 12(Suppl 9):120
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

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