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  1. Research Article

    Reconstructing cancer drug response networks using multitask learning

    Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph

    BMC Systems Biology 2017 11:96

    Published on: 10 October 2017

  2. Research

    System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia

    Molecular mechanisms of the functional alteration of hematopoietic stem cells (HSCs) in leukemic environment attract intensive research interests. As known in previous researches, Maff and Egr3 are two important ...

    Rudong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu and Lei Liu

    BMC Systems Biology 2017 11(Suppl 5):91

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  3. Research

    A systematic analysis of FDA-approved anticancer drugs

    The discovery of novel anticancer drugs is critical for the pharmaceutical research and development, and patient treatment. Repurposing existing drugs that may have unanticipated effects as potential candidate...

    Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu and Hua Xu

    BMC Systems Biology 2017 11(Suppl 5):87

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  4. Research

    Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma

    Previous studies suggested that cancer cells possess traits reminiscent of the biological mechanisms ascribed to normal embryonic stem cells (ESCs) regulated by MYC and Polycomb repressive complex 2 (PRC2). Se...

    Xinan Holly Yang, Fangming Tang, Jisu Shin and John M. Cunningham

    BMC Systems Biology 2017 11(Suppl 5):92

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  5. Research

    Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis

    Adult hippocampal neurogenesis, the process of formation of new neurons, occurs throughout life in the hippocampus. New neurons have been associated with learning and memory as well as mood control, and impair...

    Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel and Mirjana Maletic-Savatic

    BMC Systems Biology 2017 11(Suppl 5):90

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  6. Research

    Roles of alternative splicing in modulating transcriptional regulation

    The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain prote...

    Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang and Yunlong Liu

    BMC Systems Biology 2017 11(Suppl 5):89

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  7. Introduction

    The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work

    Between December 8–10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, on...

    W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao and Zhangdong Liu

    BMC Systems Biology 2017 11(Suppl 5):88

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  8. Research

    MD-Miner: a network-based approach for personalized drug repositioning

    Due to advances in next generation sequencing technologies and corresponding reductions in cost, it is now attainable to investigate genome-wide gene expression and variants at a patient-level, so as to better...

    Haoyang Wu, Elise Miller, Denethi Wijegunawardana, Kelly Regan, Philip R.O. Payne and Fuhai Li

    BMC Systems Biology 2017 11(Suppl 5):86

    Published on: 3 October 2017

    This article is part of a Supplement: Volume 11 Supplement 5

  9. Research

    Modeling and analysis of the Delta-Notch dependent boundary formation in the Drosophila large intestine

    The boundary formation in the Drosophila large intestine is widely studied as an important biological problem. It has been shown that the Delta-Notch signaling pathway plays an essential role in the formation of ...

    Fei Liu, Deshun Sun, Ryutaro Murakami and Hiroshi Matsuno

    BMC Systems Biology 2017 11(Suppl 4):80

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  10. Research

    Mimvec: a deep learning approach for analyzing the human phenome

    The human phenome has been widely used with a variety of genomic data sources in the inference of disease genes. However, most existing methods thus far derive phenotype similarity based on the analysis of bio...

    Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang and Rui Jiang

    BMC Systems Biology 2017 11(Suppl 4):76

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  11. Research

    Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations

    Predicting protein structure from amino acid sequence is a prominent problem in computational biology. The long range interactions (or non-local interactions) are known as the main source of complexity for pro...

    Yuzhen Guo, Fengying Tao, Zikai Wu and Yong Wang

    BMC Systems Biology 2017 11(Suppl 4):93

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  12. Research

    NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis

    High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as different...

    Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang and Ling-Yun Wu

    BMC Systems Biology 2017 11(Suppl 4):75

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  13. Research

    Forecasting influenza A pandemic outbreak using protein dynamical network biomarkers

    Influenza A virus is prone to mutation and susceptible to human beings and spread in the crowds when affected by the external environment or other factors. It is very necessary to forecast influenza A pandemic...

    Jie Gao, Kang Wang, Tao Ding and Shanshan Zhu

    BMC Systems Biology 2017 11(Suppl 4):85

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  14. Research

    Improvement of phylogenetic method to analyze compositional heterogeneity

    Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally ref...

    Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang and Fei Guo

    BMC Systems Biology 2017 11(Suppl 4):79

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  15. Research

    Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despit...

    Changhe Fu, Su Deng, Guangxu Jin, Xinxin Wang and Zu-Guo Yu

    BMC Systems Biology 2017 11(Suppl 4):81

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  16. Research

    A two-step framework for inferring direct protein-protein interaction network from AP-MS data

    Affinity purification-mass spectrometry (AP-MS) has been widely used for generating bait-prey data sets so as to identify underlying protein-protein interactions and protein complexes. However, the AP-MS data ...

    Bo Tian, Can Zhao, Feiyang Gu and Zengyou He

    BMC Systems Biology 2017 11(Suppl 4):82

    Published on: 21 September 2017

    This article is part of a Supplement: Volume 11 Supplement 4

  17. Research Article

    An Integrative multi-lineage model of variation in leukopoiesis and acute myelogenous leukemia

    Acute myelogenous leukemia (AML) progresses uniquely in each patient. However, patients are typically treated with the same types of chemotherapy, despite biological differences that lead to differential respo...

    Joyatee M. Sarker, Serena M. Pearce, Robert P. Nelson Jr., Tamara L. Kinzer-Ursem, David M. Umulis and Ann E. Rundell

    BMC Systems Biology 2017 11:78

    Published on: 25 August 2017

  18. Research Article

    Cooperative binding mitigates the high-dose hook effect

    The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker prot...

    Ranjita Dutta Roy, Christian Rosenmund and Melanie I. Stefan

    BMC Systems Biology 2017 11:74

    Published on: 14 August 2017

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