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Deep mining heterogeneous networks of biomedical linked data to predict novel drug–target associations

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Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Published: 18 April 2017
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Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

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Hyun-Seob Song, Noam Goldberg, Ashutosh Mahajan, Doraiswami Ramkrishna
Published: 27 March 2017
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VCNet: vector-based gene co-expression network construction and its application to RNA-seq data

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Zengmiao Wang, Huaying Fang, Nelson Leung-Sang Tang, Minghua Deng
Published: 08 March 2017
Journal Article

Stepwise inference of likely dynamic flux distributions from metabolic time series data

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Mojdeh Faraji, Eberhard O. Voit
Published: 07 March 2017
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Systematic inference of functional phosphorylation events in yeast metabolism

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Yu Chen, Yonghong Wang, Jens Nielsen
Published: 02 March 2017
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An approach to infer putative disease-specific mechanisms using neighboring gene networks

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Sahar Ansari, Michele Donato, Nafiseh Saberian, Sorin Draghici
Published: 15 February 2017
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Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells

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Pengyi Yang, Andrew Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang ...
Published: 14 February 2017
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Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway

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Sucheendra K. Palaniappan, François Bertaux, Matthieu Pichené, Eric Fabre, Gregory Batt ...
Published: 14 February 2017
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SANA: simulated annealing far outperforms many other search algorithms for biological network alignment

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Nil Mamano, Wayne B. Hayes
Published: 14 February 2017
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Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach

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Igor Marín de Mas, Eric Fanchon, Balázs Papp, Susana Kalko, Josep Roca ...
Published: 06 October 2016
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Combining multiple tools outperforms individual methods in gene set enrichment analyses

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Monther Alhamdoosh, Milica Ng, Nicholas J. Wilson, Julie M. Sheridan, Huy Huynh ...
Published: 30 September 2016
Journal Article

DEF: an automated dead-end filling approach based on quasi-endosymbiosis

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Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen
Published: 26 September 2016
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Detecting subnetwork-level dynamic correlations

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Yan Yan, Shangzhao Qiu, Zhuxuan Jin, Sihong Gong, Yun Bai ...
Published: 25 September 2016
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Assessment of cancer and virus antigens for cross-reactivity in human tissues

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Victor Jaravine, Silke Raffegerst, Dolores J. Schendel, Dmitrij Frishman
Published: 10 September 2016
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BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals

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Minsuk Kim, Gwanggyu Sun, Dong-Yup Lee, Byung-Gee Kim
Published: 07 September 2016
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Virtual exploration of early stage atherosclerosis

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Andy L. Olivares, Miguel A. González Ballester, Jérôme Noailly
Published: 29 August 2016
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Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models

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Pedro A. Saa, Lars K. Nielsen
Published: 24 August 2016
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Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes

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Yiyi Liu, Hongyu Zhao
Published: 18 August 2016
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Selective mutation accumulation: a computational model of the paternal age effect

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Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu
Published: 16 August 2016
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Predicting G protein-coupled receptor downstream signaling by tissue expression

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Yun Hao, Nicholas P. Tatonetti
Published: 02 August 2016