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2020 – today
- 2020
[j10]Aaron M. Smith
, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek, Charles K. Fisher:
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. BMC Bioinform. 21(1): 119 (2020)
2010 – 2019
- 2019
- [j9]Sahand Khakabimamaghani, Yogeshwar D. Kelkar, Bruno M. Grande, Ryan D. Morin, Martin Ester, Daniel Ziemek:
SUBSTRA: Supervised Bayesian Patient Stratification. Bioinform. 35(18): 3263-3272 (2019) - 2017
- [j8]Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek, Kourosh Zarringhalam:
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. BMC Bioinform. 18(1): 565:1-565:11 (2017) - 2016
- [j7]Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek, Kourosh Zarringhalam:
Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinform. 17: 318 (2016) - 2014
- [j6]Kourosh Zarringhalam, Ahmed Enayetallah, Padmalatha Reddy, Daniel Ziemek:
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. Bioinform. 30(12): 69-77 (2014) - 2013
- [j5]Kourosh Zarringhalam, Ahmed Enayetallah, Alex Gutteridge, Ben Sidders, Daniel Ziemek:
Molecular causes of transcriptional response: a Bayesian prior knowledge approach. Bioinform. 29(24): 3167-3173 (2013) - [j4]Vicky Wang, Li Xi, Ahmed Enayetallah, Eric Fauman, Daniel Ziemek:
GeneTopics - interpretation of gene sets via literature-driven topic models. BMC Syst. Biol. 7(S-5): S10 (2013) - 2012
- [j3]Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch S. Huang:
Causal reasoning on biological networks: interpreting transcriptional changes. Bioinform. 28(8): 1114-1121 (2012) - [j2]Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek:
Assessing statistical significance in causal graphs. BMC Bioinform. 13: 35 (2012) - [j1]Chia-Ling Huang, John Lamb, Leonid Chindelevitch, Jarek Kostrowicki, Justin Guinney, Charles DeLisi, Daniel Ziemek:
Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. BMC Bioinform. 13: 46 (2012) - 2011
- [c1]Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch S. Huang:
Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract). RECOMB 2011: 34-37 - [p1]Daniel Ziemek, Christoph Brockel:
Network-Driven Analysis Methods and their Application to Drug Discovery. Handbook of Research on Computational and Systems Biology 2011: 294-315
Coauthor Index
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