Network-Driven Analysis Methods and their Application to Drug Discovery. - Daniel Ziemek; Christoph Brockel (Handbook of Research on Computational and Systems Biology, 2011)

Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract). - Leonid Chindelevitch; Daniel Ziemek; Ahmed Enayetallah; Ranjit Randhawa; Ben Sidders; Christoph Brockel; Enoch S. Huang (RECOMB, 2011)

Causal reasoning on biological networks: interpreting transcriptional changes. - Leonid Chindelevitch; Daniel Ziemek; Ahmed Enayetallah; Ranjit Randhawa; Ben Sidders; Christoph Brockel; Enoch S. Huang (Bioinform., 2012)

Assessing statistical significance in causal graphs. - Leonid Chindelevitch; Po-Ru Loh; Ahmed Enayetallah; Bonnie Berger; Daniel Ziemek (BMC Bioinform., 2012)

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. - Chia-Ling Huang; John Lamb; Leonid Chindelevitch; Jarek Kostrowicki; Justin Guinney; Charles DeLisi; Daniel Ziemek (BMC Bioinform., 2012)

Molecular causes of transcriptional response: a Bayesian prior knowledge approach. - Kourosh Zarringhalam; Ahmed Enayetallah; Alex Gutteridge; Ben Sidders; Daniel Ziemek (Bioinform., 2013)

GeneTopics - interpretation of gene sets via literature-driven topic models. - Vicky Wang; Li Xi; Ahmed Enayetallah; Eric Fauman; Daniel Ziemek (BMC Syst. Biol., 2013)

Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. - Kourosh Zarringhalam; Ahmed Enayetallah; Padmalatha Reddy; Daniel Ziemek (Bioinform., 2014)

Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. - Carl Tony Fakhry; Parul Choudhary; Alex Gutteridge; Ben Sidders; Ping Chen 001; Daniel Ziemek; Kourosh Zarringhalam (BMC Bioinform., 2016)

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. - Tianyu Kang; Wei Ding 003; Luoyan Zhang; Daniel Ziemek; Kourosh Zarringhalam (BMC Bioinform., 2017)

SUBSTRA: Supervised Bayesian Patient Stratification. - Sahand Khakabimamaghani; Yogeshwar D. Kelkar; Bruno M. Grande; Ryan D. Morin; Martin Ester; Daniel Ziemek (Bioinform., 2019)

Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. - 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 (BMC Bioinform., 2020)