Daniel Ziemek

发表

SUBSTRA: Supervised Bayesian Patient Stratification

Martin Ester, Sahand Khakabimamaghani, Ryan D. Morin, 2019 .

GeneTopics - interpretation of gene sets via literature-driven topic models

Ahmed Enayetallah, Li Xi, Daniel Ziemek, 2013, BMC Systems Biology.

Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data

Mateusz Maciejewski, John Long, Jonathan R. Walsh, 2020, BMC Bioinformatics.

Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract)

Ahmed Enayetallah, Leonid Chindelevitch, Daniel Ziemek, 2011, RECOMB.

Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks

Ahmed Enayetallah, Kourosh Zarringhalam, Daniel Ziemek, 2014, Bioinform..

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data

Tianyu Kang, Wei Ding, Kourosh Zarringhalam, 2017, BMC Bioinformatics.

Molecular causes of transcriptional response: a Bayesian prior knowledge approach

Ahmed Enayetallah, Kourosh Zarringhalam, Alex Gutteridge, 2013, Bioinform..

Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes

Kourosh Zarringhalam, David Degras, Daniel Ziemek, 2018, Scientific Reports.

Causal reasoning on biological networks: interpreting transcriptional changes

Ahmed Enayetallah, Leonid Chindelevitch, Daniel Ziemek, 2012, Bioinform..

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

Chia-Ling Huang, Charles DeLisi, Justin Guinney, 2012, BMC Bioinformatics.

Assessing statistical significance in causal graphs

Bonnie Berger, Ahmed Enayetallah, Leonid Chindelevitch, 2012, BMC Bioinformatics.

Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks

Ping Chen, Kourosh Zarringhalam, Alex Gutteridge, 2016, BMC Bioinformatics.

Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data

Klaus-Robert Müller, Nico Görnitz, Daniel Ziemek, 2019, Scientific Reports.

Network-Driven Analysis Methods and their Application to Drug Discovery

Daniel Ziemek, Christoph Brockel, D. Ziemek, 2011, Handbook of Research on Computational and Systems Biology.

SUBSTRA: Supervised Bayesian Patient Stratification

Martin Ester, Sahand Khakabimamaghani, Ryan D. Morin, 2019, Bioinform..

Deep learning of representations for transcriptomics-based phenotype prediction

Mateusz Maciejewski, John Long, Jonathan R. Walsh, 2019, bioRxiv.

ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci

David Stacey, Karsten Suhre, Daniel Ziemek, 2018, Nucleic acids research.

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning

Daniel Ziemek, Alex Gutteridge, Alex Gutteridge, 2013, PloS one.

ProGeM: A framework for the prioritisation of candidate causal genes at molecular quantitative trait loci

David Stacey, Karsten Suhre, Daniel Ziemek, 2017, bioRxiv.

From hype to reality: data science enabling personalized medicine

Holger Fröhlich, Thomas Lengauer, Blaz Zupan, 2018, BMC Medicine.

Modeling the Mechanism of Action of a DGAT1 Inhibitor Using a Causal Reasoning Platform

Nigel Greene, Daniel Ziemek, Ranjit Randhawa, 2011, PloS one.