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

por Zarringhalam, Kourosh, Enayetallah, Ahmed, Reddy, Padmalatha, Ziemek, Daniel
Publicado 2014

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

por Zarringhalam, Kourosh, Degras, David, Brockel, Christoph, Ziemek, Daniel
Publicado 2018

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

por Wang, Vicky, Xi, Li, Enayetallah, Ahmed, Fauman, Eric, Ziemek, Daniel
Publicado 2013

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

por Kang, Tianyu, Ding, Wei, Zhang, Luoyan, Ziemek, Daniel, Zarringhalam, Kourosh
Publicado 2017

Assessing statistical significance in causal graphs

por Chindelevitch, Leonid, Loh, Po-Ru, Enayetallah, Ahmed, Berger, Bonnie, Ziemek, Daniel
Publicado 2012

What Is the Persistence to Methotrexate in Rheumatoid Arthritis, and Does Machine Learning Outperform Hypothesis‐Based Approaches to Its Prediction?

por Westerlind, Helga, Maciejewski, Mateusz, Frisell, Thomas, Jelinsky, Scott A, Ziemek, Daniel, Askling, Johan
Publicado 2021

Assessing the translatability of In vivo cardiotoxicity mechanisms to In vitro models using causal reasoning

por Enayetallah, Ahmed E, Puppala, Dinesh, Ziemek, Daniel, Fischer, James E, Kantesaria, Sheila, Pletcher, Mathew T
Publicado 2013

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

por Fakhry, Carl Tony, Choudhary, Parul, Gutteridge, Alex, Sidders, Ben, Chen, Ping, Ziemek, Daniel, Zarringhalam, Kourosh
Publicado 2016

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

por Huang, Chia-Ling, Lamb, John, Chindelevitch, Leonid, Kostrowicki, Jarek, Guinney, Justin, DeLisi, Charles, Ziemek, Daniel
Publicado 2012

Silencing of enzymes involved in ceramide biosynthesis causes distinct global alterations of lipid homeostasis and gene expression

por Ruangsiriluk, Wanida, Grosskurth, Shaun E., Ziemek, Daniel, Kuhn, Max, des Etages, Shelley G., Francone, Omar L.
Publicado 2012

Profiling of Gene Expression Biomarkers as a Classifier of Methotrexate Nonresponse in Patients With Rheumatoid Arthritis

por Plant, Darren, Maciejewski, Mateusz, Smith, Samantha, Nair, Nisha, Hyrich, Kimme, Ziemek, Daniel, Barton, Anne, Verstappen, Suzanne
Publicado 2019

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

por Mieth, Bettina, Hockley, James R. F., Görnitz, Nico, Vidovic, Marina M.-C., Müller, Klaus-Robert, Gutteridge, Alex, Ziemek, Daniel
Publicado 2019

Prediction of response of methotrexate in patients with rheumatoid arthritis using serum lipidomics

por Maciejewski, Mateusz, Sands, Caroline, Nair, Nisha, Ling, Stephanie, Verstappen, Suzanne, Hyrich, Kimme, Barton, Anne, Ziemek, Daniel, Lewis, Matthew R., Plant, Darren
Publicado 2021

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

por Stacey, David, Fauman, Eric B, Ziemek, Daniel, Sun, Benjamin B, Harshfield, Eric L, Wood, Angela M, Butterworth, Adam S, Suhre, Karsten, Paul, Dirk S
Publicado 2019

HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain

por Denk, Franziska, Huang, Wenlong, Sidders, Ben, Bithell, Angela, Crow, Megan, Grist, John, Sharma, Simone, Ziemek, Daniel, Rice, Andrew S.C., Buckley, Noel J., McMahon, Stephen B.
Publicado 2013

Early prediction of clinical response to anti-TNF treatment using multi-omics and machine learning in rheumatoid arthritis

por Yoosuf, Niyaz, Maciejewski, Mateusz, Ziemek, Daniel, Jelinsky, Scott A, Folkersen, Lasse, Müller, Malin, Sahlström, Peter, Vivar, Nancy, Catrina, Anca, Berg, Louise, Klareskog, Lars, Padyukov, Leonid, Brynedal, Boel
Publicado 2021

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

por Smith, Aaron M., Walsh, Jonathan R., Long, John, Davis, Craig B., Henstock, Peter, Hodge, Martin R., Maciejewski, Mateusz, Mu, Xinmeng Jasmine, Ra, Stephen, Zhao, Shanrong, Ziemek, Daniel, Fisher, Charles K.
Publicado 2020

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

por Gutteridge, Alex, Rukstalis, J. Michael, Ziemek, Daniel, Tié, Mark, Ji, Lin, Ramos-Zayas, Rebeca, Nardone, Nancy A., Norquay, Lisa D., Brenner, Martin B., Tang, Kim, McNeish, John D., Rowntree, Rebecca K.
Publicado 2013

Peripheral blood cellular dynamics of rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs

por Hedman, Åsa K., Winter, Eitan, Yoosuf, Niyaz, Benita, Yair, Berg, Louise, Brynedal, Boel, Folkersen, Lasse, Klareskog, Lars, Maciejewski, Mateusz, Sirota-Madi, Alexandra, Spector, Yael, Ziemek, Daniel, Padyukov, Leonid, Shen-Orr, Shai S., Jelinsky, Scott A.
Publicado 2023

GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci

por Jones, Amy V., Tilley, Mera, Gutteridge, Alex, Hyde, Craig, Nagle, Michael, Ziemek, Daniel, Gorman, Donal, Fauman, Eric B., Chen, Xing, Miller, Melissa R., Tian, Chao, Hu, Youna, Hinds, David A., Cox, Peter, Scollen, Serena
Publicado 2017