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)

A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions. - Allan Peter Davis; Thomas C. Wiegers; Phoebe M. Roberts; Benjamin L. King; Jean M. Lay; Kelley Lennon-Hopkins; Daniela Sciaky; Robin J. Johnson; Heather Keating; Nigel Greene; Robert Hernandez; Kevin J. McConnell; et al. (Database J. Biol. Databases Curation, 2013)

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)

ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. - Dennis J. Pelletier; Thomas C. Wiegers; Ahmed Enayetallah; C. Kibbey; Mark Gosink; P. Koza-Taylor; Carolyn J. Mattingly; M. Lawton (Database J. Biol. Databases Curation, 2016)