Prediction of transcription Factor Binding Sites Using genetical genomics Methods. - Peter von Rohr; Markus T. Friberg; Haja N. Kadarmideen (J. Bioinform. Comput. Biol., 2007)

PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. - Nathan S. Watson-Haigh; Haja N. Kadarmideen; Antonio Reverter (Bioinform., 2010)

FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. - Stephen J. Goodswen; Cedric Gondro; Nathan S. Watson-Haigh; Haja N. Kadarmideen (BMC Bioinform., 2010)

Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data. - Lisette J. A. Kogelman; Haja N. Kadarmideen (BMC Syst. Biol., 2014)

WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases. - Victor A. O. Carmelo; Lisette J. A. Kogelman; Majbritt Busk Madsen; Haja N. Kadarmideen (BMC Bioinform., 2018)

Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency. - S. M. Salleh; Gianluca Mazzoni; Peter Løvendahl; Haja N. Kadarmideen (BMC Bioinform., 2018)

Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach. - Pedro Morell Miranda; Francesca Bertolini; Haja N. Kadarmideen (F1000Research, 2018)

GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis. - Xiao Wang; Dan Hao 002; Haja N. Kadarmideen (J. Comput. Biol., 2021)