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Nature Biotechnology|November 10, 2012
Interpreting noncoding genetic variation in complex traits and human diseaseLucas D Ward, Manolis KellisNucleic Acids Research|December 15, 2015
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and diseaseLucas D Ward, Manolis KellisGenome Biology|August 18, 2021
CoCoA-diff: counterfactual inference for single-cell gene expression analysisYongjin P Park, Manolis KellisMolecular Biology and Evolution|July 28, 2010
A Bayesian approach for fast and accurate gene tree reconstructionMatthew D Rasmussen, Manolis KellisGenome Research|November 9, 2007
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomesMatthew D Rasmussen, Manolis KellisJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|March 10, 2011
SubMAP: aligning metabolic pathways with subnetwork mappingsFerhat Ay, Manolis Kellis, Tamer KahveciBiorxiv : the Preprint Server for Biology|December 3, 2025
sc4D: spatio-temporal single-cell transcriptomics analysis through embedded optimal transport identifies joint glial response to Alzheimer's disease pathologyIshir Rao, Manolis Kellis, Yosuke TanigawaNature Communications|May 12, 2021
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomesIrwin Jungreis, Rachel Sealfon, Manolis KellisBiorxiv : the Preprint Server for Biology|June 25, 2020
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomesIrwin Jungreis, Rachel Sealfon, Manolis KellisPageof 40