HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes. - Alexander T. Dilthey; Loukas Moutsianas; Stephen Leslie; Gil McVean (Bioinform., 2011)

Multi-Population Classical HLA Type Imputation. - Alexander T. Dilthey; Stephen Leslie; Loukas Moutsianas; Judong Shen; Charles Cox; Matthew R. Nelson; Gil McVean (PLoS Comput. Biol., 2013)

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs. - Alexander T. Dilthey; Pierre-Antoine Gourraud; Alexander J. Mentzer; Nezih Cereb; Zamin Iqbal; Gil McVean (PLoS Comput. Biol., 2016)

A fast adaptive algorithm for computing whole-genome homology maps. - Chirag Jain; Sergey Koren; Alexander T. Dilthey; Adam M. Phillippy; Srinivas Aluru (Bioinform., 2018)

NovoGraph: Genome graph construction from multiple long-read de novo assemblies. - Evan Biederstedt; Jeffrey C. Oliver; Nancy F. Hansen; Aarti Jajoo; Nathan A. Dunn; Andrew Olson; Ben Busby; Alexander T. Dilthey (F1000Research, 2018)

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. - Chirag Jain; Alexander T. Dilthey; Sergey Koren; Srinivas Aluru; Adam M. Phillippy (J. Comput. Biol., 2018)

Accelerating Sequence Alignment to Graphs. - Chirag Jain; Sanchit Misra; Haowen Zhang; Alexander T. Dilthey; Srinivas Aluru (IPDPS, 2019)

Validating Paired-End Read Alignments in Sequence Graphs. - Chirag Jain; Haowen Zhang; Alexander T. Dilthey; Srinivas Aluru (WABI, 2019)

HLA*LA - HLA typing from linearly projected graph alignments. - Alexander T. Dilthey; Alexander J. Mentzer; Raphael Carapito; Clare Cutland; Nezih Cereb; Shabir A Madhi; Arang Rhie; Sergey Koren; Seiamak Bahram; Gil McVean; Adam M. Phillippy (Bioinform., 2019)

Integer Programming Framework for Pangenome-Based Genome Inference. - Ghanshyam Chandra; Md. Helal Hossen; Stephan Scholz; Alexander T. Dilthey; Daniel Gibney; Chirag Jain (RECOMB, 2025)