Comparative genome assembly. - Mihai Pop; Adam M. Phillippy; Arthur L. Delcher; Steven Salzberg (Briefings Bioinform., 2004)

Knowledge discovery using the sand spatial browser. - Hanan Samet; Adam M. Phillippy; Jagan Sankaranarayanan (DG.O, 2007)

Comprehensive DNA Signature Discovery and Validation. - Adam M. Phillippy; Jacquline A. Mason; Kunmi Ayanbule; Daniel D. Sommer; Elisa Taviani; Anwar Huq; Rita R. Colwell; Ivor T. Knight; Steven L. Salzberg (PLoS Comput. Biol., 2007)

Efficient oligonucleotide probe selection for pan-genomic tiling arrays. - Adam M. Phillippy; Xiangyu Deng; Wei Zhang 039; Steven L. Salzberg (BMC Bioinform., 2009)

Insignia: a DNA signature search web server for diagnostic assay development. - Adam M. Phillippy; Kunmi Ayanbule; Nathan J. Edwards; Steven L. Salzberg (Nucleic Acids Res., 2009)

Interactive metagenomic visualization in a Web browser. - Brian D. Ondov; Nicholas H. Bergman; Adam M. Phillippy (BMC Bioinform., 2011)

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. - Michael C. Schatz; Adam M. Phillippy; Daniel D. Sommer; Arthur L. Delcher; Daniela Puiu; Giuseppe Narzisi; Steven L. Salzberg; Mihai Pop (Briefings Bioinform., 2013)

Automated ensemble assembly and validation of microbial genomes. - Sergey Koren; Todd J. Treangen; Christopher Michael Hill; Mihai Pop; Adam M. Phillippy (BMC Bioinform., 2014)

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

MUMmer4: A fast and versatile genome alignment system. - Guillaume Marçais; Arthur L. Delcher; Adam M. Phillippy; Rachel Coston; Steven L. Salzberg; Aleksey V. Zimin (PLoS Comput. Biol., 2018)

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)

Integrating Hi-C links with assembly graphs for chromosome-scale assembly. - Jay Ghurye; Arang Rhie; Brian Walenz; Anthony D. Schmitt; Siddarth Selvaraj; Mihai Pop; Adam M. Phillippy; Sergey Koren (PLoS Comput. Biol., 2019)

Weighted minimizer sampling improves long read mapping. - Chirag Jain; Arang Rhie; Haowen Zhang; Claudia Chu; Brian Walenz; Sergey Koren; Adam M. Phillippy (Bioinform., 2020)

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. - Mitchell R. Vollger; Peter Kerpedjiev; Adam M. Phillippy; Evan E. Eichler (Bioinform., 2022)

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. - Bryce Kille; Erik Garrison; Todd J. Treangen; Adam M. Phillippy (Bioinform., 2023)