Adam Phillippy, PhD

Professor

aphillippyjhu.edu

Adam is a professor in the departments of Computer Science, Biomedical Engineering, and Genetic Medicine at the Johns Hopkins University. His lab develops efficient methods for analyzing DNA sequencing data, including tools for genome assembly, comparative genomics, clustering, forensics, and metagenomics. He is a co-founder of the Telomere-to-Telomere (T2T) Consortium, the Human Pangenome Reference Consortium, and the Vertebrate Genomes Project, which, together, seek to enable the complete and gapless assembly of human and vertebrate genomes. He is a recipient of the U.S. Presidential Early Career Award for Scientists and Engineers, the NIH Director’s Award, the Ilchun Molecular Medicine Award from the Korean Society for Biochemistry and Molecular Biology, and a distinguished alumni award from Loyola University Maryland. He was named by TIME magazine as one of the world’s most influential people of 2022 for his work on completing the human genome, and is currently working to understand the function, evolution, and clinical relevance of the approximately 10% of the human genome newly uncovered by the T2T project.

Software

Verkko

Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.

GQC (Genome Quality Checker)

GQC is a benchmarking tool for evaluating sequence reads and assemblies against a genome benchmark.

TTT

Trivial Tangle Traverser (TTT) is a tool developed to construct model sequences for the remaining gaps in the T2T assemblies and replace error-prone and labour-intensive manual graph curation step.

AniAnn's

AniAnn's is a tandem repeat annotation and masking tool which can infer repeat structure across whole chromosomes without sequence alignment.
News posts

Filling the holes in whole genomes

August 6, 2026

We're moving!

April 19, 2026

Choose your reference wisely

October 13, 2025

The formation and propagation of human Robertsonian chromosomes

September 24, 2025
Publications
Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere
Cell, August 6, 2026
Phillippy AM, Mao Y, Kang Y, Šikić M, Miga KH
Telomere-to-telomere genome assembly and a pangenome for the rat
Cell Genomics, August 6, 2026
Li K, Ciosek JL, Koren S, Phillippy AM, Zhu Y, Lauer WA, Brooks SY, Bouffard GG, Pickett BD, Dumont BL, Smith ML, Kalbfleisch TS, Doris PA