Adam M. Phillippy, Ph.D.

Director and Senior Investigator

Center for Genomics and Data Science Research

Head

Genome Informatics Section

Education

B.S. Loyola University Maryland

M.S. University of Maryland, College Park

Ph.D. University of Maryland, College Park

Contact Info

BG 49 RM 4A22
49 CONVENT DR
BETHESDA MD 20892

Biography

Dr. Adam Phillippy is the director of the Center for Genomics and Data Science research and head of the Genome Informatics Section at the National Human Genome Research Institute. His lab develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. He is a pioneer of single-molecule sequencing for the reconstruction of complete genomes and is best known for his work on completing the human genome from “telomere to telomere”.

As a bioinformatician who bridges the fields of computer science and genomics, Dr. Phillippy has developed numerous widely-used tools for genome assembly, comparative genomics, microbial forensics, and metagenomics. Early in his career at The Institute for Genomic Research, he developed algorithms for whole-genome alignment that were used by the FBI to trace the origin of the 2001 anthrax attacks. After completing his Ph.D. in 2010, he founded a bioinformatics group at the National Bioforensic Analysis Center and pioneered the use of single-molecule sequencing for the reconstruction of complete microbial genomes. In 2015, he joined NHGRI and shifted his focus to human and vertebrate genomics. Since then, his group has assembled hundreds of reference genomes for humans, animals, and plants, including important endangered and agricultural species. In 2022, his team published the first truly complete sequence of a human genome, revealing over 200 million bases of additional sequence and enabling new studies of genomic function and disease.

Dr. Phillippy received his B.S. in computer science from Loyola University Maryland under the advising of Dr. Arthur Delcher and his M.S. and Ph.D. in computer science from the University of Maryland with Dr. Steven Salzberg. 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.

Scientific Summary

The Genome Informatics Section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. As one example, high-quality reference genomes form a fundamental basis of all genomics research, but the construction of these references, known as genome sequencing and assembly, is an error-prone process that can affect the accuracy of all downstream analyses. The section aims to improve such foundational processes and translate emerging genomic technologies into practice.

Bioinformatics has a long history of bridging fields, and the incredible growth of genomics has been inextricably linked to advances in algorithms and computing. Recognizing this, the section specializes in the development of methods for new genomic technologies and seeks to foster open and interdisciplinary collaboration between the computational, biological, and medical sciences for the advancement of global health. Members of the section are at the forefront of these fields and have made key contributions to the development of DNA sequencing and analysis technologies.

Another major focus of the section is the development of genomic resources such as the human reference genome. From its initial release in 2000 through 2022, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing this remaining 8% of the genome, the section assembled the first truly complete sequence of a human genome in 2022, unlocking all regions of the genome to variational and functional studies for the first time. However, this complete genome represents only a single haplotype and does not capture the full diversity of human genomes. This limitation can affect the accuracy of all genomic analyses, especially for underrepresented variants and populations. For the benefits of personalized genomics to be inclusive of everyone, the section is now working towards extending the human reference to a pangenome that is more representative of genomic variation.

Lastly, characterizing genomic variation and innovation across all species, not just human, is critical for fully understanding and reverse-engineering life’s genomic code. The section’s development of new sequencing and assembly technologies has resulted in a flood of complete genomes from across the tree of life, which are being used to study the functional, comparative, and population genomics of multiple species at unprecedented resolution. Even for well-studied species, the de novo assembly of multiple individuals can reveal complex structural variation missed by re-sequencing approaches. Our current projects include completing the genomes of non-human primates to better understand our own evolution; agricultural species to improve their health and resiliency; and endangered species to create an indelible record of the world’s genomic biodiversity.

Scientific Summary

The Genome Informatics Section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. As one example, high-quality reference genomes form a fundamental basis of all genomics research, but the construction of these references, known as genome sequencing and assembly, is an error-prone process that can affect the accuracy of all downstream analyses. The section aims to improve such foundational processes and translate emerging genomic technologies into practice.
Bioinformatics has a long history of bridging fields, and the incredible growth of genomics has been inextricably linked to advances in algorithms and computing. Recognizing this, the section specializes in the development of methods for new genomic technologies and seeks to foster open and interdisciplinary collaboration between the computational, biological, and medical sciences for the advancement of global health. Members of the section are at the forefront of these fields and have made key contributions to the development of DNA sequencing and analysis technologies.
Another major focus of the section is the development of genomic resources such as the human reference genome. From its initial release in 2000 through 2022, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing this remaining 8% of the genome, the section assembled the first truly complete sequence of a human genome in 2022, unlocking all regions of the genome to variational and functional studies for the first time. However, this complete genome represents only a single haplotype and does not capture the full diversity of human genomes. This limitation can affect the accuracy of all genomic analyses, especially for underrepresented variants and populations. For the benefits of personalized genomics to be inclusive of everyone, the section is now working towards extending the human reference to a pangenome that is more representative of genomic variation.
Lastly, characterizing genomic variation and innovation across all species, not just human, is critical for fully understanding and reverse-engineering life’s genomic code. The section’s development of new sequencing and assembly technologies has resulted in a flood of complete genomes from across the tree of life, which are being used to study the functional, comparative, and population genomics of multiple species at unprecedented resolution. Even for well-studied species, the de novo assembly of multiple individuals can reveal complex structural variation missed by re-sequencing approaches. Our current projects include completing the genomes of non-human primates to better understand our own evolution; agricultural species to improve their health and resiliency; and endangered species to create an indelible record of the world’s genomic biodiversity.

Publications

Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol. 2023 Feb 16. doi: 10.1038/s41587-023-01662-6. Epub ahead of print.

Nurk S, Koren S, Rhie A, Rautiainen M, et. al. The complete sequence of a human genome. Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31.

Rhie A, McCarthy SA, Fedrigo O, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28.

Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132.

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12.

Publications

Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol. 2023 Feb 16. doi: 10.1038/s41587-023-01662-6. Epub ahead of print.
Nurk S, Koren S, Rhie A, Rautiainen M, et. al. The complete sequence of a human genome. Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31.
Rhie A, McCarthy SA, Fedrigo O, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28.
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12.