# Daehwan Kim

> Daehwan Kim is a computational biologist and software engineer whose genome-alignment tools - TopHat, HISAT and HISAT2 - are cited more than 78,000 times and are used by researchers worldwide to read DNA and RNA data. A former Michael L. Rosenberg Assistant Professor in the Lyda Hill Department of Bioinformatics at UT Southwestern Medical Center, he co-founded Omphalos Lifesciences, where he invented L++, a high-level programming language meant to describe living systems the way C++ describes machines. His goal is a fully programmable, simulatable virtual cell.

- **Role:** Co-Founder and Co-CEO at Omphalos Lifesciences Inc
- **Organizations:** Omphalos Lifesciences Inc, Omphalos Korea Inc, UT Southwestern Medical Center (former)
- **Nationality:** South Korean
- **Education:** PhD, Computer Science (computational biology), University of Maryland
- **Known for:** Lead author of HISAT and HISAT2, graph-based genome aligners used across genomics, Co-developer of TopHat2 and widely used RNA-seq analysis protocols, More than 78,000 Google Scholar citations across his work

## Career timeline

- **2011-2013** — Co-developed TopHat2 and the RNA-seq analysis workflows with TopHat and Cufflinks
- **2015** — Published HISAT, a fast spliced aligner with low memory requirements
- **2016** — Co-authored the HISAT/StringTie/Ballgown transcript-level expression protocol
- **2019** — Published HISAT2 and HISAT-genotype (graph-based genome alignment) in Nature Biotechnology
- **2019-2021** — Michael L. Rosenberg Assistant Professor, Lyda Hill Department of Bioinformatics, UT Southwestern
- **2021** — Founded Omphalos Lifesciences; began building the Life Designer platform and L++ language
- **2023** — Presented programmable-biology work; L++ positioned as a high-level language for lifeforms

## Achievements

- Lead author of HISAT and HISAT2, graph-based genome aligners used across genomics
- Co-developer of TopHat2 and widely used RNA-seq analysis protocols
- More than 78,000 Google Scholar citations across his work
- Encoded 14.5 million genomic variants plus haplotypes into the HISAT2 graph FM-index
- Invented L++, a high-level programming language for describing lifeforms
- Built open-source tools (HISAT2, HISAT-genotype, Centrifuge, HISAT-3N, SeqWho) freely available to researchers

## Latest updates

- **2023-09** — Omphalos framed 'biology becomes programming,' positioning L++ as a high-level language for lifeforms co-developed with UT Southwestern's Kim Lab.
- **2022-10** — Omphalos Lifesciences associated with a Series A funding stage.

## Links

- Website: https://omphaloslifesci.com
- LinkedIn: http://www.linkedin.com/in/daehwan-kim-057555b
- GitHub: https://github.com/infphilo

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Profile page: https://yespress.io/daehwan-kim
Published by YesPress — https://yespress.io
Last updated: 2026-07-22