News

1. Feb Talk

   I give an invited talk in the Machine Learning in Genomics session at ProbGen 2026 at UC Berkeley. The talk is titled “Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.”

2. Oct Publication

   The OpenSpliceAI version of record is published in eLife. The GitHub repository and documentation are available.

3. Sep Publication

   Our Shorkie preprint describing a fungal DNA language model for predicting RNA-seq coverage from DNA sequence in S. cerevisiae is available on bioRxiv.

4. Aug Milestone

   I join Illumina AI Lab as a Senior Deep Learning Scientist & Engineer.

5. Aug Talk

   My public dissertation talk, “Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning,” is scheduled for August 25, 2025.

6. Aug Other

   I defend my Ph.D. dissertation at Johns Hopkins University on August 25, 2025, advised by Steven Salzberg and Mihaela Pertea.

7. Jul Publication

   The OpenSpliceAI paper is published in eLife. The GitHub repository and documentation are available.

8. Jun Other

   The JHU Computer Science Department spotlights LiftOn in the feature article Solving the Bottleneck in Genome Biology.

9. Apr Talk

   I present an overview of protein language models and OpenCRISPR at the Hopkins Deep Learning in Genomics Study Group. The slides are available.

10. Apr Other

    OpenSpliceAI, Splam, and LiftOn appear in the JHU Open Source Programs Office catalog.

11. Apr Award

    I deliver the Mark O. Robbins Prize recipient talk at HPC 2025. The slides are available.

12. Mar Publication

    I release OpenSpliceAI, an open-source PyTorch framework for splice-site prediction. The preprint, GitHub repository, documentation, and slides are available.

13. Feb Publication

    LiftOn is published in Genome Research. The GitHub repository, documentation, slides, and ISMB 2024 talk are available.

14. Jan Milestone

    I present work on a multi-species fungal DNA language model for ChIP-exo and RNA-seq coverage prediction at a JHU joint lab meeting. The video and slides are available.

15. Dec Publication

    Johns Hopkins publishes a feature article about Splam on the HUB, Computer Science, and Whiting School of Engineering websites.

16. Oct Talk

    I present Splam and OpenSpliceAI at Biological Data Science 2024.

17. Oct Talk

    I co-found the Deep Learning in Genomics Study Group at Hopkins with Mahler Revsine. Meeting materials are available in the study group repository, including my opening talk slides.

18. Sep Award

    The JHU Computer Science Department publishes an article highlighting my receipt of the 2024 Mark O. Robbins Prize in High-Performance Computing.

19. Sep Publication

    The Splam splice-site prediction paper is published in Genome Biology.

20. Aug Talk

    I give an invited Google Deep Dive presentation on my genomics AI research. The internal presentation and public slides are available.

21. Aug Talk

    I present my Calico internship project in a one-hour showcase talk. The slides are available.

22. Jul Release

    The video and slides are available for my ISMB 2024 talk, “Combining DNA and protein alignments to improve genome annotation with LiftOn.”

23. Jun Award

    I receive the 2024 Mark O. Robbins Prize in High-Performance Computing and present the recipient talk at the 2025 ARCH Symposium.

24. May Release

    The video and slides are available for my talk, “Predicting splice sites in DNA sequences with sequence models.”

25. May Milestone

    I join the Kelley Lab at Calico for a summer 2024 internship in South San Francisco.

26. May Publication

    LiftOn is selected for a 20-minute talk in the ISMB 2024 General Computational COSI track. The preprint is available.

27. Apr Release

    LiftOn v1.0.0 is released. The RECOMB-Seq talk slides, poster, GitHub repository, and documentation are available.

28. Mar Publication

    LiftOn, a genome annotation lift-over tool, is selected for a talk at RECOMB-Seq 2024.

29. Jan Award

    My Wheeler graph collaboration with Berkeley EECS is highlighted by the JHU Whiting School of Engineering and the JHU Computer Science Department, featuring work with Pei-Wei Chen, Ben Langmead, and Sanjit Seshia.

30. Dec Release

    I present Splam at Genome Informatics 2023. The v1.0.10 release is available on GitHub.

31. Nov Publication

    My co-authored paper introduces EASTR, a tool for identifying and removing inaccurate spliced alignments, and is published in Nature Communications.

32. Nov Other

    I complete my Graduate Board Oral exam at Johns Hopkins University, with Steven Salzberg, Mihaela Pertea, Ben Langmead, Liliana Florea, and Winston Timp serving on the committee.

33. Oct Publication

    The CHESS 3 paper describes a new human gene catalog and is published in Genome Biology.

34. Aug Publication

    My iScience paper describes fast Wheeler graph recognition using renaming heuristics and an SMT solver. The paper, GitHub repository, and RECOMB-Seq talk are available.

35. Jul Publication

    I release Splam v1.0.2, a splice-site prediction tool for improving spliced alignments. The GitHub repository, preprint, and documentation are available.

36. Jun Publication

    My co-first-author paper on protein interactome analysis from co-elution data is published in Briefings in Bioinformatics, in collaboration with the HK Tsai Lab and Jun-Yi Leu Lab. The paper is available online.

37. May Award

    Splam is accepted as a poster at MLCSB COSI, and Han1 is accepted as a highlight poster at HiTSeq COSI during ISMB/ECCB 2023.

38. Mar Publication

    The WGT paper is accepted to RECOMB-Seq as a proceedings-track paper and to RECOMB as a poster, in collaboration with the Langmead Lab and Seshia Lab.

39. Jan Publication

    My paper in G3: Genes, Genomes, Genetics describes Han1, the first gap-free assembly of a Han Chinese genome. The paper is available online.

40. Nov Talk

    I present Han1 at Biological Data Science 2022. The poster and one-minute lightning talk are available online.

41. Oct Publication

    The Wheeler Graph Toolkit, a software suite for Wheeler graph recognition and analysis, is available with a preprint on bioRxiv.

42. Aug Publication

    The Han1 preprint describes the first gapless, fully annotated Chinese Han genome and is available on bioRxiv.

43. Oct Release

    sangeranalyseR and RNASeqR are released as part of Bioconductor 3.14.

44. Sep Milestone

    I join Steven Salzberg and Mihaela Pertea’s labs as a Computer Science Ph.D. student at Johns Hopkins University.

45. Aug Award

    sangeranalyseR receives the Best Poster award at Bioc2021. The poster is available through F1000Research.

46. Jun Other

    Several Unity WebGL side projects are available, including Biobaby, Flappy Penguin, and Tank Fire.

47. Mar Publication

    My Genome Biology and Evolution paper introduces sangeranalyseR, an open-source R package for processing Sanger sequencing data, available through Bioconductor.