Updates
Papers, talks, releases, and milestones — filter by type, search, or browse by year.
I’m honored to have been part of the SpliceAI2 team, and grateful to Kishore Jaganathan for the opportunity.
The preprint, A unified framework for quantitative splicing and transcript prediction, presents quantitative splice-site usage, splice-junction usage, and transcript prediction (also available as an Illumina PDF). The announcement, code and documentation, model weights, and precomputed predictions are available through the official release resources.
It was an honor to take part in the Telomere-to-Telomere Consortium’s Q100 project, whose complete diploid HG002 genome benchmark is published in Cell. My contribution was to the gene annotation, using LiftOn to help identify additional gene copies on the maternal and paternal haplotypes. Data and code are on GitHub.
I gave an invited seminar, “Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning,” at the Agricultural Biotechnology Research Center (ABRC), Academia Sinica, in Tainan, Taiwan. The slides are available.
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.” The slides, paper, code, documentation, and interactive lab are available.
The OpenSpliceAI version of record is published in eLife. The GitHub repository and documentation are available.
Our Shorkie preprint describing a fungal DNA language model for predicting RNA-seq coverage from DNA sequence in S. cerevisiae is available on bioRxiv. Explore the published checkpoints in-browser on Shorkie Lab.
My public dissertation talk, “Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning,” is scheduled for August 25, 2025. The defense slides and dissertation are available.
I defend my Ph.D. dissertation at Johns Hopkins University on August 25, 2025, advised by Steven Salzberg and Mihaela Pertea. The defense slides are also available.
The OpenSpliceAI paper is published in eLife. The GitHub repository and documentation are available.
The JHU Computer Science Department spotlights LiftOn in the feature article Solving the Bottleneck in Genome Biology.
I present an overview of protein language models and OpenCRISPR at the Hopkins Deep Learning in Genomics Study Group. The slides are available.
I deliver the Mark O. Robbins Prize recipient talk at HPC 2025. The slides are available.
OpenSpliceAI, Splam, and LiftOn appear in the JHU Open Source Programs Office catalog.
I release OpenSpliceAI, an open-source PyTorch framework for splice-site prediction. The preprint, GitHub repository, documentation, and slides are available.
LiftOn is published in Genome Research. The GitHub repository, documentation, slides, and ISMB 2024 talk are available.
Johns Hopkins publishes a feature article about Splam on the HUB, Computer Science, and Whiting School of Engineering websites.
I present Splam and OpenSpliceAI at Biological Data Science 2024. The poster is available.
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.
The JHU Computer Science Department publishes an article highlighting my receipt of the 2024 Mark O. Robbins Prize in High-Performance Computing.
The Splam splice-site prediction paper is published in Genome Biology.
I give an invited Google Deep Dive presentation on my genomics AI research. The internal presentation and public slides are available.
I present my Calico internship project in a one-hour showcase talk. The slides are available.
I receive the 2024 Mark O. Robbins Prize in High-Performance Computing and present the recipient talk at the 2025 ARCH Symposium.
I join the Kelley Lab at Calico for a summer 2024 internship in South San Francisco.
LiftOn v1.0.0 is released. The RECOMB-Seq talk slides, poster, GitHub repository, and documentation are available.
LiftOn, a genome annotation lift-over tool, is selected for a talk at RECOMB-Seq 2024.
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.
I present Splam at Genome Informatics 2023. The poster and v1.0.10 release are available.
My co-authored paper introduces EASTR, a tool for identifying and removing inaccurate spliced alignments, and is published in Nature Communications.
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.
The CHESS 3 paper describes a new human gene catalog and is published in Genome Biology.
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.
I release Splam v1.0.2, a splice-site prediction tool for improving spliced alignments. The GitHub repository, preprint, and documentation are available.
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.
Splam is accepted as a poster at MLCSB COSI, and Han1 is accepted as a highlight poster at HiTSeq COSI during ISMB/ECCB 2023. The Splam poster and Han1 poster are available.
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. The poster and slides are available.
I present Han1 at Biological Data Science 2022. The poster and one-minute lightning talk are available online.
The Wheeler Graph Toolkit, a software suite for Wheeler graph recognition and analysis, is available with a preprint on bioRxiv.
sangeranalyseR and RNASeqR are released as part of Bioconductor 3.14.
I join Steven Salzberg and Mihaela Pertea’s labs as a Computer Science Ph.D. student at Johns Hopkins University.
sangeranalyseR receives the Best Poster award at Bioc2021. The poster is available directly and through F1000Research.
Several Unity WebGL side projects are available, including Biobaby, Flappy Penguin, and Tank Fire.
My Genome Biology and Evolution paper introduces sangeranalyseR, an open-source R package for processing Sanger sequencing data, available through Bioconductor.
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