Speaking

Talks & posters

Conference talks, invited lectures, and posters on machine learning for genomics.

Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning
[Academia Sinica 2026] ABRC Invited SeminarAgricultural Biotechnology Research Center, Academia Sinica· Tainan, TaiwanInvited talk
Slides Event page
Related resourcesHan1 · WGT · LiftOn · HG002 benchmark · Splam · OpenSpliceAI · Shorkie
Han1
Paper Publication Code Data Research Post
WGT
Paper Publication Code Research Report
LiftOn
Paper Publication Code Docs Research Post Report
HG002 benchmark
Paper Publication Code Research Post
Splam
Paper Publication Code Docs Research Post
OpenSpliceAI
Paper Publication Code Docs Research Post Report
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model
[ProbGen 2026] Probabilistic Modeling in Genomics 2026University of California, Berkeley· Berkeley, CAInvited talk
Slides
Related resourcesShorkie
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning
Doctoral Dissertation Defense Seminar: "Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning"Johns Hopkins University· Baltimore, MDTalk
Slides Defense page
Related resourcesDissertation · Han1 · WGT · LiftOn · Splam · OpenSpliceAI · Shorkie
Dissertation
Paper Publication
Han1
Paper Publication Code Data Research Post
WGT
Paper Publication Code Research Report
LiftOn
Paper Publication Code Docs Research Post Report
Splam
Paper Publication Code Docs Research Post
OpenSpliceAI
Paper Publication Code Docs Research Post Report
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Teaching machines to learn biology: splice site prediction and gene expression prediction
[HPC 2025] JHU Symposium on High-Performance Computing 2025Johns Hopkins University· Baltimore, MDTalk
Slides
Related resourcesHan1 · LiftOn · Splam · OpenSpliceAI · Shorkie
Han1
Paper Publication Code Data Research Post
LiftOn
Paper Publication Code Docs Research Post Report
Splam
Paper Publication Code Docs Research Post
OpenSpliceAI
Paper Publication Code Docs Research Post Report
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Unifying ChIP-exo DNA-Binding and RNA-Seq Coverage Predictions with a Multi-Species Fungal Language Model
[JHU 2025] JHU Joint Biostats-Genomics Lab Meeting 2025Johns Hopkins University· Baltimore, MDTalk
Slides Video
Related resourcesShorkie
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
OpenSpliceAI and Splam: Enhancing Splice Site Prediction Across Species to Improve Transcriptome Assembly
[BioData 2024] Biological Data Science 2024Biological Data Science (BioData 2024)· Cold Spring Harbor, NYPoster
Poster
Improving ChIP-exo DNA-binding and gene expression predictions with a multi-species fungi language model
[Calico project showcase 2024] Calico summer internship talk 2024Calico Life Sciences· South San Francisco, CATalk
Slides
Related resourcesShorkie
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Computational methods to improve genome annotation, splice site prediction, and gene expression prediction
[Google Deep Dive 2024] Invited Google Deep Dive Talk 2024Google Health Deep Dive· Virtual & Mountain View, CAInvited talk
Slides
Related resourcesLiftOn · Splam · OpenSpliceAI · Shorkie
LiftOn
Paper Publication Code Docs Research Post Report
Splam
Paper Publication Code Docs Research Post
OpenSpliceAI
Paper Publication Code Docs Research Post Report
Shorkie
Paper Publication Code Docs Data Research Post Latest slides
Combining DNA and protein alignments to improve genome annotation with LiftOn
[ISMB 2024] Intelligent Systems for Molecular Biology 2024Intelligent Systems for Molecular Biology (ISMB 2024)· Montréal, CanadaTalk
Slides Video
Related resourcesLiftOn
LiftOn
Paper Publication Code Docs Research Post Report
Combining DNA and protein alignments to improve genome annotation with LiftOn
[ISMB 2024] Intelligent Systems for Molecular Biology 2024Intelligent Systems for Molecular Biology (ISMB 2024)· Montréal, CanadaPoster
Poster
Predicting Splice Sites in DNA Sequences with Sequence Models
[JHU 2024] JHU Joint Biostats-Genomics Lab Meeting 2024JHU Joint Biostats-Genomics Lab Meeting (JHU 2024)· Baltimore, MDTalk
Slides Video
Related resourcesSplam · OpenSpliceAI
Splam
Paper Publication Code Docs Research Post
OpenSpliceAI
Paper Publication Code Docs Research Post Report
Combining DNA and protein alignments to improve genome annotation with LiftOn
[RECOMB 2024] Research on Computational Molecular Biology 2024Research on Computational Molecular Biology (RECOMB 2024)· Boston, MAPoster
Poster
Combining DNA and protein alignments to improve genome annotation with LiftOn
[RECOMB-Seq 2024] Research on Computational Molecular Biology on Biological Sequence Analysis 2024Research in Computational Molecular Biology Conference on Biological Sequence Analysis (RECOMB-Seq 2024)· Cambridge, MATalk
Slides
Related resourcesLiftOn
LiftOn
Paper Publication Code Docs Research Post Report
Splam: a deep-learning-based splice site predictor that improves spliced alignments
[GI 2023] Genome Informatics 2023Genome Informatics (GI 2023)· Cold Spring Harbor, New YorkPoster
Poster
Splam: a deep-learning-based splice site predictor that improves spliced alignments
[ISMB/ECCB 2023] Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2023Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB 2023)· Lyon, FrancePoster
Poster
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
[ISMB/ECCB 2023] Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2023Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB 2023) — HiTSeq COSI highlight poster· Lyon, FrancePoster
Poster
WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
[RECOMB 2023] Research on Computational Molecular Biology 2023Research in Computational Molecular Biology Conference (RECOMB 2023)· Istanbul, TürkiyePoster
Poster
WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
[RECOMB-Seq 2023] Research on Computational Molecular Biology on Biological Sequence Analysis 2023Research in Computational Molecular Biology Conference on Biological Sequence Analysis (RECOMB-Seq 2023)· Istanbul, TürkiyeTalk
Slides Video
Related resourcesWGT
WGT
Paper Publication Code Research Report
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
[BDS 2022] Biological Data Science 2022Biological Data Science (BDS 2022)· Cold Spring Harbor, New YorkPoster
Poster Video
sangeranalyseR: simple and interactive processing of Sanger sequencing data in R
[Bioc 2021] Bioconductor Conference 2021Bioconductor Conference 2021 (Bioc 2021)· VirtualPoster
Poster
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
[ICIBM 2019] International Conference on Intelligent Biology and Medicine 2019International Conference on Intelligent Biology and Medicine (ICIBM 2019)· Columbus, OhioTalk
Slides
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
[NTUCGM 2018] Summer Research Competition 2018NTU Centers of Genomics and Precision Medicine (NTUCGM) Summer Research· Taipei, TaiwanTalk
[WCIT 2017] Exhibition on smart transportation with Taipei City Government
World Congress on Information Technology (WCIT 2017)· Taipei, TaiwanExhibition
Slides Video

Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning

Han1

WGT

LiftOn

HG002 benchmark

Splam

OpenSpliceAI

Shorkie

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

Shorkie

Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning

Dissertation

Han1

WGT

LiftOn

Splam

OpenSpliceAI

Shorkie

Teaching machines to learn biology: splice site prediction and gene expression prediction

Han1

LiftOn

Splam

OpenSpliceAI

Shorkie

Unifying ChIP-exo DNA-Binding and RNA-Seq Coverage Predictions with a Multi-Species Fungal Language Model

Shorkie

OpenSpliceAI and Splam: Enhancing Splice Site Prediction Across Species to Improve Transcriptome Assembly

Improving ChIP-exo DNA-binding and gene expression predictions with a multi-species fungi language model

Shorkie

Computational methods to improve genome annotation, splice site prediction, and gene expression prediction

LiftOn

Splam

OpenSpliceAI

Shorkie

Combining DNA and protein alignments to improve genome annotation with LiftOn

LiftOn

Combining DNA and protein alignments to improve genome annotation with LiftOn

Predicting Splice Sites in DNA Sequences with Sequence Models

Splam

OpenSpliceAI

Combining DNA and protein alignments to improve genome annotation with LiftOn

Combining DNA and protein alignments to improve genome annotation with LiftOn

LiftOn

Splam: a deep-learning-based splice site predictor that improves spliced alignments

Splam: a deep-learning-based splice site predictor that improves spliced alignments

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs

WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs

WGT

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

sangeranalyseR: simple and interactive processing of Sanger sequencing data in R

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

[WCIT 2017] Exhibition on smart transportation with Taipei City Government