Yun S. Song
Professor
Develops AI and statistical methods for genomics and population genetics.
Yun S. Song's lab at UC Berkeley works on genomics & computational biology and learning theory & optimization. 36 papers since 2023, 8 at top venues, mostly PNAS and Cell. 10 PhD students. 46 alumni, most often to Google and Meta. Applications close .
At a glance
- papers, 2023–2026
- 9/ year
- at T1 venues
- 22%
- PhD students
- 10
- MS students
- 0
- alumni listed
- 46
Papers by yearfrom the lab homepage, 2023–2026
- 11 papers2026 · T1 2 · collecting
- 12 papers2025 · T1 2
- 4 papers2024 · T1 0
- 9 papers2023 · T1 4
T1 venuesOtherVenues: PNAS, Cell, Nature, Nature Communications, Nature Methods
Research focuspaper titles that use each topic's words
- Learning theory & optimization4 papers
- population2 papers
- Genomics & computational biology1 paper
- genetics1 paper
- statistical methods0 papers
Paper list
From the lab homepage.
202611 papers
- International Conference on Machine Learning (ICMLConditionally Site-Independent Neural Evolution of Antibody Sequences
- Systematic BiologyConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing (opens in a new tab)
- Nature Structural & Molecular BiologyHypervariable loop profiling decodes sequence determinants of antibody stability (opens in a new tab)
- eLifeInference of germinal center evolutionary dynamics via simulation-based deep learning (opens in a new tab)
- Nature BiotechnologyMapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression (opens in a new tab)
- Nature (T1)Predicting genome-wide functional constraints with GPN-Star (opens in a new tab)
- eLifePredicting the effect of CRISPR-Cas9-based epigenome editing (opens in a new tab)
- Cell (T1)Replaying germinal center evolution on a quantified affinity landscape (opens in a new tab)
- eLifeSeparating selection from mutation in antibody language models (opens in a new tab)
- eLifeThe Impact of Stability Considerations on Genetic Fine-Mapping (opens in a new tab)
- Genome ResearchTree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining (opens in a new tab)
202512 papers
- Nature BiotechnologyA DNA language model based on multispecies alignment predicts the effects of genome-wide variants (opens in a new tab)
- PNAS (T1)A general framework for branch length estimation in ancestral recombination graphs (opens in a new tab)
- RECOMBA phylogenetic approach to genomic language modeling (opens in a new tab)
- GeneticsA previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact (opens in a new tab)
- Molecular Biology and EvolutionA sitewise model of natural selection on individual antibodies via a transformer-encoder (opens in a new tab)
- Genes & DevelopmentActive telomere elongation by a subclass of cancer-associated POT1 mutations (opens in a new tab)
- PNAS (T1)Exact and efficient phylodynamic simulation from arbitrarily large populations (opens in a new tab)
- Trends in GeneticsGenomic Language Models: Opportunities and Challenges (opens in a new tab)
- Cell SystemsLearning antibody sequence constraints from allelic inclusion (opens in a new tab)
- PLoS Computational BiologyNucleotide context models outperform protein language models for predicting antibody affinity maturation (opens in a new tab)
- Nature GeneticsRobust and Accurate Bayesian Inference of Genome-Wide Genealogies for Hundreds of Genomes (opens in a new tab)
- Cell Reports MethodsRobust and adaptive non-parametric tests for detecting general distributional shifts in gene expression (opens in a new tab)
20244 papers
- Annals of Applied StatisticsA simple and flexible test of sample exchangeability with applications to statistical genomics (opens in a new tab)
- Human GeneticsAssessing predictions on fitness effects of missense variants in HMBS in CAGI6 (opens in a new tab)
- Proc. Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB , Lecture Notes in Computer ScienceCELL-E: A Text-to-Image Transformer for Protein Image Prediction (opens in a new tab)
- Advances in Neural Information Processing Systems (NeurIPSUltrafast classical phylogenetic method beats large protein language models on variant effect prediction
20239 papers
- PLoS Computational BiologyA fast machine-learning-guided primer design pipeline for selective whole genome amplification (opens in a new tab)
- Advances in Neural Information Processing Systems 36 (NeurIPSCELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer (opens in a new tab)
- Nature Methods (T1)CherryML: Scalable maximum likelihood estimation of phylogenetic models (opens in a new tab)
- Genome BiologyCross-protein transfer learning substantially improves disease variant prediction (opens in a new tab)
- PNAS (T1)DNA language models are powerful predictors of genome-wide variant effects (opens in a new tab)
- PLoS PathogensSelective whole-genome amplification reveals population genetics of directly from patient skin biopsies (opens in a new tab)
- Genome BiologyThe ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles (opens in a new tab)
- Nature Communications (T1)Tracing cancer evolution and heterogeneity using Hi-C (opens in a new tab)
- Cell (T1)Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation (opens in a new tab)
Where alumni went46 listed, 30% to industry
Industry 6Academia 14
Most often to
- Meta
- Optum Labs as Senior Machine Learning Scientist
Also to
- Stanford University
- Bakar Computational Biomedicine Institute as Fellow
- Carnegie Mellon University
Apply to UC BerkeleyFall 2027
UC Berkeley EECS Computer Science PhD
- Round
- Single round
- Opens
- —
- GRE
- not required
- English
- TOEFL/IELTS (non-English-country degrees)
- Fee
- See program page
Confirmed on the program page.
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