Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. - Yun S. Song; Jotun Hein (WABI, 2003)

An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. - Gerton Lunter; István Miklós; Yun S. Song; Jotun Hein (J. Comput. Biol., 2003)

Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. - Yun S. Song; Yufeng Wu; Dan Gusfield (ISMB (Supplement of Bioinformatics), 2005)

Minimum Recombination Histories by Branch and Bound. - Rune B. Lyngsø; Yun S. Song; Jotun Hein (WABI, 2005)

Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. - Yun S. Song; Yufeng Wu; Dan Gusfield (WABI, 2005)

Constructing Minimal Ancestral Recombination Graphs. - Yun S. Song; Jotun Hein (J. Comput. Biol., 2005)

A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. - Yun S. Song (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. - Yun S. Song; Rune B. Lyngsø; Jotun Hein (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. - Dan Gusfield; Vikas Bansal 001; Vineet Bafna; Yun S. Song (J. Comput. Biol., 2007)

Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. - Yun S. Song; Zhihong Ding; Dan Gusfield; Charles H. Langley; Yufeng Wu (J. Comput. Biol., 2007)

Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. - Rune B. Lyngsø; Yun S. Song; Jotun Hein (RECOMB, 2008)

Efficient whole-genome association mapping using local phylogenies for unphased genotype data. - Zhihong Ding; Thomas Mailund; Yun S. Song (Bioinform., 2008)

Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. - Anand Bhaskar; Yun S. Song (Bioinform., 2009)

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. - Junming Yin; Michael I. Jordan; Yun S. Song (Bioinform., 2009)

Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only). - Kristian Stevens; Henry Chen; Terry Filiba; Peter L. McMahon; Yun S. Song (FPGA, 2010)

SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. - Kristian Stevens; Henry Chen; Terry Filiba; Peter L. McMahon; Yun S. Song (FPL, 2010)

naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. - Wei-Chun Kao; Yun S. Song (J. Comput. Biol., 2011)

On the Genealogy of Asexual Diploids. - Fumei Lam; Charles H. Langley; Yun S. Song (J. Comput. Biol., 2011)

Telescoper: de novo assembly of highly repetitive regions. - Ma'ayan Bresler; Sara Sheehan; Andrew H. Chan; Yun S. Song (Bioinform., 2012)

Blockwise HMM computation for large-scale population genomic inference. - Joshua S. Paul; Yun S. Song (Bioinform., 2012)

Changepoint Analysis for Efficient Variant Calling. - Adam E. Bloniarz; Ameet Talwalkar; Jonathan Terhorst; Michael I. Jordan; David A. Patterson 001; Bin Yu 001; Yun S. Song (RECOMB, 2014)

Decoding Coalescent Hidden Markov Models in Linear Time. - Kelley Harris; Sara Sheehan; John A. Kamm; Yun S. Song (RECOMB, 2014)

SMaSH: a benchmarking toolkit for human genome variant calling. - Ameet Talwalkar; Jesse Liptrap; Julie Newcomb; Christopher Hartl; Jonathan Terhorst; Kristal Curtis; Ma'ayan Bresler; Yun S. Song; Michael I. Jordan; David A. Patterson 001 (Bioinform., 2014)

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. - Paula Tataru; Jasmine A. Nirody; Yun S. Song (Bioinform., 2014)

Prediction of ribosome footprint profile shapes from transcript sequences. - Tzu-Yu Liu; Yun S. Song (Bioinform., 2016)

SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. - Matthias Steinrücken; Ethan M. Jewett; Yun S. Song (Bioinform., 2016)

Orthogonal Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). - Miaoyan Wang; Yun S. Song (CoRR, 2016)

Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. - Shishi Luo; Jane A. Yu; Yun S. Song (PLoS Comput. Biol., 2016)

Deep Learning for Population Genetic Inference. - Sara Sheehan; Yun S. Song (PLoS Comput. Biol., 2016)

Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). - Miaoyan Wang; Yun S. Song (AISTATS, 2017)

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. - Jeffrey Chan; Valerio Perrone; Jeffrey P. Spence; Paul A. Jenkins; Sara Mathieson; Yun S. Song (NeurIPS, 2018)

Evaluating Protein Transfer Learning with TAPE. - Roshan Rao; Nicholas Bhattacharya; Neil Thomas; Yan Duan; Xi Chen 022; John F. Canny; Pieter Abbeel; Yun S. Song (NeurIPS, 2019)

Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and Convolutional Pooling. - Zhiqing Xu; Jinghao Wu; Yun S. Song; Radhakrishnan Mahadevan (MLBC, 2021)

Parallelizing Contextual Linear Bandits. - Jeffrey Chan; Aldo Pacchiano; Nilesh Tripuraneni; Yun S. Song; Peter L. Bartlett; Michael I. Jordan (CoRR, 2021)

A fast machine-learning-guided primer design pipeline for selective whole genome amplification. - Jane A. Dwivedi-Yu; Zachary J. Oppler; Matthew W. Mitchell; Yun S. Song; Dustin Brisson (PLoS Comput. Biol., 2023)

CELL-E: A Text-to-Image Transformer for Protein Image Prediction. - Emaad Khwaja; Yun S. Song; Bo Huang (RECOMB, 2024)

Genomic Language Models: Opportunities and Challenges. - Gonzalo Benegas; Chengzhong Ye; Carlos Albors; Jianan Canal Li; Yun S. Song (CoRR, 2024)

A Phylogenetic Approach to Genomic Language Modeling. - Carlos Albors; Jianan Canal Li; Gonzalo Benegas; Chengzhong Ye; Yun S. Song (RECOMB, 2025)

Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. - Sebastian Prillo; Kevin An; Wilson Wu; Ivan Kristanto; Matthew G. Jones; Yun S. Song; Nir Yosef (RECOMB, 2025)