Yun S. Song - RankMe

47 papers A* 2A 2B 10C 3Journal 28Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Conditionally Site-Independent Neural Evolution of Antibody Sequences. CoRR Stephen Zhewen Lu, Aakarsh Vermani, Kohei Sanno, Jiarui Lu, Frederick A. Matsen IV, Milind Jagota, Yun S. Song
2025	B	`conf`	A Phylogenetic Approach to Genomic Language Modeling. RECOMB Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song
2025	J	`jnl`	A Phylogenetic Approach to Genomic Language Modeling. CoRR Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song
2025	J	`jnl`	Nucleotide context models outperform protein language models for predicting antibody affinity maturation. PLoS Comput. Biol. Mackenzie M. Johnson, Kevin Sung, Hugh K. Haddox, Ashni A. Vora, Tatsuya Araki, Gabriel D. Victora, Yun S. Song, Julia Fukuyama, Frederick A. Matsen IV
2025	B	`conf`	Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. RECOMB Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef
2024	B	`conf`	CELL-E: A Text-to-Image Transformer for Protein Image Prediction. RECOMB Emaad Khwaja, Yun S. Song, Bo Huang
2024	J	`jnl`	Genomic Language Models: Opportunities and Challenges. CoRR Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S. Song
2023	J	`jnl`	A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput. Biol. Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson
2021	—	`conf`	Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and Convolutional Pooling. MLBC Zhiqing Xu, Jinghao Wu, Yun S. Song, Radhakrishnan Mahadevan
2021	J	`jnl`	Parallelizing Contextual Linear Bandits. CoRR Jeffrey Chan, Aldo Pacchiano, Nilesh Tripuraneni, Yun S. Song, Peter L. Bartlett, Michael I. Jordan
2019	A*	`conf`	Evaluating Protein Transfer Learning with TAPE. NeurIPS Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song
2019	J	`jnl`	Evaluating Protein Transfer Learning with TAPE. CoRR Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song
2018	A*	`conf`	A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. NeurIPS Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song
2018	J	`jnl`	A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. CoRR Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song
2017	A	`conf`	Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). AISTATS Miaoyan Wang, Yun S. Song
2016	J	`jnl`	Deep Learning for Population Genetic Inference. PLoS Comput. Biol. Sara Sheehan, Yun S. Song
2016	J	`jnl`	Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. PLoS Comput. Biol. Shishi Luo, Jane A. Yu, Yun S. Song
2016	J	`jnl`	Orthogonal Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). CoRR Miaoyan Wang, Yun S. Song
2016	J	`jnl`	Prediction of ribosome footprint profile shapes from transcript sequences. Bioinform. Tzu-Yu Liu, Yun S. Song
2016	J	`jnl`	SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. Bioinform. Matthias Steinrücken, Ethan M. Jewett, Yun S. Song
2014	B	`conf`	Changepoint Analysis for Efficient Variant Calling. RECOMB Adam E. Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David A. Patterson, Bin Yu, Yun S. Song
2014	B	`conf`	Decoding Coalescent Hidden Markov Models in Linear Time. RECOMB Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song
2014	J	`jnl`	SMaSH: a benchmarking toolkit for human genome variant calling. Bioinform. Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Christopher Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael I. Jordan, David A. Patterson
2014	J	`jnl`	diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinform. Paula Tataru, Jasmine A. Nirody, Yun S. Song
2012	J	`jnl`	Blockwise HMM computation for large-scale population genomic inference. Bioinform. Joshua S. Paul, Yun S. Song
2012	J	`jnl`	Telescoper: Bioinform. Ma'ayan Bresler, Sara Sheehan, Andrew H. Chan, Yun S. Song
2011	J	`jnl`	On the Genealogy of Asexual Diploids. J. Comput. Biol. Fumei Lam, Charles H. Langley, Yun S. Song
2011	J	`jnl`	naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. J. Comput. Biol. Wei-Chun Kao, Yun S. Song
2010	A	`conf`	Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only). FPGA Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song
2010	B	`conf`	On the Genealogy of Asexual Diploids. RECOMB Fumei Lam, Charles H. Langley, Yun S. Song
2010	B	`conf`	SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. FPL Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song
2010	B	`conf`	naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. RECOMB Wei-Chun Kao, Yun S. Song
2009	J	`jnl`	Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinform. Junming Yin, Michael I. Jordan, Yun S. Song
2009	J	`jnl`	Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. Bioinform. Anand Bhaskar, Yun S. Song
2008	B	`conf`	Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. RECOMB Rune B. Lyngsø, Yun S. Song, Jotun Hein
2008	J	`jnl`	Efficient whole-genome association mapping using local phylogenies for unphased genotype data. Bioinform. Zhihong Ding, Thomas Mailund, Yun S. Song
2007	J	`jnl`	A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song
2007	J	`jnl`	Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. J. Comput. Biol. Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu
2006	J	`jnl`	A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. IEEE ACM Trans. Comput. Biol. Bioinform. Yun S. Song
2006	B	`conf`	Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. RECOMB Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu
2006	J	`jnl`	Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE ACM Trans. Comput. Biol. Bioinform. Yun S. Song, Rune B. Lyngsø, Jotun Hein
2005	C	`conf`	Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI Yun S. Song, Yufeng Wu, Dan Gusfield
2005	J	`jnl`	Constructing Minimal Ancestral Recombination Graphs. J. Comput. Biol. Yun S. Song, Jotun Hein
2005	—	`conf`	Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. ISMB (Supplement of Bioinformatics) Yun S. Song, Yufeng Wu, Dan Gusfield
2005	C	`conf`	Minimum Recombination Histories by Branch and Bound. WABI Rune B. Lyngsø, Yun S. Song, Jotun Hein
2003	J	`jnl`	An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. J. Comput. Biol. Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein
2003	C	`conf`	Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. WABI Yun S. Song, Jotun Hein