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2020 – today
- 2024
[c17]Emaad Khwaja, Yun S. Song, Bo Huang
:
CELL-E: A Text-to-Image Transformer for Protein Image Prediction. RECOMB 2024: 185-200- [i5]Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S. Song:
Genomic Language Models: Opportunities and Challenges. CoRR abs/2407.11435 (2024) - 2023
- [j20]Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson:
A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput. Biol. 19(4) (2023) - 2021
- [c16]Zhiqing Xu, Jinghao Wu, Yun S. Song, Radhakrishnan Mahadevan:
Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and Convolutional Pooling. MLBC 2021: 78-87 - [i4]Jeffrey Chan, Aldo Pacchiano, Nilesh Tripuraneni, Yun S. Song, Peter L. Bartlett, Michael I. Jordan:
Parallelizing Contextual Linear Bandits. CoRR abs/2105.10590 (2021)
2010 – 2019
- 2019
- [c15]Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song:
Evaluating Protein Transfer Learning with TAPE. NeurIPS 2019: 9686-9698 - [i3]Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song:
Evaluating Protein Transfer Learning with TAPE. CoRR abs/1906.08230 (2019) - 2018
- [c14]Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song:
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. NeurIPS 2018: 8603-8614 - [i2]Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song:
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. CoRR abs/1802.06153 (2018) - 2017
- [c13]Miaoyan Wang, Yun S. Song:
Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). AISTATS 2017: 614-622 - 2016
- [j19]Matthias Steinrücken, Ethan M. Jewett, Yun S. Song:
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. Bioinform. 32(5): 795-797 (2016) - [j18]Tzu-Yu Liu, Yun S. Song:
Prediction of ribosome footprint profile shapes from transcript sequences. Bioinform. 32(12): 183-191 (2016) - [j17]Sara Sheehan, Yun S. Song:
Deep Learning for Population Genetic Inference. PLoS Comput. Biol. 12(3) (2016) - [j16]Shishi Luo, Jane A. Yu, Yun S. Song:
Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. PLoS Comput. Biol. 12(9) (2016) - [i1]Miaoyan Wang, Yun S. Song:
Orthogonal Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). CoRR abs/1612.03839 (2016) - 2014
- [j15]Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Christopher Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael I. Jordan, David A. Patterson:
SMaSH: a benchmarking toolkit for human genome variant calling. Bioinform. 30(19): 2787-2795 (2014) - [j14]Paula Tataru, Jasmine A. Nirody, Yun S. Song:
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinform. 30(23): 3430-3431 (2014) - [c12]Adam E. Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David A. Patterson, Bin Yu, Yun S. Song:
Changepoint Analysis for Efficient Variant Calling. RECOMB 2014: 20-34 - [c11]Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song:
Decoding Coalescent Hidden Markov Models in Linear Time. RECOMB 2014: 100-114 - 2012
- [j13]Joshua S. Paul, Yun S. Song:
Blockwise HMM computation for large-scale population genomic inference. Bioinform. 28(15): 2008-2015 (2012) - [j12]Ma'ayan Bresler, Sara Sheehan, Andrew H. Chan, Yun S. Song:
Telescoper: de novo assembly of highly repetitive regions. Bioinform. 28(18): 311-317 (2012) - 2011
- [j11]Wei-Chun Kao, Yun S. Song:
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. J. Comput. Biol. 18(3): 365-377 (2011) - [j10]Fumei Lam, Charles H. Langley, Yun S. Song:
On the Genealogy of Asexual Diploids. J. Comput. Biol. 18(3): 415-428 (2011) - 2010
- [c10]Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song:
Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only). FPGA 2010: 284 - [c9]Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song:
SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. FPL 2010: 442-447 - [c8]Wei-Chun Kao, Yun S. Song:
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. RECOMB 2010: 233-247 - [c7]Fumei Lam, Charles H. Langley, Yun S. Song:
On the Genealogy of Asexual Diploids. RECOMB 2010: 325-340
2000 – 2009
- 2009
- [j9]Anand Bhaskar, Yun S. Song:
Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. Bioinform. 25(12) (2009) - [j8]Junming Yin, Michael I. Jordan, Yun S. Song:
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinform. 25(12) (2009) - 2008
- [j7]Zhihong Ding, Thomas Mailund, Yun S. Song:
Efficient whole-genome association mapping using local phylogenies for unphased genotype data. Bioinform. 24(19): 2215-2221 (2008) - [c6]Rune B. Lyngsø, Yun S. Song, Jotun Hein:
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. RECOMB 2008: 463-477 - 2007
- [j6]Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song:
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14(10): 1247-1272 (2007) - [j5]Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu:
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. J. Comput. Biol. 14(10): 1273-1286 (2007) - 2006
- [j4]Yun S. Song:
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 186-191 (2006) - [j3]Yun S. Song, Rune B. Lyngsø, Jotun Hein:
Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE ACM Trans. Comput. Biol. Bioinform. 3(3): 239-251 (2006) - [c5]Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu:
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. RECOMB 2006: 231-245 - 2005
- [j2]Yun S. Song, Jotun Hein:
Constructing Minimal Ancestral Recombination Graphs. J. Comput. Biol. 12(2): 147-169 (2005) - [c4]Yun S. Song, Yufeng Wu, Dan Gusfield:
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. ISMB (Supplement of Bioinformatics) 2005: 413-422 - [c3]Yun S. Song, Yufeng Wu, Dan Gusfield:
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI 2005: 152-164 - [c2]Rune B. Lyngsø, Yun S. Song, Jotun Hein:
Minimum Recombination Histories by Branch and Bound. WABI 2005: 239-250 - 2003
- [j1]Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein:
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. J. Comput. Biol. 10(6): 869-889 (2003) - [c1]Yun S. Song, Jotun Hein:
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. WABI 2003: 287-302
Coauthor Index
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