Sul Treno© 2008 Yun S. Song. All rights reserved.
Lecture Notes
Recent preprints online
- Deng, Y., Nielsen, R.†, Song, Y.S.†
A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact. †Corresponding authors.
[ Preprint ] - Prillo, S., An, K., Wu, W., Kristanto, I., Jones, M.G., Song, Y.S.†, Yosef, N.†
Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining. †Corresponding authors.
[ Preprint ] - Benegas, G.*, Ye, C.*, Albors, C.*, Li, J.C.*, Song, Y.S.
Genomic Language Models: Opportunities and Challenges. *These authors contributed equally to this work.
[ Preprint ] - Deng, Y., Nielsen, R.†, Song, Y.S.†
Robust and accurate Bayesian inference of genome-wide genealogies for large samples. †Corresponding authors.
[ Preprint ] - Celentano, M., DeWitt, W.S., Prillo, S., Song, Y.S.
Exact and efficient phylodynamic simulation from arbitrarily large populations.
[ Preprint ] - Aw, A.J., McRae, J., Rahmani, E.†, Song, Y.S.†
Highly parameterized polygenic scores tend to overfit to population stratification via random effects. †Corresponding authors.
[ Preprint ] - Prillo, S., Ravoor, A., Yosef, N.†, Song, Y.S.†
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data. †Corresponding authors.
[ Preprint ] - Benegas, G., Albors, C., Aw, A.J., Ye, C., Song, Y.S.
GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction.
[ Preprint ] [ Software ] - Hartoularos, G.C., Si, Y., Zhang, F.C., Kathail, P., Lee, D., Ogorodnikov, A., Sun, Y., Song, Y.S., Kang, H.M., Ye, C.J.
Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response.
[ Preprint ] - Thomas, N.*, Agarwala, A.*, Belanger, D., Song, Y.S.†, Colwell, L.J.†
Tuned Fitness Landscapes for Benchmarking Model-Guided Protein Design.
*These authors contributed equally to this work.
†Corresponding authors.
[ Preprint ] - Fung, A.*, Koehl, A.*, Jagota, M., and Song, Y.S.
The Impact of Protein Dynamics on Residue-Residue Coevolution and Contact Prediction.
[ Preprint ] - Erdmann-Pham, D.D., Terhorst, J., and Song, Y.S.
Exact and arbitrarily accurate non-parametric two-sample tests based on rank spacings.
[ Preprint ] - Chan, J., Pacchiano, A., Tripuraneni, N., Song, Y.S., Bartlett, P., Jordan, M.I.
Parallelizing Contextual Linear Bandits.
[ Preprint ] - Mowery, C.T., Marson, A., Song, Y.S., Ye, C.J.
Improved COVID-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays using Machine Learning.
[ Preprint ] [ Rapid Reviews: Covid-19 ]
Publications
- Prillo, S.*, Wu, W.*, Song, Y.S. Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction. Advances in Neural Information Processing Systems (NeurIPS 2024), in press.
- Zhang J, Kinch L, Katsonis P, Lichtarge O, Jagota M, Song YS, Sun Y, Shen Y, Kuru N, Dereli O, Adebali O, Alladin MA, Pal D, Capriotti E, Turina MP, Savojardo C, Martelli PL, Babbi G, Casadio R Hu Z, Pucci F, Rooman M, Cia G, Tsishyn M, Strokach A, van Loggerenberg W, Roth FP, Radivojac P, Brenner SE, Cong Q, Grishin NV.
Assessing predictions on fitness effects of missense variants in HMBS in CAGI6.
Human Genetics (2024).
[ Journal ] - Khwaja, E., Song, Y.S., Huang, B.
CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction.
Proc. 28th Annual Intl. Conf. on Research in
Computational Molecular Biology (RECOMB 2024), Lecture Notes in Computer Science, Vol. 14758 (2024) 185-200
[ Proceedings ] [ Preprint ] - Aw, A.J., Spence, J.P., Song, Y.S.
A simple and flexible test of sample exchangeability with applications to statistical genomics.
Annals of Applied Statistics, Vol. 18, No. 1 (2024) 858-881.
[ Journal ] [ Preprint ] [ Software ] - Batra, S.S.*, Cabrera, A.*, Spence, J.P.*, Hilton, I.†, Song, Y.S.†
Predicting the effect of CRISPR-Cas9-based epigenome editing. eLife 12:RP92991 (2023). (Under revision)
*These authors contributed equally to this work.
†Corresponding authors.
[ Journal ] [ Preprint ] - Erdmann-Pham, D.D.*, Batra, S.S.*, Turkalo, T.K., Durbin, J., Blanchette, M., Yeh, I., Shain, H., Bastian, B., Song, Y.S.†, Rokhsar, D.S.†, Hockemeyer, D.†
Tracing cancer evolution and heterogeneity using Hi-C.
Nature Communications, 14, Article Number: 7111 (2023).
*These authors contributed equally to this work.
†Corresponding authors.
[ Journal ] [ Preprint ] [ Software ] - Khwaja, E., Song, Y.S., Agarunov, A., Huang, B.
CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer.
Advances in Neural Information Processing Systems 36 (NeurIPS 2023).
[ Proceedings ] [ Preprint ] [ Software ] - Benegas, G., Batra, S.S., and Song, Y.S.
DNA language models are powerful predictors of genome-wide variant effects.
PNAS, Vol. 120, No. 44 (2023) e2311219120.
[ Journal ] [ Preprint ] [ Software ] - Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N. and Song, Y.S.
Cross-protein transfer learning substantially improves disease variant prediction. Genome Biology, 24, Article Number: 182 (2023). *These authors contributed equally to this work.
[ Journal ] [ Preprint ] [ Software and data ] - Prillo, S., Deng, Y., Boyeau, P., Li, X., Chen, P.-Y., Song, Y.S.
CherryML: Scalable maximum likelihood estimation of phylogenetic models. Nature Methods, 20 (2023) 1232-1236.
[ Journal ] [ Preprint ] [ Software ] - Aw, A., Jin, C., Ioannidis, N.†, Song, Y.S.†
The Impact of Stability Considerations on Genetic Fine-Mapping.
eLife 12:RP88039 (2023). (Under revision)
†Corresponding authors.
[ Journal ] [ Preprint ] - Dwivedi-Yu, J.A.*, Oppler, Z.J.*, Mitchell, M.W., Song, Y.S.†, Brisson, D.†
A fast machine-learning-guided primer design pipeline for selective whole genome amplification.
PLoS Computational Biology, Vol. 19, No. 4 (2023) e1010137.
*These authors contributed equally to this work.
†Corresponding authors.
[ Journal ] [ Preprint ] [ Software ] - Schreiber, J.M. et al.
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Genome Biology, 24, Article number: 79 (2023).
[ Journal ] [ Preprint ] - Pilling, O.A. et al.
Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.
PLoS Pathogens, Vol. 19, No. 3 (2023) e1011230.
[ Journal ] [ Preprint ] -
Fan, S.*, Spence, J.P.*, Feng, Y., Hansen, M.E.B., Terhorst, J., Beltrame, M.H., Ranciaro, A., Hirbo, J., Beggs, W., Thomas, N., Nyambo, T., Mpoloka, S.W., Mokone, G.G., Njamnshi, A., Folkunang, C., Meskel, D.W., Belay, G., Song, Y.S., Tishkoff, S.A.
Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation,
Cell, Vol. 186, Issue 5, (2023) 923-939.e14.
Cover article.
[ Journal ] [ Cover ] - Koleske, M.L., McInnes, G., Brown, J.E.H., Thomas, N., Hutchinson, K., Chin, M.Y., Koehl, A., Arkin, M.R., Schlessinger, A., Gallagher, R.C., Song, Y.S., Altman, R.B., Giacomini, K.M.
Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency,
PNAS, Vol. 119, No. 46, (2022) e2210247119.
[ Journal ] - Benegas, G., Fischer, J., Song., Y.S.
Robust and annotation-free analysis of alternative splicing across diverse cell types in mice,
eLife 11:e73520 (2022).
[ Journal ] [ Preprint ] [ Software: scQuint ] [ Analysis Results ] - Koehl, A.*, Jagota, M.*, Erdmann-Pham, D.D.*, Fung, A., Song, Y.S.
Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions.
Pacific Symposium on Biocomputing (PSB), 27 (2022) 22-33.
[ Proceedings ] [ Preprint ] - Bhattacharya, N., Thomas, N., Rao, R., Dauparas, J., Koo, P., Baker, D., Song, Y.S., Ovchinnikov, S.
Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention.
Pacific Symposium on Biocomputing (PSB), 27 (2022) 34-45.
[ Proceedings ] [ Preprint ] - Xu, Z., Wu, J., Song, Y.S., Mahadevan, R.
Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and
Convolutional Pooling.
Proceedings of the 16th Machine Learning in Computational Biology (MLCB) meeting, PMLR, 165 (2022) 78-87.
[ Proceedings ] - van der Wijst, M.G.P., et al.
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.
Science Translational Medicine, Vol. 13, eabh2624 (2021).
[ Journal ] [ Preprint ] - Erdmann-Pham, D.D.*, Fischer, J.*, Hong, J., and Song, Y.S.
Likelihood-based deconvolution of bulk gene expression data using single-cell references.
Genome Research, Vol. 31 (2021) 1794-1806.
[ Journal ] [ Preprint ] [ Software: RNA-Sieve ] - Hwang, B., Lee, D.S., Tamaki, W., Sun, Y., Ogorodnikov, A., Hartoularos, G.C., Winters, A.,
Yeung, B.Z., Nazor, K.L., Song, Y.S., Chow, E.D., Spitzer, M.H., Ye, C.J.
SCITO-seq: single-cell combinatorial indexed cytometry sequencing.
Nature Methods, Vol. 18 (2021) 903-911.
[ Journal ] [ Preprint ] - Deng, Y., Song, Y.S., Nielsen, R.
The distribution of waiting distances in ancestral recombination graphs.
Theoretical Population Biology, Vol. 141 (2021) 34-43.
[ Journal ] [ Preprint ] - Lee, Y.*, Bogdanoff, D.*, Wang*, Y., Hartoularos, G., Woo, J.M., Mowery, C.T., Nisonoff, H.M., Lee, D.S., Sun, Y., Lee, J., Mehdizadeh, S., Cantlon, J., Shifrut, E., Ngyuen, D.N.,
Roth, T.L., Song, Y.S., Marson, A., Chow, E.D., Ye, C.J.
XYZeq: Spatially-resolved single-cell RNA-sequencing reveals expression heterogeneity in the tumor microenvironment,
Science Advances , Vol. 7, eabg4755 (2021).
[ Journal ] - Erdmann-Pham, D.D., Son, W., Dao Duc, K., and Song, Y.S.
EGGTART: A computational tool to visualize the dynamics of biophysical transport processes under the inhomogeneous ℓ-TASEP.
Biophysical Journal, Vol. 120, No. 8 (2021) 1309-1313.
[ Journal ] [ Preprint ] [ Software ] - Crits-Christoph, A., Bhattacharya, N., Olm, M.R., Song, Y.S., Banfield, J.F.
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity.
Genome Research, Vol. 31, No. 2 (2021) 239-250.
[ Journal ] [ Preprint ] - Batra, S.S., Levy-Sakin, M., Robinson, J., Guillory, J., Durinck, S., Kwok, P.-Y., Cox, L.A., Seshagiri, S., Song, Y.S., Wall, J.D.
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data.
GigaScience, Vol. 9, No. 12, (2020) giaa134.
[ Journal ] [ Preprint ] - Batra, S.S., Spence, J., Song, Y.S.
Learning putatively causal gene regulatory programs
using permutation-equivariant neural networks.
Machine Learning in Computational Biology (MLCB), 2020. Selected as Spotlight
[ Abstract ] - Kamm, J.A., Terhorst, J., Durbin, R, and Song, Y.S.
Efficiently inferring the demographic history of many populations with allele count data.
Journal of the American Statistical Association,
Vol. 115, No. 531, (2020) 1472-1487.
[ Journal ] [ Preprint ] [ Software: momi2 ] - Fischer, J., Song, Y.S., Yosef, N., di Iulio, J., Churchman, L.S., Choder, M.
The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.
J. Biol. Chem., Vol. 295 (2020) 11435-11454.
[ Journal ] [ Preprint ] - Erdmann-Pham, D.D., Dao Duc, K., and Song, Y.S.
The key parameters that govern translation efficiency.
Cell Systems, Vol. 10, Issue 2, (2020) 183-192.
[ Journal ] [ Preprint ] - Olm, M.R., Bhattacharya, N., Crits-Christoph, A., Firek, B.A., Baker, R. Song, Y.S., Morowitz, M.J., and Banfield, J.F.
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.
Science Advances, Vol. 5, No. 12, (2019) eaax5727.
[ Journal ] [ Preprint ] - Spence, J.P. and Song, Y.S.
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations.
Science Advances, Vol. 5, No. 10, (2019) eaaw9206.
[ Journal ] [ Preprint ] [ Software: pyrho ] - Rao, R., Bhattacharya, N., Thomas, N., Duan, Y., Chen, X., Canny, J., Abbeel, P., and Song, Y.S.
Evaluating Protein Transfer Learning with TAPE.
Advances in Neural Information Processing Systems 32 (NeurIPS 2019).
Selected as Spotlight. (2.4% of submissions)
[ Proceedings ] [ Preprint ] [ Data & Code ] - Steinrücken, M., Kamm, J., Spence, J.P., and Song, Y.S.
Inference of complex population histories using whole-genome sequences from multiple populations.
PNAS, Vol. 116, No. 34 (2019) 17115-17120.
[ Journal ] [ Preprint ] [ Software: diCal2 ] - Dao Duc, K., Batra, S.S., Bhattacharya, N., Cate, J.H.D., and Song, Y.S.
Differences in the path to exit the ribosome across the three domains of life.
Nucleic Acids Research, Vol. 47, Issue 8 (2019) 4198-4210.
[ Journal ] [ Preprint ]
- Wang, M., Fischer, J., and Song, Y.S.
Three-way clustering of multi-tissue multi-individual gene expression data using semi-nonnegative tensor decomposition.
Annals of Applied Statistics, Vol. 13, No. 2 (2019) 1103-1127.
[ Journal ] [ PDF ] [ Preprint ] - Luo, S., Yu, J.A., Li, H., and Song, Y.S.
Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans.
Life Science Alliance, Vol 2, No 2 (2019) e201800221.
[ Journal ] [ Preprint ] - Chan, J., Perrone, V., Spence, J.P., Jenkins, P.A., Mathieson, S., and Song, Y.S.
A likelihood-free inference framework for population genetic data using exchangeable neural networks.
Advances in Neural Information Processing Systems 31 (NIPS 2018).
Selected as Spotlight. (3.5% of submissions)
[ Proceedings ] [ Preprint ] -
Moreno-Mayar, J.V.*, Vinner, L.*, de Barros Damgaard, P.*, de la Fuente, C.*, Chan, J.*, Spence, J.P.*, ... (45 authors) ..., Song, Y.S.†, Meltzer, D.J.†, Willerslev, E.†
Early human dispersals within the Americas.
Science, Vol. 362, Issue 6419, eaav2621 (2018).
*These authors contributed equally to this work.
†Corresponding authors.
[ Journal ] - Steinrücken, M., Spence, J.P., Kamm, J.A., Wieczorek, E., and Song, Y.S.
Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans.
Molecular Ecology, Vol. 27, No. 19 (2018) 3873-3888.
[ Journal ] [ Preprint ] [ diCal-admix ] - Rosen, Z.*, Bhaskar, A.*, Roch, S., and Song, Y.S.
Geometry of the sample frequency spectrum and the perils of demographic inference.
Genetics, Vol. 210, No. 2 (2018) 665-682. *Authors contributed equally.
Selected as October 2018 Highlight.
[ Journal ] [ Preprint ] - Palamara, P.F., Terhorst, J., Song, Y.S., Price, A.L.
High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.
Nature Genetics, Vol. 50 (2018) 1311-1317.
[ Journal ] [ Preprint ] - Spence, J.P., Steinrücken, M., Terhorst, J., and Song, Y.S.
Inference of population history using coalescent HMMs: review and outlook.
Current Opinion in Genetics & Development, Vol. 53 (2018) 70-76.
[ Journal ] [ Preprint ] - Moreno-Mayar, J.V., Potter, B.A., Vinner, L, Steinrücken, M. Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., and Willerslev, E.
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.
Nature, Vol. 553 (2018) 203-207.
[ Journal ] - Dao Duc, K., and Song, Y.S.
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.
PLoS Genetics, Vol. 14 No. 1 (2018) e1007166
[ Journal ] [ Preprint ] - Dao Duc, K., Saleem, Z.H., and Song, Y.S.
Theoretical analysis of the distribution of isolated particles in totally asymmetric exclusion processes: Application to mRNA translation rate estimation.
Phys. Rev. E, Vol. 97, No. 1, (2018) 012106.
Selected as Editor's Suggestion.
[ Journal ] [ Preprint ] - Crawford et al.
Loci associated with skin pigmentation identified in African populations. Science, Vol. 358, Issue 6365, eaan8433 (2017).
[ Journal ] - Liu, T.-Y.*, Huang, H.H.*, Wheeler, D., Xu, Y., Wells, J.A., Song, Y.S.†, and Wiita, A.P.†
Time-resolved proteomics extends ribosomal profiling-based measurements of protein synthesis dynamics.
Cell Systems, Vol. 4, Issue 6 (2017) 636-644.
†Corresponding authors. *Authors contributed equally.
Cover article.
Nick Ingolia's Preview of our article.
[ Journal ] [ Cover ] [ Preprint ] - Wang, M., and Song, Y.S.
Tensor decompositions via two-mode higher-order SVD (HOSVD).
Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (AISTATS),
PMLR, Vol. 54 (2017) 614-622.
[ Journal ] [ Preprint ] [ Software ] - Kamm, J.A., Terhorst, J., and Song, Y.S.
Efficient computation of the joint sample frequency spectra for multiple populations.
Journal of Computational and Graphical Statistics, Vol. 26, No. 1 (2017) 182-194.
[ Journal ] [ Preprint ] [ Software: momi ] (Note: The journal version is substantially different from the preprint.) - Terhorst, J., Kamm, J.A., and Song, Y.S.
Robust and scalable inference of population history from hundreds of unphased whole genomes.
Nature Genetics, Vol. 49 (2017) 303-309.
[ Journal ] [ Software: SMC++ ] - Wang, M., Dao Duc, K., Fischer, J., and Song, Y.S.
Operator norm inequalities between tensor unfoldings on the partition lattice.
Linear Algebra and its Applications, Vol. 520 (2017) 44-66.
[ Journal ] [ Preprint ] - Mallick et al.
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Nature, Vol. 538 (2016) 201-206.
[ Journal ] - Jewett, E.M., Steinrücken, M. and Song, Y.S.
The effects of population size histories on estimates of selection coefficients from time-series genetic data.
Molecular Biology and Evolution, Vol. 33 No.11 (2016) 3002-3027.
[ Journal ] [ Preprint ] - Luo, S., Yu, J.A., and Song, Y.S.
Estimating copy number and allelic variation at the immunoglobulin heavy chain locus using short reads.
PLoS Comput Biol, Vol. 12 No. 9 (2016) e1005117
[ Journal ] [ Preprint ] (Note: The preprint has a different title.) - Song, Y.S.
Na Li and Matthew Stephens on Modeling Linkage Disequilibrium.
Genetics, Vol. 203 No. 3 (2016) 1005-1006.
[ Journal ] - Kamm, J.A.*, Spence, J.P.*, Chan, J., and Song, Y.S.
Two-locus likelihoods under variable population size and fine-scale recombination rate estimation.
Genetics, Vol. 203 No. 3 (2016) 1381-1399. *These authors contributed equally to this work.
[ Journal ] [ Preprint ] [ Software: LDpop ] - Liu, T.-Y. and Song, Y.S.
Prediction of ribosome footprint profile shapes from transcript sequences.
Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191.
[ Journal ] [ Software: riboShape ] - Liu, T.-Y.*, Dodson, A.E.*, Terhorst, J., Song, Y.S.† , and Rine, J.†
Riches of phenotype computationally extracted from microbial colonies.
PNAS, Vol. 113, No. 20 (2016) E2822-E2831. †Corresponding authors. *These authors contributed equally to this work.
[ Journal ] - Spence, J.P.*, Kamm, J.A.*, and Song, Y.S.
The site frequency spectrum for general coalescents.
Genetics, Vol. 202 No. 4 (2016) 1549-1561.
*These authors contributed equally to this work.
[ Journal ] [ Preprint ]
- Sheehan, S. and Song, Y.S.
Deep learning for population genetic inference.
PLoS Comput Biol, Vol. 12, No. 5 (2016) e1004845.
[ Journal ] [ Preprint ] [ Software: evoNet ] - Steinrücken, M.*, Jewett, E.M.*, and Song, Y.S.
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes.
Bioinformatics, Vol. 32, No. 5 (2016) 795-797.
*These authors contributed equally to this work.
[ Journal ] [ Preprint ] [ Software: spectralTDF ] - Zou, J.Y., Park, D.S., Burchard, E.G., Torgerson, D.G., Pino-Yanes, M., Song, Y.S., Sankararaman, S., Halperin, E., and Zaitlen, N.
Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns.
PNAS, Vol. 112, No. 44 (2015) 13621-13626.
[ Journal ] - Raghavan, M.*, Steinrücken, M.*, Harris, K.*, Schiffels, S.*,
...(94 authors)... , Song, Y.S.†, Nielsen, R.†, Willerslev, E.†
Genomic evidence for the Pleistocene and recent population history of Native Americans. Science Vol. 349, Issue 6250, aab3884 (2015).
†Corresponding authors. *These authors contributed equally to this work.
[ Journal ] Media Coverage articles - Terhorst, J. and Song, Y.S.
Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. PNAS, Vol. 112, No. 25 (2015) 7677-7682.
[ Journal ] [ Preprint ] - Živković, D., Steinrücken, M., Song, Y.S., and Stephan, W.
Transition densities and sample frequency spectra of diffusion processes with selection and variable population size.
Genetics, Vol. 200, No. 2 (2015) 601-617.
[ Journal ] [ PDF ] [ Preprint ] - Jenkins, P.A., Fearnhead, P., and Song, Y.S.
Tractable diffusion and coalescent processes for weakly correlated loci.
Electronic Journal of Probability, Vol. 20, No. 58 (2015) 1-26.
[ Journal ] [ Preprint ] - Terhorst, J., Schlötterer, C., Song, Y.S.
Multi-locus analysis of genomic time series data from experimental evolution. PLoS Genetics, Vol. 11, No. 4 (2015) e1005069.
[ Journal ] [ Preprint ] - Bhaskar, A., Wang, Y.X.R. and Song, Y.S.
Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.
Genome Research, Vol. 25, No. 2 (2015) 268-279.
[ Journal ] [ Preprint ] [ Software: fastNeutrino ] - Bhaskar, A. and Song, Y.S.
Descartes' rule of signs and the identifiability of population demographic models from genomic variation data.
Annals of Statistics, Vol. 42, No. 6 (2014) 2469-2493.
[ Journal ] [ PDF ] [ Preprint ] - Steinrücken, M., Bhaskar, A. and Song, Y.S.
A novel spectral method for inferring general diploid selection from time series genetic data.
Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222.
[ Journal ] [ PDF ] [ Preprint ] [ Software: spectralHMM ] - Tataru, P., Nirody, J.A., and Song, Y.S.
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.
Bioinformatics, Vol. 30, No. 23 (2014) 3430-3431.
[ Journal ] [ Preprint ] [ Software: diCal-IBD ] - Talwalkar, A., Liptrap, J., Newcomb, J. Hartl, C., Terhorst, T., Curtis, K., Bresler, M., Song, Y.S., Jordan, M.I., and Patterson, D.
SMaSH: A benchmarking toolkit for human genome variant calling.
Bioinformatics, Vol. 30, No. 19 (2014) 2787-2795.
[ Journal ] [ Preprint ] [ Software: SMaSH ] - Bhaskar, A., Clark, A.G., and Song, Y.S.
Distortion of genealogical properties when the sample is very large.
PNAS, Vol. 111, No. 6 (2014) 2385-2390.
[ Journal ] [ Preprint ] [ Software ] - Harris, K., Sheehan, S., Kamm, J.A., Song, Y.S.,
Decoding coalescent hidden Markov models in linear time,
Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB),
LNBI Vol. 8394, 2014, pp 100-114.
[ Journal ] [ Preprint ] -
Bloniarz, A., Talwalkar, A., Terhorst, J., Jordan, M.I., Patterson, D., Yu, B., and Song, Y.S.
Changepoint analysis for efficient variant calling,
Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB), LNBI Vol. 8394, 2014, pp. 20-34.
[ Journal ] - Jenkins, P.A., Mueller, J.W, and Song, Y.S.
General triallelic frequency spectrum under demographic models with variable population size. Genetics, 196 (2014) 295-311.
[ Journal ] [ Preprint ] Research Highlight by Nature Reviews Genetics - Rohlfs, R.V., Murphy, E., Song, Y.S., and Slatkin, M.
The influence of relatives on the efficiency and error rate of familial searching.
PLoS ONE, Vol. 8 No. 8 (2013) e70495
[ Journal ] Media Coverage: LA Times, LiveScience - Steinrücken, M., Paul, J.S., and Song, Y.S.
A sequentially Markov conditional sampling distribution for structured populations with migration and recombination.
Theoretical Population Biology 87 (2013) 51-61.
[ Journal ] [ PDF ] [ Preprint ] - Sheehan, S.*, Harris, K.*, Song, Y.S.
Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach.
Genetics, 194 (2013) 647-662.
*These authors contributed equally to this work.
[ Journal ] [ Software: diCal ] - Steinrücken, M., Wang, Y.X.R., and Song, Y.S.
An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection. Theoretical Population Biology, 83 (2013) 1-14.
[ Journal ] [ PDF ] [ Preprint ] -
Chan, A.H.*, Jenkins, P.A.*, and Song, Y.S.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, Vol. 8 No. 12 (2012) e1003090. *These authors contributed equally to this work.
[ Journal ] [ Supporting Information ] [ Software: LDhelmet ] -
Jenkins, P.A., Song, Y.S., and Brem, R.
Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. PLoS ONE, Vol. 7 No. 11 (2012) e46947.
[ Journal ] - Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S.
Telescoper: De novo Assembly of Highly Repetitive Regions.
ECCB'12 Special Issue, Bioinformatics 28 (2012) i311-i317.
[ Journal ] [ PDF ] - Paul, J.S. and Song, Y.S.
Blockwise HMM computation for large-scale population genomic inference.
Bioinformatics, 28 (2012) 2008-2015.
[ Journal ] [ PDF ] -
Langley, C.H., Stevens, K., Cardeno, C., Lee, Y.C.G, Schrider, D.R., Pool, J.E., Langley, S.A., Suarez, C. Corbett-Detig, R.B., Kolaczkowski, B., Fang, S., Nista, P.M., Holloway, A.K., Kern, A.D., Dewey, C.N., Song, Y.S., Hahn, M.W., Begun, D.J.
Genomic variation in natural populations of Drosophila melanogaster.
Genetics, Vol. 192 No. 2 (2012) 533-598.
[ Journal ] [ PDF ] - Song, Y.S. and Steinrücken, M.
A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.
Genetics 190 (2012) 1117-1129.
[ Journal ] [ PDF ] - Bhaskar, A. and Song, Y.S.
Closed-form asymptotic sampling distributions under the coalescent with recombination for an arbitrary number of loci.
Advances in Applied Probability 44 (2012) 391-407
[ Journal ] [ PDF ] [ Preprint ] - Bhaskar, A., Kamm, J.A., and Song, Y.S.
Approximate sampling formulae for general finite-alleles models of mutation.
Advances in Applied Probability 44 (2012) 408-428.
[ Journal ] [ PDF ] [ Preprint ] - Jenkins, P.A. and Song, Y.S.
Padé approximants and exact two-locus sampling distributions.
Annals of Applied Probability 22 (2012) 576-607.
(Technical Report 793, Department of Statistics, University of California, Berkeley, 2010.)
[ Journal ] [ PDF ] [ Preprint ] - Nielsen, R., Paul, J.S., Albrechtsen, A., and Song, Y.S.
Genotype and SNP calling from next-generation sequencing data.
Nature Reviews Genetics 12 (2011) 443-451.
[ Journal ] - Jenkins, P.A. and Song, Y.S.
The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele.
Theoretical Population Biology 80 (2011) 158-173.
[ Journal ] [ PDF ] - Kao, W.-C., Chan, A.H., and Song, Y.S.
ECHO: A reference-free short-read error correction algorithm
Genome Research 21 (2011) 1181-1192
[ Journal ] [ PDF ] [ Software: ECHO ] - Paul, J.S., Steinrücken, M., and Song, Y.S.
An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.
Genetics 187 (2011) 1115-1128
[ Journal ] [ PDF ] [ Proof of Proposition 1] - Malaspinas, A.-S., Slatkin, M., and Song, Y.S.
Match probabilities in a finite, subdivided population.
Theoretical Population Biology 79 (2011) 55-63
[ Journal ] - Kao, W.C. and Song, Y.S.
naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing.
J. Comput. Biol. 18 (2011) 365-377.
(Extended Journal version of a RECOMB 2010 conference paper.)
[ Journal ] [ PDF ] - Lam, F., Langley, C.H., and Song, Y.S.
On the genealogy of asexual diploids.
J. Comput. Biol. 18 (2011) 415-428.
(Extended Journal version of a RECOMB 2010 conference paper.)
[ Journal ] [ PDF ] - Song, Y.S., Wang, F., and Slatkin, M.
General epistatic models of the risk of complex diseases.
Genetics 186 (2010) 1467-1473.
[ Journal ] [ PDF ] - Paul, J.S. and Song, Y.S.
A principled approach to deriving approximate conditional sampling
distributions in population genetics models with recombination.
Genetics 186 (2010) 321-338.
[ Journal ] [ PDF ] - Jenkins, P.A. and Song, Y.S.
An asymptotic sampling formula for the coalescent with recombination.
Annals of Applied Probability 20 (2010) 1005-1028.
(Technical Report 775, Department of Statistics, University of California, Berkeley, 2009.)
[ Journal ] [ PDF ] [ Preprint ] [ Tech Report Version ] - Stevens, K., Chen, H., Filiba, T., McMahon, P., Song, Y.S.
SeqHive: A reconfigurable computer cluster for genome re-sequencing.
IEEE Proceedings of the 20th International Conference
on Field Programmable Logic and Applications (FPL 2010), pages 442-447, 2010.
[ Journal ] [ PDF ] - Kao, W.-C. and Song, Y.S.
naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing.
Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology
(RECOMB 2010),
Lecture Notes in Computer Science 6044, pages 233-247, 2010.
(A new base-calling algorithm that builds on our previous method BayesCall to achieve scalability.)
[ Journal ] [ PDF ] [ Software: naiveBayesCall ]
- Lam, F., Langley, C.H., and Song, Y.S.
On the genealogy of asexual diploids.
Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology
(RECOMB 2010),
Lecture Notes in Computer Science 6044, pages 325-340, 2010.
[ Journal ] [ PDF ]
- Jenkins, P.A. and Song, Y.S.
Closed-form two-locus sampling distributions: accuracy and universality.
Genetics 183 (2009) 1087-1103.
[ Journal ] [ PDF ] [ Software ] - Kao, W.-C., Stevens, K. and Song, Y.S.
BayesCall: A model-based basecalling algorithm for high-throughput short-read sequencing.
Genome Research
19 (2009) 1884-1895.
[ Journal ] [ PDF ] [ Software: BayesCall ] - Bhaskar, A. and Song, Y.S.
Multi-locus match probability in a finite population: A fundamental
difference between the Moran and Wright-Fisher models.
Proceedings of
ISMB 2009, Bioinformatics 25 (2009) i187-i195.
[ Journal ] [ PDF ] [ Software ] - Yin, J., Jordan, M.I., and Song, Y.S.
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.
Proceedings of
ISMB 2009, Bioinformatics 25 (2009) i231-i239.
[ Journal ] [ PDF ] [ Software ] -
Song, Y.S., Patil, A., Murphy, E.E., and Slatkin, M.
Average probability that a "cold hit" in a DNA database search results in an erroneous attribution. J. Forensic Sciences 54 (2009) 22-27.
[ Journal ] - Krane DE, Bahn V, Balding D, Barlow B, Cash H, Desportes BL, D'Eustachio P, Devlin K, Doom TE, Dror I, Ford S, Funk C, Gilder J, Hampikian G, Inman K, Jamieson A, Kent PE, Koppl R, Kornfield I, Krimsky S, Mnookin J, Mueller L, Murphy E, Paoletti DR, Petrov DA, Raymer M, Risinger DM, Roth A, Rudin N, Shields W, Siegel JA, Slatkin M, Song YS, Speed T, Spiegelman C, Sullivan P, Swienton AR, Tarpey T, Thompson WC, Ungvarsky E, Zabell S.
Time for DNA disclosure.
Science 326, No.5960 (2009) 1631-1632.
[ PDF ] - Griffiths, R.C, Jenkins, P.A., and Song, Y.S.
Importance sampling and the two-locus model
with subdivided population structure.
Advances in Applied Probability 40 (2008) 473-500.
[ Journal ] [ PDF ] - Ding, Z., Mailund, T., and Song, Y.S.
Efficient whole-genome association mapping using local
phylogenies for unphased genotype data.
Bioinformatics 24 (2008) 2215-2221.
[ Journal ] [ PDF ] -
Lyngsø, R., Song, Y.S., and Hein, J.
Accurate computation of likelihoods in the coalescent with recombination via parsimony.
Proc. 12th Annual Intl. Conf. on Research in
Computational Molecular Biology (RECOMB 2008), Lecture Notes
in Computer Science 4955, pages 463--477.
[ Journal ] [ PDF ] [ Software ] -
Anderson, J.A., Song, Y.S., and Langley, C.H.
Molecular population genetics of Drosophila
subtelomeric DNA.
Genetics 178 (2008) 477-487.
[ Journal ] -
Gusfield, D, Bansal, V., Bafna, V., and Song, Y.S.
A decomposition theory for phylogenetic
networks and incompatible characters.
J. Comput. Biol. 14 (2007) 1247-1272.
[ Journal ] [ PDF ] -
Song, Y.S. and Slatkin, M.
A graphical approach to multi-locus match
probability computation: revisiting the product rule.
Theoretical Population Biology 72 (2007) 96-110.
[ Journal ] [ PDF ] -
Song, Y.S. and Song, J.S.
Analytic computation of the expectation of the linkage
disequilibrium coefficient r2.
Theoretical Population Biology 71 (2007) 49-60.
[ Journal ] [ PDF ] -
Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y.
Algorithms to distinguish the role of
gene-conversion from single-crossover recombination in the
derivation of SNP sequences in populations.
J. Comput. Biol. 14 (2007) 1273-1286.
(Extended journal version of a RECOMB 2006 conference paper.)
[ Journal ] [ PDF ] [ Software ] -
Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y.
Algorithms to distinguish the role of gene-conversion from
single-crossover recombination in the derivation of SNP sequences in populations.
Proc. 10th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2006).
Lecture Notes in Computer Science 3909, (2006) 231-245.
[ Journal ] [ PDF ] [ Software ]
-
Stephan, W., Song, Y.S., and Langley, C.H.
The hitchhiking effect on linkage disequilibrium between
linked neutral loci.
Genetics 172 (2006) 2647-2663.
[ Journal ] [ PDF ] -
Song, Y.S.
A concise necessary and sufficient
condition for the existence of a galled-tree.
IEEE/ACM Transactions on Computational Biology and Bioinformatics
3 (2006) 186-191.
[ Journal ] [ PDF ] -
Song, Y.S., Lyngsø, R., and Hein, J.
Counting all possible ancestral
configurations of sample sequences in population genetics.
IEEE/ACM Transactions on Computational
Biology and Bioinformatics 3 (2006) 239-251.
[ Journal ] [ PDF ] -
Song, Y.S.
A sufficient condition for reducing recursions
in hidden Markov models.
Bulletin of Mathematical Biology 68 (2006) 361-384.
[ Journal ] [ PDF ] -
Song, Y.S.
Properties of subtree-prune-and-regraft operations on
totally-ordered phylogenetic trees.
Annals of Combinatorics 10 (2006) 147-163.
[ Journal ] [ PDF ] -
Li, J. and Song, Y.S.
Open string instantons and relative stable morphisms.
Geometry and Topology Monographs
8, (2006) 49-72.
(Invited reprint of the 2001 paper shown below.)
[ Link ] [ PDF ] -
Lyngsø, R., Song, Y.S., and Hein, J.
Minimum recombination histories by branch and bound.
Proceedings of
Workshop on Algorithms in Bioinformatics 2005,
Lecture Notes in Computer Science 3692 (2005) 239-250.
[ Journal ] [ PDF ] [ Software ] -
Song, Y.S., Wu, Y. and Gusfield, D.
Algorithms for imperfect phylogeny haplotyping (IPPH) with a
single homoplasy or recombination event.
Proceedings of
Workshop on Algorithms in Bioinformatics 2005,
Lecture Notes in Computer Science 3692 (2005) 152-164.
[ Journal ] [ PDF ] -
Song, Y.S., Wu, Y. and Gusfield, D.
Efficient computation of close lower and upper bounds on the minimum
number of recombinations in biological sequence evolution.
Proceedings of
ISMB 2005.
Bioinformatics 21, Suppl.1, (2005) i413-i422.
[ Journal ] [ PDF ] [ Software ] -
Song, Y.S. and Hein, J.
Constructing minimal ancestral recombination graphs.
J. Comput. Biol. 12 (2005) 147-169.
[ Journal ] [ PDF ] -
Song, Y.S. and Hein, J.
On the minimum number of recombination events in the
evolutionary history of DNA sequences.
J. Math. Biol. 48 (2004) 160-186.
[ Journal ] [ PDF ] -
Song, J.S. and Song, Y.S.
On a conjecture of Givental.
J. Math. Phys. 45 (2004) 4539-4550.
[ Journal ] [ PDF ] [ Preprint ] -
Monni, S., Song, J.S., and Song, Y.S.
The Hurwitz enumeration problem of branched covers and Hodge integrals.
J. Geometry and Physics 50 (2004) 223-256.
[ Journal ] [ PDF ] [ Preprint ] -
Song, Y.S. and Hein, J.
Phylogenetics. (Review of Charles Semple and Mike Steel's
book.)
Systematic Biology 53, No.6 (2004) 1003-1006.
[ PDF ] -
Lunter, G.A, Miklós, I., Song, Y.S. and Hein, J.
An efficient algorithm for statistical multiple alignment on
arbitrary phylogenetic trees.
J. Comput. Biol. 10 (2003) 869-889.
[ Journal ] [ PDF ] -
Song, Y.S. and Hein, J.
Parsimonious reconstruction of sequence evolution and haplotype blocks.
Algorithms in Bioinformatics, Proceedings of
Workshop on Algorithms in Bioinformatics 2003,
Lecture Notes in Computer Science 2812 (2003) 287-302.
[ Journal ] [ PDF ] -
Song, Y.S.
On the combinatorics of rooted binary phylogenetic trees.
Annals of Combinatorics 7 (2003) 365-379.
[ Journal ] [ PDF ] -
Li, J. and Song, Y.S.
Open string instantons and relative stable morphisms.
Adv. Theor. Math. Phys.
5 (2001) 67-91.
[ Journal ] [ Preprint ]
-
Silverstein, E. and Song, Y.S.
On the critical behavior of D1-brane theories.
J. High Energy Phys. 03 (2000) 029.
[ Journal ] [ Preprint ]
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Prior to 2008
Theses
- Ph.D. Thesis. Physics, Stanford University, 2001.
Topological String Theory and Enumerative Geometry
[ PDF ] - B.S. Thesis. Physics, MIT, 1996.
Differential Renormalization of Supersymmetric Gauge Theories in Superspace
[ PDF ]