Yun S Song (Yun Song)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 28

Top Venues

bioRxiv : the preprint server for biology

Science advances

Proceedings of the National Academy of Sciences of the United States of America

Science (New York, N.Y.)

University of California Berkeley

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California Berkeley Jul 01 2007

United States

Professor :: Computer Science, Statistics, and Integrative Biology

Publications

Annika Martin, Johannes Schabort, Rebecca Bartke-Croughan, Stella Tran, Atul Preetham, Robert Lu, Richard Ho, Jianpu Gao, Shirin Jenkins, John Boyle, George E Ghanim, Milind Jagota, Yun S Song, Hanqin Li, Dirk Hockemeyer
Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis. bioRxiv : the preprint server for biology (2024)
Alan J Aw, Jeremy McRae, Elior Rahmani, Yun S Song
Highly parameterized polygenic scores tend to overfit to population stratification via random effects. bioRxiv : the preprint server for biology (2024)
Alan J Aw, Jeremy McRae, Elior Rahmani, Yun S Song
Highly parameterized polygenic scores tend to overfit to population stratification via random effects. bioRxiv : the preprint server for biology (2024)
Gonzalo Benegas, Sanjit Singh Batra, Yun S Song
DNA language models are powerful predictors of genome-wide variant effects. Proceedings of the National Academy of Sciences of the United States of America 120 (44) (2023)
Emaad Khwaja, Yun S Song, Bo Huang
CELL-E: zero-shot sequence-to-image synthesis for protein localization prediction. Research square (2023)
Milind Jagota, Chengzhong Ye, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah Ioannidis, Yun S Song
Cross-protein transfer learning substantially improves disease variant prediction. Genome biology 24 (1) (2023)
Alan Aw, Lionel Chentian Jin, Nilah Ioannidis, Yun S Song
The Impact of Stability Considerations on Genetic Fine-Mapping. bioRxiv : the preprint server for biology (2023)
Dan Daniel Erdmann-Pham, Sanjit Singh Batra, Timothy K Turkalo, James Durbin, Marco Blanchette, Iwei Yeh, Hunter Shain, Boris C Bastian, Yun S Song, Daniel S Rokhsar, Dirk Hockemeyer
Tracing cancer evolution and heterogeneity using Hi-C. Nature communications 14 (1) (2023)
Alan Aw, Lionel Chentian Jin, Nilah Ioannidis, Yun S Song
The Impact of Stability Considerations on Genetic Fine-Mapping. bioRxiv : the preprint server for biology (2023)
Sebastian Prillo, Yun Deng, Pierre Boyeau, Xingyu Li, Po-Yen Chen, Yun S Song
CherryML: scalable maximum likelihood estimation of phylogenetic models. Nature methods (2023)
Sebastian Prillo, Akshay Ravoor, Nir Yosef, Yun S Song
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data. bioRxiv : the preprint server for biology (2023)
Gonzalo Benegas, Carlos Albors, Alan J Aw, Chengzhong Ye, Yun S Song
GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction. bioRxiv : the preprint server for biology (2023)
Sanjit Singh Batra, Alan Cabrera, Jeffrey P Spence, Isaac B Hilton, Yun S Song
Predicting the effect of CRISPR-Cas9-based epigenome editing. bioRxiv : the preprint server for biology (2023)
Alan Aw, Lionel Chentian Jin, Nilah Ioannidis, Yun S Song
The Impact of Stability Considerations on Genetic Fine-Mapping. bioRxiv : the preprint server for biology (2023)
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 computational biology 19 (4) (2023)
Gonzalo Benegas, Jonathan Fischer, Yun S Song
Robust and annotation-free analysis of alternative splicing across diverse cell types in mice. eLife 11 (2022)
Megan L Koleske, Gregory McInnes, Julia E H Brown, Neil Thomas, Keino Hutchinson, Marcus Y Chin, Antoine Koehl, Michelle R Arkin, Avner Schlessinger, Renata C Gallagher, Yun S Song, Russ B Altman, Kathleen M Giacomini
Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency. Proceedings of the National Academy of Sciences of the United States of America 119 (46) (2022)
Youjin Lee, Derek Bogdanoff, Yutong Wang, George C Hartoularos, Jonathan M Woo, Cody T Mowery, Hunter M Nisonoff, David S Lee, Yang Sun, James C Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N Nguyen, Theodore L Roth, Yun S Song, Alexander Marson, Eric D Chow, Chun Jimmie Ye
XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Science advances 7 (17) (2021)
Byungjin Hwang, David S Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George C Hartoularos, Aidan Winters, Bertrand Z Yeung, Kristopher L Nazor, Yun S Song, Eric D Chow, Matthew H Spitzer, Chun Jimmie Ye
SCITO-seq: single-cell combinatorial indexed cytometry sequencing. Nature methods 18 (8) (2021)
Monique G P van der Wijst, Sara E Vazquez, George C Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno, David S Lee, John R Greenland, Yang Sun, Richard Perez, Anton Ogorodnikov, Alyssa Ward, Sabrina A Mann, Kara L Lynch, Cassandra Yun, Diane V Havlir, Gabriel Chamie, Carina Marquez, Bryan Greenhouse, Michail S Lionakis, Philip J Norris, Larry J Dumont, Kathleen Kelly, Peng Zhang, Qian Zhang, Adrian Gervais, Tom Le Voyer, Alexander Whatley, Yichen Si, Ashley Byrne, Alexis J Combes, Arjun Arkal Rao, Yun S Song, null null, Gabriela K Fragiadakis, Kirsten Kangelaris, Carolyn S Calfee, David J Erle, Carolyn Hendrickson, Matthew F Krummel, Prescott G Woodruff, Charles R Langelier, Jean-Laurent Casanova, Joseph L Derisi, Mark S Anderson, Chun Jimmie Ye
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv : the preprint server for biology (2021)
Monique G P van der Wijst, Sara E Vazquez, George C Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno, David S Lee, John R Greenland, Yang Sun, Richard K Perez, Anton Ogorodnikov, Alyssa Ward, Sabrina A Mann, Kara L Lynch, Cassandra Yun, Diane V Havlir, Gabriel Chamie, Carina Marquez, Bryan Greenhouse, Michail S Lionakis, Phillip J Norris, Larry J Dumont, Kathleen K Kelly, Peng Zhang, Qian Zhang, Adrian Gervais, Tom Le Voyer, Alexander Whatley, Yichen Si, Ashley Byrne, Alexis J Combes, Arjun Arkal Rao, Yun S Song, Gabriela K Fragiadakis, Kirsten Kangelaris, Carolyn S Calfee, David J Erle, Carolyn M Hendrickson, Matthew F Krummel, Prescott G Woodruff, Charles R Langelier, Jean Laurent Casanova, Joseph L Derisi, Mark S Anderson, Chun Jimmie Ye, null null
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Science translational medicine 13 (612) (2021)
Matthias Steinrücken, Jack Kamm, Jeffrey P Spence, Yun S Song
Inference of complex population histories using whole-genome sequences from multiple populations. Proceedings of the National Academy of Sciences of the United States of America 116 (34) (2019)
Shishi Luo, Jane A Yu, Heng Li, Yun S Song
Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans. Life science alliance 2 (2) (2019)
Matthew R Olm, Nicholas Bhattacharya, Alexander Crits-Christoph, Brian A Firek, Robyn Baker, Yun S Song, Michael J Morowitz, Jillian F Banfield
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Science advances 5 (12) (2019)
Jeffrey P Spence, Yun S Song
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Science advances 5 (10) (2019)
J Víctor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente Castro, Jeffrey Chan, Jeffrey P Spence, Morten E Allentoft, Tharsika Vimala, Fernando Racimo, Thomaz Pinotti, Simon Rasmussen, Ashot Margaryan, Miren Iraeta Orbegozo, Dorothea Mylopotamitaki, Matthew Wooller, Clément P Bataille, Lorena Becerra-Valdivia, David Chivall, Daniel Comeskey, Thibaut Deviese, Donald K Grayson, Len George, Harold Harry, Verner Alexandersen, Charlotte Primeau, Jon M Erlandson, Claudia Rodrigues-Carvalho, Silvia Reis, Murilo Q R Bastos, Jerome Cybulski, Carlos Vullo, Flavia Morello, Miguel Vilar, Spencer Wells, Kristian Gregersen, Kasper Lykke Hansen, Niels Lynnerup, Marta Mirazón Lahr, Kurt H Kjær, André Strauss, Marta Alfonso-Durruty, Antonio Salas, Hannes Schroeder, Thomas Higham, Ripan Singh Malhi, Jeffrey T Rasic, Luiz Souza, Fabricio R Santos, Anna-Sapfo Malaspinas, Martin Sikora, Rasmus Nielsen, Yun S Song, David J Meltzer, Eske Willerslev
Early human dispersals within the Americas. Science (New York, N.Y.) 362 (6419) (2018)
Khanh Dao Duc, Yun S Song
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. PLoS genetics 14 (1) (2018)
Nicholas G Crawford, Derek E Kelly, Matthew E B Hansen, Marcia Holsbach Beltrame, Shaohua Fan, Shanna L Bowman, Ethan Jewett, Alessia Ranciaro, Simon Thompson, Yancy Lo, Susanne P Pfeifer, Jeffrey D Jensen, Michael C Campbell, William Beggs, Farhad Hormozdiari, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Jake Haut, null null, Harriet T Rothschild, Leonard I Zon, Yi Zhou, Michael A Kovacs, Mai Xu, Tongwu Zhang, Kevin Bishop, Jason Sinclair, Cecilia Rivas, Eugene Elliot, Jiyeon Choi, Shengchao A Li, Belynda D Hicks, Jason W Sinclair, Christian C Abnet, Dawn E Watkins-Chow, Elena Oancea, Yun S Song, Eleazar Eskin, Kevin K Brown, Michael S Marks, Stacie K Loftus, William J Pavan, Meredith Yeager, Stephen Chanock, Sarah A Tishkoff
Loci associated with skin pigmentation identified in African populations. Science (New York, N.Y.) 358 (6365) (2017)

Yun S Song.css-eqlu8i{font-size:small;padding-left:4px;} (Yun Song)

Publication Activity (10 Years)

Top Topics

Top Venues

Yun S Song (Yun Song)