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Yun S. Song

University of California

52H-index
313Paper Count
1.4WCitation Count
Published Papers 81
Publication Date
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Hypervariable loop profiling decodes sequence determinants of antibody stability
errNATURE STRUCTURAL & MOLECULAR BIOLOGY
IF10.1
err2026-04-30
err0
PREAI
errYue Wan; Jiahao Liang; Yile Dai; Karthik Srinivasan; Christian Billesbølle; Ju-Fen Zhu; Jung-Eun Shin; Steffanie Paul; Debora Marks; Yun S. Song; Benjamin R. Myers; Antoine Koehl; Aashish Manglik
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Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression
errNature Biotechnology
IF41.7
err2026-03-27
err0
errOAAI
errEvan D. Groover; David Ding; Flora Z. Wang; Gonzalo Benegas; Joseph Rivera; Shahar Schwartz; Stephen Chen; Michael F. Moubarak; Viktoriya Georgieva; Peggy G. Lemaux; Brian J. Staskawicz; Krishna K. Niyogi; Yun S. Song; David F. Savage
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errSave
Nucleotide context models outperform protein language models for predicting antibody affinity maturation
errPLOS COMPUTATIONAL BIOLOGY
IF3.6
err2025-12-01
err0
PREAI
errJohnson, Mackenzie M.; Sung, Kevin; Haddox, Hugh K.; Vora, Ashni A.; Araki, Tatsuya; Victora, Gabriel D.; Song, Yun S.; Fukuyama, Julia; Matsen Iv, Frederick A.
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Moronic acid alleviates non-alcoholic fatty liver disease and fibrosis through PPARs-mediated lipidomic reprogramming
errPhytomedicine
IF8.3
err2025-11-07
err0
PREAI
errJinlu Han; Jiong Chen; Hong Hu; Yun Song; Mengyan Chen; De Zhao; Wen Shan; Qinghui Zhang; Ling Xu
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errSave
Author Correction: Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
errNature Genetics
IF29
err2025-10-10
err0
errOAAI
errYun Deng; Rasmus Nielsen; Yun S. Song
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errSave
Robust and adaptive non-parametric tests for detecting general distributional shifts in gene expression
errCell Reports Methods
IF4.5
err2025-09-02
err0
errOAAI
errFanding Zhou; Alan J. Aw; Dan D. Erdmann-Pham; Jonathan Fischer; Yun S. Song
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errSave
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing
errSYSTEMATIC BIOLOGY
IF5.7
err2025-09-01
err1
PREAI
errPrillo, Sebastian; Ravoor, Akshay; Yosef, Nir; Song, Yun S.
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Learning antibody sequence constraints from allelic inclusion
errCell Systems
IF7.7
err2025-08-13
err0
PREAI
errMilind Jagota; Chloe Hsu; Thomas Mazumder; Kevin Sung; William S. DeWitt; Jennifer Listgarten; Frederick A. Matsen IV; Chun Jimmie Ye; Yun S. Song
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errSave
Dynamic covalent interaction induced formation of a bortezomib–andrographolide complex and construction of the dual-drug delivery system
errRSC Adv.
IF4.6
err2025-08-13
err0
errOAAI
errShihui Qiao †; Hui Long †; Yun Song †; Xu Dong †; Huamin Zhong; Huanfeng Meng; Jingwen Gong; Yong Wang; Yiheng Liu; Haiying Zhang
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errSave
A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder
errMOLECULAR BIOLOGY AND EVOLUTION
IF5.3
err2025-08-01
err0
errOAAI
errMatsen IV, Frederick A.; Sung, Kevin; Johnson, Mackenzie M.; Dumm, Will; Rich, David; Starr, Tyler N.; Song, Yun S.; Bradley, Philip; Fukuyama, Julia; Haddox, Hugh K.
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errSave
Exact and efficient phylodynamic simulation from arbitrarily large populations
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2025-05-14
err0
errOAAI
errCelentano, Michael; Dewitt, William S.; Prillo, Sebastian; Song, Yun S.
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errSave
Active telomere elongation by a subclass of cancer-associated POT1 mutations
errGENES & DEVELOPMENT
IF7.7
err2025-02-27
err0
errOAAI
errMartin, Annika; Schabort, Johannes; Bartke-Croughan, Rebecca; Tran, Stella; Preetham, Atul; Lu, Robert; Ho, Richard; Gao, Jianpu; Jenkins, Shirin; Boyle, John; Ghanim, George E.; Jagota, Milind; Song, Yun S.; Li, Hanqin; Hockemeyer, Dirk
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errSave
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles ( vol 24 , 79 , 2023)
errGENOME BIOLOGY
IF9.4
err2025-02-13
err0
errOAAI
errSchreiber, Jacob Matthew; Boix, Carles A.; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Schoelkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jefrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard S.; Farrell, Nina P.; Halow, Jessica M.; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles B.; Strattan, J. Seth; Bernstein, Bradley E.; Snyder, Michael P.; Kellis, Manolis; Noble, William S.; Kundaje, Anshul Bharat; ENCODE Imputat Challenge Participants
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A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact
errGENETICS
IF5.1
err2024-12-16
err1
errOAAI
errDeng, Yun; Nielsen, Rasmus; Song, Yun S.
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errSave
Assessing predictions on fitness effects of missense variants in HMBS in CAGI6
errHUMAN GENETICS
IF3.6
err2024-08-07
err0
PREAI
errZhang, Jing; Kinch, Lisa; Katsonis, Panagiotis; Lichtarge, Olivier; Jagota, Milind; Song, Yun S.; Sun, Yuanfei; Shen, Yang; Kuru, Nurdan; Dereli, Onur; Adebali, Ogun; Alladin, Muttaqi Ahmad; Pal, Debnath; Capriotti, Emidio; Turina, Maria Paola; Savojardo, Castrense; Martelli, Pier Luigi; Babbi, Giulia; Casadio, Rita; Pucci, Fabrizio; Rooman, Marianne; Cia, Gabriel; Tsishyn, Matsvei; Strokach, Alexey; Hu, Zhiqiang; van Loggerenberg, Warren; Roth, Frederick P.; Radivojac, Predrag; Brenner, Steven E.; Cong, Qian; Grishin, Nick V.
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errSave
Tracing cancer evolution and heterogeneity using Hi-C
errNATURE COMMUNICATIONS
IF15.7
err2023-11-06
err5
errOAAI
errErdmann-Pham, Dan Daniel; Batra, Sanjit Singh; Turkalo, Timothy K.; Durbin, James; Blanchette, Marco; Yeh, Iwei; Shain, Hunter; Bastian, Boris C.; Song, Yun S.; Rokhsar, Daniel S.; Hockemeyer, Dirk
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errSave
DNA language models are powerful predictors of genome-wide variant effects
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2023-10-26
err17
errOAAI
errBenegas, Gonzalo; Batra, Sanjit Singh; Song, Yun S.
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errSave
Cross-protein transfer learning substantially improves disease variant prediction
errGENOME BIOLOGY
IF9.4
err2023-08-07
err15
errOAAI
errJagota, Milind; Ye, Chengzhong; Albors, Carlos; Rastogi, Ruchir; Koehl, Antoine; Ioannidis, Nilah; Song, Yun S.
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errSave
CherryML: scalable maximum likelihood estimation of phylogenetic models
errNATURE METHODS
IF32.1
err2023-06-29
err2
errOAAI
errPrillo, Sebastian; Deng, Yun; Boyeau, Pierre; Li, Xingyu; Chen, Po-Yen; Song, Yun S.
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errSave
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
errGENOME BIOLOGY
IF9.4
err2023-04-18
err7
errOAAI
errSchreiber, Jacob; Boix, Carles; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Scholkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jeffrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard; Farrell, Nina; Halow, Jessica; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles; Strattan, J. Seth; Bernstein, Bradley; Snyder, Michael; Kellis, Manolis; Stafford, William; Kundaje, Anshul
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Research Directions

No research directions
Co-authors
Cooperation Journals
M
M Snyder
H-index: 210 · Papers: 3.3K
J
Jean‐Laurent Casanova
H-index: 171 · Papers: 1.4K
J
Jillian F. Banfield
H-index: 154 · Papers: 935
R
Rasmus Nielsen
H-index: 151 · Papers: 525
R
Richard Durbin
H-index: 149 · Papers: 465
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