Yun S. Song

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

10.8Author DataRank

Indexed papers

4in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 4 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Nature(2016)10.1038/nature18964

Top 2%

8.6DataRank

Top 2%1785 citations

Alexandra P. Lewis, Mark Lipson, Iain Mathieson, Madhusudan Gujral, Fernando Racimo +86 more

Papers

Driven by 69 papers — median percentile 79. Top paper: “The Simons Genome Diversity Project: 300 genomes from 142 diverse populations”.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Nature(2016)10.1038/nature18964

Top 2%

8.6DataRank

Top 2%1785 citations

Alexandra P. Lewis, Mark Lipson, Iain Mathieson, Madhusudan Gujral, Fernando Racimo +86 more

Accurate assembly of the olive baboon ( Papio anubis ) genome using long-read and Hi-C data

GigaScience(2020)10.1093/gigascience/giaa134

Top 19%

1.1DataRank

Top 19%39 citations

Michal Levy‐Sakin, Jacqueline A. Robinson, Joseph Guillory, Steffen Durinck, Tauras P. Vilgalys +6 more

Robust and annotation-free analysis of alternative splicing across diverse cell types in mice

eLife(2022)10.7554/elife.73520

Top 24%

0.852DataRank

Top 24%23 citations

Jonathan Fischer, Yun S. Song, Gonzalo Benegas

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

Genome Biology(2023)10.1186/s13059-023-02915-y

N/A

0.692DataRank · unranked

17 citations

Carles B. Adsera, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang +46 more

Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia

Nature Communications(2024)10.1038/s41467-024-53566-x

N/A

0.549DataRank · unranked

16 citations

Alexandra Tsitsiklis, Victoria Chu, Hoang Van Phan, Catherine DeVoe, Christina Love +87 more

Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans

Life Science Alliance(2019)10.26508/lsa.201800221

N/A

0.524DataRank · unranked

32 citations

Jane A. Yu, Alexandra P. Lewis, Yun S. Song, Shishi Luo

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.30.502157

N/A

0.190DataRank · unranked

2 citations

Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang +40 more

Robust and annotation-free analysis of alternative splicing across diverse cell types in mice

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.27.441683

Top 67%

0.173DataRank

Top 67%1 citations

Jonathan Fischer, Yun S. Song, Gonzalo Benegas

Predicting the effect of CRISPR-Cas9-based epigenome editing

eLife(2023)10.7554/elife.92991

N/A

0.170DataRank · unranked

2 citations

Alan Cabrera, Jeffrey P. Spence, Jacob Goell, Selvalakshmi S Anand, Isaac B. Hilton +2 more

Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19

Science Translational Medicine(2021)10.1126/scitranslmed.abh2624

N/A

0DataRank · unranked

239 citations

Sara E. Vazquez, George C. Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno +40 more

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment

Science Advances(2021)10.1126/sciadv.abg4755

N/A

0DataRank · unranked

118 citations

Derek Bogdanoff, Yutong Wang, George C. Hartoularos, Jonathan M. Woo, Cody T. Mowery +14 more

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

Nature Methods(2021)10.1038/s41592-021-01222-3

N/A

0DataRank · unranked

63 citations

David Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George C. Hartoularos +8 more

The distribution of waiting distances in ancestral recombination graphs

Theoretical Population Biology(2021)10.1016/j.tpb.2021.06.003

N/A

0DataRank · unranked

45 citations

Yun S. Song, Rasmus Nielsen, Yun Deng

EGGTART: A tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP

Biophysical Journal(2021)10.1016/j.bpj.2021.02.004

N/A

0DataRank · unranked

6 citations

Won-Jun Son, Khanh Dao Duc, Yun S. Song, Dan D. Erdmann-Pham

Likelihood-based deconvolution of bulk gene expression data using single-cell references

Genome Research(2021)10.1101/gr.272344.120

N/A

0DataRank · unranked

50 citations

Jonathan Fischer, Justin Hong, Yun S. Song, Dan D. Erdmann-Pham

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.09.434529

N/A

0DataRank · unranked

29 citations

Sara E. Vazquez, George C. Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno +40 more

Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.01.462692

N/A

0DataRank · unranked

1 citations

Milind Jagota, Dan D. Erdmann-Pham, Alexander Fung, Yun S. Song, Antoine Koehl

A simple and flexible test of sample exchangeability with applications to statistical genomics

arXiv (Cornell University)(2021)10.48550/arxiv.2109.15261

N/A

0DataRank · unranked

1 citations

Jeffrey P. Spence, Yun S. Song, Alan J. Aw

Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2210247119

N/A

0DataRank · unranked

34 citations

Gregory McInnes, Julia E. H. Brown, Neil Thomas, Keino Hutchinson, Marcus Y. Chin +8 more

DNA language models are powerful predictors of genome-wide variant effects

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.22.504706

N/A

0DataRank · unranked

26 citations

Sanjit Singh Batra, Yun S. Song, Gonzalo Benegas

Cross-protein transfer learning substantially improves disease variant prediction

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.15.516532

N/A

0DataRank · unranked

9 citations

Chengzhong Ye, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah M. Ioannidis +2 more

Tuned Fitness Landscapes for Benchmarking Model-Guided Protein Design

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.28.514293

N/A

0DataRank · unranked

8 citations

Atish Agarwala, David Belanger, Yun S. Song, Lucy J. Colwell, Neil Thomas

The Impact of Protein Dynamics on Residue-Residue Coevolution and Contact Prediction

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.16.512436

N/A

0DataRank · unranked

6 citations

Antoine Koehl, Milind Jagota, Yun S. Song, Alexander Fung

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.27.489632

N/A

0DataRank · unranked

3 citations

Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson, Jane A. Yu

CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.21.521328

N/A

0DataRank · unranked

1 citations

Yun Deng, Pierre Boyeau, Xingyu Li, Po‐Yen Chen, Yun S. Song +1 more

DNA language models are powerful predictors of genome-wide variant effects

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2311219120

N/A

0DataRank · unranked

135 citations

Sanjit Singh Batra, Yun S. Song, Gonzalo Benegas

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

Cell(2023)10.1016/j.cell.2023.01.042

N/A

0DataRank · unranked

98 citations

Jeffrey P. Spence, Yuanqing Feng, Matthew E.B. Hansen, Jonathan Terhorst, Márcia Holsbach Beltrame +14 more

Cross-protein transfer learning substantially improves disease variant prediction

Genome biology(2023)10.1186/s13059-023-03024-6

N/A

0DataRank · unranked

72 citations

Chengzhong Ye, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah M. Ioannidis +2 more

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

PLoS Computational Biology(2023)10.1371/journal.pcbi.1010137

N/A

0DataRank · unranked

24 citations

Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson, Jane A. Dwivedi-Yu

CherryML: scalable maximum likelihood estimation of phylogenetic models

Nature Methods(2023)10.1038/s41592-023-01917-9

N/A

0DataRank · unranked

15 citations

Yun Deng, Pierre Boyeau, Xingyu Li, Po‐Yen Chen, Yun S. Song +1 more

Tracing cancer evolution and heterogeneity using Hi-C

Nature Communications(2023)10.1038/s41467-023-42651-2

N/A

0DataRank · unranked

15 citations

Sanjit Singh Batra, Timothy K. Turkalo, J. Durbin, Marco Blanchette, Iwei Yeh +6 more

GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.10.561776

N/A

0DataRank · unranked

29 citations

Carlos Albors, Alan J. Aw, Chengzhong Ye, Yun S. Song, Gonzalo Benegas

ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.03.569785

N/A

0DataRank · unranked

10 citations

Akshay Ravoor, Nir Yosef, Yun S. Song, Sebastian Prillo

Predicting the effect of CRISPR-Cas9-based epigenome editing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.03.560674

N/A

0DataRank · unranked

5 citations

Alan Cabrera, Jeffrey P. Spence, Jacob Goell, Selvalakshmi Selvaraj Anand, Isaac B. Hilton +2 more

CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.05.561066

N/A

0DataRank · unranked

3 citations

Yun S. Song, Aaron Agarunov, Bo Huang, Emaad Khwaja

Tracing cancer evolution and heterogeneity using Hi-C

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.20.529175

N/A

0DataRank · unranked

1 citations

Sanjit Singh Batra, Timothy K. Turkalo, J. Durbin, Marco Blanchette, Iwei Yeh +6 more

The Impact of Stability Considerations on Genetic Fine-mapping

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.11.536456

N/A

0DataRank · unranked

0 citations

Lionel Chentian Jin, Nilah M. Ioannidis, Yun S. Song, Alan J. Aw

The impact of stability considerations on genetic fine-mapping

eLife(2023)10.7554/elife.88039

N/A

0DataRank · unranked

0 citations

Lionel Chentian Jin, Nilah M. Ioannidis, Yun S. Song, Alan J. Aw

Reviewer #1 (Public Review): Predicting the effect of CRISPR-Cas9-based epigenome editing

(2023)10.7554/elife.92991.1.sa1

N/A

0DataRank · unranked

0 citations

Alan Cabrera, Jeffrey P. Spence, Isaac B. Hilton, Yun S. Song, Sanjit Singh Batra

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19

Nature Communications(2024)10.1038/s41467-024-49756-2

N/A

0DataRank · unranked

19 citations

Ravi K. Patel, Aartik Sarma, K. Mark Ansel, Stephanie A. Christenson, Michael Adkisson +75 more

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact

Genetics(2024)10.1093/genetics/iyae192

N/A

0DataRank · unranked

9 citations

Rasmus Nielsen, Yun S. Song, Yun Deng

A simple and flexible test of sample exchangeability with applications to statistical genomics

The Annals of Applied Statistics(2024)10.1214/23-aoas1817

N/A

0DataRank · unranked

2 citations

Jeffrey P. Spence, Yun S. Song, Alan J. Aw

Assessing predictions on fitness effects of missense variants in HMBS in CAGI6

Human Genetics(2024)10.1007/s00439-024-02680-3

N/A

0DataRank · unranked

2 citations

Lisa N. Kinch, Panagiotis Katsonis, Olivier Lichtarge, Milind Jagota, Yun S. Song +26 more

Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.16.585351

N/A

0DataRank · unranked

44 citations

Rasmus Nielsen, Yun S. Song, Yun Deng

Highly parameterized polygenic scores tend to overfit to population stratification via random effects

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.27.577589

N/A

0DataRank · unranked

9 citations

Jeremy F. McRae, Elior Rahmani, Yun S. Song, Alan J. Aw

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.01.615851

N/A

0DataRank · unranked

4 citations

Rasmus Nielsen, Yun S. Song, Yun Deng

Learning antibody sequence constraints from allelic inclusion

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.22.619760

N/A

0DataRank · unranked

1 citations

Chloe Hsu, Thomas Mazumder, Kevin Sung, William S. DeWitt, Jennifer Listgarten +4 more

Genomic language models: opportunities and challenges

Trends in Genetics(2025)10.1016/j.tig.2024.11.013

N/A

0DataRank · unranked

94 citations

Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S. Song, Gonzalo Benegas

A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder

Molecular Biology and Evolution(2025)10.1093/molbev/msaf186

N/A

0DataRank · unranked

7 citations

Kevin Sung, Mackenzie M. Johnson, Will Dumm, David Rich, Tyler N. Starr +5 more

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes

Nature Genetics(2025)10.1038/s41588-025-02317-9

N/A

0DataRank · unranked

17 citations

Rasmus Nielsen, Yun S. Song, Yun Deng

ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing

Systematic Biology(2025)10.1093/sysbio/syaf054

N/A

0DataRank · unranked

6 citations

Akshay Ravoor, Nir Yosef, Yun S. Song, Sebastian Prillo

Learning antibody sequence constraints from allelic inclusion

Cell Systems(2025)10.1016/j.cels.2025.101368

N/A

0DataRank · unranked

1 citations

Chloe Hsu, Thomas Mazumder, Kevin Sung, William S. DeWitt, Jennifer Listgarten +4 more

Exact and efficient phylodynamic simulation from arbitrarily large populations

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2412978122

N/A

0DataRank · unranked

2 citations

William S. DeWitt, Sebastian Prillo, Yun S. Song, Michael Celentano

A general framework for branch length estimation in Ancestral Recombination Graphs

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2504461122

N/A

0DataRank · unranked

1 citations

William S. DeWitt, Yun S. Song, Rasmus Nielsen, Yun Deng

Nucleotide context models outperform protein language models for predicting antibody affinity maturation

PLoS Computational Biology(2025)10.1371/journal.pcbi.1013758

N/A

0DataRank · unranked

1 citations

Kevin Sung, Hugh K. Haddox, A. B. Vora, Tatsuya Araki, Gabriel D. Victora +4 more

Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.11.637758

N/A

0DataRank · unranked

17 citations

Gökçen Eraslan, Yun S. Song, Gonzalo Benegas

Active telomere elongation by a subclass of cancer-associated POT1 mutations

Genes & Development(2025)10.1101/gad.352492.124

N/A

0DataRank · unranked

8 citations

Johannes J. Schabort, Rebecca Bartke-Croughan, Stella Tran, Atul Preetham, Robert Lu +10 more

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.21.677619

N/A

0DataRank · unranked

6 citations

Gonzalo Benegas, Carlos Albors, Jianan Canal Li, Sebastian Prillo, Peter D. Fields +3 more

CPI-Pred: A deep learning framework for predicting functional parameters of compound-protein interactions

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.16.633372

N/A

0DataRank · unranked

1 citations

Rana Barghout, Jinghao Wu, Dhruv Garg, Yun S. Song, Radhakrishnan Mahadevan +1 more

Robust and adaptive non-parametric tests for detecting general distributional shifts in gene expression

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101147

N/A

0DataRank · unranked

0 citations

Alan J. Aw, Dan D. Erdmann-Pham, Jonathan Fischer, Yun S. Song, Fanding Zhou

A Phylogenetic Approach to Genomic Language Modeling

arXiv (Cornell University)(2025)10.48550/arxiv.2503.03773

N/A

0DataRank · unranked

0 citations

Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song, Carlos Albors

Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

Genome Biology(2025)10.1186/s13059-025-03494-w

N/A

0DataRank · unranked

0 citations

Carles B. Adsera, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang +45 more

The Key Parameters that Govern Translation Efficiency

Cell Systems(2020)10.1016/j.cels.2019.12.003

N/A

0DataRank · unranked

63 citations

Khanh Dao Duc, Yun S. Song, Dan D. Erdmann-Pham

The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5‘ and 3‘ gene regions

Journal of Biological Chemistry(2020)10.1074/jbc.ra120.013426

N/A

0DataRank · unranked

45 citations

Yun S. Song, Nir Yosef, Julia di Iulio, L. Stirling Churchman, Mordechai Choder +1 more

Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity

Genome Research(2020)10.1101/gr.268169.120

N/A

0DataRank · unranked

71 citations

Nicholas Bhattacharya, Matthew R. Olm, Yun S. Song, Jillian F. Banfield, Alexander Crits‐Christoph

Single Layers of Attention Suffice to Predict Protein Contacts

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.21.423882

N/A

0DataRank · unranked

35 citations

Neil Thomas, Roshan Rao, Justas Dauparas, Peter K. Koo, David Baker +3 more

Improved COVID-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays using Machine Learning

medRxiv(2020)10.1101/2020.07.15.20154773

N/A

0DataRank · unranked

4 citations

Alexander Marson, Yun S. Song, Chun Jimmie Ye, Cody T. Mowery

A likelihood-based deconvolution of bulk gene expression data using single-cell references

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.01.322867

N/A

0DataRank · unranked

2 citations

Jonathan Fischer, Justin Hong, Yun S. Song, Dan D. Erdmann-Pham

The distribution of waiting distances in ancestral recombination graphs and its applications

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.24.424361

N/A

0DataRank · unranked

2 citations

Yun S. Song, Rasmus Nielsen, Yun Deng

Yun S. Song

Indexed papers

Top data-sharing exemplar

Papers