🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Nilah M. Ioannidis

Berkeley College

ORCID: 0000-0001-9628-8229

Also affiliated with University of California, Santa Cruz, Chan Zuckerberg Initiative (United States), Santa Cruz County Office of Education, University of California, Berkeley, Stanford University

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 100%percentile
0Author DataRank

Indexed papers

2in 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 2 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 →

Top data-sharing exemplar

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

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

UNC Libraries(2020)10.17615/gd7n-3n77
Top 100%
0DataRank
Top 100%0 citations

Olivier Cussenot, Diptasri Mandal, Nilah M. Ioannidis, Graham G. Giles, Shannon K. McDonnell +36 more

Papers

Driven by 20 papers — median percentile 0. Top paper: “Tissue-specific impacts of aging and genetics on gene expression patterns in humans”.

Tissue-specific impacts of aging and genetics on gene expression patterns in humans

Nature Communications(2022)10.1038/s41467-022-33509-0
N/A
0.665DataRank · unranked
83 citations

Ryan Chung, Juan Manuel Vazquez, Huanjie Sheng, Philippa L. Steinberg, Nilah M. Ioannidis +2 more

Strategies for effectively modelling promoter-driven gene expression using transfer learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.24.529941
N/A
0.385DataRank · unranked
12 citations

Michael H. Herschl, Xinyang Geng, Sathvik Kolli, Amy X. Lu, Aviral Kumar +4 more

GUANinE v1.0: Benchmark Datasets for Genomic AI Sequence-to-Function Models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.12.562113
N/A
0.345DataRank · unranked
9 citations

Nilah M. Ioannidis, Eyes S Robson

Cross-protein transfer learning substantially improves disease variant prediction

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.15.516532
N/A
0.345DataRank · unranked
9 citations

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

Personal transcriptome variation is poorly explained by current genomic deep learning models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.30.547100
N/A
0DataRank · unranked
18 citations

Richard W. Shuai, Parth Baokar, Ryan Chung, Ruchir Rastogi, Pooja Kathail +2 more

Characterizing uncertainty in predictions of genomic sequence-to-activity models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.21.572730
N/A
0DataRank · unranked
4 citations

Ruchir Rastogi, Pooja Kathail, Richard W. Shuai, Nilah M. Ioannidis, Ayesha Bajwa

Predicting target genes of non-coding regulatory variants with IRT

Bioinformatics(2020)10.1093/bioinformatics/btaa254
N/A
0DataRank · unranked
8 citations

Nilah M. Ioannidis, James Zou, Zhenqin Wu

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

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Nature Genetics(2024)10.1038/s41588-024-01904-6
N/A
0DataRank · unranked
27 citations

Pooja Kathail, Richard W. Shuai, Ryan Chung, Reinier J. Grona, Sailaja Peddada +14 more

Current genomic deep learning models display decreased performance in cell type-specific accessible regions

Genome biology(2024)10.1186/s13059-024-03335-2
N/A
0DataRank · unranked
17 citations

Richard W. Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B. Loeb, Nilah M. Ioannidis +1 more

Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.23.600232
N/A
0DataRank · unranked
6 citations

Xinyang Geng, Michael H. Herschl, Sathvik Kolli, Aviral Kumar, Patrick D. Hsu +3 more

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.18.599625
N/A
0DataRank · unranked
5 citations

Pooja Kathail, Richard W. Shuai, Ryan Chung, Reinier J. Grona, Sailaja Peddada +14 more

Critical assessment of missense variant effect predictors on disease-relevant variant data

Human Genetics(2025)10.1007/s00439-025-02732-2
N/A
0DataRank · unranked
21 citations

Ryan Chung, Sindy Li, Chang Li, Kyoungyeul Lee, Junwoo Woo +31 more

Machine learning-based prediction of human structural variation and characterization of associated sequence determinants

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.09.693295
N/A
0DataRank · unranked
1 citations

Runyang Nicolas Lou, Nilah M. Ioannidis, Peter H. Sudmant, Daven Lim

Integrated analysis of multimodal long-read epigenetic assays

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.09.687458
N/A
0DataRank · unranked
0 citations

Oberon Dixon-Luinenburg, Nathan Gamarra, Jacob Schwartz, Michal Rozenwald, Annie Maslan +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

Two-stage Study of Familial Prostate Cancer by Whole-exome Sequencing and Custom Capture Identifies 10 Novel Genes Associated with the Risk of Prostate Cancer

European Urology(2020)10.1016/j.eururo.2020.07.038
N/A
0DataRank · unranked
42 citations

Shannon K. McDonnell, Liesel M. FitzGerald, Lissa DeRycke, Zachary C. Fogarty, Graham G. Giles +34 more

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

UNC Libraries(2020)10.17615/gd7n-3n77
Top 100%
0DataRank
Top 100%0 citations

Olivier Cussenot, Diptasri Mandal, Nilah M. Ioannidis, Graham G. Giles, Shannon K. McDonnell +36 more

Personal transcriptome variation is poorly explained by current genomic deep learning models

Nature Genetics(2023)10.1038/s41588-023-01574-w
N/A
0DataRank · unranked
110 citations

Richard W. Shuai, Parth Baokar, Ryan Chung, Ruchir Rastogi, Pooja Kathail +2 more