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

Lydia Freddolino

University of Illinois Urbana-Champaign

ORCID: 0000-0002-5821-4226

Also affiliated with Washington University in St. Louis, University of Michigan, Michigan United, The University of Texas at Austin

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 2%percentile
3.2Author 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 →

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.

BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Nucleic Acids Research(2023)10.1093/nar/gkad630
Top 7%
3.0DataRank
Top 7%140 citations

Xi Zhang, Lydia Freddolino, Yang Zhang, Chengxin Zhang

Papers

Driven by 36 papers — median percentile 30. Top paper: “BioLiP2: an updated structure database for biologically relevant ligand–protein interactions”.

BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Nucleic Acids Research(2023)10.1093/nar/gkad630
Top 7%
3.0DataRank
Top 7%140 citations

Xi Zhang, Lydia Freddolino, Yang Zhang, Chengxin Zhang

Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding

Biophysical Journal(2009)10.1016/j.bpj.2009.08.012
N/A
0.747DataRank · unranked
144 citations

Klaus Schulten, Lydia Freddolino

Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine

mBio(2023)10.1128/mbio.02690-22
N/A
0.549DataRank · unranked
12 citations

Lydia Freddolino, Christine A. Ziegler

Deep mutational scanning highlights a role for cytosolic regions in Hrd1 function

Cell Reports(2023)10.1016/j.celrep.2023.113451
N/A
0.426DataRank · unranked
14 citations

Jiwon Hwang, Jennifer E. Russ, Jeremy W. Schroeder, Lydia Freddolino, Ryan D. Baldridge +1 more

Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex

RNA(2024)10.1261/rna.079813.123
N/A
0.330DataRank · unranked
8 citations

Catherine Barnier, Nathan D. Elrod, Hua Luo, Madeline K. Jensen, Ping Ji +6 more

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Nucleic Acids Research(2025)10.1093/nar/gkaf647
N/A
0.165DataRank · unranked
2 citations

Tatiana Julien, Sahana Suraj, Judith F. Kribelbauer, Saeed Tavazoie, Lydia Freddolino +2 more

FURNA: A database for functional annotations of RNA structures

PLoS Biology(2024)10.1371/journal.pbio.3002476
Top 70%
0.141DataRank
Top 70%1 citations

Lydia Freddolino, Chengxin Zhang

FURNA: a database for function annotations of RNA structures

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.19.572314
Top 78%
0.104DataRank
Top 78%1 citations

Lydia Freddolino, Chengxin Zhang

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00658
N/A
0DataRank · unranked
98 citations

John E. Stone, João V. Ribeiro, Jan Saam, Lydia Freddolino, Rafael C. Bernardi +2 more

Protein target highlights in CASP15 : Analysis of models by structure providers

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26545
N/A
0DataRank · unranked
35 citations

Janani Durairaj, Andriy Kryshtafovych, Luciano A. Abriata, Yusupha Bayo, Gira Bhabha +46 more

Nutrigenomic regulation of sensory plasticity

eLife(2023)10.7554/elife.83979
N/A
0DataRank · unranked
17 citations

Anoumid Vaziri, Daniel Wilinski, Riley K.R. Woerner, Lydia Freddolino, Monica Dus +1 more

Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.08.531771
N/A
0DataRank · unranked
2 citations

Melissa Seman, Ali Farhat, Yekaterina Fyodorova, Saikat Biswas, Alexander Levashkevich +4 more

A large-scale assessment of sequence database search tools for homology-based protein function prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.14.567021
N/A
0DataRank · unranked
2 citations

Lydia Freddolino, Chengxin Zhang

Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.29.555372
N/A
0DataRank · unranked
0 citations

Catherine Barnier, Nathan D. Elrod, Hua Luo, Madeline K. Jensen, Ping Ji +6 more

A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited

Microbiology and Molecular Biology Reviews(2020)10.1128/mmbr.00030-17
N/A
0DataRank · unranked
24 citations

Christine A. Ziegler, Lydia Freddolino, Alan J. Wolfe, Mario Zamora

Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae

mSphere(2024)10.1128/msphere.00011-24
N/A
0DataRank · unranked
9 citations

Drew T. Dunham, Kimberley D. Seed, Lydia Freddolino, Yulduz Rakibova

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

EcoSal Plus(2024)10.1128/ecosalplus.esp-0001-2022
N/A
0DataRank · unranked
3 citations

Lydia Freddolino, Sonya Royzenblat

Enricherator: A Bayesian Method for Inferring Regularized Genome-wide Enrichments from Sequencing Count Data

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168567
N/A
0DataRank · unranked
3 citations

Lydia Freddolino, Jeremy W. Schroeder

Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2023.12.30.573743
N/A
0DataRank · unranked
1 citations

Drew T. Dunham, Kimberley D. Seed, Lydia Freddolino, Yulduz Rakibova

Polyphosphate: The “Dark Matter” of Bacterial Chromatin Structure

Molecular Microbiology(2025)10.1111/mmi.15350
N/A
0DataRank · unranked
10 citations

Lydia Freddolino, Lisa R. Racki

Viperin expression leads to downregulation of mitochondrial genes through misincorporation of ddhCTP by mitochondrial RNA polymerase

Journal of Biological Chemistry(2025)10.1016/j.jbc.2025.108359
N/A
0DataRank · unranked
3 citations

Pronay Roy, Minshik Jo, Jiying Liu, Rebecca L. Hurto, Lydia Freddolino +2 more

Highlights of Model Quality Assessment in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70035
N/A
0DataRank · unranked
1 citations

Recep Adiyaman, Shaima N Alhaddad, Bijan Behzadi, Jianlin Cheng, Xinyue Cui +19 more

StoPred: Accurate Stoichiometry Prediction for Protein Complexes Using Protein Language Models and Graph Attention

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.20.683515
N/A
0DataRank · unranked
2 citations

Chunxiang Peng, Wei Zheng, Chengxin Zhang, Lydia Freddolino, Quancheng Liu

Conserved Heterochromatin-like Structures with Local Regulators Mediate the Iron Stress Response in Mycobacteria

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.23.671944
N/A
0DataRank · unranked
1 citations

Agata Turula, Jeremy W. Schroeder, Rebecca L. Hurto, Quancheng Liu, Lydia Freddolino +2 more

DNA methylation affects gene expression but not global chromatin structure in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.06.631547
N/A
0DataRank · unranked
0 citations

Haley M. Amemiya, Lydia Freddolino, Willow Jay Morgan

Correction to: High-Throughput Mapping of Chromosomal Conformations in E. coli Under Physiological Conditions Using Massively Multiplexed Mu Transposition

Methods in molecular biology(2025)10.1007/978-1-0716-3930-6_30
N/A
0DataRank · unranked
0 citations

Sonya Royzenblat, Brady Wilkins, Rasika M. Harshey, Lydia Freddolino, Khang Ho

The lac operon in uropathogenic Escherichia coli enhances intracellular growth by enabling host glycan utilization

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.03.691977
N/A
0DataRank · unranked
0 citations

Devina Puri, Taylor M. Nye, Rebecca L. Hurto, Jennie E. Hazen, Nathaniel C. Gualberto +6 more

The Algorithm for Reversible Jump Inference of Motifs

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.25.696506
N/A
0DataRank · unranked
0 citations

Lydia Freddolino, Ali Farhat

Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data

Nature Methods(2024)10.1038/s41592-023-02130-4
N/A
0DataRank · unranked
130 citations

Qiqige Wuyun, Yang Li, Chengxin Zhang, Lydia Freddolino, Yang Zhang +1 more

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

PLoS Biology(2021)10.1371/journal.pbio.3001306
N/A
0DataRank · unranked
43 citations

Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie, Lydia Freddolino

CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks

Nature Methods(2022)10.1038/s41592-021-01389-9
N/A
0DataRank · unranked
76 citations

Biao Zhang, Lydia Freddolino, Yang Zhang, Xi Zhang

Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape

mBio(2022)10.1128/mbio.00135-22
N/A
0DataRank · unranked
64 citations

Guilhem Faure, Yuri I. Wolf, Lydia Freddolino, Feng Zhang, Eugene V. Koonin +1 more

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation

Nucleic Acids Research(2022)10.1093/nar/gkac248
N/A
0DataRank · unranked
41 citations

Qiqige Wuyun, Xiaogen Zhou, Yang Li, Lydia Freddolino, Yang Zhang +1 more

Genetic context effects can override canonical cis regulatory elements in Escherichia coli

Nucleic Acids Research(2022)10.1093/nar/gkac787
N/A
0DataRank · unranked
21 citations

Chase D. Lindeboom, Lydia Freddolino, Scott A. Scholz

Intracellular acidification is a hallmark of thymineless death in E. coli

PLoS Genetics(2022)10.1371/journal.pgen.1010456
N/A
0DataRank · unranked
11 citations

Lydia Freddolino, Saeed Tavazoie, Alexandra Ketcham

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

Nature Communications(2023)10.1038/s41467-023-41303-9
N/A
0DataRank · unranked
106 citations

Chengxin Zhang, Chenjie Feng, Robin Pearce, Lydia Freddolino, Yang Zhang +1 more