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

Julio Collado‐Vides

Boston University

ORCID: 0000-0001-8780-7664

Also affiliated with Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Centre for Genomic Regulation, Universidad Autónoma del Estado de Morelos, Universidad Nacional Autónoma de México

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
26.6Author DataRank

Indexed papers

9in 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 9 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.

The Complete Genome Sequence of Escherichia coli K-12

Science(1997)10.1126/science.277.5331.1453
Top 1%
14.2DataRank
Top 1%7525 citations

Guy Plunkett, Craig A. Bloch, Nicole T. Perna, Valerie Burland, Monica Riley +16 more

Papers

Driven by 15 papers — median percentile 89. Top paper: “The Complete Genome Sequence of Escherichia coli K-12”.

The Complete Genome Sequence of Escherichia coli K-12

Science(1997)10.1126/science.277.5331.1453
Top 1%
14.2DataRank
Top 1%7525 citations

Guy Plunkett, Craig A. Bloch, Nicole T. Perna, Valerie Burland, Monica Riley +16 more

The EcoCyc Database in 2021

Frontiers in Microbiology(2021)10.3389/fmicb.2021.711077
Top 5%
4.2DataRank
Top 5%236 citations

Socorro Gama‐Castro, Amanda Mackie, Richard Billington, César Bonavides-Martínez, Ron Caspi +14 more

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

Microbial Genomics(2022)10.1099/mgen.0.000833
Top 8%
2.9DataRank
Top 8%117 citations

Claire Rioualen, Heladia Salgado, Paloma Lara, Socorro Gama‐Castro, Patrick Lally +17 more

The EcoCyc Database (2023)

EcoSal Plus(2023)10.1128/ecosalplus.esp-0002-2023
Top 10%
2.1DataRank
Top 10%97 citations

Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter Midford +16 more

RegulonDB v12.0: a comprehensive resource of transcriptional regulation inE. coliK-12

Nucleic Acids Research(2023)10.1093/nar/gkad1072
Top 11%
1.9DataRank
Top 11%113 citations

Socorro Gama‐Castro, Paloma Lara, Citlalli Mejía-Almonte, Gabriel Alarcón-Carranza, Andrés G. López-Almazo +20 more

The EcoCyc database (2025)

EcoSal Plus(2025)10.1128/ecosalplus.esp-0019-2024
Top 38%
0.512DataRank
Top 38%22 citations

Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter Midford +18 more

Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli

Nature Communications(2025)10.1038/s41467-025-58862-8
Top 50%
0.351DataRank
Top 50%8 citations

Laura Gómez-Romero, Víctor H. Tierrafría, Patricia Aquino, Claire Rioualen, Xiaoman Zhang +9 more

Missing Links Between Gene Function and Physiology in Genomics

Frontiers in Physiology(2022)10.3389/fphys.2022.815874
Top 55%
0.296DataRank
Top 55%4 citations

Pascale Gaudet, Vı́ctor de Lorenzo, Julio Collado‐Vides

Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.23.594371
Top 62%
0.223DataRank
Top 62%3 citations

Laura Gómez-Romero, Víctor H. Tierrafría, Patricia Aquino, Claire Rioualen, Xiaoman Zhang +9 more

Lisen&Curate: A platform to facilitate knowledge tools for curation of regulation of transcription initiation in bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.28.065243
N/A
0DataRank · unranked
0 citations

Martín Díaz-Rodríguez, Francisco Guadarrama-García, Oscar Lithgow-Serrano, Socorro Gama‐Castro, Hilda Solano-Lira +3 more

A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.21.614188
N/A
0DataRank · unranked
3 citations

Víctor H. Tierrafría, Laura Gómez-Romero, Anne M. Stringer, Julio Collado‐Vides, Joseph T. Wade +2 more

L-Regulon: A novel “soft-curation” approach supported by a semantic enriched reading for RegulonDB literature

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.26.062745
N/A
0DataRank · unranked
3 citations

Socorro Gama‐Castro, Cecilia Ishida-Gutiérrez, Julio Collado‐Vides, Oscar Lithgow-Serrano

Sensory Systems and Transcriptional Regulation in Escherichia coli

Frontiers in Bioengineering and Biotechnology(2022)10.3389/fbioe.2022.823240
N/A
0DataRank · unranked
9 citations

Socorro Gama‐Castro, Paloma Lara, Daniela Ledezma-Tejeida, Víctor H. Tierrafría, Luis Muñiz-Rascado +3 more

Redefining fundamental concepts of transcription initiation in bacteria

Nature Reviews Genetics(2020)10.1038/s41576-020-0254-8
N/A
0DataRank · unranked
157 citations

Stephen Busby, Joseph T. Wade, Jacques van Helden, Adam P. Arkin, Gary D. Stormo +5 more

Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms(2021)10.1016/j.bbagrm.2021.194753
N/A
0DataRank · unranked
3 citations

Oscar Lithgow-Serrano, Francisco Guadarrama-García, Víctor H. Tierrafría, Socorro Gama‐Castro, Hilda Solano-Lira +5 more