Author

Patricia Aquino

Boston UniversityORCID 0000-0003-1065-4967Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 2 Organism:E. coli· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Research Focus:software / tool· 1

Frequent Co-Authors

James E. GalaganiD· 2 shared Julio Collado‐VidesiD· 2 shared Víctor H. TierrafríaiD· 2 shared Alberto Santos-ZavaletaiD· 1 shared Bernhard Ørn PalssoniD· 1 shared Carol Smith· 1 shared Claire RioualeniD· 1 shared David A. Velázquez-RamíreziD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersBioinformatics

James E. GalaganORCID

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2 papers

Recent·Most cited

BioinformaticsNature CommunicationsPeer-reviewedMay 7, 2025

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

Patrick Lally, Laura Gómez-Romero, Víctor H. Tierrafría…·James E. Galagan

The paper maps DNA binding of 139 E. coli TFs using ChIP-Seq and trains BoltzNet, a neural network that predicts TF binding energy from DNA sequence, validated with biophysical experiments.

13 citations

E. coliChIP-seq

𝕏 PostBluesky

Systems BiologyBMC BiologyPeer-reviewedAug 16, 2018

Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB.

Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado…·Julio Collado‐Vides

The paper expands RegulonDB to integrate high-throughput binding data with existing knowledge on gene regulation in E. coli K-12, enhancing its comprehensiveness and utility.

40 citations

E. coliChIP-seq

𝕏 PostBluesky