Luis Amaral
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About
Professor Luis Amaral is a faculty member at Northwestern University in the United States. His research focuses on computational biology, artificial intelligence, and the ethical implications of these technologies in genomic studies. Recent publications address the limitations of convolutional neural networks, the need for scientifically driven methodologies in AI, and the impact of energy metabolism on gene expression. He also explores the dynamics of protein interactions and gene transcription in relation to aging and other biological processes.
Recent Grants
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A1: Systematic Content Analysis of Litigation Events (SCALES) Open Knowledge Network to Enable Transparency and Access to Court Records
Open Date: 2020-09-01
Close Date: 2022-08-31
Grant: Close
SCISIPBIO: A data-science approach to evaluating the likelihood of fraud and error in published studies
Open Date: 2020-09-01
Close Date: 2022-08-31
Grant: Close
EAGER: Investigating the Hinge Mechanics of the Spike Protein to Understand the Coronavirus Infection Mechanism
Open Date: 2020-06-15
Close Date: 2021-11-30
Grant: Close
Convergence Accelerator Phase I (RAISE): Northwestern Open Access to Court Records Initiative
Open Date: 2019-09-01
Close Date: 2021-05-31
Grant: Close
Successful Clinical Response In Pneumonia Therapy (SCRIPT) Systems Biology Center
Open Date: 2018-01-17
Close Date: 2022-12-31
Articles (15)
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2024
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2024
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2024
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2024
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2024
Cell state transitions are often triggered by large changes in the concentrations of transcription factors and therefore large differences in their stoichiometric ratios. Whether cells can elicit transitions using modest changes in the ratios of co-expressed factors is unclear. Here, we investigate how cells in the Drosophila eye resolve state transitions by quantifying the expression dynamics of the ETS transcription factors Pnt and Yan. Eye progenitor cells maintain a relatively constant ratio of Pnt/Yan protein, despite expressing both proteins with pulsatile dynamics. A rapid and sustained twofold increase in the Pnt/Yan ratio accompanies transitions to photoreceptor fates. Genetic perturbations that modestly disrupt the Pnt/Yan ratio produce fate transition defects consistent with the hypothesis that transitions are normally driven by a twofold shift in the ratio. A biophysical model based on cooperative Yan-DNA binding coupled with non-cooperative Pnt-DNA binding illustrates how twofold ratio changes could generate ultrasensitive changes in target gene transcription to drive fate transitions. Thus, coupling cell state transitions to the Pnt/Yan ratio sensitizes the system to modest fold-changes, conferring robustness and ultrasensitivity to the developmental program.
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2023
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2023
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2023
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2022
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2022
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2021
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2020
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2020
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2020
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2020
Collaborators (6)
Richard W. Carthew
-
Michael Schwake
Bielefeld University
Thomas Stoeger
Assistant Professor
Northwestern University
Kristi Holmes
Professor
Northwestern University Feinberg School of Medicine
Sinan Keten
-
Cleber Zanchettin
Adjunct Associate Professor
Northwestern University
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