Publications by authors named "Gregory Fonseca"

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SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbation.
Yasmin Jolasun, Kailu Song, Yumin Zheng, Jingtao Wang, Gregory J Fonseca

Nat Commun· December 2025

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scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization.
Guo Jiang, Kailu Song, Gregory J Fonseca, Darcy E Wagner, Iain C Clark

Nat Commun· November 2025

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DENetwork unveils non-differentially expressed genes with functional relevance across conditions through information flow perturbation.
Bowen Zhao, Ting-Yi Su, Jingtao Wang, Quazi S Islam, Kailu Song, Gregory J Fonseca

Nucleic Acids Res· November 2025

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Biological responses during high-dose protein nutrition in the critically ill: a randomized controlled trial.
Arnold S Kristof, Mengyin Hong, Nadia Boufaied, Nihad Tousson-Abouelazm, Surya Dandamudi, Gregory J Fonseca

Am J Clin Nutr· August 2025

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Machine-guided cell-fate engineering.
Evan Appleton, Jenhan Tao, Songlei Liu, Christopher Glass, Gregory Fonseca

Cell Rep· June 2025

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Efficient and scalable construction of clinical variable networks for complex diseases with RAMEN.
Yiwei Xiong, Jingtao Wang, Xiaoxiao Shang, Tingting Chen, Douglas D Fraser, Gregory J Fonseca

Cell Rep Methods· April 2025

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Crash testing machine learning force fields for molecules, materials, and interfaces: molecular dynamics in the TEA challenge 2023.
Igor Poltavsky, Mirela Puleva, Anton Charkin-Gorbulin, Grégory Fonseca, Ilyes Batatia

Chem Sci· February 2025

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Crash testing machine learning force fields for molecules, materials, and interfaces: model analysis in the TEA Challenge 2023.
Igor Poltavsky, Anton Charkin-Gorbulin, Mirela Puleva, Grégory Fonseca, Ilyes Batatia

Chem Sci· February 2025

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Younger epigenetic age is associated with higher cardiorespiratory fitness in individuals with airflow limitation.
Ana I Hernandez Cordero, Carli Peters, Xuan Li, Chen Xi Yang, Amirthagowri Ambalavanan, Gregory J Fonseca

iScience· October 2024

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scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning.
Jingtao Wang, Gregory J Fonseca, Jun Ding

Nat Commun· July 2024

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In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells.
Juan Carlos Jado, Michelle Dow, Krypton Carolino, Adam Klie, Gregory J Fonseca

Sci Rep· June 2024

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Induction of a memory-like CD4 T-cell phenotype by airway smooth muscle cells.
Joyce H Jang, Michael Zhou, Kosuke Makita, Rui Sun, Mikal El-Hajjar, Gregory Fonseca

Eur J Immunol· April 2024

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Regulation of long non-coding RNA expression by aryl hydrocarbon receptor activation.
Aeshah Alluli, Gregory Fonseca, Jason Matthews, David H Eidelman, Carolyn J Baglole

Toxicol Lett· January 2024

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Force Field Analysis Software and Tools (FFAST): Assessing Machine Learning Force Fields under the Microscope.
Gregory Fonseca, Igor Poltavsky, Alexandre Tkatchenko

J Chem Theory Comput· December 2023

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Differences in the Tumor Microenvironment of EBV-Associated Gastric Cancers Revealed Using Single-Cell Transcriptome Analysis.
Mikhail Y Salnikov, Gregory J Fonseca, Joe S Mymryk

Cancers (Basel)· June 2023

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Receptor-mediated effects of Δ -tetrahydrocannabinol and cannabidiol on the inflammatory response of alveolar macrophages.
Matthew W Preteroti, Hussein Traboulsi, Patrick Greiss, Orsolya Lapohos, Gregory J Fonseca

Immunol Cell Biol· February 2023

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DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal.
Paola Cattaneo, Michael G B Hayes, Nina Baumgarten, Dennis Hecker, Sofia Peruzzo, Gregory Fonseca

Nat Commun· December 2022

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Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity.
Danielle Karo-Atar, Shaida Ouladan, Tanvi Javkar, Loick Joumier, Macy K Matheson, Gregory J Fonseca

J Exp Med· September 2022

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TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy.
Salyan Bhattarai, Qian Li, Jun Ding, Feng Liang, Ekaterina Gusev, Gregory J Fonseca

Nat Commun· February 2022

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Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs.
Zeyang Shen, Rick Z Li, Thomas A Prohaska, Marten A Hoeksema, Nathan J Spann, Gregory J Fonseca

Elife· January 2022

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A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19.
Jun Ding, David Earl Hostallero, Mohamed Reda El Khili, Gregory Joseph Fonseca, Simon Milette

PLoS Comput Biol· March 2021

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Challenges for machine learning force fields in reproducing potential energy surfaces of flexible molecules.
Valentin Vassilev-Galindo, Gregory Fonseca, Igor Poltavsky, Alexandre Tkatchenko

J Chem Phys· March 2021

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Improving molecular force fields across configurational space by combining supervised and unsupervised machine learning.
Gregory Fonseca, Igor Poltavsky, Valentin Vassilev-Galindo, Alexandre Tkatchenko

J Chem Phys· March 2021

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Angiotensin-converting enzyme 2 expression in COPD and IPF fibroblasts: the forgotten cell in COVID-19.
Noof Aloufi, Hussein Traboulsi, Jun Ding, Gregory J Fonseca, Parameswaran Nair

Am J Physiol Lung Cell Mol Physiol· January 2021

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Infiltrating Hematogenous Macrophages Aggregate Around β-Amyloid Plaques in an Age- and Sex-Dependent Manner in a Mouse Model of Alzheimer Disease.
Natalie Kozyrev, Shawn Albers, Jennifer Yang, Vania F Prado, Marco A M Prado, Gregory J Fonseca

J Neuropathol Exp Neurol· November 2020

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