Latest Publications

Artificial intelligence-enabled automated analysis of transmission electron micrographs to evaluate chemotherapy impact on mitochondrial morphology in triple negative breast cancer.

Argenis Arriojas, Lily Baek, Mariah Berner, Alexander Zhurkevich, Antentor Hinton, Matthew D. Meyer, Lacey E. Dobrolecki, Michael T. Lewis, Kourosh Zarringhalam, Gloria Echeverria.

bioRxiv.

Feb 19, 2025 in Computational Biology, Machine Learning, Cancer Biology, Image Analysis
Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver.

Jingjing Lou, Yasaman Rezvani, Argenis Arriojas, Yihan Wu, David Degras, Caroline Keroack, Manoj T Duraisingh, Kourosh Zarringhalam, Marc‑Jan Gubbels.

Nature Communications, 15(1), 7419 (2024).

Feb 20, 2024 in Computational Biology, Genomics, Parasitology
A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data.

Argenis Arriojas, Susan Palatano, Jill Macoska, Kourosh Zarringhalam.

NAR Genomics and Bioinformatics, 5(4), lqad106 (2023).

Nov 3, 2023 in Computational Biology, Bayesian Methods, Genomics, Transcriptomics
Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles.

Yasaman Rezvani, Caroline Keroack, Brendan Elsworth, Argenis Arriojas, Marc‑Jan Gubbels, Manoj T Duraisingh, Kourosh Zarringhalam.

PLOS Biology, 20(9), e3001816 (2022).

Sep 28, 2022 in Computational Biology, Parasitology, Single-cell Genomics
The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming.

Vincent A. Primo Jr., Yasaman Rezvani, Andrew Farrell, Connor Q. Murphy, Jingjing Lou, Amir Vajdi, Gabor T. Marth, Kourosh Zarringhalam, Marc‑Jan Gubbels.

mSystems 6:e01196-21 (2021).

Dec 21, 2021 in Computational Biology, Parasite Biology, Genomics, Experimental Evolution