Publications

Enhancing generative perturbation models with LLM-informed gene embeddings

Authors: Kaspar Märtens, Rory Donovan-Maiye, and Jesper Ferkinghoff-Borg

ICLR 2024 Workshop on Machine Learning for Genomics Explorations • 2024

Integrated intracellular organization and its variations in human ips cells

Authors: Matheus P Viana, Jianxu Chen, Theo A Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Eva M Brown, et al. (including Rory Donovan-Maiye)

Nature • 2023

Nature, 613(7943):345–354, 2023.

A deep generative model of 3d single-cell organization

Authors: Rory M Donovan-Maiye, Jackson M Brown, Caleb K Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A Theriot, Mary M Maleckar, Theo A Knijnenburg, and Gregory R Johnson

PLOS Computational Biology • 2022

PLOS Computational Biology, 18(1):e1009155, 2022.

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hipsc-derived cardiomyocytes

Authors: Kaytlyn A Gerbin, Tanya Grancharova, Rory M Donovan-Maiye, Melissa C Hendershott, Helen G Anderson, Jackson M Brown, Jianxu Chen, Stephanie Q Dinh, Jamie L Gehring, Gregory R Johnson, et al.

Cell Systems • 2021

Cell Systems, 12(6):670–687, 2021.

Atlas of transcription factor binding sites from encode dnase hypersensitivity data across 27 tissue types

Authors: Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, et al.

Cell Reports • 2020

Cell Reports, 32(7), 2020.

Systematic testing of belief-propagation estimates for absolute free energies in atomistic peptides and proteins

Authors: Rory M Donovan-Maiye, Christopher J Langmead, and Daniel Zuckerman

Journal of Chemical Theory and Computation • 2017

Biophysical comparison of atp synthesis mechanisms shows a kinetic advantage for the rotary process

Authors: Ramu Anandakrishnan, Zining Zhang, Rory Donovan-Maiye, and Daniel M Zuckerman

Proceedings of the National Academy of Sciences • 2016

PNAS, 113(40):11220–11225, 2016.

Unbiased rare event sampling in spatial stochastic systems biology models using a weighted ensemble of trajectories

Authors: Rory M Donovan, Jose-Juan Tapia, Devin P Sullivan, James R Faeder, Robert F Murphy, Markus Dittrich, and Daniel M Zuckerman

PLoS Computational Biology • 2016

Learning mixed graphical models with separate sparsity parameters and stability-based model selection

Authors: Andrew J Sedgewick, Ivy Shi, Rory M Donovan, and Panatiotis V Benos

BMC Genomics • 2014

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

Authors: Rory M Donovan, Andrew J Sedgewick, James R Faeder, and Daniel M Zuckerman

The Journal of Chemical Physics • 2013

The Journal of Chemical Physics, 139(11):115105, 2013.