The paper introduces an interactive Data Integrator for uniform processing and integration of bulk RNA-seq datasets from the MorPhiC program and external sources.

bioRxiv · Oct 19, 2026 · PreprintBioinformatics

DIANNE: Segmentation-Free Localization of Histology Differential Attributes

Sergii Domanskyi, Jill Carol Rubinstein, Todd Sheridan, Adam H. Thiesen, Javad Noorbakhsh, Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Dylan S. Baker, Riley Sheldon, Qian Wu, George A. Kuchel, Nicolas Musi, Sara E Espinoza, Francisco G. Cigarroa, Paul Robson, Jeffrey H. Chuang

DIANNE enables rapid training and inference of spatial differential attributes in histology images without manual annotations, using mixup augmentation and foundation models.

bioRxiv · Jul 23, 2026 · PreprintPathology

A human and mouse subpopulation of senescent β-cells induces pathologic dysfunction through targetable paracrine signaling

Kanako Iwasaki, Priscila Carapeto, Cristian Abarca, Francesko Hela, Stephanie Sanjines, Sebastian Pena, Sandra M. Le, Hui Pan, Christopher Cahill, Ayush D. Midha, Juliana Alcoforado Diniz, Dylan S. Baker, Sergii Domanskyi, Sara Espinoza, Alejandro Pena, , Cristina Aguayo‐Mazzucato

The paper identifies senescent β-cell subpopulations in humans and mice that induce pathologic dysfunction through paracrine signaling and shows JAK inhibitors can reverse this effect.

bioRxiv · May 7, 2025 · PreprintDevelopmental Biology

A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening

Bruno Boivin, Kasper C. D. Roet, Xuan Huang, Kyle W. Karhohs, Mohammad Hossein Rohban, Jackson Sandoe, Ole Wiskow, Rie K. Maeda, Alyssa Grantham, Mary Kate Dornon, Jenny Shao, Devlin Frost, Dylan S. Baker, Kevin C. Eggan, Anne Elizabeth Carpenter, Clifford J. Woolf

The paper introduces a cloud-based platform for analyzing calcium activity in motor neurons to identify compounds that reverse disease phenotypes in amyotrophic lateral sclerosis.

Molecular Biology of the Cell · Dec 15, 2021Peer-reviewedNeuroscience

A Cellular Reference Resource for the Mouse Urinary Bladder

Dylan S. Baker, Iman M. Al‐Naggar, Santhosh K. Sivajothi, William F. Flynn, Anahita Amiri, Diane Luo, Cara C. Hardy, George A. Kuchel, Phillip P. Smith, Paul Robson

This paper defines the cellular composition of the mouse urinary bladder using single-cell profiling and spatial analysis, identifying novel cell types and fibroblast populations associated with aging.

bioRxiv · Sep 20, 2021 · PreprintGenomics

Hyperexcitable phenotypes in iPSC-derived neurons from patients with 15q11-q13 duplication syndrome, a genetic form of autism

James J. Fink, Jeremy D. Schreiner, Judy E. Bloom, Jadin James, Dylan S. Baker, Tiwanna M. Robinson, Richard Lieberman, Leslie M. Loew, Stormy J. Chamberlain, Eric S. Levine

This study investigates hyperexcitability in iPSC-derived neurons from Dup15q patients, identifying mechanisms like delayed action potential maturation and KCNQ2 channel disruption.

bioRxiv · Mar 21, 2018Neuroscience