The paper introduces SPACE-Tag, a spatial CUT&Tag method for chromatin profiling, and applies it to the mouse brain to reveal age-related chromatin and transcriptome changes.

bioRxiv · Nov 7, 2026 · PreprintGenomics

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Benjamin Kumar Wesley, Frank Wos, Søren Germer, Jade Carter, Silas Maniatis, Khanh Ngoc Dinh, James S. Roche, Timothy R. Chu, Nicolas Robine, Rebecca Claire Fitzgerald, Lizhe Zhuang, Simon Tavaré, Karol Nowicki-Osuch

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

Nucleic Acids Research · Sep 22, 2026Peer-reviewedBioinformatics

Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis

Maithê Rocha Monteiro de Barros, Katharina Bosch, Salima Soualhi, Shirin Issa Bhaloo, Thomas Chu, Tanya Hemrajani, Jin Cho, Kurtay Ozuner, Rui Fu, Heather M. Geiger, Nicolas Robine, Jade Carter, Silas Maniatis, Sandra W. Ryeom, Simon Tavaré, Karol Nowicki-Osuch

bioRxiv · Apr 27, 2026 · PreprintGenomics

Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord

John F. Tuddenham, Masashi Fujita, Emily Lee, Nivedita Nimmagadda, Anthony Khairallah, Claire Harbison, Xena E. Flowers, Guillermo Coronas‐Samano, Silas Maniatis, Aidan C. Daly, Julie A. Schneider, Andrew F. Teich, Jean Paul Vonsattel, Peter A. Sims, Wassim Elyaman, , Marta Olah

The paper identifies microglia subsets in ALS brain and spinal cord, finding an undifferentiated phenotype and enrichment of interferon response microglia in aggressive cases.

Acta Neuropathologica · Jul 29, 2025Peer-reviewedNeuroscience

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan Avi Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi

This paper introduces NTT-seq, a method to measure multiple chromatin features at single-cell resolution, and demonstrates its application in immune cells.

bioRxiv · Mar 8, 2022 · PreprintGenomics

PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms.

Kunal Pandit, Joana Petrescu, Miguel Cuevas, William Stephenson, Peter Smibert, Hemali P. Phatnani, Silas Maniatis

PySeq2500 converts the HiSeq 2500 into an open platform for programmable fluidics and imaging, enabling automated multi-day workflows for multiplexed imaging of biological samples.

bioRxiv · Aug 27, 2021 · PreprintGenomics

Splotch: Robust estimation of aligned spatial temporal gene expression data.

Tarmo Äijö, Silas Maniatis, Sanja Vicković, Kristy Kang, Miguel Cuevas, Catherine Braine, Hemali P. Phatnani, Joakim Lundeberg, Richard Bonneau

Splotch aligns spatial transcriptomics data across tissue sections and timepoints to improve gene expression estimates and study optimal experimental design.

bioRxiv · Sep 5, 2019 · PreprintBioinformatics

Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

Silas Maniatis, Tarmo Äijö, Sanja Vicković, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro, Miguel Cuevas, Aaron Watters, Joakim Lundeberg, Richard Bonneau, Hemali P. Phatnani

Analysis of the ALS spinal cord using Spatial Transcriptomics reveals spatiotemporal dynamics of disease driven gene regulation.

Science · Apr 4, 2019Peer-reviewedNeuroscience