Publications

2025

DNA methylation influences human centromere positioning and function

Salinas-Luypaert, C., Dubocanin, D*., Lee, R.J*…Altemose N, Fachinetti D . 

Nature Genetics. https://doi.org/10.1038/s41588-025-02324-w

Principles and functional consequences of plasmid chromatinization in mammalian cells

Benjamin J Mallory, Thomas W Tullius, Carina G Biar, Jonas A Gustafson, Stephanie C Bohaczuk, Danilo Dubocanin, Lea M Starita, Andrew B Stergachis

bioRxiv. https://doi.org/10.1101/2025.05.27.656122

Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition

Danilo Dubocanin, Anna Kalygina, J. Matthew Franklin, Cy Chittenden, Mitchell R Vollger, Shane Neph, Andrew B Stergachis, Nicolas Altemose  

bioRxiv. https://doi.org/10.1101/2025.02.26.640261

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

Gabrielle A. Hartley, Maryam Okhovat, Samuel J. Hoyt, Emily Fuller, Niall Pauloski, Nicholas Alexandre, Ilya Alexandrov, Russell Drennan, Danilo Dubocanin, Diana M. Gilbert, Yizi Mao, Craig McCann, Shane Neph, Fedor Ryabov, Takashi Sasaki, Jackson M. Storer, David Svendsen, William Troy, Jacob Wells, Jason Core, Andrew Stergachis, Lucia Carbone, Rachel J. O’Neill  

Cell Genomics. https://doi.org/10.1101/2024.08.29.610280

Heterochromatin boundaries maintain centromere position, size, and number

Ben L Carty, Danilo Dubocanin, Marina Murillo-Pineda, Marie Dumont, Emilia Volpe, Pawel Mikulski, Julia Humes, Oliver Whittingham, Daniele Fachinetti, Simona Giunta, Nicolas Altemose, Lars E.T. Jansen  

bioRxiv. https://doi.org/10.1101/2025.02.03.635667

Conservation of dichromatin organization along regional centromeres 

Danilo Dubocanin,  Gabrielle A. Hartley,  Adriana E. Sedeno Cortes,  Yizi Mao,  Sabrine Hedouin, Jane Ranchalis, Aman Agarwal,  Glennis A. Logsdon, Katherine M. Munson, Taylor Real,  Benjamin J. Mallory,  Evan E. Eichler,  Sue Biggins,  Rachel J. O’Neill,  Andrew B. Stergachis

Cell Genomics. https://doi.org/10.1101/2023.04.20.537689


2024

Mapping enhancer-gene regulatory interactions from single-cell data

Monika U. Sheth, Wen-Ling Qiu, Xiaotian Ma, Andreas R. Gschwind, Ewy Jagoda, Adrian S. Tan, Helga Einarsson, Bart L. Gorissen, Danilo Dubocanin, Clinton S. McGinnis, Dorj-Amgalan Amgalan, Anslem T. Satpathy, Tomas R. Jones, Lars M. Steinmetz, Anshul Kundaje, Burak Ustun, Jesse M. Engreitz, Robin Andersson  

bioRxiv. https://doi.org/10.1101/2024.11.23.624931

Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms  

J. Matthew Franklin, Danilo Dubocanin, Cy Chittenden, Alice Barillas, Rose J. Lee, Rahul Pratyush Ghosh, Jennifer L. Gerton, Kun-Liang Guan, Nicolas Altemose  

bioRxiv. https://doi.org/10.1101/2024.10.22.616524

Single-molecule states link transcription factor binding to gene expression

Bernhard R. Doughty, Megan H. Hinks, Jonathan M. Schaepe, Georg K. Marinov, Amir R. Thurm, Carlos Rios-Martinez, Ben E. Parks, Yixin Tan, Emelie Marklund, Danilo Dubocanin, Leighton B. Bintu, William J. Greenleaf  

Nature. https://doi.org/10.1038/s41586-024-08219-w

RNA polymerases reshape chromatin architecture and couple transcription on individual fibers

Tyler W. Tullius, Robert S. Isaac, Danilo Dubocanin, Jared Ranchalis, Sarah Churchman, Andrew B. Stergachis  

Molecular Cell. https://doi.org/10.1016/j.molcel.2024.08.013

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

Amit Jha, Stephanie C. Bohaczuk, Yizi Mao, Jared Ranchalis, Ben J. Mallory, Athena T. Min, Marie O. Hamm, Emily Swanson, Danilo Dubocanin, David Finkbeiner, Tongtong Li, Daniel Whittington, William S. Noble, Andrew B. Stergachis, Mitchell R. Vollger  

Genome Research. https://doi.org/10.1101/2023.04.20.537673

Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA  

Robert S. Isaac, Tyler W. Tullius, Kyle G. Hansen, Danilo Dubocanin, Michael Couvillion, Andrew B. Stergachis, Sarah Churchman  

Nature Structural & Molecular Biology. https://doi.org/10.1038/s41594-024-01225-6


2023

Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion

Roger Volden, Kayla D. Schimke, Ashley Byrne, Danilo Dubocanin, Matthew Adams, Christopher Vollmers  

Genome Biology 24(1): 167. https://doi.org/10.1186/s13059-023-02999-6


2022

Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin

Danilo Dubocanin, Adriana E. Sedeno Cortes, Jared Ranchalis, Taylor Real, Ben Mallory, Andrew B. Stergachis  

bioRxiv. https://doi.org/10.1101/2022.05.09.491186


2021

Evidence of disrupted rhombic lip development in the pathogenesis of Dandy–Walker malformation

Parthiv Haldipur, Silvia Bernardo, Kimberly A. Aldinger, Tarika Sivakumar, Jake Millman, Alexandria H. Sjoboen, Derek Dang, Danilo Dubocanin, Mei Deng, Andrew E. Timms, ..., Kenneth J. Millen  

Acta Neuropathologica. 142: 761-776. https://doi.org/10.1007/s00401-021-02355-7