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