Publications
(* denotes equal contribution)
First Author Publications
Sohn M-H*, Dubocanin D*, Vollger MR, Kwon Y, Minkina A, Munson KM, Hart SFM, Ranchalis JE, Parmalee NL, Sedeno-Cortes AE, Ou J, Au NYT, Bohaczuk S, Carroll B, Frazar CD, Harvey WT, Hoekzema K, Huang M-F, Jacques CN, Jensen DM, Kolar JT, Lee R, Lin J, Loy K, Mack T, Mao Y, Pham MM, Ryke E, Smith JD, Sutherlin L, Swanson EG, Weiss JM, SMaHT Assembly Working Group, Carvalho C, Coorens THH, Harris K, Wei C-L, Eichler EE, Altemose N, Bennett JT, Stergachis AB.
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer.
bioRxiv (2025). https://doi.org/10.1101/2025.10.10.681725
Dubocanin D, Kalygina A, Franklin JM, Chittenden C, Vollger MR, Neph S, Stergachis AB, Altemose N.
Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.
bioRxiv (2025). https://doi.org/10.1101/2025.02.26.640261
Dubocanin D, … , Stergachis AB.
Conservation of dichromatin organization along regional centromeres.
Cell Genomics (2025). https://doi.org/10.1101/2023.04.20.537689
Dubocanin D, Sedeno Cortes AE, Ranchalis J, Real T, Mallory B, Stergachis AB.
Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin.
bioRxiv (2022). https://doi.org/10.1101/2022.05.09.491186
Second Author Publications
Salinas-Luypaert, C., Dubocanin, D*., Lee, R.J*…Altemose N, Fachinetti D
DNA methylation influences human centromere positioning and function.
Nature Genetics (2025). https://doi.org/10.1038/s41588-025-02324-w
Carty BL, Dubocanin D, Murillo-Pineda M, Dumont M, Volpe E, Mikulski P, Humes J, Whittingham O, Fachinetti D, Giunta S, Altemose N, Jansen LET.
Heterochromatin boundaries maintain centromere position, size, and number.
Nature Structural & Molecular Biology (2025). https://doi.org/10.1101/2025.02.03.635667
Franklin JM, Dubocanin D, Chittenden C, Barillas A, Lee RJ, Ghosh RP, Gerton JL, Guan K-L, Altemose N.
Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms.
bioRxiv (2024). https://doi.org/10.1101/2024.10.22.616524
Additional Publications
Real TD, Hebbar P, Yoo D, Antonacci F, Pacar I, Dubocanin D, Diekhans M, Mikol GJ, Popoola OG, Mallory BJ, Vollger MR, Dishuck PC, Guitart X, Rozanski AN, Munson KM, Hoekzema K, Ranchalis JE, Neph SJ, Sedeno-Cortes AE, Paten B, Salama SR, Stergachis AB, Eichler EE.
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications.
Cell Genomics (2026). https://doi.org/10.1016/j.xgen.2026.101194
Xu Y, Loucks H, Menendez J, Ryabov F, Lucas JK, Cechova M, Morina L, Xu E, Dubocanin D, Chittenden C, Asri M, Violich I, Ortiz C, Gardner JMV, Hillaker T, O'Rourke S, McNulty B, Potapova TA, Mitchell MW, Schwartz JP, Straight AF, Gerton JL, Timp W, Alexandrov IA, Altemose N, Miga KH.
Haplotype-resolved centromeric chromatin organization from a complete diploid human genome.
bioRxiv (2026). https://doi.org/10.64898/2026.03.27.714900
Tullius TW, Heuer RA, Bohaczuk SC, Mallory B, Dubocanin D, Ranchalis J, Ayaz A, Mason C, Seli E, Phillippy AM, Stergachis AB, Lesch BJ.
Protamine lacunae preserve the paternal chromatin landscape in sperm.
bioRxiv (2025). https://doi.org/10.1101/2025.10.10.667890
Mallory BJ, Tullius TW, Biar CG, Gustafson JA, Bohaczuk SC, Dubocanin D, Starita LM, Stergachis AB.
Principles and functional consequences of plasmid chromatinization in mammalian cells.
bioRxiv (2025). https://doi.org/10.1101/2025.05.27.656122
Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O’Neill RJ.
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.
Cell Genomics (2025). https://doi.org/10.1101/2024.08.29.610280
Sheth MU, Qiu W-L, Ma XR, Gschwind AR, Jagoda E, Tan AS, Einarsson H, Gorissen BL, Dubocanin D, McGinnis CS, Amgalan D, Satpathy AT, Jones TR, Steinmetz LM, Kundaje A, Ustun B, Engreitz JM, Andersson R.
Mapping enhancer-gene regulatory interactions from single-cell data.
bioRxiv (2024). https://doi.org/10.1101/2024.11.23.624931
Doughty BR, Hinks MH, Schaepe JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L, Greenleaf WJ.
Single-molecule states link transcription factor binding to gene expression.
Nature (2024). https://doi.org/10.1038/s41586-024-08219-w
Tullius TW, Isaac RS, Dubocanin D, Ranchalis J, Churchman S, Stergachis AB.
RNA polymerases reshape chromatin architecture and couple transcription on individual fibers.
Molecular Cell (2024). https://doi.org/10.1016/j.molcel.2024.08.013
Jha A, Bohaczuk SC, Mao Y , Ranchalis J, Mallory BJ, Min AT, Hamm MO, Swanson E, Dubocanin D, Finkbeiner D, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR.
DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.
Genome Research (2024). https://doi.org/10.1101/2023.04.20.537673
Isaac, RS, Tullius, TW, Hansen KG, Dubocanin D, Couvillion M , Stergachis AB, Churchman S.
Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.
Nature Structural & Molecular Biology (2024). https://doi.org/10.1038/s41594-024-01225-6
Volden R, Schimke K, Byrne A, Dubocanin D, Adams M, Vollmers C.
Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion.
Genome Biology (2023). https://doi.org/10.1186/s13059-023-02999-6
Haldipur P, Bernardo S, Aldinger KA, Sivakumar T, Millman J, Sjoboen AH, Dang D, Dubocanin D, …, Millen KJ.
Evidence of disrupted rhombic lip development in the pathogenesis of Dandy-Walker malformation.
Acta Neuropathol (2021). 10.1007/s00401-021-02355-7