Publications
FIRST-AUTHOR PUBLICATIONS (* denotes equal contribution, ‡ denotes co-corresponding)
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 SC, 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.
Cell (In Press, 2026). https://doi.org/10.1101/2025.10.10.681725
Dubocanin D, Vollger MR, Neph SJ, Del Rio Pisula MS, Lucas JK, Sedeno-Cortes AE, Mallory BJ, Real TD, Human Pangenome Reference Consortium, Barthel FP, Altemose N‡, Stergachis AB‡.
Single-molecule variation in telomeric sequence and structure across humans.
bioRxiv. https://doi.org/10.64898/2026.05.01.722200
Dubocanin D, Hartley GA, Sedeno-Cortes AE, Mao Y, Hedouin S, Ranchalis JE, Agarwal A, Logsdon GA, Munson KM, Real TD, Mallory BJ, Eichler EE, Biggins S, O’Neill RJ, Stergachis AB.
Conservation of dichromatin organization along regional centromeres.
Cell Genomics 5, 100819 (2025). https://doi.org/10.1016/j.xgen.2025.100819
Dubocanin D, Kalygina A, Franklin JM, Chittenden C, Vollger MR, Neph SJ, 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
SECOND-AUTHOR PUBLICATIONS
Salinas-Luypaert C, Dubocanin D*, Lee RJ*, Ruiz LA, Gamba R, Grison M, Velikovsky L, Angrisani A, Scelfo A, Xu Y, Dumont M, Barra V, Wilhelm T, Velasco G, Losito M, Wardenaar R, Francastel C, Foijer F, Kops GJPL, Miga KH, Altemose N‡, Fachinetti D‡.
DNA methylation influences human centromere positioning and function.
Nature Genetics 57, 2509–2521 (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 33, 220–234 (2026). https://doi.org/10.1038/s41594-025-01706-2
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 (In Review at Nature, 2024). https://doi.org/10.1101/2024.10.22.616524
ADDITIONAL PUBLICATIONS
SMaHT Consortium (consortium member), Sedlazeck FJ, Coorens THH, Park PJ, Stergachis AB.
Integrated map of somatic mosaicism across human tissues in 25 individuals.
bioRxiv (2026). https://doi.org/10.64898/2026.09.01.748636
Lucas JK, Hebbar P, Liao WW, Macias-Velasco JF, Novak AM, Asri M, …, Dubocanin D, …, Altemose N, Stergachis AB, …, Paten B.
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.
bioRxiv (2026). https://doi.org/10.64898/2026.07.21.739710
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.
Nature Genetics 58, 1941–1952 (2026). https://doi.org/10.1038/s41588-026-02695-8
Vollger MR, Swanson EG, Neph SJ, Mallory BJ, Dubocanin D, Ho C-H, Cheng YHH, Ranchalis JE, Munson KM, Sedeno-Cortes AE, Mudeppa DG, Fondrie WE, Bohaczuk SC, Dippel MA, Mao Y, Parmalee NL, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB.
Somatic epimutations cap genetic determinism in the human diploid chromatin epigenome.
bioRxiv (2026). https://doi.org/10.1101/2024.06.14.599122
Mallory BJ, Tullius TW, Biar CG, Herlihy CP, Gustafson JA, Bohaczuk SC, Dubocanin D, Beliveau BJ, Schweppe DK, Starita LM‡, Stergachis AB‡.
Chromatin architectures underlying plasmid-based assays for regulatory variant effects.
Molecular Cell 86, 2041–2054.e9 (2026). https://doi.org/10.1016/j.molcel.2026.04.027
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 6, 101194 (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 DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.
Cell Genomics 6, 101324 (2026). https://doi.org/10.1016/j.xgen.2026.101324
Tullius TW, Heuer RA, Bohaczuk SC, Mallory BJ, Dubocanin D, Ranchalis JE, 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
Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov IA, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph SJ, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis AB, Carbone L, O’Neill RJ.
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.
Cell Genomics 5, 100808 (2025). https://doi.org/10.1016/j.xgen.2025.100808
Doughty BR, Hinks MM, 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 636, 745–754 (2024). https://doi.org/10.1038/s41586-024-08219-w
Tullius TW, Isaac RS, Dubocanin D, Ranchalis JE, Churchman LS‡, Stergachis AB‡.
RNA polymerases reshape chromatin architecture and couple transcription on individual fibers.
Molecular Cell 84, 3209–3222.e5 (2024). https://doi.org/10.1016/j.molcel.2024.08.013
Jha A, Bohaczuk SC, Mao Y, Ranchalis JE, Mallory BJ, Min AT, Hamm MO, Swanson EG, Dubocanin D, Finkbeiner C, 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 34, 1976–1986 (2024). https://doi.org/10.1101/gr.279095.124
Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB‡, Churchman LS‡.
Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.
Nature Structural & Molecular Biology 31, 568–577 (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 24, 167 (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, Deng M, Timms AE, Davis BD, Plummer JT, Mankad K, Oztekin O, Manganaro L, Guimiot F, Adle-Biassette H, Russo R, Siebert JR, Kidron D, Petrilli G, Roux N, Razavi F, Glass IA, Di Gioia C, Silvestri E, Millen KJ.
Evidence of disrupted rhombic lip development in the pathogenesis of Dandy-Walker malformation.
Acta Neuropathologica 142, 761–776 (2021). https://doi.org/10.1007/s00401-021-02355-7