papers

Postdoc

2024

Lin, K.N., Volkel, K., Cao, C., Hook, P.W., Polak, R.E., Clark, A.S., San Miguel, A., Timp, W., Tuck, J.M., Velev, O.D., et al. (2024). A primordial DNA store and compute engine. Nat. Nanotechnol., 1–11. https://doi.org/10.1038/s41565-024-01771-6


Volkel, K.D., Hook, P.W., Keung, A., Timp, W., and Tuck, J.M. (2024). Nanopore Decoding with Speed and Versatility for Data Storage. bioRxiv, 2024.06.18.599582. https://doi.org/10.1101/2024.06.18.599582


Guerrero Zuniga, A., Aikin, T.J., McKenney, C., Lendner, Y., Phung, A., Hook, P.W., Meltzer, A., Timp, W., and Regot, S. (2024). Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication. Developmental Cell 59, 1–13. https://doi.org/10.1016/j.devcel.2024.03.032


Kovaka, S., Hook, P.W., Jenike, K.M., Shivakumar, V., Morina, L.B. Razaghi, R., Timp, W., Schatz, M .C (2024). Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. bioRxiv, 2024.03.05.58351. https://doi.org/10.1101/2024.03.05.583511


2023

Volkel, K.D, Lin, K.N., Hook, P.W., Timp, W., Keung, A.J., and Tuck, J.M (2023). FrameD: framework for DNA-based data storage design, verification, and validation. Bioinformatics, Volume 39, Issue 10, October 2023, btad572. https://doi.org/10.1093/bioinformatics/btad572


Rhie, A., Nurk, S., Cechova, M., Hoyt, S.J., Taylor, D.J., Altemose, N., Hook, P.W., Koren, S., Rautiainen, M., Alexandrov, I.A., …, Eichler, E.E, O’Neill, R., Schatz, M.C., Miga, K.H., Makova, K.D., and Phillippy, A.M. (2023). The complete sequence of a human Y chromosome. Nature 621, 344–354. https://doi.org/10.1038/s41586-023-06457-y


Hook, P.W., and Timp, W. (2023). Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat. Rev. Genet. 24, 627–641. https://doi.org/10.1038/s41576-023-00600-1


Boyd, R.J., McClymont, S.A., Barrientos, N.B., Hook, P.W., Law, W.D., Rose, R.J., Waite, E.L., Rathinavelu, J., Avramopoulos, D., and McCallion, A.S. (2023). Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. BMC Genomics 24, 306. https://doi.org/10.1186/s12864-023-09398-y


2022

Razaghi, R., Hook, P.W., Ou, S., Schatz, M. C., Hansen, K. D., Jain, M., & Timp, W. (2022). Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering. bioRxiv, 2022.07.07.499188. https://www.biorxiv.org/content/10.1101/2022.07.07.499188


Gershman, A., Sauria, M.E.G., Guitart, X., Vollger, M.R., Hook, P.W., Hoyt, S.J., Jain, M., Shumate, A., Razaghi, R., Koren, S., Altemose, N., Caldas, G.V., Logsdon, G.A., Rhie, A., Eichler, E.E., Schatz, M.C., O’Neill, R.J., Phillippy, A.M., Miga, K.H., & Timp, W. (2022). Epigenetic patterns in a complete human genome. Science, 376 (6588), eabj5089. https://doi.org/10.1126/science.abj5089



Grad school

2020

Soto-Beasley, A.I., Walton, R.L., Valentino, R.R., Hook, P.W., Labbé, C., Heckman, M.G., Johnson, P.W., Goff, L.A., Uitti, R.J., McLean, P.J., Springer, W., McCallion, A.S., Wszolek, Z.K., & Ross, O.A. (2020). Screening non-MAPT genes of the Chr17q21 H1 haplotype in Parkinson’s disease. Parkinsonism & Related Disorders, 78, 138–144. https://doi.org/10.1016/j.parkreldis.2020.07.022


Hook, P.W., & McCallion, A.S. (2020). Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia. Genome Res. 30, 528–539. https://doi.org/10.1101/gr.256578.119

Previous preprint versions can be found on bioRxiv. doi: https://doi.org/10.1101/427484


2018

McClymont, S.A., Hook, P.W., Soto, A.I., Reed, X., Law, W.D., Kerans, S.J., Waite, E.L., Briceno, N.J., Thole, J.F., Heckman, M.G., Diehl, N.N., Wszolek, Z.K., Moore, C.D., Zhu, H., Akiyama, J.A., Dickel, D.E., Visel, A., Pennacchio, L.A., Ross, O.A., Beer, M.A., McCallion, A.S. (2018). Parkinson Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. Am. J. Hum. Genet., 103(6), 874–892. doi: 10.1016/j.ajhg.2018.10.018


Hook, P.W., McClymont, S.A., Cannon, G.H., Law, W.D., Morton, A.J., Goff, L.A., and McCallion, A.S. (2018). Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease. Am. J. Hum. Genet. 102, 427-446. doi: http://dx.doi.org/10.1016/j.ajhg.2018.02.001


2016

Turner, T.N., Hormozdiari, F., Duyzend, M.H., McClymont, S.A., Hook, P.W., Iossifov, I., Raja, A., Baker, C., Hoekzema, K., Stessman, H.A., et al. (2016). Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. Am. J. Hum. Genet. 98, 58-74. doi: 10.1016/j.ajhg.2015.11.023



Before Grad school

2014 (Lab technician)

Maragh, S., Miller, R.A., Bessling, S.L., Wang, G., Hook, P.W., and McCallion, A.S. (2014) Rbm24a and Rbm24b Are Required for Normal Somitogenesis. PLOS ONE 9(8): e105460. doi: 10.1371/journal.pone.0105460


2012 (Undergrad)

Van Wagenen, J., Miller, T.W., Hobbs, S., Hook, P., Crowe, B., and Huesemann, M. (2012). Effects of light and temperature on fatty acid production in Nannochloropsis salina. Energies 5, 731-740. doi: 10.3390/en5030731