•  Lumpkin, C.J., Patel, H., Potts, G.K. et al. Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson’s disease pathogenesis. Mol Brain 17, 26 (2024). https://doi.org/10.1186/s13041-024-01099-1

  • Fleischmann, Zoë, Auden Cote-L’Heureux, Melissa Franco, Sergey Oreshkov, Sofia Annis, Mark Khrapko, Dylan Aidlen, et al. “Reanalysis of mtDNA Mutations of Human Primordial Germ Cells (PGCs) Reveals NUMT Contamination and Suggests That Selection in PGCs May Be Positive.” Mitochondrion 74 (2024): 101817. https://doi.org/10.1016/j.mito.2023.10.005.

  • Shamanskiy, Victor, Konstantin Gunbin, Evgenii O. Tretiakov, Ilya Mazunin, Viktoria Skripskaya, Alina A. Mikhailova, Alina G. Mikhailova, et al. "Mitochondrial Direct Repeat Reduction as a Strategy for Enhancing Human Longevity: The Case of the Common Repeat." bioRxiv (2024): 2024.09.02.610808. https://doi.org/10.1101/2024.09.02.610808.

  • Ree, Natalia, Maxim Ri, Jonathan Tilly, Ilya Mazunin, and Konstantin Popadin. "Maternal Age-Independent Human Aneuploidies Are Common and Associated with Mitochondrial Disfunctions: Analysis of 11,610 Genomes of Human Embryos-Virtual." Paper presented at the EUROPEAN JOURNAL OF HUMAN GENETICS, 2024.

  • Capelluto, Fausto, Hannah Alberico, Paula Ledo-Hopgood, Jonathan L. Tilly, and Dori C. Woods. “Lineage-Mismatched Mitochondrial Replacement in an Inducible Mitochondrial Depletion Model Effectively Restores the Original Proteomic Landscape of Recipient Cells.” Advanced Biology 7, no. 6 (2023): 2200246. https://doi.org/10.1002/adbi.202200246.

  • Sheehan, H.C., Tilly, J.L., Woods, D.C. (2023). Assaying Mitochondrial Function by Multiparametric Flow Cytometry. In: Friedrich, O., Gilbert, D.F. (eds) Cell Viability Assays. Methods in Molecular Biology, vol 2644. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3052-5_5

  • Shamanskiy, V., Mikhailova, A.A., Tretiakov, E.O. et al. Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biol 21, 103 (2023). https://doi.org/10.1186/s12915-023-01606-1

  • Auden Cote-L’Heureux, Yogesh NK Maithania, Melissa Franco, Konstantin Khrapko (2023) Mitochondrial DNA: Are some mutations more equal than others? eLife 12:e87194. https://doi.org/10.7554/eLife.87194

  • Cote-L’Heureu, Auden, Melissa Franco, Yogesh N. K. Maithania, Konstantin Popadin, Dori Woods, Jonathan Tilly, and Konstantin Khrapko. "The ‘Stem’ and the ‘Workers’ of the Mtdna Population of the Cell. Evidence from Mutational Analysis." bioRxiv (2023): 2023.04.14.536897. https://doi.org/10.1101/2023.04.14.536897.

  • MacDonald, Julie A., et al. "Characterization of Oogonial Stem Cells in Adult Mouse Ovaries with Age and Comparison to In Silico Data on Human Ovarian Aging." Stem Cells and Development 32.5-6 (2023): 99-114.

  • Woods, Dori C, and Jonathan L Tilly. “Revisiting Claims of the Continued Absence of Functional Germline Stem Cells in Adult Ovaries.” Stem Cells 41, no. 2 (December 2022): 200–204. https://doi.org/10.1093/stmcls/sxac083.

  • Ri, Maxim, Natalia Ree, Sergey Oreshkov, Maria Tofilo, Irina Zvereva, Anastasia Kirillova, Konstantin Gunbin, et al. "Aneuploidy in Human Embryos Is Associated with a Maternal Age-Independent Increase in Mitochondrial DNA Content and an Enrichment of Ultra-Rare Mitochondrial DNA Variants." bioRxiv (2023): 2022.10.14.512116. https://doi.org/10.1101/2022.10.14.512116.

  • Franco, Melissa, Sarah J Pickett, Zoe Fleischmann, Mark Khrapko, Auden Cote-L’Heureux, Dylan Aidlen, David Stein, et al. "Dynamics of the Most Common Pathogenic Mtdna Variant M.3243a ≫ G Demonstrate Frequency-Dependency in Blood and Positive Selection in the Germline." Human Molecular Genetics 31, no. 23 (2022): 4075-86. https://doi.org/10.1093/hmg/ddac149.

  • Logan, R., Fleischmann, Z., Annis, S. et al. 3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data. BMC Bioinformatics 23, 95 (2022). https://doi.org/10.1186/s12859-022-04637-7

  • Mikhailova, Alina G, Alina A Mikhailova, Kristina Ushakova, Evgeny O Tretiakov, Dmitrii Iliushchenko, Victor Shamansky, Valeria Lobanova, et al. "A Mitochondria-Specific Mutational Signature of Aging: Increased Rate of A ≫ g Substitutions on The heavy Strand." Nucleic Acids Research 50, no. 18 (2022): 10264-77. https://doi.org/10.1093/nar/gkac779.

  • Popadin, K., Gunbin, K., Peshkin, L., Annis, S., Fleischmann, Z., Franco, M., Kraytsberg, Y., Markuzon, N., Ackermann, R. R., & Khrapko, K. (2022). Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors. Genes, 13(5), 810. https://doi.org/10.3390/genes13050810

  • Voronka, Alexandr, Bogdan Efimenko, Sergey Oreshkov, Melissa Franco, Zoe Fleischmann, Valerian Yurov, Arina Trufanova, et al. "Direction Mutation Pressure of Sars-Cov-2 Helps to Understand the Past and Predict the Future Evolution: C≫U and G≫U Biased Mutagenesis Forces the Majority of Amino-Acid Substitutions to Be from Cg-Rich Losers to U-Rich Gainers." bioRxiv (2022): 2022.08.22.504819. https://doi.org/10.1101/2022.08.22.504819.

  • Annis S, Fleischmann Z, Logan R, et al. LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules. Aging (Albany NY). 2020;12(8):7603-7613. doi:10.18632/aging.103171

  •        Satirapod C, Wang N, MacDonald JA, Sun M, Woods DC, Tilly JL. Estrogen regulation of germline stem cell differentiation as a mechanism contributing to female reproductive aging. Aging (Albany NY). 2020;12(8):7313-7333.

  •        Franco M, Pickett S, Fleischmann Z, Khrapko M, Annis S, Woods DC, Markuzon N, Turnbull D, Khrapko K. Can detrimental mtDNA mutations be under positive selection in the germline? Biochemistry and Molecular Biology. 2020.

  •        Tilly JL, Woods DC. The obligate need for accuracy in reporting preclinical studies relevant to clinical trials: autologous germline mitochondrial supplementation for assisted human reproduction as a case study. Therapeutic Advances in Reproductive Health. January 2020.

  •        Bothun A, Woods DC. Inherent mitochondrial activity influences specification of the germ line in pluripotent stem cells. Heliyon. 2020. 6(4): E03651.

  •        Annis S, Fleischmann Z, Khrapko M, Franco M, Wasko K, Woods DC, Kunz WS, Ellis P, Khrapko K. Quasi-Mendelian paternal inheritance of mitochondrial DNA: A notorious artifact, or anticipated behavior? PNAS. 2019.

  •        MacDonald JA, Bothun AM, Annis SN, Sheehan H, Ray S, Gao Y, Ivanov AR, Khrapko K, Tilly JL, Woods DC. A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics. Commun. Biol. 2019. 2(258).

  •        Akahori T, Woods DC, Tilly JL. Female Fertility Preservation through Stem Cell-based Ovarian Tissue Reconstitution In Vitro and Ovarian Regeneration In Vivo. Clin. Med. Insights: Reprod. Health. 2019. 13: 1179558119848007.

  •        MacDonald JA, Take Y, Ishihara O, Seki H, Woods DC, Tilly JL. Extracellular matrix signaling activates differentiation of adult ovary-derived oogonial stem cells in a species-specific manner. Fertil Steril. 2019. 111(4): 794–805.

  •        Martin JJ, Woods DC, Tilly JL. Implications and Current Limitations of Oogenesis from Female Germline or Oogonial Stem Cells in Adult Mammalian Ovaries. Cells. 2019. 8(2): 93.

  •        MacDonald JA, Kura N, Sussman C, Woods DC. Mitochondrial membrane depolarization enhances TRAIL-induced cell death in adult human granulosa tumor cells, KGN, through inhibition of BIRC5. J Ovarian Res. 11(1): 89.

  •        Bothun AM and Woods DC. Dynamics of WNT signaling components in the human ovary from development to adulthood. Histochem and Cell Bio. 2018. 1–9

  •        Faraci C, Jin J, Woods DC. Calorie restriction does not influence oocyte quality in oocytes from POLG mitochondrial mutator mice. PloS one. 13(9): e0204373.

  •        Faraci C, Annis S, Jin J, Li H, Khrapko K, Woods DC. Impact of exercise on oocyte quality in the POLG mitochondrial DNA mutator mouse. Reproduction. 2018. 156(2): 185–194

  •        Woods DC, Khrapko K, Tilly JL. Influence of maternal aging on mitochondrial heterogeneity, inheritance, and function in oocytes and preimplantation embryos. Genes. 2018. 9(5):265. 

  •        MacDonald JA, Fowle WH, Shin E, Woods DC. A method for freeze-fracture and scanning electron microscopy of isolated mitochondria. MethodsX. 2018. 5: 593.

  •        Bothun AM, Gao Y, Takai Y, Ishihara O, Seki H, Karger B, Tilly JL, Woods DC. Quantitative proteomic profiling of the human ovary from early to mid-gestation reveals protein expression dynamics of oogenesis and folliculogenesis. Stem Cells Dev. 2018. 27(11): 723–735.

  •        Wang N, Satirapod C, Ohguchi Y, Park E, Woods DC, Tilly JL. Genetic studies in mice directly link oocytes produced during adulthood to ovarian function and natural fertility. Sci Reports. 2017. 7(1):10011.

  •        MacDonald JA, Fowle WH, Woods DC. New insights on mitochondrial heterogeneity observed in prepared mitochondrial samples following a method for freeze-fracture and scanning electron microscopy. Micron. 2017. (101): 25–31.  

  •        Truman AM, Tilly JL, Woods DC. Ovarian regeneration: the potential for stem cell contribution in the postnatal ovary to sustained endocrine function. Molecular and cellular endocrinology. 2017. 445: 74–84.

  •        Truman AM, Johnson AL, Woods DC.  Granulosa Cell Tumors. Encyclopedia of Cancer, M. Schwab, Ed. Springer-Verlag Berlin and Heidelberg GmbH & Co. K; 4th Revised edition, 2016.

  •        Woods DC, Tilly JL. Autologous Germline Mitochondrial Energy Transfer (AUGMENT) in Human Assisted Reproduction. Semin Reprod Med. 2015. 33(6):410–21. 

  •        Woods DC, Tilly JL. Woods and Tilly reply. Nat Med. 2015. 21(10):1118–21. 

  •        Best MW, Wu J, Pauli SA, Kane MA, Pierzchalski K, Session DR, Woods DC, Shang W, Taylor RN, Sidell N. A role for retinoids in human oocyte fertilization: regulation of connexin 43 by retinoic acid in cumulus granulosa cells. Mol Hum Reprod. 2015. 21(6): 527–34. 

  •        Park ES, Woods DC, Tilly JL. Bone morphogenetic protein 4 promotes mammalian oogonial stem cell differentiation via Smad1/5/8 signaling. Fertil Steril. 2013 100(5):1468–75. 

  •        Imudia AN, Wang N, Tanaka Y, White YA, Woods DC, Tilly JL. Comparative gene expression profiling of adult mouse ovary-derived oogonial stem cells supports a distinct cellular identity. Fertil Steril. 2013. 100(5): 1451–8. 

  •        Woods DC, Tilly JL. Isolation, characterization and propagation of mitotically active germ cells from adult mouse and human ovaries. Nat Protoc. 2013 8(5): 966–88. 

  •        Woods DC, White YA, Niikura Y, Kiatpongsan S, Lee HJ, Tilly JL. Embryonic stem cell-derived granulosa cells participate in ovarian follicle formation in vitro and in vivo. Reprod Sci. 2013 20(5): 524–35. 

  •        Woods DC, Tilly JL. An evolutionary perspective on adult female germline stem cell function from flies to humans. Semin Reprod Med. 2013. 31(1): 24–32.

  •        Woods DC, White YA, Tilly JL. Purification of oogonial stem cells from adult mouse and human ovaries: an assessment of the literature and a view toward the future. Reprod Sci. 2013. 20(1): 7–15. 

  •        Nehra D, Le HD, Fallon EM, Carlson SJ, Woods D, White YA, Pan AH, Guo L, Rodig SJ, Tilly JL, Rueda BR, Puder M. Prolonging the female reproductive lifespan and improving egg quality with dietary omega-3 fatty acids. Aging Cell. 2012. 11(6): 1046–54. 

  •        Woods DC, Telfer EE, Tilly JL. Oocyte family trees: old branches or new stems? PLoS Genet. 2012. 8(7):e1002848. 

  •        Woods DC, Tilly JL. The next (re)generation of ovarian biology and fertility in women: is current science tomorrow's practice? Fertil Steril. 2012. 98(1): 3–10. 

  •        White YA, Woods DC, Takai Y, Ishihara O, Seki H, Tilly JL. Oocyte formation by mitotically active germ cells purified from ovaries of reproductive-age women. Nat Med. 2012. 26;18(3): 413–21. 

  •        White YA, Woods DC, Wood AW. A transgenic zebrafish model of targeted oocyte ablation and de novo oogenesis. Dev Dyn. 2011. 240(8): 1929–37. 

  •        Woods DC, White YA, Dau C, Johnson AL. TLR4 activates NF-κB in human ovarian granulosa tumor cells. Biochem Biophys Res Commun. 2011. 409(4): 675–80. 

  •        Woods DC, Schorey JS, Johnson AL. Toll-like receptor signaling in hen ovarian granulosa cells is dependent on stage of follicle maturation. Reproduction. 2009. 137(6): 987–96. 

  •        Johnson AL, Woods DC. Dynamics of avian ovarian follicle development: cellular mechanisms of granulosa cell differentiation. Gen Comp Endocrinol. 2009. 163(1-2): 12–7. 

  •        Johnson AL, Haugen MJ, Woods DC. Role for inhibitor of differentiation/deoxyribonucleic acid-binding (Id) proteins in granulosa cell differentiation. Endocrinology. 2008. 149(6): 3187–95. 

  •        Woods DC, Alvarez C, Johnson AL. Cisplatin-mediated sensitivity to TRAIL-induced cell death in human granulosa tumor cells. Gynecol Oncol. 2008. 108(3): 632–40. 

  •        Woods DC, Liu HK, Nishi Y, Yanase T, Johnson AL. Inhibition of proteasome activity sensitizes human granulosa tumor cells to TRAIL-induced cell death. Cancer Lett. 2008. 260(1-2): 20–7. 

  •        Woods DC, Johnson AL. Protein kinase C activity mediates LH-induced ErbB/Erk signaling in differentiated hen granulosa cells. Reproduction. 2007. 133(4): 733–41. 

  •        Woods DC, Haugen MJ, Johnson AL. Actions of epidermal growth factor receptor/mitogen-activated protein kinase and protein kinase C signaling in granulosa cells from Gallus gallus are dependent upon stage of differentiation. Biol Reprod. 2007. 77(1): 61–70. 

  •        Johnson AL, Ratajczak C, Haugen MJ, Liu HK, Woods DC. Tumor necrosis factor-related apoptosis inducing ligand expression and activity in hen granulosa cells. Reproduction. 2007. 133(3): 609–16. 

  •        Woods DC, Johnson AL. Phosphatase activation by epidermal growth factor family ligands regulates extracellular regulated kinase signaling in undifferentiated hen granulosa cells. Endocrinology. 2006. 147(10): 4931–40. 

  •        Woods DC, Haugen MJ, Johnson AL. Opposing actions of TGFbeta and MAP kinase signaling in undifferentiated hen granulosa cells. Biochem Biophys Res Commun. 2005. 336(2): 450–7. 

  •        Woods DC, Johnson AL. Regulation of follicle-stimulating hormone-receptor messenger RNA in hen granulosa cells relative to follicle selection. Biol Reprod. 2005. 72(3): 643–50. 

Recent Publications