publications

Relevant publications from the Doan Lab or co-authored by Dr. Doan.

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  1. Ganz J, Maury EA, Becerra B, Bizzotto S, Doan RN, Kenny CJ, Shin T, Kim J, Zhou Z, Ligon KL, Lee EA, Walsh CA. Rates and Patterns of Clonal Oncogenic Mutations in the Normal Human Brain. Cancer Discov. 2022 Jan;12(1):172-185. doi: 10.1158/2159-8290.CD-21-0245. Epub 2021 Aug 13. PMID: 34389641; PMCID: PMC8758513.

  2. St Jean SC, Jortner BS, Doan RN, Dindot SV, Johnson GS, Bullock G, Whitley DB, Levine JM, Hancock SK, Ambrus A, Porter BF. Pathologic characterization of canine multiple system degeneration in the Ibizan hound. Vet Pathol. 2022 Jan;59(1):132-137. doi: 10.1177/03009858211043088. Epub 2021 Sep 7. PMID: 34490804.

  3. Girskis K.M., Stergachis A.B., DeGennaro E.M., Doan R.N., Qian X., Johnson M.B., Wang P.P., Sejourne G.M.,  Nagy M.A., Pollina E.A., Sousa A.M.M., Shin T., Kenny C.J., Scotellaro J.L., Debo B.M., Gonzalez D.M., Rento L.M., Yeh R.C., Song J.H.T., Beaudin M., Fan J., Kharchenko P.V., Sestan N., Greenberg M.E., Walsh C.A. (2021). Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron 109, 1-13.

  4. Wang, Y., Bae, T., Thorpe, J., Sherman, M.A., Jones, A.G., Cho, S., Daily, K., Dou, Y., Ganz, J., Galor, A., Lobon, I., Pattni, R., Rosenbluh, C., Tomasi, S., Tomasini, L., Yang, X., Zhou, B., Akbarian, S., Ball, L.L., Bizzotto, S., Emery, S.B., Doan, R., Fasching, L., Jang, Y., Juan, D., Lizano, E., Moldovan, J.B., Narurkar, R., Oetjens, M.T., Sekar, S., Shin, J.H., Soriano, E., Straub, R.E., Zhou, W., Chess, A., Gleeson, J.G., Marquès-Bonet, T., Park, P.J., Peters, M.A., Pevsner, J., Walsh, C.A., Weinberger, D.R., Vaccarino, F.M., Moran, J.V., Urban, A.E., Kidd, J.M., Mills, R.E., and Abyzov, A. (2021). Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome biology 22, 1-32.

  5. Blumcke, I., Coras, R., Busch, R.M., Morita-Sherman, M., Lal, D., Prayson, R., Cendes, F., Lopes-Cendes, I., Rogerio, F., Almeida, V.S., Rocha, C.S., Sim, N.S., Lee, J.H., Kim, S.H., Baulac, S., Baldassari, S., Adle-Biassette, H., Walsh, C.A., Bizzotto, S., Doan, R.N., Morillo, K.S., Aronica, E., Muhlebner, A., Becker, A., Cienfuegos, J., Garbelli, R., Giannini, C., Honavar, M., Jacques, T.S., Thom, M., Mahadevan, A., Miyata, H., Niehusmann, P., Sarnat, H.B., Soylemezoglu, F., and Najm, I. (2021). Toward a better definition of focal cortical dysplasia: An iterative histopathological and genetic agreement trial. Epilepsia 62, 1416-1428.

  6. Bizzotto, S., Dou, Y., Ganz, J., Doan, R.N., Kwon, M., Bohrson, C.L., Kim, S.N., Bae, T., Abyzov, A., and Network, N.B.S.M. (2021). Landmarks of human embryonic development inscribed in somatic mutations. Science 371, 1249-1253.

  7. Doan, R. N., M. B. Miller, S. N. Kim, R. E. Rodin, J. Ganz, S. Bizzotto, K. S. Morillo, A. Y. Huang, R. Digumarthy, Z. Zemmel and C. A. Walsh (2021). MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics 14(1): 47.

  8. Rodin, R. E., Y. Dou, M. Kwon, M. A. Sherman, A. M. D'Gama, R. N. Doan, L. M. Rento, K. M. Girskis, C. L. Bohrson, S. N. Kim, A. Nadig, L. J. Luquette, D. C. Gulhan, N. Brain Somatic Mosaicism, P. J. Park and C. A. Walsh (2021). The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neuroscience.

  9. Shao, D.D., Achkar, C.M., Lai, A., Srivastava, S., Doan, R.N., Rodan, L.H., Chen, A.Y., the Brain Development Study, G., Poduri, A., Yang, E., et al. (2020). Polymicrogyria is Associated With Pathogenic Variants in PTEN. Annals of Neurology 88, 1153-1164.

  10. Schmitz-Abe, K., Sanchez-Schmitz, G., Doan, R.N., Hill, R.S., Chahrour, M.H., Mehta, B.K., Servattalab, S., Ataman, B., Lam, A.-T.N., Morrow, E.M., et al. (2020). Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder. Scientific Reports 10, 14045.

  11. Fombonne, E., Goin-Kochel, R.P., O'Roak, B.J., Abbeduto, L., Aberbach, G., Acampado, J., Ace, A.J., Albright, C., Alessandri, M., and Amaral, D.G. (2020). Beliefs in vaccine as causes of autism among SPARK cohort caregivers. Vaccine.

  12. Satterstrom, F.K., Kosmicki, J.A., Wang, J., Breen, M.S., De Rubeis, S., An, J.-Y., Peng, M., Collins, R., Grove, J., and Klei, L. (2020). Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell 180, 568-584. e523.

  13. Dou, Y., Kwon, M., Rodin, R.E., Cortés-Ciriano, I., Doan, R., Luquette, L.J., Galor, A., Bohrson, C., Walsh, C.A., and Park, P.J. (2020). Accurate detection of mosaic variants in sequencing data without matched controls. Nature Biotechnology, 1-6.

  14. Doan RN, Lim ET, De Rubeis S, Betancur C, Cutler DJ, Chiocchetti AG, Overman LM, Soucy A, Goetze S, Freitag CM, Daly MJ, Walsh CA, Buxbaum JD, Yu TW. Recessive gene disruptions in autism spectrum disorder. Nature genetics. 2019 Jun 17:1.

  15. Feliciano, P., Zhou, X., Astrovskaya, I., Turner, T.N., Wang, T., Brueggeman, L., Barnard, R., Hsieh, A., Snyder, L.G., Muzny, D.M., et al. (2019). Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ Genom Med 4, 19.

  16. Smith, R.S., Kenny, C.J., Ganesh, V., Jang, A., Borges-Monroy, R., Partlow, J.N., Hill, R.S., Shin, T., Chen, A.Y., Doan, R.N., Anttonen, A.-K., Ignatius, J., Medne, L., Bönnemann, C.G., Hecht, J.L., Salonen, O., Barkovich, A.J., Poduri, A., Wilke, M., de Wit, M.C.Y., Mancini, G.M.S., Sztriha, L., Im, K., Amrom, D., Andermann, E., Paetau, R., Lehesjoki, A.-E., Walsh, C.A., Lehtinen, M.K. Sodium Channel SCN3A (NaV1.3) Regulation of Human Cerebral Cortical Folding and Oral Motor Development. Neuron 1–17. doi:10.1016/j.neuron.2018.07.052.

  17. Dindot SV, Doan RN, Kuskie KR, Hillman PR, Whitfield CM, McQueen CC, Bordin AI, Bourquin JR, Cohen ND. Postnatal changes in epigenetic modifications of neutrophils of foals are associated with increased ROS function and regulation of neutrophil function. Dev Comp Immunol. 2018;87:182-7.

  18. Hillman PR, Christian SGB, Doan R, Cohen ND, Konganti K, Douglas K, Wang X, Samollow PB, Dindot SV. Genomic imprinting does not reduce the dosage of UBE3A in neurons, Epigenetics & Chromatin 2017:10 (1), 27.

  19. Lakhani S*, Doan R*, Almureikhi M, Partlow JN, Al Saffar M, Elsaid MF, Alaaraj N, Barkovich AJ, Walsh CA, Ben-Omran T. Identification of a novel CNTNAP1 mutation causing arthrogryposis multiplex congenita with cerebral and cerebellar atrophy, European Journal of Medical Genetics 2017;60 (5), 245-249.

  20. Alves BRC, Cardoso RC, Doan R, Zhang Y, Dindot SV, Williams GL, Amstalden M. Nutritional programming of accelerated puberty in heifers: alterations in DNA methylation in the arcuate nucleus. Biology of reproduction. 2017;96(1):174-84.

  21. Ault JG, Felt KD, Doan RN, Nedo AO, Ellison CA, Paliulis LV. Co-segregation of sex chromosomes in the male black widow spider Latrodectus mactans (Araneae, Theridiidae). Chromosoma. 2017. doi: 10.1007/s00412-017-0628-7.

  22. Doan RN*, Quist E*, Pool R, Porter B, Dindot SV. Identification of a candidate mutation in the COL1A2 gene of a Chow Chow with osteogenesis imperfecta. Journal of Heredity. 2017.

  23. Doan RN, Bae BI, Cubelos B, Chang C, Hossain AA, Al-Saad S, Mukaddes NM, Oner O, Al-Saffar M, Balkhy S, Gascon GG, Nieto M, Walsh CA. Mutations in Human Accelerated Regions (HARs) Disrupt Cognition and Social Behavior. Cell 2016;167.2:341-354.

  24. Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter JF, Black L, Kharchenko PV, Sharp PA, Walsh CA. Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 2016;166(5):1147-62 e15.

  25. Johnson MB, Wang PP, Atabay KD, Murphy EA, Doan RN, Hecht JL, Walsh CA. Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex. Nature Neuroscience. 2015.

  26. McQueen CM, Doan R, Dindot SV, Bourquin JR, Zlatev ZZ, Chaffin MK, Blodgett GP, Ivanov I, Cohen ND. Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PloS One. 2014;9(6):e98710.

  27. Ghaffari N, Sanchez-Flores A, Doan R, Garcia-Orozco KD, Chen PL, Ochoa-Leyva A, Lopez-Zavala AA, Carrasco JS, Hong C, Brieba LG, Rudino-Pinera E, Blood PD, Sawyer JE, Johnson CD, Dindot SV, Sotelo-Mundo RR, Criscitiello MF. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Scientific Reports. 2014;4:7081.

  28. Doan R. The identification and characterization of copy number variants in the bovine genome. TAMU Dissertation Thesis.

  29. Doan R, Cohen N, Harrington J, Veazey K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV. Identification of copy number variants in horses. Genome Research. 2012;22(5):899-907.

  30. Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, Dindot SV. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC Genomics. 2012;13:78. 2012/02/22.

  31. Doan RN, Paliulis LV. Micromanipulation reveals an XO-XX sex determining system in the orb-weaving spider Neoscona arabesca (Walckenaer). Hereditas. 2009;146(4):180-2.