Lab Publications

Selected Research manuscripts (peer-reviewed, *equal contributions) 

  1. Co M, Barnard RA, Jahncke JN, Grindstaff S, Fedorov LM, Adey AC, Wright KM, O’Roak BJ. Shared and distinct functional effects of patient-specific Tbr1 mutations on cortical development. J Neurosci. 2022 Sep;42(37):7166-7181. PMCID: PMC9480892. Note: Selected for cover image of issue.  

  2. Zhou X*, Feliciano P*, Wang T*, Astrovskaya I*, Shu C*, Hall J, Obiajulu JU, Wright J, Murali S, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, Green Snyder L, Han B, Chang TS, Turner TN, Harvey W, Nishida A, O’Roak BJ, Geschwind DH, The SPARK Consortium, Michaelson JJ, Volfovsky N, Eichler EE, Shen Y, Chung WK. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat Genet. 2022 Sep;54(9):1305-1319. PMCID: PMC9470534.  

  3. Mighell TL, Nishida A, O’Connell BL, Miller CV, Grindstaff S, Thornton CA, Adey AC, Doherty D, O’Roak BJ. Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing. CRISPR J. 2022 Aug;5(4):548-557. PMCID: PMC9419982. 

  4. Mighell TL, Thacker S, Fombonne E, Eng C, O'Roak BJ. An Integrated Deep-Mutational-Scanning Approach Provides Clinical Insights on PTEN Genotype-Phenotype Relationships. Am J Hum Genet. 2020 Jun 4;106(6):818-829. PMCID: PMC7273526. 

  5. Fombonne E, Goin-Kochel RP, O'Roak BJ; SPARK Consortium. Beliefs in vaccine as causes of autism among SPARK cohort caregivers. Vaccine. 2020 Feb;38(7):1794-1803. PMID: 31924427. 

  6. Mighell TL, Evans-Dutson S, O'Roak BJ. A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships. Am J Hum Genet. 2018 May;102(5):943-955. PMCID: PMC5986715. 

  7. Mulqueen RM, Pokholok D, Norberg S, Fields AJ, Sun D, Torkenczy KA, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC. Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing. Nat. Biotech. 2018 Jun;36(5):428-431. PMCID: PMC5938134. 

  8. *Krupp DR, *Barnard RA, Duffourd Y, Evans SA, Mulqueen RM, Bernier R, Rivière JB, Fombonne E, O'Roak BJ. Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder. Am J Hum Genet. 2017 Sep;101(3):369-390. PMCID: PMC5590950. 

  9. Iossifov I*, O'Roak BJ*, Sanders SJ*, Ronemus M*, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee Y, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The burden of de novo coding mutations in autism spectrum disorder. Nature. 2014 Nov;515(7526):216-21. PMCID: PMC4313871. 

  10. O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science. 2012 Dec;338(6114):1619-22. PMCID: PMC3528801.  

  11. O’Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012 Apr;485(7397):246-50 PMCID: PMC3350576.  

Preprints (published works that originally appeared as preprints excluded) 

  1. Mulqueen RM, DeRosa BA, Thornton CA, Sayar Z, Torkenczy KA, Fields AJ, Wright KM, Nan X, Ramji R, Steemers F, O’Roak BJ, Adey AC. Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis. bioRxiv. 2019 May. DOI: 10.1101/637256