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Andrew Farrell

 https://orcid.org/0000-0003-3895-4208
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20122022

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  • 2022

    Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia

    Nicholas, T. J., Al-Sweel, N., Farrell, A., Mao, R., Bayrak-Toydemir, P., Miller, C. E., Bentley, D., Palmquist, R., Moore, B., Hernandez, E. J., Cormier, M. J., Fredrickson, E., Noble, K., Rynearson, S., Holt, C., Karren, M., Bonkowsky, J. L., Tristani-Firouzi, M., Yandell, M. & Marth, G. & 7 others, Quinlan, A. R., Brunelli, L., Toydemir, R., Shayota, B. J., Carey, J. C., Boyden, S. E. & Malone Jenkins, S., Apr 2022, In: Molecular Genetics and Genomic Medicine. 10, 4, e1888.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    5 Scopus citations

  • Rapid genome sequencing identifies a novel de novo SNAP25 variant for neonatal congenital myasthenic syndrome

    Reynolds, H. M., Wen, T., Farrell, A., Mao, R., Moore, B., Boyden, S. E., Bayrak-Toydemir, P., Nicholas, T. J., Rynearson, S., Holt, C., Miller, C., Noble, K., Bentley, D., Palmquist, R., Ostrander, B., Manberg, S., Bonkowsky, J. L., Shayota, B. J. & Jenkins, S. M., Dec 2022, In: Cold Spring Harbor Molecular Case Studies. 8, 7, a006242.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    4 Scopus citations
  • 2021

    Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies

    Huang, X., Qiao, Y., Brady, S. W., Factor, R. E., Downs-Kelly, E., Farrell, A., McQuerry, J. A., Shrestha, G., Jenkins, D., Johnson, W. E., Cohen, A. L., Bild, A. H. & Marth, G. T., Dec 2021, In: Genome Medicine. 13, 1, 170.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    6 Scopus citations

  • The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming

    Primo, V. A., Rezvani, Y., Farrell, A., Murphy, C. Q., Lou, J., Vajdi, A., Marth, G. T., Zarringhalam, K. & Gubbels, M. J., Dec 2021, In: mSystems. 6, 6, e01196-21.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    14 Scopus citations
  • 2020

    Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias

    Bogenschutz, E. L., Fox, Z. D., Farrell, A., Wynn, J., Moore, B., Yu, L., Aspelund, G., Marth, G., Yandell, M., Shen, Y., Chung, W. K. & Kardon, G., Oct 22 2020, In: Human Genetics and Genomics Advances. 1, 1, 100008.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    9 Scopus citations

  • Genomic analyses implicate noncoding de novo variants in congenital heart disease

    Richter, F., Morton, S. U., Kim, S. W., Kitaygorodsky, A., Wasson, L. K., Chen, K. M., Zhou, J., Qi, H., Patel, N., DePalma, S. R., Parfenov, M., Homsy, J., Gorham, J. M., Manheimer, K. B., Velinder, M., Farrell, A., Marth, G., Schadt, E. E., Kaltman, J. R. & Newburger, J. W. & 15 others, Giardini, A., Goldmuntz, E., Brueckner, M., Kim, R., Porter, G. A., Bernstein, D., Chung, W. K., Srivastava, D., Tristani-Firouzi, M., Troyanskaya, O. G., Dickel, D. E., Shen, Y., Seidman, J. G., Seidman, C. E. & Gelb, B. D., Aug 1 2020, In: Nature Genetics. 52, 8, p. 769-777 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    96 Scopus citations

  • The effects of common structural variants on 3D chromatin structure

    Shanta, O., Noor, A., Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F. & Lee, D. & 77 others, Wenger, A. M., Hastie, A. R., Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeey, T., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E., Lee, C. & Sebat, J., Jan 30 2020, In: BMC Genomics. 21, 1, 95.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    20 Scopus citations
  • 2019

    Multi-platform discovery of haplotype-resolved structural variation in human genomes

    Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A. M. & Hastie, A. R. & 77 others, Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D. U., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Qiu, Y., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Ren, B., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E. & Lee, C., Dec 1 2019, In: Nature Communications. 10, 1, 1784.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    522 Scopus citations

  • Pedigree-based estimation of human mobile element retrotransposition rates

    Feusier, J., Watkins, W. S., Thomas, J., Farrell, A., Witherspoon, D. J., Baird, L., Ha, H., Xing, J. & Jorde, L. B., 2019, In: Genome Research. 29, 10, p. 1567-1577 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    69 Scopus citations

  • Phenotype of CM-AVM2 caused by variants in EPHB4: how much overlap with hereditary hemorrhagic telangiectasia (HHT)?

    Wooderchak-Donahue, W. L., Akay, G., Whitehead, K., Briggs, E., Stevenson, D. A., O’Fallon, B., Velinder, M., Farrell, A., Shen, W., Bedoukian, E., Skrabann, C. M., Antaya, R. J., Henderson, K., Pollak, J., Treat, J., Day, R., Jacher, J. E., Hannibal, M., Bontempo, K. & Marth, G. & 2 others, Bayrak-Toydemir, P. & McDonald, J., Sep 1 2019, In: Genetics in Medicine. 21, 9, p. 2007-2014 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    47 Scopus citations
  • 2018

    An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

    Werling, D. M., Brand, H., An, J. Y., Stone, M. R., Zhu, L., Glessner, J. T., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., Farrell, A., Schwartz, G. B., Wang, H. Z., Currall, B. B., Zhao, X., Dea, J., Duhn, C., Erdman, C. A., Gilson, M. C. & Yadav, R. & 27 others, Handsaker, R. E., Kashin, S., Klei, L., Mandell, J. D., Nowakowski, T. J., Liu, Y., Pochareddy, S., Smith, L., Walker, M. F., Waterman, M. J., He, X., Kriegstein, A. R., Rubenstein, J. L., Sestan, N., McCarroll, S. A., Neale, B. M., Coon, H., Willsey, A. J., Buxbaum, J. D., Daly, M. J., State, M. W., Quinlan, A. R., Marth, G. T., Roeder, K., Devlin, B., Talkowski, M. E. & Sanders, S. J., May 1 2018, In: Nature Genetics. 50, 5, p. 727-736 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    175 Scopus citations

  • Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia

    Wooderchak-Donahue, W. L., McDonald, J., Farrell, A., Akay, G., Velinder, M., Johnson, P., Vansant-Webb, C., Margraf, R., Briggs, E., Whitehead, K. J., Thomson, J., Lin, A. E., Pyeritz, R. E., Marth, G. & Bayrak-Toydemir, P., Dec 1 2018, In: Journal of Medical Genetics. 55, 12, p. 824-830 7 p.

    Research output: Contribution to journal › Article › peer-review

    13 Scopus citations

  • Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

    Ostrander, B. E. P., Butterfield, R. J., Pedersen, B. S., Farrell, A. J., Layer, R. M., Ward, A., Miller, C., DiSera, T., Filloux, F. M., Candee, M. S., Newcomb, T., Bonkowsky, J. L., Marth, G. T. & Quinlan, A. R., Dec 1 2018, In: npj Genomic Medicine. 3, 1, 22.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    67 Scopus citations
  • 2015

    Analysis of archived residual newborn screening blood spots after whole genome amplification

    Cantarel, B. L., Lei, Y., Weaver, D., Zhu, H., Farrell, A., Benstead-Hume, G., Reese, J. & Finnell, R. H., Aug 13 2015, In: BMC Genomics. 16, 1, 602.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    6 Scopus citations
  • 2014

    Forward Genetic Screening Identifies a Small Molecule That Blocks Toxoplasma gondii Growth by Inhibiting Both Host- and Parasite-Encoded Kinases

    Brown, K. M., Suvorova, E., Farrell, A., McLain, A., Dittmar, A., Wiley, G. B., Marth, G., Gaffney, P. M., Gubbels, M. J., White, M. & Blader, I. J., Jun 2014, In: PLoS Pathogens. 10, 6, e1004180.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    32 Scopus citations

  • Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii

    Farrell, A., Coleman, B. I., Benenati, B., Brown, K. M., Blader, I. J., Marth, G. T. & Gubbels, M. J., May 10 2014, In: BMC Genomics. 15, 1, 354.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    27 Scopus citations
  • 2013

    Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains

    Yang, N., Farrell, A., Niedelman, W., Melo, M., Lu, D., Julien, L., Marth, G. T., Gubbels, M. J. & Saeij, J. P. J., Jul 10 2013, In: BMC Genomics. 14, 1, 467.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    39 Scopus citations
  • 2012

    A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis

    Farrell, A., Thirugnanam, S., Lorestani, A., Dvorin, J. D., Eidell, K. P., Ferguson, D. J. P., Anderson-White, B. R., Duraisingh, M. T., Marth, G. T. & Gubbels, M. J., Jan 13 2012, In: Science. 335, 6065, p. 218-221 4 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    110 Scopus citations