Publications

Tracing the lab's work from human gene expression genetics to RNA biology and disease.

2020 - Present

International Human RNome Project Consortium. Unlocking the Regulatory Code of RNA: Launching the Human RNome Project. Genome Biology 26:367.
Hengesbach M, Chan CK, Bhandari T, Bruzel A, Demott M, Podoprygorina G, Sun G, Tabeling E, Cheung VG, Dedon P, Helm M, Limbach PA. Towards standardized epitranscriptomic analysis: an inter-laboratory comparison of mass spectrometric detection and quantitation of modified ribonucleosides in human RNA. Nucleic Acids Research, 53(17):gkaf895.
Winkelsas A, Apfel A, Johnson B, Harmison G, Li D, Cheung VG, Grunseich C. Allele-specific silencing of a dominant SETXmutation in familial amyotrophic lateral sclerosis type 4. HGG Advances 6(3): 100434, 2025.
Snyder R, Delker D, Burdick JT, Cheung VG, Watts JA. Guanine quadruplexes mediate mitochondrial RNA polymerase pausing. BMC Biology23(1): 129, 2025.
Wan M, Liu Y, Li D, Snyder RJ, Elkin LB, Day CR, Rodriguez J, Grunseich C, Mahley RW, Watts JA, Cheung VG. The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia. Nucleic Acids Research, 52: 10235-10254, 2024.
Abdulghani M, Razavian NB, Burdick JT, Domingo E, Cheung VG Humphrey TC. Isoform-switching regulates response to ionizing radiation through SRSF1. Int J Radiat Oncol Biol Phys. 2024 Aug 1;119(5):1517-1529.
Burdick JT, Comai A, Bruzel A, Sun G, Dedon PC & Cheung VG. Nanopore-based direct sequencing of RNA transcripts with ten different modified nucleotides reveals gaps in existing technology. G3 Sept; jkad200, 2023.
Watts JA, Grunseich C, Rodriguez Y, Liu Y, Li D, Burdick JT, Bruzel A, Crouch RJ, Mahley RW, Wilson SH, Cheung VG. A gene regulatory mechanism involving an R-loop, m6A modification and formation of an RNA abasic site as exemplified by APOEexpression. Nucleic Acid Research, 50:12497-12514, 2022.
Alfonzo JD, Brown JA, Byers PH, Cheung VG, Maraia R, Ross RL. A call for direct sequencing of full-length RNAs. Nature Genetics, 53: 1113-1116, 2021. (communicating author)
Lee MH., Perl DP., Nair G., Li W., Maric D.., Murray H, Dodd SJ., Koretsky AP., Watts JA., Cheung VG., Masliah E., Rentas F., Horkayne-Szakaly I., Jones R., Stram MN., Moncur J., Hefti M., Folkerth RD. & Nath A. Microvascular injury in the Brains of Patients with COVID-19. New Engl J Med, 384(5):481-483, 2021.
Ramirez P.,Crouch RJ., Cheung VG. & Grunseich C. R-loop by dot-blot analysis. JOVE, (167):10.3791/62069, 2021.

2011 - 2020

Liu Y., Rodriguez Y., Ross RL., Zhao R., Grunseich C., Bruzel A., Li D., Watts JA., Prasad R., Crouch RJ., Limbach PA., Wilson SH & Cheung VG. RNA abasic sites in yeast and human cells. Proceedings of the National Academy of Sciences of the United States of America, 17:20689-20695, 2020.
Grunseich C, Patankar A, Amaya J, Watts JA, Li D, Ramirez P, Schindler AB, Fischbeck KH & Cheung VG. Clinical and molecular aspects of senataxin mutation in ALS4. Annal of Neurology, 87: 547-555, 2020.
Watts JA., Burdick J., Diagneault J., Bruzel A., Zhu Z., Grunseich C. & Cheung VG. Cis elements that mediate RNA polymerase II pausing regulate human gene expression. Am. J Human Genetics, 105: 677-688, 2019.
Wang IX., Grunseich C., Fox J., Burdick J., Zhu Z., Razavian N., Hafner M. & Cheung VG. Human proteins that interact with RNA/DNA hybrids. Genome Research, 28: 1405-1414, 2018.
Grunseich C., Wang IX., Watts JA., Guber RD., Burdick JT., Zhu Z., Bruzel A., Lanman T., Chen K., Schindler AB., Edwards N., Ray-Chaudhury A., Yao J., Lehky T., Piszczek G., Crain B., Fischbeck KH. & Cheung VG. Senataxin mutation reveals how R-loops promote transcription by blocking DNA methylation at gene promoters. Molecular Cell, 69: 426-437, 2018.
Wang IX., Grunseich C., Chung YG., Kwak H., Ramrattan G., Zhu Z. & Cheung VG. RNA-DNA sequence differences in Saccharomyces cerevisiae. Genome Research, 26: 1544-1554, 2016.
Begum F., Chowdhury R., Cheung VG., Sherman SL. & Feingold E. Genome-wide association study of meiotic recombination phenotypes. G3 (Bethesda), 6: 3995-4007, 2016.
Booth GT., Wang IX., Cheung VG. & Lis JL. Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Research, 26: 799-811, 2016.
Wang IX., Ramrattan G. & Cheung VG. Genetic variation in insulin-induced kinase signaling. Mol. Syst. Biol., 11: 820, 2015.
Danko CG., Hyland SL., Core LJ., Martins AL., Waters CT., Lee HW., Cheung VG., Kraus WL., Lis JT. & Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nature Methods, 12: 433-438, 2015.
Oliver TR., Middlebrooks CD., Tinker SW., Allen EG., Bean LJ., Begum F., Feingold E., Chowdhury R., Cheung V. & Sherman SL. An examination of the relationship between hotspots and recombination associated with chromosome 21 nondisjunction. PLoS One,9: e99560, 2014.
Middlebrooks CD., Mukhopadhyay N., Tinker SW., Allen EG., Bean LJ., Begum F., Chowdhury R., Cheung V., Doheny K., Adams M., Feingold E. & Sherman SL. Evidence for dysregulation of genome-wide recombination in oocytes with nondisjoined chromosomes 21. Human Molecular Genetics, 23: 408-17, 2014.
Wang IX., Core LJ., Kwak H., Brady L., Bruzel A., McDaniel L., Richards AL., Wu M., Grunseich C., Lis JT. & Cheung VG. RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. Cell Reports, 6: 906-915, 2014.
Gregory BL., Cheung VG. Natural variation in the histone demethylase, KDM4C, influences expression levels of specific genes including those that affect cell growth. Genome Research, 24: 52-63, 2014.
Nayak RR., Bernal WE., Kearns M. & Cheung VG. Stress-induced changes in gene interactions in human cells.Nucleic Acids Research, 42: 1757-1771, 2014.
Wang IX., So E., Devlin JL., Zhao Y., Wu M. & Cheung VG. ADAR regulates RNA editing, transcript stability, and gene expression. Cell Reports, 5: 849-60, 2013.
Oliver TR., Tinker SW., Allen EG., Hollis N., Locke AE., Bean LJ., Chowdhury R., Begum F., Marazita M., Cheung V., Feingold E. & Sherman SL. Altered patterns of multiple recombinant events are associated with nondisjunction of chromosome 21. Human Genetics, 131(7): 1039-46, 2012.
Smirnov DA., Brady L., Halasa K., Morley M., Solomon S. & Cheung VG. Genetic variation in radiation-induced cell death. Genome Research, 22: 332-339, 2012.
Li M., Wang IX., Li Y., Bruzel A., Richards AL., Toung JM. & Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science, 333: 53-58, 2011.
Toung JM., Morley M., Li M. & Cheung VG. RNA-sequence analysis of human B-cells. Genome Research, 21: 991-998, 2011.

2000 - 2010

Cheung VG., Nayak RR., Wang IX., Elwyn S., Cousins SM., Morley M. & Spielman RS. Polymorphic cis and trans regulation of human gene expression. PLoS Biology, e1000480, 2010.
Krewski D., Acosta D Jr., Andersen M., Anderson H., Bailar JC 3rd., Boekelheide K., Brent R., Charnley G., Cheung VG., Green S Jr, Kelsey KT., Kerkvliet NI., Li AA., McCray L., Meyer O., Patterson RD., Pennie W., Scala RA., Solomon GM., Stephens M., Yager J. & Zeise L. Toxicity testing in the 21st century: a vision and a strategy. J Toxicol Environ Health B Crit Rev, 13: 51-138, 2010.
Dombroski BA., Nayak RR., Ewens KG., Ankener W., Cheung VG. & Spielman RS. Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells. Amer J Hum Genet, 86: 719-729, 2010.
Cheung VG., Sherman SL. & Feingold E. Genetic control of hotspots. Science, 327: 791-792, 2010.
Nayak RR., Kearns M., Spielman RS. & Cheung VG. Coexpression network based on natural variation in human gene expression reveals gene interactions and functions. Genome Research, 19: 1953-1962, 2009.
Chowdhury R., Bois PR., Feingold E., Sherman SL. & Cheung VG. Genetic analysis of variation in human meiotic recombination. PLoS Genet, 5:e1000648, 2009.
Smirnov DA., Morley M., Shin E., Spielman RS. & Cheung VG. Genetic analysis of radiation-induced changes in human gene expression. Nature, 459: 587-591, 2009.
Price AL., Patterson N., Hancks DC., Myers S., Reich D., Cheung VG. & Spielman RS. Effects of cis and transgenetic ancestry on gene expression in African Americans. PLoS Genet, 4: e1000294, 2008.
Smirnov DA. & Cheung VG. ATM gene mutations result in both recessive and dominant expression phenotypes of genes and microRNAs. Amer J Hum Genet, 83: 243-253, 2008.
Cheung VG., Bruzel A., Burdick JT., Morley M., Devlin JL. & Spielman RS. Monozygotic twins reveal germline contribution to allelic expression differences. Amer J Hum Genet, 82: 1357-1360, 2008.
Oliver TR., Feingold E., Yu K., Cheung V., Tinker S., Yadav-Shah M., Masse N. & Sherman SL. New insights into human nondisjunction of chromosome 21 in oocytes. PLoS Genet, 4: e1000033, 2008.
Bastone LA., Putt ME., Ten Have TR., Cheung VG. & Spielman RS. Genetic heterogeneity and trans regulators of gene expression. BMC Proceedings, 1 Suppl 1: S80, 2007.
Wang X., Tomso DJ., Chorley BN., Cho HY., Cheung VG., Kleeberger SR. & Bell DA. Identification of polymorphic antioxidant response elements in the human genome. Human Molecular Genetics, 16: 1188-1200, 2007.
Cheung VG., Burdick JT., Hirschmann D. & Morley M. Polymorphic variation in human meiotic recombination. Amer J Hum Genet, 80: 526-530, 2007.
Spielman RS., Bastone LA., Burdick JT., Morley M., Ewens WJ. & Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nature Genetics, 39: 226-231, 2007.
Burdick JT., Chen W., Abecasis GR. & Cheung VG. In silico method for inferring genotypes in pedigrees. Nature Genetics, 38: 1002-1004, 2006.
Cheung VG. & Ewens WJ. Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype. Genome Research, 16: 973-979, 2006.
Bruzel A. & Cheung VG. DNA Reassociation using oscillating phenol emulsions. Genomics, 87: 286-289, 2006.
Cheung VG., Spielman RS., Ewens KG., Weber TM., Morley M. & Burdick JT. Mapping determinants of human gene expression by regional and genome-wide association. Nature, 437: 1365-1369, 2005.
Jen KY. & Cheung VG. Identification of novel P53 target genes involved in ionizing radiation response. Cancer Research, 65: 7666-7673, 2005.
Correa CR. & Cheung VG. Genetic variation in radiation-induced expression phenotypes. Amer J Hum Genet, 75: 885-90, 2004.
Morley M., Molony CM., Weber T., Devlin JL., Ewens KG., Spielman RS. & Cheung VG. Genetic analysis of genome-wide variation in human gene expression. Nature, 430: 743-747, 2004.
Smirnov DA., Burdick JT., Morley M. & Cheung VG. Method for manufacturing whole-genome microarrays by rolling circle amplification. Genes, Chromosomes & Cancer, 40: 72-77, 2004.
Smirnov D., Bruzel A., Morley M. & Cheung VG. Direct IBD Mapping: An identical-by-descent mapping method without genotyping. Genomics, 83: 335-345, 2004.
Jen KY. & Cheung VG. Transcriptional response of lymphoblastoid cells to ionizing radiation. Genome Research, 13: 2092-2100, 2003.
Cheung VG., Conlin LK., Weber TM., Arcaro M., Jen KY., Morley M. & Spielman RS. Natural variation in human gene expression assessed in lymphoblastoid cells. Nature Genetics, 33: 422-425, 2003.
Cheung VG., Jen KY., Weber TM., Morley M., Devlin JL., Ewens KG. & Spielman RS. Genetics of quantitative variation in human gene expression. Cold Spring Harbor Symposia on Quantitative Biology, 68: 403-407, 2003.
Watts JA., Morley M., Burdick JT., Fiori JL., Ewens WJ., Spielman RS. & Cheung VG. Gene expression phenotype in heterozygous carriers of ataxia telangiectasia. Amer J Hum Genet, 71: 791-800, 2002.
Cheung VG., Nowak N., Jang W., et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature, 409: 953-958, 2001.
International Human Genome Mapping Consortium. A physical map of the human genome. Nature, 409: 934-941, 2001.
Morley M., Arcaro M., Burdick J., Yonescu R., Reid T., Kirsch IR. & Cheung VG. GenMapDB: a database of mapped human BAC clones. Nucleic Acids Research, 29: 144-147, 2001.
Cheung VG., Dalrymple HL., Narasimhan S., Watts J., Schuler G., Raap AK., Morley M. & Bruzel A. A resource of mapped human bacterial artificial chromosome clones. Genome Research, 9: 989-993, 1999.
Grant GR., Manduchi E., Cheung VG. & Ewens WJ. Significance testing for direct identity-by-descent mapping.Annals of Human Genetics, 63: 441-454, 1999.
Cheung VG., Gregg JP., Gogolin-Ewens KJ., Bandong J., Stanley CA., Baker L., Higgins MJ., Nowak NJ., Shows TB., Ewens WJ., Nelson SF. & Spielman RS. Linkage-disequilibrium mapping without genotyping. Nature Genetics, 18: 225-230, 1998.

Before 2000

Cheung VG., Dalrymple HL., Narasimhan S., Watts J., Schuler G., Raap AK., Morley M. & Bruzel A. A resource of mapped human bacterial artificial chromosome clones. Genome Research, 9: 989-993, 1999.
Grant GR., Manduchi E., Cheung VG. & Ewens WJ. Significance testing for direct identity-by-descent mapping.Annals of Human Genetics, 63: 441-454, 1999.
Cheung VG., Gregg JP., Gogolin-Ewens KJ., Bandong J., Stanley CA., Baker L., Higgins MJ., Nowak NJ., Shows TB., Ewens WJ., Nelson SF. & Spielman RS. Linkage-disequilibrium mapping without genotyping. Nature Genetics, 18: 225-230, 1998.