Research

Parker Lab Researchers
 Parker Lab Researchers

Department of Human Genetics faculty are involved in widely diverse areas of research, from Genome Structure and Function research to Evolutionary and Population Genetics. Please select an area of interest from the list below to explore the research of individual laboratories.

You may also explore The Department of Human Genetic's research profile and collaboration network on the Michigan Experts website (Michigan Experts is a searchable database of research expertise across disciplines from several schools/colleges or institutes at the University of Michigan.)

 

Recent Publications  

He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang HH, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Sci Data. 2020 Jun 12;7(1):181. doi: 10.1038/s41597-020-0523-6. PMID: 32533075; PMCID: PMC7293349.

Moon SL, Morisaki T, Stasevich TJ, Parker R. Coupling of translation quality control and mRNA targeting to stress granules. J Cell Biol. 2020 Aug 3;219(8):e202004120. doi: 10.1083/jcb.202004120. PMID: 32520986.

Shami AN, Zheng X, Munyoki SK, Ma Q, Manske GL, Green CD, Sukhwani M, Orwig KE, Li JZ, Hammoud SS. Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis. Dev Cell. 2020 Jun 5:S1534-5807(20)30399-3. doi: 10.1016/j.devcel.2020.05.010. Epub ahead of print. PMID: 32504559.

Vallianatos CN, Raines B, Porter RS, Bonefas KM, Wu MC, Garay PM, Collette KM, Seo YA, Dou Y, Keegan CE, Tronson NC, Iwase S. Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. Commun Biol. 2020 Jun 1;3(1):278. doi: 10.1038/s42003-020-1001-6. Erratum in: Commun Biol. 2020 Jun 22;3(1):331. PMID: 32483278; PMCID: PMC7264178.

Desch K, Ozel AB, Halvorsen M, Jacobi PM, Golden KL, Underwood MI, Germain M, Trégouët DA, Reitsma PH, Kearon C, Mokry L, Richards B, Williams F, Li J, Goldstein DB, Ginsburg D. Whole exome sequencing identifies rare variants in STAB2 associated with venous thromboembolic disease. Blood. 2020 May 26:blood.2019004161. doi: 10.1182/blood.2019004161. Epub ahead of print. PMID:32457982.

Brinkmeier ML, Bando H, Camarano AC, Fujio S, Yoshimoto K, de Souza FSJ, Camper SA. Rathke's cleft-like cysts arise from Isl1 deletion in murine pituitary progenitors. J Clin Invest. 2020 May 26:136745. doi: 10.1172/JCI136745. Epub ahead of print. PMID: 32453714.

Tseng-Rogenski SS, Munakata K, Choi DY, Martin PK, Mehta S, Koi M, Zheng W, Zhang Y, Carethers JM. The Human DNA Mismatch Repair Protein MSH3 Contains Nuclear Localization and Export Signals That Enable Nuclear-Cytosolic Shuttling in Response to Inflammation. Mol Cell Biol. 2020 Jun 15;40(13):e00029-20. doi: 10.1128/MCB.00029-20. PMID: 32284349.

Arlt MF, Brogley MA, Stark-Dykema ER, Hu YC, Mueller JL. Genomic Structure, Evolutionary Origins, and Reproductive Function of a Large Amplified Intrinsically Disordered Protein-Coding Gene on the X Chromosome (<i>Laidx</i>) in Mice. G3 (Bethesda). 2020 Jun 1;10(6):1997-2005. doi: 10.1534/g3.120.401221. PMID: 32253194; PMCID: PMC7263670.

Kregel S, Bagamasbad P, He S, LaPensee E, Raji Y, Brogley M, Chinnaiyan A, Cieslik M, Robins DM. Differential modulation of the androgen receptor for prostate cancer therapy depends on the DNA response element. Nucleic Acids Res. 2020 May 21;48(9):4741-4755. doi: 10.1093/nar/gkaa178. PMID: 32198885; PMCID: PMC7229860.

Diehl AG, Ouyang N, Boyle AP. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat Commun. 2020 Apr 14;11(1):1796. doi: 10.1038/s41467-020-15520-5. PMID: 32286261;PMCID: PMC7156512. https://pubmed.ncbi.nlm.nih.gov/32286261/

Bando H, Gergics P, Bohnsack BL, Toolan KP, Richter CE, Shavit JA, Camper SA. Otx2b mutant zebrafish have pituitary, eye and mandible defects that model mammalian disease. Hum Mol Genet. 2020 Jun 27;29(10):1648-1657. doi: 10.1093/hmg/ddaa064. PMID: 32277752. https://pubmed.ncbi.nlm.nih.gov/32277752/

Tseng-Rogenski SS, Munakata K, Choi DY, Martin PK, Mehta S, Koi M, Zheng W,Zhang Y, Carethers JM. The human DNA mismatch repair protein MSH3 contains nuclear localization and export signals that enable nuclear-cytosolic shuttling in response to inflammation. Mol Cell Biol. 2020 Apr 13:MCB.00029-20. doi:10.1128/MCB.00029-20. Epub ahead of print. PMID: 32284349. https://pubmed.ncbi.nlm.nih.gov/32284349/

Leonard D, Huang W, Izadmehr S, O'Connor CM, Wiredja DD, Wang Z, Zaware N,Chen Y, Schlatzer DM, Kiselar J, Vasireddi N, Schüchner S, Perl AL, Galsky MD,Xu W, Brautigan DL, Ogris E, Taylor DJ, Narla G. Selective PP2A Enhancement through Biased Heterotrimer Stabilization. Cell. 2020 Apr 30;181(3):688-701.e16.doi: 10.1016/j.cell.2020.03.038. Epub 2020 Apr 20. PMID: 32315618; PMCID:PMC7243596. https://pubmed.ncbi.nlm.nih.gov/32315618/

Roberts JS, Patterson AK, Uhlmann WR. Genetic testing for neurodegenerative diseases: Ethical and health communication challenges. Neurobiol Dis. 2020 Apr 14;141:104871. doi: 10.1016/j.nbd.2020.104871. Epub ahead of print. PMID:32302673. https://pubmed.ncbi.nlm.nih.gov/32302673/

Sheldon JP, Oliver M, Yashar BM. Rewards and challenges of parenting a child with Down syndrome: a qualitative study of fathers' perceptions. Disabil Rehabil. 2020 Apr 7:1-12. doi: 10.1080/09638288.2020.1745907. Epub ahead of print. PMID: 32255374. https://pubmed.ncbi.nlm.nih.gov/32255374/

Samanta M, Kalantry S. Generating primed pluripotent epiblast stem cells: A methodology chapter. Curr Top Dev Biol. 2020;138:139-174. doi: 10.1016/bs.ctdb.2020.01.005. Epub 2020 Feb 27. PubMed PMID: 32220296.

Orchard P, Kyono Y, Hensley J, Kitzman JO, Parker SCJ. Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. Cell Syst. 2020 Mar 25;10(3):298-306.e4. doi: 10.1016/j.cels.2020.02.009. PubMed PMID: 32213349.

Norton EL, Hornsby WE, Wu X, Wolford BN, Graham SE, Willer CJ, Yang B. Aortic progression and reintervention in patients with pathogenic variants after a thoracic aortic dissection. J Thorac Cardiovasc Surg. 2020 Feb 20. pii: S0022-5223(20)30471-2. doi: 10.1016/j.jtcvs.2020.01.094. [Epub ahead of print] PubMed PMID: 32199657.

Kregel S, Bagamasbad P, He S, LaPensee E, Raji Y, Brogley M, Chinnaiyan A, Cieslik M, Robins DM. Differential modulation of the androgen receptor for prostate cancer therapy depends on the DNA response element. Nucleic Acids Res. 2020 Mar 21. pii: gkaa178. doi: 10.1093/nar/gkaa178. [Epub ahead of print] PubMed PMID: 32198885.

Swanepoel CM, Gerlinger ER, Mueller JL. Large X-linked palindromes undergo arm-to-arm gene conversion across Mus lineages. Mol Biol Evol. 2020 Mar 7. pii: msaa059. doi: 10.1093/molbev/msaa059. [Epub ahead of print] PubMed PMID: 32145018.

Rai V, Quang DX, Erdos MR, Cusanovich DA, Daza RM, Narisu N, Zou LS, Didion JP, Guan Y, Shendure J, Parker SCJ, Collins FS. Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Mol Metab. 2020 Feb; 32:109-121. doi: 10.1016/j.molmet.2019.12.006. Epub 2019 Dec 20. PubMed PMID: 32029221; PubMed Central PMCID: PMC6961712.

Prasov L, Ullah E, Turriff AE, Warner BM, Conley J, Mark PR, Hufnagel RB, Huryn LA. Expanding the genotypic spectrum of Jalili syndrome: Novel CNNM4 variants and uniparental isodisomy in a north American patient cohort. Am J Med Genet A. 2020 Mar;182(3):493-497. doi: 10.1002/ajmg.a.61484. Epub 2020 Feb 5. PubMed PMID: 32022389.

Lenk GM, Jafar-Nejad P, Hill SF, Huffman LD, Smolen CE, Wagnon JL, Petit H, Yu W, Ziobro J, Bhatia K, Parent J, Giger RJ, Rigo F, Meisler MH. Scn8a Antisense Oligonucleotide Is Protective in Mouse Models of SCN8A Encephalopathy and Dravet Syndrome. Ann Neurol. 2020 Mar;87(3):339-346. doi: 10.1002/ana.25676. Epub 2020 Feb 6. PubMed PMID: 31943325; PubMed Central PMCID: PMC7064908.

Cheung LYM, Camper SA. PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression. Endocrinology. 2020 Feb 1;161(2). pii: bqaa002. doi: 10.1210/endocr/bqaa002. PubMed PMID: 31913463; PubMed Central PMCID: PMC7029777.

Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res. 2020 Feb 20;48(3):1146-1163. doi: 10.1093/nar/gkz1173. PubMed PMID: 31853540; PubMed Central PMCID: PMC7026601.

Kuo ME, Antonellis A. Ubiquitously Expressed Proteins and Restricted Phenotypes: Exploring Cell-Specific Sensitivities to Impaired tRNA Charging. Trends Genet. 2020 Feb;36(2):105-117. doi: 10.1016/j.tig.2019.11.007. Epub 2019 Dec 12. Review. PubMed PMID: 31839378; PubMed Central PMCID: PMC6980692.

Meisner JK, Martin DM. Congenital heart defects in CHARGE: The molecular role of CHD7 and effects on cardiac phenotype and clinical outcomes. Am J Med Genet C  Semin Med Genet. 2020 Mar;184(1):81-89. doi: 10.1002/ajmg.c.31761. Epub 2019 Dec 13. PubMed PMID: 31833191.

Ho SS, Urban AE, Mills RE. Structural variation in the sequencing era. Nat Rev Genet. 2020 Mar;21(3):171-189. doi: 10.1038/s41576-019-0180-9. Epub 2019 Nov 15. Review. PubMed PMID: 31729472.

Read P, Yashar BM, Robinson L, Marvin M. Optimizing efficiency and skill utilization: Analysis of genetic counselors' attitudes regarding delegation in a clinical setting. J Genet Couns. 2020 Feb;29(1):67-77. doi: 10.1002/jgc4.1181. Epub 2019 Nov 13. PubMed PMID: 31721370.

Kuo ME, Antonellis A, Shakkottai VG. Alanyl-tRNA Synthetase 2 (AARS2)-Related Ataxia Without Leukoencephalopathy. Cerebellum. 2020 Feb;19(1):154-160. doi: 10.1007/s12311-019-01080-y. PubMed PMID: 31705293; PubMed Central PMCID: PMC6982554.

Ziats MN, Ahmad A, Bernat JA, Fisher R, Glassford M, Hannibal MC, Jacher JE, Weiser N, Keegan CE, Lee KN, Marzulla TB, O'Connor BC, Quinonez SC, Seemann L, Turner L, Bielas S, Harris NL, Ogle JD, Innis JW, Martin DM. Genotype-phenotype analysis of 523 patients by genetics evaluation and clinical exome sequencing. Pediatr Res. 2020 Mar;87(4):735-739. doi: 10.1038/s41390-019-0611-5. Epub 2019 Oct 16. PubMed PMID: 31618753; PubMed Central PMCID: PMC7082194.

Wilson TE, Sunder S. Double-strand breaks in motion: implications for chromosomal rearrangement. Curr Genet. 2020 Feb;66(1):1-6. doi: 10.1007/s00294-019-01015-4. Epub 2019 Jul 18. Review. PubMed PMID: 31321486; PubMed Central PMCID: PMC6980467.

Lenk GM, Jafar-Nejad P, Hill SF, Huffman LD, Smolen CE, Wagnon JL, Petit H, Yu W, Ziobro J, Bhatia K, Parent J, Giger RJ, Rigo F, Meisler MH. Scn8a antisense oligonucleotide is protective in mouse models of SCN8A Encephalopathy and Dravet Syndrome. Ann Neurol. 2020 Jan 14. doi: 10.1002/ana.25676. [Epub ahead of print] PMID: 31943325 

Kruger et al., A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice, Current Biology (2019), https://doi.org/10.1016/j.cub.2019.08.057

Moldovan JB, Wang Y, Shuman S, Mills RE, Moran JV. RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. Proc Natl Acad Sci U S A. 2019 Sep 23. pii: 201805404. doi: 10.1073/pnas.1805404116. [Epub ahead of print] PubMed PMID: 31548405.

Watts JA, Burdick J, Daigneault J, Zhu Z, Grunseich C, Bruzel A, Cheung VG. cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression. Am J Hum Genet. 2019 Aug 26. pii: S0002-9297(19)30306-4. doi:10.1016/j.ajhg.2019.08.003. [Epub ahead of print] PubMed PMID: 31495490.

Miyoshi T, Makino T, Moran JV. Poly(ADP-Ribose) Polymerase 2 Recruits Replication Protein A to Sites of LINE-1 Integration to Facilitate Retrotransposition. Mol Cell. 2019 Sep 19;75(6):1286-1298.e12. doi: 10.1016/j.molcel.2019.07.018. Epub 2019 Aug 28. PubMed PMID: 31473101; PubMed Central PMCID: PMC6754305.

Watts JA, Burdick J, Daigneault J, Zhu Z, Grunseich C, Bruzel A, Cheung VG. cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression. Am J Hum Genet. 2019 Aug 26. pii: S0002-9297(19)30306-4. doi:10.1016/j.ajhg.2019.08.003. [Epub ahead of print] PubMed PMID: 31495490.

Emmer BT, Ginsburg D. Genome Editing and Hematologic Malignancy. Annu Rev Med. 2019 Aug 30. doi: 10.1146/annurev-med-052318-100741. [Epub ahead of print] PubMed PMID: 31469969.

Mazzola SE, O'Connor B, Yashar BM. Primary care physicians' understanding and utilization of pediatric exome sequencing results. J Genet Couns. 2019 Aug 30. doi: 10.1002/jgc4.1163. [Epub ahead of print] PubMed PMID: 31469212.

Carethers JM. Fecal DNA Testing for Colorectal Cancer Screening. Annu Rev Med. 2019 Aug 26. doi: 10.1146/annurev-med-103018-123125. [Epub ahead of print] PubMed PMID: 31451044.

Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res. 2019 Sep 13. doi: 10.1021/acs.jproteome.9b00434. [Epub ahead of print] PubMed PMID: 31430157.

Innis JW. Hand-Foot-Genital Syndrome. 2006 Jul 11 [updated 2019 Aug 8]. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens K, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2019. Available from http://www.ncbi.nlm.nih.gov/books/NBK1423/ PubMed PMID: 20301596.

Nishizaki SS, Ng N, Dong S, Porter RS, Morterud C, Williams C, Asman C, Switzenberg JA, Boyle AP. Predicting the effects of SNPs on transcription factor binding affinity. Bioinformatics. 2019 Aug 2. pii: btz612. doi: 10.1093/bioinformatics/btz612. [Epub ahead of print] PubMed PMID: 31373606.

Dong S, Boyle AP. Predicting functional variants in enhancer and promoter elements using RegulomeDB. Hum Mutat. 2019 Sep;40(9):1292-1298. doi: 10.1002/humu.23791. Epub 2019 Jun 22. PubMed PMID: 31228310; PubMed Central PMCID: PMC6744346.

Khoriaty R, Ozel AB, Ramdas S, Ross C, Desch K, Shavit JA, Everett L, Siemieniak D, Li JZ, Ginsburg D. Genome-wide linkage analysis and whole-exome sequencing identifies an ITGA2B mutation in a family with thrombocytopenia. Br J Haematol. 2019 Aug;186(4):574-579. doi: 10.1111/bjh.15961. Epub 2019 May 23. PubMed PMID: 31119735; PubMed Central PMCID: PMC6679728.

Wilson TE, Sunder S. Double-strand breaks in motion: implications for chromosomal rearrangement. Curr Genet. 2019 Jul 18. doi: 10.1007/s00294-019-01015-4. [Epub ahead of print] Review. PubMed PMID: 31321486.

Jacher JE, Roy N, Ghaziuddin M, Innis JW. Expanding the phenotypic spectrum of MBOAT7-related intellectual disability. Am J Med Genet B Neuropsychiatr Genet. 2019 Jul 8. doi: 10.1002/ajmg.b.32749. [Epub ahead of print] PubMed PMID: 31282596.

Lenk GM, Park YN, Lemons R, Flynn E, Plank M, Frei CM, Davis MJ, Gregorka B, Swanson JA, Meisler MH, Kitzman JO. CRISPR knockout screen implicates three genes in lysosome function. Sci Rep. 2019 Jul 3;9(1):9609. doi: 10.1038/s41598-019-45939-w. PubMed PMID: 31270356; PubMed Central PMCID: PMC6610096. 

Sunder S, Wilson TE. Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast. Proc Natl Acad Sci U S A. 2019 Apr 24. pii: 201818595. doi: 10.1073/pnas.1818595116. [Epub ahead of print] PubMed PMID: 31019070. 

Ramdas S, Ozel AB, Treutelaar MK, Holl K, Mandel M, Woods LCS, Li JZ. Extended regions of suspected mis-assembly in the rat reference genome. Sci Data. 2019 Apr 23;6(1):39. doi: 10.1038/s41597-019-0041-6. PubMed PMID: 31015470; PubMed Central PMCID: PMC6478900. 

Graham SE, Nielsen JB, Zawistowski M, Zhou W, Fritsche LG, Gabrielsen ME, Skogholt AH, Surakka I, Hornsby WE, Fermin D, Larach DB, Kheterpal S, Brummett CM, Lee S, Kang HM, Abecasis GR, Romundstad S, Hallan S, Sampson MG, Hveem K, Willer CJ. Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis. Nat Commun. 2019 Apr 23;10(1):1847. doi: 10.1038/s41467-019-09861-z. PubMed PMID: 31015462; PubMed Central PMCID: PMC6478837. 

Flasch DA, Macia Á, Sánchez L, Ljungman M, Heras SR, García-Pérez JL, Wilson TE, Moran JV. Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication. Cell. 2019 May 2;177(4):837-851.e28. doi: 10.1016/j.cell.2019.02.050. Epub 2019 Apr 4. PubMed PMID: 30955886. 

Harris C, Cloutier M, Trotter M, Hinten M, Gayen S, Du Z, Xie W, Kalantry S. Conversion of random X-inactivation to imprinted X-inactivation by maternal PRC2. Elife. 2019 Apr 2;8. pii: e44258. doi: 10.7554/eLife.44258. [Epub ahead of print] PubMed PMID: 30938678. 

Caglayan AO, Gumus H, Sandford E, Kubisiak TL, Ma Q, Ozel AB, Per H, Li JZ, Shakkottai VG, Burmeister M. COQ4 Mutation Leads to Childhood-Onset Ataxia Improved by CoQ10 Administration. Cerebellum. 2019 Mar 8. doi: 10.1007/s12311-019-01011-x. [Epub ahead of print] PubMed PMID: 30847826. 

Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet. 2019 Mar 7;104(3):520-529. doi: 10.1016/j.ajhg.2019.01.006. Epub 2019 Feb 26. PubMed PMID: 30824121; PubMed Central PMCID: PMC6407526. 

Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology. 2019 Mar 7;16(1):6. doi: 10.1186/s12977-019-0468-z. PMID: 30845962.