Student Publications

Student Spotlight Articles

Student Publication Archive 

The publications below are from current and past Genetics & Genomics PhD students who were in the graduate program at the time of their article being published. New publications added regularly.

2021

Kondratov O, Kondratova L, Mandel RJ, Coleman K, Savage MA, Gray-Edwards HL, Ness TJ, Rodriguez-Lebron E, Bell RD, Rabinowitz J, Gamlin PD, Zolotukhin S. A comprehensive study of a 29-capsid AAV library in a non-human primate central nervous system. Mol Ther. 2021 Jul 21:S1525-0016(21)00364-6. doi: 10.1016/j.ymthe.2021.07.010. Online ahead of print. PMID: 34298128

Stribling D*, Chang PL*, Dalton JE, Conow CA, Rosenthal M, Hebets E, Graze RM, Arbeitman MN. The brain transcriptome of the wolf spider, Schizocosa ocreata. BMC Res Notes. 2021 Jun 23;14(1):236. doi: 10.1186/s13104-021-05648-y. PMID: 34162407

Malik I*, Kelley CP*, Wang ET, Todd PK. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat Rev Mol Cell Biol. 2021 Jun 17. doi: 10.1038/s41580-021-00382-6. Online ahead of print. PMID: 34140671 Review.

Linzer N, Trumbull A, Nar R, Gibbons MD, Yu DT, Strouboulis J, Bungert J. Regulation of RNA Polymerase II Transcription Initiation and Elongation by Transcription Factor TFII-I. Front Mol Biosci. 2021 May 13;8:681550. doi: 10.3389/fmolb.2021.681550. eCollection 2021. PMID: 34055891

Stribling D, Lei Y, Guardia CM, Li L, Fields CJ, Nowialis P, Opavsky R, Renne R, Xie M. A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor. RNA. 2021 Jun;27(6):694-709. doi: 10.1261/rna.078694.121. Epub 2021 Apr 1. PMID: 33795480

Claudio-Campos K, Stevens D, Koo SW, Valko A, Bienvenu OJ, Budman CB, Cath DC, Darrow S, Geller D, Goes FS, Grados MA, Greenberg BD, Greenberg E, Hirschtritt ME, Illmann C, Ivankovic F, King RA, Knowles JA, Krasnow J, Lee PC, Lyon GJ, McCracken JT, Robertson MM, Osiecki L, Riddle MA, Rouleau G, Sandor P, Nestadt G, Samuels J, Scharf JM, Mathews CA; Tourette Association of America International Consortium for Genetics (TAAICG) and the OCD Collaborative Genetics Association Study (OCGAS). Is Persistent Motor or Vocal Tic Disorder a Milder Form of Tourette Syndrome? Mov Disord. 2021 May 4. doi: 10.1002/mds.28593. Online ahead of print. PMID: 33942911

Miller BR, Morse AM, Borgert JE, Liu Z, Sinclair K, Gamble G, Zou F, Newman JRB, León-Novelo LG, Marroni F, McIntyre LM. Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele specific expression (BayesASE). G3 (Bethesda). 2021 Mar 27:jkab096. doi: 10.1093/g3journal/jkab096. Online ahead of print. PMID: 33772539

Liu Y, Xing H, Sheng W, Singh KN, Korkmaz AG, Comeau C, Anika M, Ernst A, Yokoi F, Vaillancourt DE, Frazier CJ, Li Y. Alteration of the cholinergic system and motor deficits in cholinergic neuron-specific Dyt1 knockout mice. Neurobiol Dis. 2021 Mar 20;154:105342. doi: 10.1016/j.nbd.2021.105342. Online ahead of print. PMID: 33757902

Hu Y, Colantonio V, Müller BSF, Leach KA, Nanni A, Finegan C, Wang B, Baseggio M, Newton CJ, Juhl EM, Hislop L, Gonzalez JM, Rios EF, Hannah LC, Swarts K, Gore MA, Hennen-Bierwagen TA, Myers AM, Settles AM, Tracy WF, Resende MFR Jr. Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nat Commun. 2021 Feb 23;12(1):1227. doi: 10.1038/s41467-021-21380-4. PMID: 33623026

Gay LA, Stribling D, Turner PC, Renne R. Kaposi’s Sarcoma-associated Herpesvirus microRNA mutants modulate cancer hallmark phenotypic differences in human endothelial cells. J Virol. 2021 Feb 10:JVI.02022-20. doi: 10.1128/JVI.02022-20. Online ahead of print. PMID: 33568509

Gurumurthy A, Yu DT, Stees JR, Chamales P, Gavrilova E, Wassel P, Li L, Stribling D, Chen J, Brackett M, Ishov AM, Xie M, Bungert J. Super-enhancer mediated regulation of adult β-globin gene expression: the role of eRNA and Integrator. Nucleic Acids Res. 2021 Jan 21:gkab002. doi: 10.1093/nar/gkab002. Epub ahead of print. PMID: 33476375.

Otero BA, Poukalov K, Hildebrandt RP, Thornton CA, Jinnai K, Fujimura H, Kimura T, Hagerman KA, Sampson JB, Day JW, Wang ET. Transcriptome alterations in myotonic dystrophy frontal cortex. Cell Rep. 2021 Jan 19;34(3):108634. doi: 10.1016/j.celrep.2020.108634. PMID: 33472074.

Liu Y, Xing H, Yokoi F, Vaillancourt DE, Li Y. Investigating the role of striatal dopamine receptor 2 in motor coordination and balance: Insights into the pathogenesis of DYT1 dystonia. Behav Brain Res. 2021 Jan 18;403:113137. doi: 10.1016/j.bbr.2021.113137. Epub ahead of print. PMID: 33476687.

Grippin AJ, Dyson KA, Qdaisat S, McGuiness J, Wummer B, Mitchell DA, Mendez-Gomez HR, Sayour EJ. Nanoparticles as immunomodulators and translational agents in brain tumors. J Neurooncol. 2021 Jan;151(1):29-39. doi: 10.1007/s11060-020-03559-9. Epub 2020 Aug 5. PMID: 32757093.

2020

Lyu S, Xing H, Liu Y, Girdhar P, Zhang K, Yokoi F, Xiao R, Li Y. Deficiency of Meis1, a transcriptional regulator, in mice and worms: Neurochemical and behavioral characterizations with implications in the restless legs syndrome. J Neurochem. 2020 Dec;155(5):522-537. doi: 10.1111/jnc.15177. Epub 2020 Sep 23. PMID: 32910473.

Liu Y, Xing H, Wilkes BJ, Yokoi F, Chen H, Vaillancourt DE, Li Y. The abnormal firing of Purkinje cells in the knockin mouse model of DYT1 dystonia. Brain Res Bull. 2020 Dec;165:14-22. doi: 10.1016/j.brainresbull.2020.09.011. Epub 2020 Sep 22. PMID: 32976982; PMCID: PMC7674218.

Liu L, Amorín R, Moriel P, DiLorenzo N, Lancaster PA, Peñagaricano F. Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition. BMC Genomics. 2020 Oct 2;21(1):684. doi: 10.1186/s12864-020-07068-x. PMID: 33008289; PMCID: PMC7531131.

Zhang X, He Y, Zhang P, Budamagunta V, Lv D, Thummuri D, Yang Y, Pei J, Yuan Y, Zhou D, Zheng G. Discovery of IAP-recruiting BCL-XL PROTACs as potent degraders across multiple cancer cell lines. Eur J Med Chem. 2020 Aug 1;199:112397. doi: 10.1016/j.ejmech.2020.112397. Epub 2020 May 4. PMID: 32388279; PMCID: PMC7325632.

He Y, Koch R, Budamagunta V, Zhang P, Zhang X, Khan S, Thummuri D, Ortiz YT, Zhang X, Lv D, Wiegand JS, Li W, Palmer AC, Zheng G, Weinstock DM, Zhou D. DT2216-a Bcl-xL-specific degrader is highly active against Bcl-xL-dependent T cell lymphomas. J Hematol Oncol. 2020 Jul 16;13(1):95. doi: 10.1186/s13045-020-00928-9. PMID: 32677976; PMCID: PMC7364785.

Wimberly K, Choe KP. Gel-free genotyping of deletion alleles in Caenorhabditis elegans with real-time PCR. MicroPubl Biol. 2020 Jul 11;2020:10.17912/micropub.biology.000274. doi: 10.17912/micropub.biology.000274. PMID: 32666047; PMCID: PMC7354062.

Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. PMID: 32381734; PMCID: PMC7293693.

Sebastian M, Hsiao CJ, Futch HS, Eisinger RS, Dumeny L, Patel S, Gobena M, Katikaneni DS, Cohen J, Carpenter AM, Spiryda L, Heldermon CD, Jin L, Brantly ML. Obesity and STING1 genotype associate with 23-valent pneumococcal vaccination efficacy. JCI Insight. 2020 May 7;5(9):e136141. doi: 10.1172/jci.insight.136141. PMID: 32376795; PMCID: PMC7253011.

He Y, Zhang X, Chang J, Kim HN, Zhang P, Wang Y, Khan S, Liu X, Zhang X, Lv D, Song L, Li W, Thummuri D, Yuan Y, Wiegand JS, Ortiz YT, Budamagunta V, Elisseeff JH, Campisi J, Almeida M, Zheng G, Zhou D. Using proteolysis-targeting chimera technology to reduce navitoclax platelet toxicity and improve its senolytic activity. Nat Commun. 2020 Apr 24;11(1):1996. doi: 10.1038/s41467-020-15838-0. PMID: 32332723; PMCID: PMC7181703.

Sznajder ŁJ, Scotti MM, Shin J, Taylor K, Ivankovic F, Nutter CA, Aslam FN, Subramony SH, Ranum LPW, Swanson MS. Loss of MBNL1 induces RNA misprocessing in the thymus and peripheral blood. Nat Commun. 2020 Apr 24;11(1):2022. doi: 10.1038/s41467-020-15962-x. PMID: 32332745; PMCID: PMC7181699.

Mavian C, Paisie TK, Alam MT, Browne C, Beau De Rochars VM, Nembrini S, Cash MN, Nelson EJ, Azarian T, Ali A, Morris JG Jr, Salemi M. Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems. Proc Natl Acad Sci U S A. 2020 Apr 7;117(14):7897-7904. doi: 10.1073/pnas.1918763117. Epub 2020 Mar 30. PMID: 32229557; PMCID: PMC7149412.

Califar B, Sng NJ, Zupanska A, Paul AL, Ferl RJ. Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana. Front Plant Sci. 2020 Mar 4;11:239. doi: 10.3389/fpls.2020.00239. PMID: 32194611; PMCID: PMC7064724.

He Y, Li W, Lv D, Zhang X, Zhang X, Ortiz YT, Budamagunta V, Campisi J, Zheng G, Zhou D. Inhibition of USP7 activity selectively eliminates senescent cells in part via restoration of p53 activity. Aging Cell. 2020 Mar;19(3):e13117. doi: 10.1111/acel.13117. Epub 2020 Feb 16. PMID: 32064756; PMCID: PMC7059172.

James TG, Sullivan MK, Dumeny L, Lindsey K, Cheong J, Nicolette G. Health insurance literacy and health service utilization among college student J Am Coll Health. 2020 Feb-Mar;68(2):200-206. doi: 10.1080/07448481.2018.1538151. Epub 2018 Dec 10. PMID: 30526397.

Yokoi F, Oleas J, Xing H, Liu Y, Dexter KM, Misztal C, Gerard M, Efimenko I, Lynch P, Villanueva M, Alsina R, Krishnaswamy S, Vaillancourt DE, Li Y. Decreased number of striatal cholinergic interneurons and motor deficits in dopamine receptor 2-expressing-cell-specific Dyt1 conditional knockout mice. Neurobiol Dis. 2020 Feb;134:104638. doi: 10.1016/j.nbd.2019.104638. Epub 2019 Oct 13. PMID: 31618684; PMCID: PMC7323754.

Louvandini H, Corrêa PS, Amorín R, Liu L, Ieda EH, Jimenez CR, Tsai SM, McManus CM, Peñagaricano F. Gestational and lactational exposure to gossypol alters the testis transcriptome. BMC Genomics. 2020 Jan 17;21(1):59. doi: 10.1186/s12864-020-6487-2. PMID: 31952482; PMCID: PMC6969474.

Lyu S, Xing H, DeAndrade MP, Perez PD, Zhang K, Liu Y, Yokoi F, Febo M, Li Y. The role of BTBD9 in the cerebral cortex and the pathogenesis of restless legs syndrome. Exp Neurol. 2020 Jan;323:113111. doi: 10.1016/j.expneurol.2019.113111. Epub 2019 Nov 9. PMID: 31715135; PMCID: PMC6899185.

2019

Ge Y, Paisie TK, Chen S, Concannon P. UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes. J Immunol. 2019 Dec 1;203(11):2827-2836. doi: 10.4049/jimmunol.1801338. Epub 2019 Oct 28. PMID: 31659016; PMCID: PMC6938261.

Nutter CA, Bubenik JL, Oliveira R, Ivankovic F, Sznajder ŁJ, Kidd BM, Pinto BS, Otero BA, Carter HA, Vitriol EA, Wang ET, Swanson MS. Cell-type-specific dysregulation of RNA alternative splicing in short tandem repeat mouse knockin models of myotonic dystrophy. Genes Dev. 2019 Dec 1;33(23-24):1635-1640. doi: 10.1101/gad.328963.119. Epub 2019 Oct 17. PMID: 31624084; PMCID: PMC6942047.

Reddy K, Jenquin JR, McConnell OL, Cleary JD, Richardson JI, Pinto BS, Haerle MC, Delgado E, Planco L, Nakamori M, Wang ET, Berglund JA. A CTG repeat-selective chemical screen identifies microtubule inhibitors as selective modulators of toxic CUG RNA levels. Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):20991-21000. doi: 10.1073/pnas.1901893116. Epub 2019 Sep 30. PMID: 31570586; PMCID: PMC6800345.

Sebastian M, Robinson MA, Dumeny L, Dyson KA, Fantone JC, McCormack WT, Stratford May W. Training methods that improve MD-PhD student self-efficacy for clinical research skills. J Clin Transl Sci. 2019 Oct 14;3(6):316-324. doi: 10.1017/cts.2019.419. PMID: 31827905; PMCID: PMC6885998.

Lyu S, Xing H, DeAndrade MP, Liu Y, Perez PD, Yokoi F, Febo M, Walters AS, Li Y. The Role of BTBD9 in Striatum and Restless Legs Syndrome. eNeuro. 2019 Oct 10;6(5):ENEURO.0277-19.2019. doi: 10.1523/ENEURO.0277-19.2019. PMID: 31444227; PMCID: PMC6787346

Kondratova L, Kondratov O, Ragheb R, Zolotukhin S. Removal of Endotoxin from rAAV Samples Using a Simple Detergent-Based Protocol. Mol Ther Methods Clin Dev. 2019 Sep 6;15:112-119. doi: 10.1016/j.omtm.2019.08.013. PMID: 31649960; PMCID: PMC6804492.

Wu CW, Wimberly K, Pietras A, Dodd W, Atlas MB, Choe KP. RNA processing errors triggered by cadmium and integrator complex disruption are signals for environmental stress. BMC Biol. 2019 Jul 16;17(1):56. doi: 10.1186/s12915-019-0675-z. PMID: 31311534; PMCID: PMC6631800.

Denes LT, Riley LA, Mijares JR, Arboleda JD, McKee K, Esser KA, Wang ET. Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation. Skelet Muscle. 2019 Jun 7;9(1):17. doi: 10.1186/s13395-019-0203-4. PMID: 31174599; PMCID: PMC6555731.

2018

Meneely S, Dinkins ML, Kassai M, Lyu S, Liu Y, Lin CT, Brewer K, Li Y, Clemens S. Differential Dopamine D1 and D3 Receptor Modulation and Expression in the Spinal Cord of Two Mouse Models of Restless Legs Syndrome. Front Behav Neurosci. 2018 Sep 4;12:199. doi: 10.3389/fnbeh.2018.00199. PMID: 30233336; PMCID: PMC6131574.

Johnson LM, Chandler LM, Davies SK, Baer CF. Network Architecture and Mutational Sensitivity of the elegans Metabolome. Front Mol Biosci. 2018 Jul 31;5:69. doi: 10.3389/fmolb.2018.00069. PMID: 30109234; PMCID: PMC6079199.

Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA. An engineered RNA binding protein with improved splicing regulation. Nucleic Acids Res. 2018 Apr 6;46(6):3152-3168. doi: 10.1093/nar/gkx1304. PMID: 29309648; PMCID: PMC5888374.

Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. Curr Opin Plant Biol. 2018 Apr;42:81-89. doi: 10.1016/j.pbi.2018.04.003. Epub 2018 Apr 27. PMID: 29694936.

Dodd W, Tang L, Lone JC, Wimberly K, Wu CW, Consalvo C, Wright JE, Pujol N, Choe KP. A Damage Sensor Associated with the Cuticle Coordinates Three Core Environmental Stress Responses in Caenorhabditis elegans. Genetics. 2018 Apr;208(4):1467-1482. doi: 10.1534/genetics.118.300827. Epub 2018 Feb 27. PMID: 29487136; PMCID: PMC5887142.

Singh S, McDonough CW, Gong Y, Alghamdi WA, Arwood MJ, Bargal SA, Dumeny L, Li WY, Mehanna M, Stockard B, Yang G, de Oliveira FA, Fredette NC, Shahin MH, Bailey KR, Beitelshees AL, Boerwinkle E, Chapman AB, Gums JG, Turner ST, Cooper-DeHoff RM, Johnson JA. Genome Wide Association Study Identifies the HMGCS2 Locus to be Associated With Chlorthalidone Induced Glucose Increase in Hypertensive Patients. J Am Heart Assoc. 2018 Mar 9;7(6):e007339. doi: 10.1161/JAHA.117.007339. PMID: 29523524; PMCID: PMC5907544.

Nicolini P, Amorín R, Han Y, Peñagaricano F. Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle. BMC Genet. 2018 Feb 27;19(1):14. doi: 10.1186/s12863-018-0600-4. PMID: 29486732; PMCID: PMC5830072.

Shen Y, Nar R, Fan AX, Aryan M, Hossain MA, Gurumurthy A, Wassel PC, Tang M, Lu J, Strouboulis J, Bungert J. Functional interrelationship between TFII-I and E2F transcription factors at specific cell cycle gene loci. J Cell Biochem. 2018 Jan;119(1):712-722. doi: 10.1002/jcb.26235. Epub 2017 Jul 31. PMID: 28657656; PMCID: PMC5705458.

2017

Pinto BS, Saxena T, Oliveira R, Méndez-Gómez HR, Cleary JD, Denes LT, McConnell O, Arboleda J, Xia G, Swanson MS, Wang ET. Impeding Transcription of Expanded Microsatellite Repeats by Deactivated Cas9. Mol Cell. 2017 Nov 2;68(3):479-490.e5. doi: 10.1016/j.molcel.2017.09.033. Epub 2017 Oct 19. PMID: 29056323; PMCID: PMC6013302.

Ge Y, Paisie TK, Newman JRB, McIntyre LM, Concannon P. UBASH3A Mediates Risk for Type 1 Diabetes Through Inhibition of T-Cell Receptor-Induced NF-κB Signaling. Diabetes. 2017 Jul;66(7):2033-2043. doi: 10.2337/db16-1023. Epub 2017 Jun 12. PMID: 28607106; PMCID: PMC5482087.

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