Student Publications

First author publications by Genetics and Development students

2022

Lee W, de Prisco N, Gennarino VA.  Identifying patients and assessing variant pathogenicity for an autosomal dominant disease-driving gene. STAR Protocols 3(1):101150. DOI: 10.1016/j.xpro.2022.101150

Lee W, Zernant J, Su PY, Nagasaki T, Tsang SH, Allikmets R. A genotype-phenotype correlation matrix for ABCA4 disease based on long-term prognostic outcomes. JCI Insight. 2022 Jan 25;7(2):e156154. doi: 10.1172/jci.insight.156154.

2021

Capdevila C, Trifas M, Miller J, Anderson T, Sims PA, Yan KS. Cellular origins and lineage relationships of the intestinal epithelium. Am J Physiol Gastrointest Liver Physiol. 2021 Oct 1;321(4):G413-G425. doi: 10.1152/ajpgi.00188.2021. Epub 2021 Aug 25. Review. PubMed PMID: 34431400; PubMed Central PMCID: PMC8560372.

Ulgherait M, Midoun AM, Park SJ, Gatto JA, Tener SJ, Siewert J, Klickstein N, Canman JC, Ja WW, Shirasu-Hiza M. Circadian autophagy drives iTRF-mediated longevity. Nature. 2021 Oct;598(7880):353-358. doi: 10.1038/s41586-021-03934-0. Epub 2021 Sep 29. PubMed PMID: 34588695; NIHMSID:NIHMS1767810.

Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet. 2021 Aug 5;108(8):1436-1449. doi: 10.1016/j.ajhg.2021.06.006. Epub 2021 Jul 2. PubMed PMID: 34216551; PubMed Central PMCID: PMC8387463.

Lee W, Zernant J, Nagasaki T, Molday LL, Su PY, Fishman GA, Tsang SH, Molday RS, Allikmets R. Cis-acting modifiers in the ABCA4 locus contribute to the penetrance of the major disease-causing variant in Stargardt disease. Hum Mol Genet. 2021 Jun 26;30(14):1293-1304. doi: 10.1093/hmg/ddab122. PubMed PMID: 33909047; PubMed Central PMCID: PMC8255130.

Lee W, Zernant J, Nagasaki T, Allikmets R. Reevaluating the Association of Sex With ABCA4 Alleles in Patients With Stargardt Disease. JAMA Ophthalmol. 2021 Jun 1;139(6):654-657. doi: 10.1001/jamaophthalmol.2021.0460. PubMed PMID: 33792637; PubMed Central PMCID: PMC8017480.

Guo Z, Tong C, Jackow J, Doucet Y, Abaci H, Zeng W, Hansen C, Hayashi R, DeLorenzo D, Rami A, Pappalardo A, Lumpkin E, Christiano A. Engineering human skin model innervated with itch sensory neuron-like cells differentiated from induced pluripotent stem cells. Bioengineering & Translational Medicine. 2021 April.

Tang Q, Efe G, Chiarella AM, Leung J, Chen M, Yamazoe T, Su Z, Pitarresi JR, Li J, Islam M, Karakasheva T, Klein-Szanto AJ, Pan S, Hu J, Natsugoe S, Gu W, Stanger BZ, Wong KK, Diehl JA, Bass AJ, Nakagawa H, Murphy ME, Rustgi AK. Mutant p53 regulates Survivin to foster lung metastasis. Genes Dev. 2021 Apr 1;35(7-8):528-541. doi: 10.1101/gad.340505.120. Epub 2021 Mar 18. PubMed PMID: 33737385; PubMed Central PMCID: PMC8015716.

Cuella-Martin R, Hayward SB, Fan X, Chen X, Huang JW, Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A. Functional interrogation of DNA damage response variants with base editing screens. Cell. 2021 Feb 18;184(4):1081-1097.e19. doi: 10.1016/j.cell.2021.01.041. PubMed PMID: 33606978; PubMed Central PMCID: PMC8018281.

Zazhytska M, Kodra A, Hoagland DA, Fullard JF, Shayya H, Omer A, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Overdevest JB, Lomvardas S. Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. bioRxiv. 2021 Feb 9;. doi: 10.1101/2021.02.09.430314. PubMed PMID: 33594368; PubMed Central PMCID: PMC7885920.

Tang Q, Lento A, Suzuki K, Efe G, Karakasheva T, Long A, Giroux V, Islam M, Wileyto EP, Klein-Szanto AJ, Nakagawa H, Bass A, Rustgi AK. Rab11-FIP1 mediates epithelial-mesenchymal transition and invasion in esophageal cancer. EMBO Rep. 2021 Feb 3;22(2):e48351. doi: 10.15252/embr.201948351. Epub 2021 Jan 6. PubMed PMID: 33403789; PubMed Central PMCID: PMC7857540.

2020

Dhindsa RS, Zoghbi AW, Krizay DK, Vasavda C, Goldstein DB. A Transcriptome-Based Drug Discovery Paradigm for Neurodevelopmental Disorders. Ann Neurol. 2021 Feb;89(2):199-211. doi: 10.1002/ana.25950. Epub 2020 Nov 18. PubMed PMID: 33159466; PubMed Central PMCID: PMC8122510.

Wang W, Frankel WN. Overlaps, gaps, and complexities of mouse models of Developmental and Epileptic Encephalopathy. Neurobiol Dis. 2021 Jan;148:105220. doi: 10.1016/j.nbd.2020.105220. Epub 2020 Dec 7. Review. PubMed PMID: 33301879; PubMed Central PMCID: PMC8547712.

Kodra A, de la Cova C, Gerhold AR, Johnston LA. Widely Used Mutants of eiger, Encoding the Drosophila Tumor Necrosis Factor, Carry Additional Mutations in the NimrodC1 Phagocytosis Receptor. G3 (Bethesda). 2020 Dec 3;10(12):4707-4712. doi: 10.1534/g3.120.401800. PubMed PMID: 33127847; PubMed Central PMCID: PMC7718733.

Garcia-Diaz A, Efe G, Kabra K, Patel A, Lowry ER, Shneider NA, Corneo B, Wichterle H. Standardized Reporter Systems for Purification and Imaging of Human Pluripotent Stem Cell-derived Motor Neurons and Other Cholinergic Cells. Neuroscience. 2020 Dec 1;450:48-56. doi: 10.1016/j.neuroscience.2020.06.028. Epub 2020 Jun 30. PubMed PMID: 32615233; PubMed Central PMCID: PMC7688562.

Koleilat A, Dugdale JA, Christenson TA, Bellah JL, Lambert AM, Masino MA, Ekker SC, Schimmenti LA. L-type voltage-gated calcium channel agonists mitigate hearing loss and modify ribbon synapse morphology in the zebrafish model of Usher syndrome type 1. Dis Model Mech. 2020 Nov 27;13(11). doi: 10.1242/dmm.043885. PubMed PMID: 33361086; PubMed Central PMCID: PMC7710014.

Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res. 2020 Nov;79:100861. doi: 10.1016/j.preteyeres.2020.100861. Epub 2020 Apr 9. Review. PubMed PMID: 32278709; PubMed Central PMCID: PMC7544654.

Aimiuwu OV, Fowler AM, Sah M, Teoh JJ, Kanber A, Pyne NK, Petri S, Rosenthal-Weiss C, Yang M, Harper SQ, Frankel WN. RNAi-Based Gene Therapy Rescues Developmental and Epileptic Encephalopathy in a Genetic Mouse Model. Mol Ther. 2020 Jul 8;28(7):1706-1716. doi: 10.1016/j.ymthe.2020.04.007. Epub 2020 Apr 16. PubMed PMID: 32353324; PubMed Central PMCID: PMC7335739.

Amador A, Bostick CD, Olson H, Peters J, Camp CR, Krizay D, Chen W, Han W, Tang W, Kanber A, Kim S, Teoh J, Sah M, Petri S, Paek H, Kim A, Lutz CM, Yang M, Myers SJ, Bhattacharya S, Yuan H, Goldstein DB, Poduri A, Boland MJ, Traynelis SF, Frankel WN. Modelling and treating GRIN2A developmental and epileptic encephalopathy in mice. Brain. 2020 Jul 1;143(7):2039-2057. doi: 10.1093/brain/awaa147. PubMed PMID: 32577763; PubMed Central PMCID: PMC7363493.

Huang JW, Acharya A, Taglialatela A, Nambiar TS, Cuella-Martin R, Leuzzi G, Hayward SB, Joseph SA, Brunette GJ, Anand R, Soni RK, Clark NL, Bernstein KA, Cejka P, Ciccia A. MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage. Nat Commun. 2020 Jun 11;11(1):2948. doi: 10.1038/s41467-020-16718-3. PubMed PMID: 32528060; PubMed Central PMCID: PMC7290032.

Kushnir A, Todd JJ, Witherspoon JW, Yuan Q, Reiken S, Lin H, Munce RH, Wajsberg B, Melville Z, Clarke OB, Wedderburn-Pugh K, Wronska A, Razaqyar MS, Chrismer IC, Shelton MO, Mankodi A, Grunseich C, Tarnopolsky MA, Tanji K, Hirano M, Riazi S, Kraeva N, Voermans NC, Gruber A, Allen C, Meilleur KG, Marks AR. Intracellular calcium leak as a therapeutic target for RYR1-related myopathies. Acta Neuropathol. 2020 Jun;139(6):1089-1104. doi: 10.1007/s00401-020-02150-w. Epub 2020 Mar 31. PubMed PMID: 32236737; PubMed Central PMCID: PMC7788518.

García-Carracedo D, Cai Y, Qiu W, Saeki K, Friedman RA, Lee A, Li Y, Goldberg EM, Stratikopoulos EE, Parsons R, Lu C, Efstratiadis A, Philipone EM, Yoon AJ, Su GH. PIK3CA and p53 Mutations Promote 4NQO-Initated Head and Neck Tumor Progression and Metastasis in Mice. Mol Cancer Res. 2020 Jun;18(6):822-834. doi: 10.1158/1541-7786.MCR-19-0549. Epub 2020 Mar 9. PubMed PMID: 32152233; PubMed Central PMCID: PMC7272268.

Billon P, Nambiar TS, Hayward SB, Zafra MP, Schatoff EM, Oshima K, Dunbar A, Breinig M, Park YC, Ryu HS, Tschaharganeh DF, Levine RL, Baer R, Ferrando A, Dow LE, Ciccia A. Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures. Cell Rep. 2020 Mar 10;30(10):3280-3295.e6. doi: 10.1016/j.celrep.2020.02.068. PubMed PMID: 32160537; PubMed Central PMCID: PMC7108696.

2019

Van Soldt BJ, Cardoso WV. Hippo-Yap/Taz signaling: Complex network interactions and impact in epithelial cell behavior. Wiley Interdiscip Rev Dev Biol. 2019 Dec 11:e371. doi: 10.1002/wdev.371. [Epub ahead of print] Review.

Nambiar TS, Billon P, Diedenhofen G, Hayward SB, Taglialatela A, Cai K, Huang JW, Leuzzi G, Cuella-Martin R, Palacios A, Gupta A, Egli D, Ciccia A. Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant. Nat Commun. 2019 Jul 30;10(1):3395. doi: 10.1038/s41467-019-11105-z.

Van Soldt BJ, Qian J, Li J, Tang N, Lu J, Cardoso WV. Yap and its subcellular localization have distinct compartment-specific roles in the developing lung. Development. 2019 May 1;146(9). pii: dev175810. doi: 10.1242/dev.175810.

2018

Hirsch SM, Sundaramoorthy S, Davies T, Zhuravlev Y, Waters JC, Shirasu-Hiza M, Dumont J, Canman JC.FLIRT: fast local infrared thermogenetics for subcellular control of protein function. Nat Methods. 2018 Nov;15(11):921-923. doi: 10.1038/s41592-018-0168-y. Epub 2018 Oct 30.

Dugger SA, Platt A, Goldstein DB. Drug development in the era of precision medicine. Nat Rev Drug Discov. 2018 Mar;17(3):183-196. doi: 10.1038/nrd.2017.226. Epub 2017 Dec 8. Review.

Concepcion, D, Hamada H, Papaioannou, VE. Tbx6 controls left-right asymmetry through regulation of GDF1. Biology Open 2018 7: bio032565 doi: 10.1242/bio.032565 Published 4 May 2018 doi: 10.1242/bio.032565.

Yang Y, Cardoso WV. Stem Cells Sheltered from Air-Raids Repair Airways. Cell Stem Cell. 2018 May 3; 22(5):613-614. doi:10.1016/j.stem.2018.04.010

Yang Y, Riccio P, Schotsaert M, Mori M, Lu J, Lee DK, García-Sastre A, Xu J, Cardoso WV. Spatial-Temporal Lineage Restrictions of Embryonic p63+ Progenitors Establish Distinct Stem Cell Pools in Adult Airways. Dev Cell. 2018 Mar 26;44(6):752-761.e4. doi: 10.1016/j.devcel.2018.03.001. PubMed PMID: 29587145; PubMed Central PMCID: PMC5875454.

2017

Smith MJ, Rothstein R. Poetry in motion: Increased chromosomal mobility after DNA damage. DNA Repair (Amst). 2017 Aug;56:102-108. doi: 10.1016/j.dnarep.2017.06.012. Epub 2017 Jun 9. Review. PubMed PMID: 28663070; PubMed Central PMCID: PMC5567867.

Sallee MD, Littleford HE, Greenwald I. A bHLH Code for Sexually Dimorphic Form and Function of the C. elegans Somatic Gonad.Curr Biol. 2017 Jun 19;27(12):1853-1860.e5. doi: 10.1016/j.cub.2017.05.059. Epub 2017 Jun 8. PubMed PMID: 28602651; PubMed Central PMCID: PMC5531766.

Stupnikov MR, Cardoso WV. Sensing oxygen inside and out. Elife. 2017 May 19;6. pii: e27467. doi: 10.7554/eLife.27467. PubMed PMID: 28525315; PubMed Central PMCID: PMC5438245.

Zhuravlev Y, Hirsch SM, Jordan SN, Dumont J, Shirasu-Hiza M, Canman JC. CYK-4 regulates Rac, but not Rho, during cytokinesis. Mol Biol Cell. 2017 May 1;28(9):1258-1270. doi: 10.1091/mbc.E17-01-0020. Epub 2017 Mar 15. PubMed PMID: 28298491; PubMed Central PMCID: PMC5415020.

Patel T, Hobert O. Coordinated control of terminal differentiation and restriction of cellular plasticity. Elife. 2017 Apr 19;6. pii: e24100. doi: 10.7554/eLife.24100. PubMed PMID: 28422646; PubMed Central PMCID: PMC5397285.

Coleman RT, Struhl G. Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene. Science. 2017 Apr 7;356(6333). pii: eaai8236. doi: 10.1126/science.aai8236. Epub 2017 Mar 16. PubMed PMID: 28302795; PubMed Central PMCID: PMC5595140.

2016

Jabbari A, Cerise JE, Chen JC, Mackay-Wiggan J, Duvic M, Price V, Hordinsky M, Norris D, Clynes R, Christiano AM. Molecular signatures define alopecia areata subtypes and transcriptional biomarkers. EBioMedicine. 2016 May;7:240-7. doi: 10.1016/j.ebiom.2016.03.036. Epub 2016 Mar 31. PubMed PMID: 27322477; PubMed Central PMCID: PMC4909368.

Borok MJ, Papaioannou VE, Sussel L. Unique functions of Gata4 in mouse liver induction and heart development. Dev Biol. 2016 Feb 15;410(2):213-222. doi: 10.1016/j.ydbio.2015.12.007. Epub 2015 Dec 11. PubMed PMID: 26687508; PubMed Central PMCID: PMC4758879.

2015

Sallee MD, Aydin T, Greenwald I. Influences of LIN-12/Notch and POP-1/TCF on the Robustness of Ventral Uterine Cell Fate Specification in Caenorhabditis elegans Gonadogenesis. G3 (Bethesda). 2015 Oct 19;5(12):2775-82. doi: 10.1534/g3.115.022608. PubMed PMID: 26483009; PubMed Central PMCID: PMC4683648.

Sallee MD, Greenwald I. Dimerization-driven degradation of C. elegans and human E proteins. Genes Dev. 2015 Jul 1;29(13):1356-61. doi: 10.1101/gad.261917.115. PubMed PMID: 26159995; PubMed Central PMCID: PMC4511211.