Publications

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization.

Cheng X, Ferrell JE Jr. J Vis Exp. 2021 Jun 6;(172). doi: 10.3791/61923. PMID: 34152312 [PubMed]

Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies.

Pokhrel S, Kraemer BR, Burkholz S, Mochly-Rosen D. Sci Rep. 2021 Jun 23;11(1):13120. doi: 10.1038/s41598-021-92641-x. PMID: 34162970 [PubMed]

Immunoglobulin Y for Potential Diagnostic and Therapeutic Applications in Infectious Diseases.

Lee L, Samardzic K, Wallach M, Frumkin LR, Mochly-Rosen D. Front Immunol. 2021 Jun 9;12:696003. doi: 10.3389/fimmu.2021.696003. eCollection 2021. PMID: 34177963 [PubMed]

Paired SARS-CoV-2 spike protein mutations observed during ongoing SARS-CoV-2 viral transfer from humans to minks and back to humans.

Burkholz S, Pokhrel S, Kraemer BR, Mochly-Rosen D, Carback RT 3rd, Hodge T, Harris P, Ciotlos S, Wang L, Herst CV, Rubsamen R. Infect Genet Evol. 2021 May 7;93:104897. doi: 10.1016/j.meegid.2021.104897. Online ahead of print. PMID: 33971305 [PubMed]

Increased elastase sensitivity and decreased intramolecular interactions in the more transmissible 501Y.V1 and 501Y.V2 SARS-CoV-2 variants’ spike protein-an in silico analysis.

Pokhrel S, Kraemer BR, Lee L, Samardzic K, Mochly-Rosen D. PLoS One. 2021 May 26;16(5):e0251426. doi: 10.1371/journal.pone.0251426. eCollection 2021. PMID: 34038453 [PubMed]

Eliminating hypoxic tumor cells improves response to PARP inhibitors in homologous recombination-deficient cancer models.

Mehibel M, Xu Y, Li CG, Moon EJ, Thakkar KN, Diep AN, Kim RK, Bloomstein JD, Xiao Y, Bacal J, Saldivar JC, Le QT, Cimprich KA, Rankin EB, Giaccia AJ. J Clin Invest. 2021 Jun 1;131(11):146256. doi: 10.1172/JCI146256. PMID: 34060485 [PubMed]

3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies.

Hoskens H, Liu D, Naqvi S, Lee MK, Eller RJ, Indencleef K, White JD, Li J, Larmuseau MHD, Hens G, Wysocka J, Walsh S, Richmond S, Shriver MD, Shaffer JR, Peeters H, Weinberg SM, Claes P. PLoS Genet. 2021 May 13;17(5):e1009528. doi: 10.1371/journal.pgen.1009528. eCollection 2021 May. PMID: 33983923 [PubMed]

Real-Time Monitoring of APC /C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts.

Kamenz J, Qiao R, Yang Q, Ferrell JE Jr. Methods Mol Biol. 2021;2329:29-38. doi: 10.1007/978-1-0716-1538-6_3. PMID: 34085213 [PubMed]

CRISPR-based genome editing in primary human pancreatic islet cells.

Bevacqua RJ, Dai X, Lam JY, Gu X, Friedlander MSH, Tellez K, Miguel-Escalada I, Bonàs-Guarch S, Atla G, Zhao W, Kim SH, Dominguez AA, Qi LS, Ferrer J, MacDonald PE, Kim SK. Nat Commun. 2021 Apr 23;12(1):2397. doi: 10.1038/s41467-021-22651-w. PMID: 33893274 [PubMed]

Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains.

Nano PR, Johnson TK, Kudo T, Mooney NA, Ni J, Demeter J, Jackson PK, Chen JK. PLoS One. 2021 May 17;16(5):e0251684. doi: 10.1371/journal.pone.0251684. PMID: 33999959. [PubMed]

An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens.

Niclas Olsson, Marlene L. Heberling, Lichao Zhang, Suchit Jhunjhunwala, Qui T. Phung, Sarah Lin, Veronica G. Anania, Jennie R. Lill, and Joshua E. Elias. Front. Immunol.,15 April 2021 | https://doi.org/10.3389/fimmu.2021.662443 URL=https://www.frontiersin.org/article/10.3389/fimmu.2021.662443

A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses.

Lin X, Liu Y, Chemparathy A, Pande T, La Russa M, Qi LS. Cell Rep Med. 2021 Mar 23:100245. doi: 10.1016/j.xcrm.2021.100245. Online ahead of print. PMID: 33778788 Free PMC article. [PubMed]

Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.

Gokhman D, Agoglia RM, Kinnebrew M, Gordon W, Sun D, Bajpai VK, Naqvi S, Chen C, Chan A, Chen C, Petrov DA, Ahituv N, Zhang H, Mishina Y, Wysocka J, Rohatgi R, Fraser HB. Nat Genet. 2021 Mar 17. doi: 10.1038/s41588-021-00804-3. Online ahead of print. PMID: 33731941 [PubMed]

The Intersection of the Genetic Architectures of Orofacial Clefts and Normal Facial Variation.

Indencleef K, Hoskens H, Lee MK, White JD, Liu C, Eller RJ, Naqvi S, Wehby GL, Moreno Uribe LM, Hecht JT, Long RE Jr, Christensen K, Deleyiannis FW, Walsh S, Shriver MD, Richmond S, Wysocka J, Peeters H, Shaffer JR, Marazita ML, Hens G, Weinberg SM, Claes P. Front Genet. 2021 Feb 22;12:626403. doi: 10.3389/fgene.2021.626403. eCollection 2021. PMID: 33692830 Free PMC article. [PubMed]

Novel and prevalent non-East Asian ALDH2 variants; Implications for global susceptibility to aldehydes’ toxicity.

Chen CH, Ferreira JCB, Joshi AU, Stevens MC, Li SJ, Hsu JH, Maclean R, Ferreira ND, Cervantes PR, Martinez DD, Barrientos FL, Quintanares GHR, Mochly-Rosen D. EBioMedicine. 2020 May;55:102753. doi: 10.1016/j.ebiom.2020.102753. Epub 2020 May 8. PMID: 32403082 Free PMC article. [PubMed]

A Novel ALDH2 Activator AD-9308 Improves Diastolic and Systolic Myocardial Functions in Streptozotocin-Induced Diabetic Mice.

Lee HL, Hee SW, Hsuan CF, Yang W, Huang JY, Lin YL, Hsu CN, Hwang JJ, Chen SM, Ding ZZ, Lee TY, Lin YC, Tsai FC, Su WL, Chueh LY, Hsieh ML, Chen CH, Mochly-Rosen D, Chang YC, Chuang LM. Antioxidants (Basel). 2021 Mar 13;10(3):450. doi: 10.3390/antiox10030450. PMID: 33805825 [PubMed]

Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling.

Weber EW, Parker KR, Sotillo E, Lynn RC, Anbunathan H, Lattin J, Good Z, Belk JA, Daniel B, Klysz D, Malipatlolla M, Xu P, Bashti M, Heitzeneder S, Labanieh L, Vandris P, Majzner RG, Qi Y, Sandor K, Chen LC, Prabhu S, Gentles AJ, Wandless TJ, Satpathy AT, Chang HY, Mackall CL. Science. 2021 Apr 2;372(6537):eaba1786. doi: 10.1126/science.aba1786. PMID: 33795428 [PubMed]

Organic wastewater treatment by single-atom catalysis and electrolytically produced H2O2.

Xu, J., Zheng, X., Feng, Z., Lu, Z., Zhang, Z., Huang W., Li, Y., Vuckovic, D, Li, Y., Dai, S., Chen, G., Wang, K., WAng, H., Chen, J.K., Mitch, W., and Cui, Y. (2021) Nat. Sustain. 4: 233-241.

Engineering 3D genome organization.

Wang H, Han M, Qi LS. Nat Rev Genet. 2021 Feb 8. doi: 10.1038/s41576-020-00325-5. Epub ahead of print. PMID: 33558716. [PubMed]

The hunt for ancient prions: Archaeal prion-like domains form amyloid-based epigenetic elements.

Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ. Mol Biol Evol. 2021 Jan 22:msab010. doi: 10.1093/molbev/msab010. Online ahead of print. PMID: 33480998 [PubMed]

Protein self-assembly: A new frontier in cell signaling.

Saad S, Jarosz DF. Curr Opin Cell Biol. 2021 Jan 22;69:62-69. doi: 10.1016/j.ceb.2020.12.013. Online ahead of print. PMID: 33493989 Review. [PubMed]

CRISPR technologies for precise epigenome editing.

Nakamura M, Gao Y, Dominguez AA, Qi LS. Nat Cell Biol. 2021 Jan;23(1):11-22. doi: 10.1038/s41556-020-00620-7. Epub 2021 Jan 8. PMID: 33420494 Review. [PubMed]

Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes.

Sundaram V, Wysocka J. Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190347. doi: 10.1098/rstb.2019.0347. Epub 2020 Feb 10. PMID: 32075564 Free PMC article. Review. [PubMed]

Epigenomic and Transcriptomic Changes During Human RPE EMT in a Stem Cell Model of Epiretinal Membrane Pathogenesis and Prevention by Nicotinamide.

Boles NC, Fernandes M, Swigut T, Srinivasan R, Schiff L, Rada-Iglesias A, Wang Q, Saini JS, Kiehl T, Stern JH, Wysocka J, Blenkinsop TA, Temple S. Stem Cell Reports. 2020 Apr 14;14(4):631-647. doi: 10.1016/j.stemcr.2020.03.009. Epub 2020 Apr 2. PMID: 32243845 Free PMC article. [PubMed]

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements.

Thomas HF, Kotova E, Jayaram S, Pilz A, Romeike M, Lackner A, Penz T, Bock C, Leeb M, Halbritter F, Wysocka J, Buecker C. Mol Cell. 2021 Jan 18:S1097-2765(20)30989-8. doi: 10.1016/j.molcel.2020.12.047. Online ahead of print. PMID: 33482114 [PubMed]