Many Vagelos MLS scholars have co-authored papers during their undergraduate research at Penn. The publication list below shows the work of recent MLS graduates.
For MLS graduates and students, if you would like to share your publications, please send an email to vs-mol@sas.upenn.edu.
2024
Ahn, J., Johnny, C., and Chenoweth, D. (2024). Duo-Chol: A Photoconvertible Live Cell Imaging Tool for Tracking Cholesterol. Bioconjugate Chem. 35, 890-896. 10.1021/acs.bioconjchem.4c00207.
Berrios, K.N., Barka, A., Gill, J., Serrano, J.C., Bailer, P.F., Parker, J.B., Evitt, N.H., Gajula, K.S., Shi, J.W., and Kohli, R.M. (2024). Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res. 52, 2078-2090. 10.1093/nar/gkae024.
Brody, E., Seo, Y., Suh, E., Amari, N., Hartstone, W., Skrinak, R., Zhang, H., Diaz-Ortiz, M., Weintraub, D., Tropea, T., Van Deerlin, V., and Chen-Plotkin, A. (2024). GPNMB Biomarker Levels in GBA1 Carriers with Lewy Body Disorders. Mov Disord. 39, 1065-1070. 10.1002/mds.29773.
Jolley, M.A., Sulentic, A., Amin, S., Gupta, M., Ching, S.P., Cianciulli, A., Wang, Y., Sabin, P., Zelonis, C., Daemer, M., Silvestro, E., Coleman, K., Ford, L.K., Edelson, J.B., Ruckdeschel, E.S., Cohen, M.S., Nicolson, S.C., and Gillespie, M.J. (2024). Introduction of transcatheter edge-to-edge repair in patients with congenital heart disease at a children’s hospital. Catheter Cardiovasc Interv. 103, 326-334. 10.1002/ccd.30935.
Moriwaki, K., Beane, A., and Lidz, A. (2024). Insights into the 21 cm field from the vanishing cross-power spectrum at the epoch of reionization. MNRAS 530, 3183-3194. 10.1093/mnras/stae1050.
Niu, Z., O’Farrell, A., Li, J., Reffsin, S., Jain, N., Dardani, I., Goyal, Y., and Raj, A. (2024). Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning. bioRxiv, 10.1101/2024.01.31.578123.
Schaff, D.L., Fasse, A.J., White, P.E., Vander Velde, R.J., and Shaffer, S.M. (2024). Clonal differences underlie variable responses to sequential and prolonged treatment. Cell Syst. 15, 213-226. 10.1016/j.cels.2024.01.011.
Woodie, L., Melink, L., Alberto, A., Burrows, M., Fortin, S., Chan, C., Hayes, M., and Lazar, M. (2024). Hindbrain REV-ERB nuclear receptors regulate sensitivity to diet-induced obesity and brown adipose tissue pathophysiology. Mol Metab. 79. 10.1016/j.molmet.2023.101861.
2023
Agarwal, A., Büdd, H., Capo, J., Chong, P., Christodoulou, G., Danilov, M., Dergacheva, A., De Roeck, A., Dokania, N., Douqa, D., Dugas, K., Fedotov, S., Gwon, S., Howell, R., Iwamoto, K., Jesus-Valls, C., Jung, C., Kasetti, S.P., Khabibullin, M., Khotjantsev, A., Kikawa, T., Kose, U., Kudenko, Y., Kuribayashi, S., Kutter, T., Last, D., Lin, L., Lin, S., Lux, T., Manly, S., Caicedo, D.A.M., Martynenko, S., Matsubara, T., Mauger, C., McFarland, K., McGrew, C., Mefodiev, A., Mineev, O., Nakadaira, T., Noah, E., Olivier, A., Paolone, V., Palestini, S., Paul-Torres, A., Pellegrino, R., Ramírez, M.A., Riccio, C., Rondon, J.R., Sanchez, F., Sgalaberna, D., Shorrock, W., Sitraka, A., Siyeon, K., Skrobova, N., Suvorov, S., Teklu, A., Tzanov, M., Uchida, Y., Wret, C., Yang, G., Yershov, N., Yokoyama, M., and Zilberman, P. (2023). Total neutron cross-section measurement on CH with a novel 3D-projection scintillator detector. Phys. Lett. B 840, 137843. 10.1016/j.physletb.2023.137843.
Baltrusaitis, E.E., Ravitch, E.E., Fenton, A.R., Perez, T.A., Holzbaur, E.L.F., and Dominguez, R. (2023). Interaction between the mitochondrial adaptor MIRO and the motor adaptor TRAK. J. Biol. Chem. 299, 105441. 10.1016/j.jbc.2023.105441.
Barka, A., Kohli, R.M., and Shi, J.W. (2023). CRISPR tiling screen reveals cancer epigenetic Goldilocks’ state. Trends Pharmacol. Sci. 44, 555-557. 10.1016/j.tips.2023.05.007.
Choi, Y., Kim, M., Rhoades, J., Johnson, N., Berry, C., Root, S., Chen, Q., Tian, Y., Fernandez, R., Cramer, Z., Adams-Tzivelekidis, S., Li, N., Johnson, F., and Lengner, C. (2023). Patient-Induced Pluripotent Stem Cell-Derived Hepatostellate Organoids Establish a Basis for Liver Pathologies in Telomeropathies. Cell Mol. Gastroenterol. Hepatol. 16, 451-472. 10.1016/j.jcmgh.2023.06.003.
Dickens, O.O., Bajwa, I., Garcia-Ramos, K., Suh, Y., Wen, C.Y., Cheng, A.N., Fethke, V., Yi, Y.J., Collman, R.G., and Johnson, A.T.C. (2023). Label-free detection of synthetic, full genomic length HIV-1 RNA at the few-copy level. Sens. Actuator B-Chem. 390, 134001. 10.1016/j.snb.2023.134001.
Etersque, J., Lee, I., Sharma, N., Xu, K., Ruff, A., Northrup, J., Sarkar, S., Nguyen, T., Lauman, R., Burslem, G., and Sellmyer, M. (2023). Regulation of eDHFR-tagged proteins with trimethoprim PROTACs. Nat. Commun. 14, 7071. 10.1038/s41467-023-42820-3.
Fare, C., Rhine, K., Lam, A., Myong, S., and Shorter, J. (2023). A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity. J. Biol. Chem. 299, 102806. 10.1016/j.jbc.2022.102806.
Fujiwara, R., Zhai, S.N., Liang, D.M., Shah, A.P., Tracey, M., Ma, X.K., Mendoza-Figueroa, M.S., Fields, C.J., Meline, M.C., Tatomer, D.C., Yang, L., and Wilusz, J.E. (2023). IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol. Cell. 83, 4445-4460. 10.1016/j.molcel.2023.10.035.
Himmelstein, D., Zietz, M., Rubinetti, V., Kloster, K., Heil, B., Alquaddoomi, F., Hu, D., Nicholson, D., Hao, Y., Sullivan, B., Nagle, M., and Greene, C. (2023). Hetnet connectivity search provides rapid insights into how biomedical entities are related. Gigascience 12. 10.1093/gigascience/giad047.
Hogan, M., Maheshwari, N., Begg, B., Nicastri, A., Muramatsu, H., Pardi, N., Miller, M., Reilly, S., Brossay, L., Lynch, K., Ternette, N., and Eisenlohr, L. (2023). Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response. Nat. Immunol. 24, 1933-1946. 10.1038/s41590-023-01644-5.
Lu, J.C., Atochina-Vasserman, E.N., Maurya, D.S., Shalihin, M.I., Zhang, D.P., Chenna, S.S., Adamson, J., Liu, M.T., Shah, H.U.R., Shah, H.E., Xiao, Q., Queeley, B., Ona, N.A., Reagan, E.K., Ni, H.P., Sahoo, D., Peterca, M., Weissman, D., and Percec, V. (2023). Screening Libraries to Discover Molecular Design Principles for the Targeted Delivery of mRNA with One-Component Ionizable Amphiphilic Janus Dendrimers Derived from Plant Phenolic Acids. Pharmaceutics 15, 1572. 10.3390/pharmaceutics15061572.
Mageswaran, S.K., Martinez, M., Guérin, A., Chen, W., Theveny, L., Cova, M., Molnár, P., John, A., Striepen, B., Lebrun, M., and Chang, Y.W. (2023). Rhoptry secretion system structures and regulatory mechanisms in Apicomplexan parasites revealed using cryo-ET. Biophys. J. 122 (1). 10.1016/j.bpj.2022.11.244.
May, S., Climent, C., Tao, Z., Vinogradov, S., and Subotnik, J. (2023). Spin-Orbit versus Hyperfine Coupling-Mediated Intersystem Crossing in a Radical Pair. J. Phys. Chem. A 127, 3591-3597. 10.1021/acs.jpca.3c00294.
Miles, L., Powell, J., Kozak, C., and Song, Y. (2023). Mechanosensitive Ion Channels, Axonal Growth, and Regeneration. Neuroscientist. 29, 421-444. 10.1177/10738584221088575.
Nair, D., Diaz-Rosado, A., Varella-Branco, E., Ramos, I., Black, A., Angireddy, R., Park, J., Murali, S., Yoon, A., Ciesielski, B., O’Brien, W.T., Passos-Bueno, M.R., and Bhoj, E. (2023). Heterozygous variants in TBCK cause a mild neurologic syndrome in humans and mice. Am. J. Med. Genet. A 191, 2508-2517. 10.1002/ajmg.a.63320.
Narayan, K.B., Mondal, S., James, H.P., Baeyens, L., Zheng, J.S., and Baumgart, T. (2023). Complex multivalent protein interactions involving endophilin, lamellipodin and VASP regulate membrane shaping phenomena and actin assembly. Biophys. J. 122. 10.1016/j.bpj.2022.11.2586.
Osman, A., Mervosh, N., Strat, A., Euston, T., Zipursky, G., Pollak, R., Meckel, K., Tyler, S., Chan, K., Grice, A., Drapeau, E., Litichevskiy, L., Gill, J., Zeldin, S., Thaiss, C., Buxbaum, J., Breen, M., and Kiraly, D. (2023). Acetate supplementation rescues social deficits and alters transcriptional regulation in prefrontal cortex of Shank3 deficient mice. Brain Behav. Immun. 114, 311-324. 10.1016/j.bbi.2023.08.020.
Ramirez, J., Pancoe, S.X., Rhoades, E., and Petersson, E.J. (2023). The Effects of Lipids on α-Synuclein Aggregation In Vitro. Biomolecules 13, 1476. 10.3390/biom13101476.
Trombley, S., Powell, J., Guttipatti, P., Matamoros, A., Lin, X., O’Harrow, T., Steinschaden, T., Miles, L., Wang, Q., Wang, S., Qiu, J., Li, Q., Li, F., and Song, Y. (2023). Glia instruct axon regeneration via a ternary modulation of neuronal calcium channels in Drosophila. Nat. Commun. 14, 6490. 10.1038/s41467-023-42306-2.
Winn, A., Konkol, A., and Katifori, E. (2023). From localized to well mixed: How commuter interactions shape disease spread. Phys. Rev. E 108, 044305. 10.1103/PhysRevE.108.044305.
Wong, A.C., Devason, A.S., Umana, I.C., Cox, T.O., Dohnalová, L., Litichevskiy, L., Perla, J., Lundgren, P., Etwebi, Z., Izzo, L.T., Kim, J., Tetlak, M., Descamps, H.C., Park, S.L., Wisser, S., McKnight, A.D., Pardy, R.D., Blank, N., Patel, S., Thum, K., Mason, S., Beltra, J.C., Michieletto, M.F., Ngiow, S.F., Miller, B.M., Liou, M.J., Madhu, B., Dmitrieva-Posocco, O., Huber, A.S., Hewins, P., Petucci, C., Chu, C.P., Baraniecki-Zwil, G., Giron, L.B., Baxter, A.E., Greenplate, A.R., Kearns, C., Montone, K., Litzky, L.A., Feldman, M., Henao-Mejia, J., Striepen, B., Ramage, H., Jurado, K.A., Wellen, K.E., O’Doherty, U., Abdel-Mohsen, M., Landay, A.L., Keshavarzian, A., Henrich, T.J., Deeks, S.G., Peluso, M.J., Meyer, N.J., Wherry, E.J., Abramoff, B.A., Cherry, S., Thaiss, C.A., and Levy, M. (2023). Serotonin reduction in post-acute sequelae of viral infection. Cell 186, 4851-4867. 10.1016/j.cell.2023.09.013.
Zhang, D.P., Xiao, Q., Rahimzadeh, M., Liu, M.T., Rodriguez-Emmenegger, C., Miyazaki, Y., Shinoda, W., and Percec, V. (2023). Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes. J. Am. Chem. Soc. 145, 4311-4323. 10.1021/jacs.3c00389.
2022
Aubin, R., Troisi, E., Montelongo, J., Alghalith, A., Nasrallah, M., Santi, M., and Camara, P. (2022). Pro-inflammatory cytokines mediate the epithelial-to-mesenchymal-like transition of pediatric posterior fossa ependymoma. Nat. Commun. 13, 3936. 10.1038/s41467-022-31683-9.
Barka, A., Berríos, K.N., Bailer, P., Schutsky, E.K., Wang, T., and Kohli, R.M. (2022). The Base-Editing Enzyme APOBEC3A Catalyzes Cytosine Deamination in RNA with Low Proficiency and High Selectivity. ACS Chem. Biol. 17, 629-636. 10.1021/acschembio.1c00919.
Beck, L., Lee, J., Coté, C., Dunagin, M., Lukonin, I., Salla, N., Chang, M., Hughes, A., Mornin, J., Gartner, Z., Liberali, P., and Raj, A. (2022). Systematically quantifying morphological features reveals constraints on organoid phenotypes. Cell Syst. 13, 547-560. 10.1016/j.cels.2022.05.008.
Copley, K.E., Smirnov, A., and Shorter, J. (2022). Developing RNA Therapeutics for TDP-43 Proteinopathy in ALS/FTD. Faseb J. 36. 10.1096/fasebj.2022.36.S1.R4365.
Diaz-Ortiz, M., Seo, Y., Posavi, M., Cordon, M., Clark, E., Jain, N., Charan, R., Gallagher, M., Unger, T., Amari, N., Skrinak, R., Davila-Rivera, R., Brody, E., Han, N., Zack, R., Van Deerlin, V., Tropea, T., Luk, K., Lee, E., Weintraub, D., and Chen-Plotkin, A. (2022). GPNMB confers risk for Parkinson’s disease through interaction with α-synuclein. Science 377, eabk0637. 10.1126/science.abk0637.
Esposito, V., McHenry, T., and Lester, M. (2022). Photoionization energetics and dissociation pathways of hydroperoxyethyl formate produced in the reaction of CH3CHOO+ formic acid. Chem. Phys. Lett. 809, 140179. 10.1016/j.cplett.2022.140179.
Fernandez, R., Gardner, Z., Slovik, K., Liberti, D., Estep, K., Yang, W., Chen, Q., Santini, G., Perez, J., Root, S., Bhatia, R., Tobias, J., Babu, A., Morley, M., Frank, D., Morrisey, E., Lengner, C., and Johnson, F. (2022). GSK3 inhibition rescues growth and telomere dysfunction in dyskeratosis congenita iPSC-derived type II alveolar epithelial cells. Elife 11, e64430. 10.7554/eLife.64430.
Ghassemi, S., Durgin, J., Nunez-Cruz, S., Patel, J., Leferovich, J., Pinzone, M., Shen, F., Cummins, K., Plesa, G., Cantu, V., Reddy, S., Bushman, F., Gill, S., O’Doherty, U., O’Connor, R., and Milone, M. (2022). Rapid manufacturing of non-activated potent CAR T cells. Nat. Biomed. Eng. 6, 118-128. 10.1038/s41551-021-00842-6.
Goff, K.M., Zheng, C.Q., and Alonso-Basanta, M. (2022). Proton radiotherapy for glioma and glioblastoma. Chin. Clin. Oncol. 11, 46. 10.21037/cco-22-92.
Konkol, A., Schwenk, J., Katifori, E., and Shaw, J. (2022). Interplay of River and Tidal Forcings Promotes Loops in Coastal Channel Networks. Geophys. Res. Lett. 49, e2022GL098284. 10.1029/2022GL098284.
Lougee, M.G., Pagar, V.V., Kim, H.J., Pancoe, S.X., Chia, W.K., Mach, R.H., Garcia, B.A., and Petersson, E.J. (2022). Harnessing the intrinsic photochemistry of isoxazoles for the development of chemoproteomic crosslinking methods. Chem. Commun. 58, 9116-9119. 10.1039/d2cc02263j.
Metlay, A.S., Chyi, B., Yoon, Y., Wycisk, R.J., Pintauro, P.N., and Mallouk, T.E. (2022). Three-Chamber Design for Aqueous Acid-Base Redox Flow Batteries. ACS Energy Lett. 7, 908-913. 10.1021/acsenergylett.2c00040.
Mondal, S., Narayan, K., Botterbusch, S., Powers, I., Zheng, J.S., James, H.P., Jin, R., and Baumgart, T. (2022). Multivalent interactions between molecular components involved in fast endophilin mediated endocytosis drive protein phase separation. Nat. Commun. 13, 5017. 10.1038/s41467-022-32529-0.
Pancoe, S.X., Wang, Y.J., Shimogawa, M., Perez, R.M., Giannakoulias, S., and Otzen, D. (2022). Effects of Mutations and Post-Transla- tional Modifications on a-Synuclein In Vitro Aggregation. J. Mol. Biol. 434, 167859. 10.1016/j.jmb.2022.167859.
Qian, W., Lynn, C.W., Klishin, A.A., Stiso, J., Christianson, N.H., and Bassett, D.S. (2022). Optimizing the human learnability of abstract network representations. Proceedings of the National Academy of Sciences of the United States of America 119, e2121338119. 10.1073/pnas.2121338119.
Qian, W., Papadopoulos, L., Lu, Z.X., Kroma-Wiley, K.A., Pasqualetti, F., and Bassett, D.S. (2022). Path-dependent dynamics induced by rewiring networks of inertial oscillators. Phys. Rev. E 105, 024304. 10.1103/PhysRevE.105.024304.
Serrano, J.C., von Trentini, D., Berríos, K.N., Barka, A., Dmochowski, I.J., and Kohli, R.M. (2022). Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem. Biol. 17, 3379-3388. 10.1021/acschembio.2c00796.
Shreiber, S.T., Granados, A., Matsuo, B., Majhi, J., Campbell, M.W., Patel, S., and Molander, G.A. (2022). Visible-Light-Induced C-F Bond Activation for the Difluoroalkylation of Indoles. Org. Lett. 24, 8542-8546. 10.1021/acs.orglett.2c03549.
Sparvoli, D., Delabre, J., Penarete-Vargas, D.M., Mageswaran, S.K., Tsypin, L.M., Heckendorn, J., Theveny, L., Maynadier, M., Cova, M.M., Berry-Sterkers, L., Guérin, A., Dubremetz, J.F., Urbach, S., Striepen, B., Turkewitz, A.P., Chang, Y.W., and Lebrun, M. (2022). An apical membrane complex for triggering rhoptry exocytosis and invasion in Toxoplasma. EMBO J. 41. 10.15252/embj.2022111158.
Theveny, L.M., Mageswaran, S.K., Chen, W.D., Martinez, M., Guérin, A., and Chang, Y.W. (2022). Parasitology meets cryo-electron tomography-exciting prospects await. Trends Parasitol. 38, 365-378. 10.1016/j.pt.2022.01.006.
Zhang, D.P., Atochina-Vasserman, E.N., Lu, J.C., Maurya, D.S., Xiao, Q., Liu, M., Adamson, J., Ona, N., Reagan, E.K., Ni, H.P., Weissman, D., and Percec, V. (2022). The Unexpected Importance of the Primary Structure of the Hydrophobic Part of One-Component Ionizable Amphiphilic Janus Dendrimers in Targeted mRNA Delivery Activity. J. Am. Chem. Soc. 144, 4746-4753. 10.1021/jacs.2c00273.
2021
Barber, A., Fong, S., Kolesnik, A., Fetchko, M., and Sehgal, A. (2021). Drosophila clock cells use multiple mechanisms to transmit time-of-day signals in the brain. Proceedings of the National Academy of Sciences of the United States of America 118, e2019826118. 10.1073/pnas.2019826118.
Barbosa, R., Acevedo, L.A., and Marmorstein, R. (2021). The MEK/ERK Network as a Therapeutic Target in Human Cancer. Mol. Cancer Res. 19, 361-374. 10.1158/1541-7786.mcr-20-0687.
Berríos, K.N., Evitt, N.H., DeWeerd, R.A., Ren, D.Q., Luo, M.Q., Barka, A., Wang, T., Bartman, C.R., Lan, Y.M., Green, A.M., Shi, J.W., and Kohli, R.M. (2021). Controllable genome editing with split-engineered base editors. Nat. Chem. Biol. 17, 1262-1270. 10.1038/s41589-021-00880-w.
Campbell, M.W., Polites, V.C., Patel, S., Lipson, J.E., Majhi, J., and Molander, G.A. (2021). Photochemical C-F Activation Enables Defluorinative Alkylation of Trifluoroacetates and -Acetamides. J. Am. Chem. Soc. 143, 19648-19654. 10.1021/jacs.1c11059.
Cason, S.E., Carman, P.J., van Duyne, C., Goldsmith, J., Dominguez, R., and Holzbaur, E.L.F. (2021). Sequential dynein effectors regulate axonal autophagosome motility in a maturation-dependent pathway. J. Cell Biol. 220, e202010179. 10.1083/jcb.202010179.
Fouad, A., Liu, A., Du, A., Bhirgoo, P., and Fang-Yen, C. (2021). Thermal laser ablation with tunable lesion size reveals multiple origins of seizure-like convulsions in Caenorhabditis elegans. Sci. Rep. 11, 5084. 10.1038/s41598-021-84516-y.
Giannakoulias, S., Shringari, S.R., Ferrie, J.J., and Petersson, E.J. (2021). Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine. Sci. Rep. 11, 18406. 10.1038/s41598-021-97965-2.
Huang, W., Wong, S., Pather, S., Nguyen, P., Zhang, F., Zhang, D., Zhang, Z., Lu, L., Fang, W., Chen, L., Fernandes, A., Su, Y., Song, H., and Ming, G. (2021). Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells. Cell Stem Cell 28, 1657-1670.e1610. 10.1016/j.stem.2021.04.006.
Ji, H., Fouad, A., Teng, S., Liu, A., Alvarez-Illera, P., Yao, B., Li, Z., and Fang-Yen, C. (2021). Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans. Elife 10, e69905. 10.7554/eLife.69905.sa2.
Jones, C., Robkis, D., Blizzard, R., Munari, M., Venkatesh, Y., Mihaila, T., Eddins, A., Mehl, R., Zagotta, W., Gordon, S., and Petersson, E.J. (2021). Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells. Chem. Sci. 12, 11955-11964. 10.1039/d1sc01914g..
Jones, D., Palatnick, S., Chen, R., Beane, A., and Lidz, A. (2021). Fuzzy Dark Matter and the 21 cm Power Spectrum. Astrophys. J. 913, 7. 10.3847/1538-4357/abf0a9.
Lee, Y., Fong, S., Shon, J., Zhang, S., Brooks, R., Lahens, N., Chen, D., Van Dang, C., Field, J., and Sehgal, A. (2021). Time-of-day specificity of anticancer drugs may be mediated by circadian regulation of the cell cycle. Science Advances 7.
Lee, Y., Fong, S., Shon, J., Zhang, S., Brooks, R., Lahens, N., Chen, D., Van Dang, C., Field, J., and Sehgal, A. (2021). Time-of-day specificity of anticancer drugs may be mediated by circadian regulation of the cell cycle. Sci. Adv. 7, eabd2645. 10.1126/sciadv.abd2645.
Mageswaran, S.K., Guérin, A., Theveny, L.M., Chen, W.D., Martinez, M., Lebrun, M., Striepen, B., and Chang, Y.W. (2021). In situ ultrastructures of two evolutionarily distant apicomplexan rhoptry secretion systems. Nat. Commun. 12, 4983. 10.1038/s41467-021-25309-9.
Mondrinos, M., Alisafaei, F., Yi, A., Ahmadzadeh, H., Lee, I., Blundell, C., Seo, J., Osborn, M., Jeon, T., Kim, S., Shenoy, V., and Huh, D. (2021). Surface-directed engineering of tissue anisotropy in microphysiological models of musculoskeletal tissue. Sci. Adv. 7, eabe9446. 10.1126/sciadv.abe9446.
Nair, D., Li, D., Erdogan, H., Yoon, A., Harr, M.H., Bergant, G., Peterlin, B., Pusenjak, M.S., Jayakar, P., Pfundt, R., Jansen, S., McWalter, K., Sidhu, A., Saliganan, S., Agolini, E., Jacob, A., Pasquier, J., Arash, R., Kahrizi, K., Najmabadi, H., Ropers, H.H., and Bhoj, E.J. (2021). Discovery of a neuromuscular syndrome caused by biallelic variants in ASCC3. Hum. Genet. Genom. Adv. 2, 100024. 10.1016/j.xhgg.2021.100024.
Patel, S., Badir, S.O., and Molander, G.A. (2021). Developments in Photoredox-Mediated Alkylation for DNA-Encoded Libraries. Trends Chem. 3, 161-175. 10.1016/j.trechm.2020.11.010.
Qian, W., Bhowmick, S., O’Neill, M., Ramisetty-Mikler, S., and Mikler, A.R. (2021). Applying a Probabilistic Infection Model for studying contagion processes in contact networks. J. Comput. Sci. 54, 101419. 10.1016/j.jocs.2021.101419.
Saikumar, J., Kim, J., Byrns, C.N., Hemphill, M., Meaney, D.F., and Bonini, N.M. (2021). Inducing different severities of traumatic brain injury in Drosophila using a piezoelectric actuator. Nat. Protoc. 16, 263-282. 10.1038/s41596-020-00415-y.
Sojli, E., Soattin, L., Patel, S., Lo, C., Kirshner, S.N., Oehmke, T.B., Kim, J., Waiho, K., Zhang, J., Easun, T.L., Neves-Costa, A., Adamowicz, B., Jensen, M.M., Richter, W.E., Barbosa, R.L., Baeyens, L., and Cardinal, B.J. (2021). Forging remote relationships. Science 372, 24-26. 10.1126/science.abi4726.
Zhang, D.P., Atochina-Vasserman, E.N., Maurya, D.S., Huang, N., Xiao, Q., Ona, N., Liu, M., Shahnawaz, H., Ni, H.P., Kim, K., Billingsley, M.M., Pochan, D.J., Mitchell, M.J., Weissman, D., and Percec, V. (2021). One-Component Multifunctional Sequence-Defined Ionizable Amphiphilic Janus Dendrimer Delivery Systems for mRNA. J. Am. Chem. Soc. 143, 12315-12327. 10.1021/jacs.1c05813.
Zhang, D.P., Atochina-Vasserman, E.N., Maurya, D.S., Liu, M., Xiao, Q., Lu, J.C., Lauri, G., Ona, N., Reagan, E.K., Ni, H., Weissman, D., and Percec, V. (2021). Targeted Delivery of mRNA with One-Component Ionizable Amphiphilic Janus Dendrimers. J. Am. Chem. Soc. 143, 17975-17982. 10.1021/jacs.1c09585.
2020
Barber, V., Esposito, V., Trabelsi, T., Hansen, A., McHenry, T., Francisco, J., and Lester, M. (2020). Experimental and computational investigation of vinoxy and 1-methylvinoxy radicals from the unimolecular decay of alkyl-substituted Criegee intermediates.Chem. Phys. Lett. 751, 137478. 10.1016/j.cplett.2020.137478.
Bernardinelli, P., Bernstein, G., Sako, M., Liu, T., Saunders, W., Khain, T., Lin, H., Gerdes, D., Brout, D., Adams, F., Belyakov, M., Somasundaram, A., Sharma, L., Locke, J., Franson, K., Becker, J., Napier, K., Markwardt, L., Annis, J., Abbott, T., Avila, S., Brooks, D., Burke, D., Rosell, A., Kind, M., Castander, F., da Costa, L., De Vicente, J., Desai, S., Diehl, H., Doel, P., Everett, S., Flaugher, B., García-Bellido, J., Gruen, D., Gruendl, R., Gschwend, J., Gutierrez, G., Hollowood, D., James, D., Johnson, M., Johnson, M., Krause, E., Kuropatkin, N., Maia, M., March, M., Miquel, R., Paz-Chinchón, F., Plazas, A., Romer, A., Rykoff, E., Sánchez, C., Sanchez, E., Scarpine, V., Serrano, S., Sevilla-Noarbe, I., Smith, M., Sobreira, F., Suchyta, E., Swanson, M., Tarle, G., Walker, A., Wester, W., Zhang, Y., and Collaboration, D. (2020). Trans-Neptunian Objects Found in the First Four Years of the Dark Energy Survey. Astrophys. J. Supplement Series 247, 32. 10.3847/1538-4365/ab6bd8.
Ghassemi, S., O’Connor, R., Nunez-Cruz, S., Leferovich, J., Patel, J., and Milone, M. (2020). Chimeric Antigen Receptor (CAR) T cells on demand: developing potent CAR T cells in less than 24 hr for adoptive immunotherapy. Cytotherapy 22, S34-S35. 10.1016/j.jcyt.2020.03.025.
Giannakoulias, S., Shringari, S.R., Liu, C.X., Phan, H.A.T., Barrett, T.M., Ferrie, J.J., and Petersson, E.J. (2020). Rosetta Machine Learning Models Accurately Classify Positional Effects of Thioamides on Proteolysis. J. Phys. Chem. B 124, 8032-8041. 10.1021/acs.jpcb.0c05981.
Gouma, S., Kim, K., Weirick, M., Gumina, M., Branche, A., Topham, D., Martin, E., Monto, A., Cobey, S., and Hensley, S. (2020). Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility. Nat. Commun. 11, 4566. 10.1038/s41467-020-18465-x.
Hashmi, S.K., Barka, V., Yang, C.S., Schneider, S., Syitkina, T.M., and Heuckeroth, R.O. (2020). Pseudo-obstruction-inducing ACTG2 R257C alters actin organization and function. JCI Insight 5, e140604. 10.1172/jci.insight.140604.
Huffman, A., Lin, J., Kim, S., Byrne, K., and Vonderheide, R. (2020). CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity. JCI Insight 5, e137263. 10.1172/jci.insight.137263.
Li, S.D., Xia, B.A., Javed, B., Hasley, W.D., Melendez-Davila, A., Liu, M., Kerzner, M., Agarwal, S., Xiao, Q., Torre, P., Bermudez, J.G., Rahimi, K., Kostina, N.Y., Möller, M., Rodriguez-Emmenegger, C., Klein, M.L., Percec, V., and Good, M. (2020). Direct Visualization of Vesicle Disassembly and Reassembly Using Photocleavable Dendrimers Elucidates Cargo Release Mechanisms. ACS Nano 14, 7398-7411. 10.1021/acsnano.0c02912.
Muir, A., Cohen, J., Sheppard, S., Guttipatti, P., Lo, T., Weed, N., Doherty, D., DeMarzo, D., Fagerberg, C., Kjærsgaard, L., Larsen, M., Rump, P., Löhner, K., Hirsch, Y., Zeevi, D., Zackai, E., Bhoj, E., Song, Y., and Mefford, H. (2020). Bi-allelic Loss-of-Function Variants in NUP188 Cause a Recognizable Syndrome Characterized by Neurologic, Ocular, and Cardiac Abnormalities. Am. J. Hum. Genet. 106, 623-631. 10.1016/j.ajhg.2020.03.009.
Qian, J., and Akçay, E. (2020). The balance of interaction types determines the assembly and stability of ecological communities. Nat. Ecol. Evol. 4, 356-365.
Rabadán, R., Mohamedi, Y., Rubin, U., Chu, T., Alghalith, A., Elliott, O., Arnés, L., Cal, S., Obaya, A., Levine, A., and Cámara, P. (2020). Identification of relevant genetic alterations in cancer using topological data analysis. Nat. Commun. 11, 3808. 10.1038/s41467-020-17659-7.
Robinson, M., Lee, M., and DaSilva, S. (2020). Glutamate Transporters and Mitochondria: Signaling, Co-compartmentalization, Functional Coupling, and Future Directions. Neurochem. Res. 45, 526-540. 10.1007/s11064-020-02974-8.
Seo, Y., Ortiz, M., Weintraub, D., Van Deerlin, V., Trojanowski, J., and Chen-Plotkin, A. (2020). GPNMB protein levels in CNS are modulated by PD risk variant rs199347. Mov. Disord. 35, S211-S212.
Shringari, S.R., Giannakoulias, S., Ferrie, J.J., and Petersson, E.J. (2020). Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning. Chem. Commun. 56, 6774-6777. 10.1039/d0cc01959c.
Vrooman, L., Rhon-Calderon, E., Chao, O., Nguyen, D., Narapareddy, L., Dahiya, A., Putt, M., Schultz, R., and Bartolomei, M. (2020). Assisted reproductive technologies induce temporally specific placental defects and the preeclampsia risk marker sFLT1 in mouse. Development 147, dev186551. 10.1242/dev.186551.
Way, G., Zietz, M., Rubinetti, V., Himmelstein, D., and Greene, C. (2020). Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biol. 21, 109. 10.1186/s13059-020-02021-3.
Zemerov, S.D., Roose, B.W., Farenhem, K.L., Zhao, Z., Stringer, M.A., Goldman, A.R., Speicher, D.W., and Dmochowski, I.J. (2020). 129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration. Anal. Chem. 92, 12817-12824. 10.1021/acs.analchem.0c00967.
Zhao, Z.Y., Roose, B.W., Zemerov, S.D., Stringer, M.A., and Dmochowski, I.J. (2020). Detecting protein-protein interactions by Xe-129 NMR. Chem. Commun. 56, 11122-11125. 10.1039/d0cc02988b.
2019
Akera, T., Trimm, E., and Lampson, M. (2019). Molecular Strategies of Meiotic Cheating by Selfish Centromeres. Cell 178, 1132-144.e10. 10.1016/j.cell.2019.07.001.
Beane, A., Villaescusa-Navarro, F., and Lidz, A. (2019). Measuring the EoR Power Spectrum without Measuring the EoR Power Spectrum. Astrophys. J. 874. 10.3847/1538-4357/ab0a08.
Jaiswal, N., Gavin, M., Quinn, W., Luongo, T., Gelfer, R., Baur, J., and Titchenell, P. (2019). The role of skeletal muscle Akt in the regulation of muscle mass and glucose homeostasis. Mol. Metab. 28, 1-13. 10.1016/j.molmet.2019.08.001.
Symmons, O., Chang, M., Mellis, I., Kalish, J., Park, J., Suszták, K., Bartolomei, M., and Raj, A. (2019). Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. PLoS Genet. 15, e1007874. 10.1371/journal.pgen.1007874.
Zost, S., Lee, J., Gumina, M., Parkhouse, K., Henry, C., Wu, N., Lee, C., Wilson, I., Wilson, P., Bloom, J., and Hensley, S. (2019). Identification of Antibodies Targeting the H3N2 Hemagglutinin Receptor Binding Site following Vaccination of Humans. Cell Rep. 29, 4460-4470.e8. 10.1016/j.celrep.2019.11.084.
2018
Beane, A., and Lidz, A. (2018). Extracting Bias Using the Cross-bispectrum: An EoR and 21 cm-[C II]-[C II] Case Study. Astrophys. J. 867, 26. 10.3847/1538-4357/aae388.
Ching, T., Himmelstein, D., Beaulieu-Jones, B., Kalinin, A., Do, B., Way, G., Ferrero, E., Agapow, P., Zietz, M., Hoffman, M., Xie, W., Rosen, G., Lengerich, B., Israeli, J., Lanchantin, J., Woloszynek, S., Carpenter, A., Shrikumar, A., Xu, J., Cofer, E., Lavender, C., Turaga, S., Alexandari, A., Lu, Z., Harris, D., DeCaprio, D., Qi, Y., Kundaje, A., Peng, Y., Wiley, L., Segler, M., Boca, S., Swamidass, S., Huang, A., Gitter, A., and Greene, C. (2018). Opportunities and obstacles for deep learning in biology and medicine. J. R. Soc. Interface. 15, 20170387. 10.1098/rsif.2017.0387.
Davis, A., McCormick, K., Gumina, M., Petrie, J., Martin, E., Xue, K., Bloom, J., Monto, A., Bushman, F., and Hensley, S. (2018). Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo. Virol. J. 92, e00859-18. 10.1128/JVI.00859-18.
Fouad, A., Teng, S., Mark, J., Liu, A., Alvarez-Illera, P., Ji, H., Du, A., Bhirgoo, P., Cornblath, E., Guan, S., and Fang-Yen, C. (2018). Distributed rhythm generators underlie Caenorhabditis elegans forward locomotion. Elife 7, e29913. 10.7554/eLife.29913.
Li, D., Li, F., Guttipatti, P., and Song, Y. (2018). A Drosophila In Vivo Injury Model for Studying Neuroregeneration in the Peripheral and Central Nervous System. J. Vis. Exp. 135, e57557. 10.3791/57557.
Qian, J., and Akçay, E. (2018). Competition and niche construction in a model of cancer metastasis. PLOS ONE 13, e0198163. 10.1371/journal.pone.0198163.
Tcyganov, E., Mastio, J., Chen, E., and Gabrilovich, D. (2018). Plasticity of myeloid-derived suppressor cells in cancer. Curr. Opin. Microbiol. 51, 76-82. 10.1016/j.coi.2018.03.009.
2017
Akera, T., Chmátal, L., Trimm, E., Yang, K., Aonbangkhen, C., Chenoweth, D., Janke, C., Schultz, R., and Lampson, M. (2017). Spindle asymmetry drives non-Mendelian chromosome segregation. Science 358, 668-672. 10.1126/science.aan0092.
Karpowicz, R., Haney, C., Mihaila, T., Sandler, R., Petersson, E.J., and Lee, V. (2017). Selective imaging of internalized proteopathic α-synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies. J. Biol. Chem. 292, 13482-13497. 10.1074/jbc.M117.780296.
Quinn, W., Wan, M., Shewale, S., Gelfer, R., Rader, D., Birnbaum, M., and Titchenell, P. (2017). mTORC1 stimulates phosphatidylcholine synthesis to promote triglyceride secretion.
J. Clin. Invest. 127, 4207-4215. 10.1172/JCI96036.
Zost, S., Parkhouse, K., Gumina, M., Kim, K., Perez, S., Wilson, P., Treanor, J., Sant, A., Cobey, S., and Hensley, S. (2017). Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. Proceedings of the National Academy of Sciences of the United States of America 114, 12578-12583. 10.1073/pnas.1712377114.