Department of Biochemistry & Molecular Biophysics

2024

AI is a viable alternative to high throughput screening: a 318-target study

Wallach, I., Bernard, D., Nguyen, K., Ho, G., Morrison, A., Stecula, A., Rosnik, A., O’Sullivan, A. M., Davtyan, A., Samudio, B., Thomas, B., Worley, B., Butler, B., Laggner, C., Thayer, D., Moharreri, E., Friedland, G., Truong, H., van den Bedem, H. & Ng, H. L. & 668 others, Stafford, K., Sarangapani, K., Giesler, K., Ngo, L., Mysinger, M., Ahmed, M., Anthis, N. J., Henriksen, N., Gniewek, P., Eckert, S., de Oliveira, S., Suterwala, S., PrasadPrasad, S. V. K., Shek, S., Contreras, S., Hare, S., Palazzo, T., O’Brien, T. E., Van Grack, T., Williams, T., Chern, T. R., Kenyon, V., Lee, A. H., Cann, A. B., Bergman, B., Anderson, B. M., Cox, B. D., Warrington, J. M., Sorenson, J. M., Goldenberg, J. M., Young, M. A., DeHaan, N., Pemberton, R. P., Schroedl, S., Abramyan, T. M., Gupta, T., Mysore, V., Presser, A. G., Ferrando, A. A., Andricopulo, A. D., Ghosh, A., Ayachi, A. G., Mushtaq, A., Shaqra, A. M., Toh, A. K. L., Smrcka, A. V., Ciccia, A., de Oliveira, A. S., Sverzhinsky, A., de Sousa, A. M., Agoulnik, A. I., Kushnir, A., Freiberg, A. N., Statsyuk, A. V., Gingras, A. R., Degterev, A., Tomilov, A., Vrielink, A., Garaeva, A. A., Bryant-Friedrich, A., Caflisch, A., Patel, A. K., Rangarajan, A. V., Matheeussen, A., Battistoni, A., Caporali, A., Chini, A., Ilari, A., Mattevi, A., Foote, A. T., Trabocchi, A., Stahl, A., Herr, A. B., Berti, A., Freywald, A., Reidenbach, A. G., Lam, A., Cuddihy, A. R., White, A., Taglialatela, A., Ojha, A. K., Cathcart, A. M., Motyl, A. A. L., Borowska, A., D’Antuono, A., Hirsch, A. K. H., Porcelli, A. M., Minakova, A., Montanaro, A., Müller, A., Fiorillo, A., Virtanen, A., O’Donoghue, A. J., Del Rio Flores, A., Garmendia, A. E., Pineda-Lucena, A., Panganiban, A. T., Samantha, A., Chatterjee, A. K., Haas, A. L., Paparella, A. S., John, A. L. S., Prince, A., ElSheikh, A., Apfel, A. M., Colomba, A., O’Dea, A., Diallo, B. N., Ribeiro, B. M. R. M., Bailey-Elkin, B. A., Edelman, B. L., Liou, B., Perry, B., Chua, B. S. K., Kováts, B., Englinger, B., Balakrishnan, B., Gong, B., Agianian, B., Pressly, B., Salas, B. P. M., Duggan, B. M., Geisbrecht, B. V., Dymock, B. W., Morten, B. C., Hammock, B. D., Mota, B. E. F., Dickinson, B. C., Fraser, C., Lempicki, C., Novina, C. D., Torner, C., Ballatore, C., Bon, C., Chapman, C. J., Partch, C. L., Chaton, C. T., Huang, C., Yang, C. Y., Kahler, C. M., Karan, C., Keller, C., Dieck, C. L., Huimei, C., Liu, C., Peltier, C., Mantri, C. K., Kemet, C. M., Müller, C. E., Weber, C., Zeina, C. M., Muli, C. S., Morisseau, C., Alkan, C., Reglero, C., Loy, C. A., Wilson, C. M., Myhr, C., Arrigoni, C., Paulino, C., Santiago, C., Luo, D., Tumes, D. J., Keedy, D. A., Lawrence, D. A., Chen, D., Manor, D., Trader, D. J., Hildeman, D. A., Drewry, D. H., Dowling, D. J., Hosfield, D. J., Smith, D. M., Moreira, D., Siderovski, D. P., Shum, D., Krist, D. T., Riches, D. W. H., Ferraris, D. M., Anderson, D. H., Coombe, D. R., Welsbie, D. S., Hu, D., Ortiz, D., Alramadhani, D., Zhang, D., Chaudhuri, D., Slotboom, D. J., Ronning, D. R., Lee, D., Dirksen, D., Shoue, D. A., Zochodne, D. W., Krishnamurthy, D., Duncan, D., Glubb, D. M., Gelardi, E. L. M., Hsiao, E. C., Lynn, E. G., Silva, E. B., Aguilera, E., Lenci, E., Abraham, E. T., Lama, E., Mameli, E., Leung, E., Christensen, E. M., Mason, E. R., Petretto, E., Trakhtenberg, E. F., Rubin, E. J., Strauss, E., Thompson, E. W., Cione, E., Lisabeth, E. M., Fan, E., Kroon, E. G., Jo, E., García-Cuesta, E. M., Glukhov, E., Gavathiotis, E., Yu, F., Xiang, F., Leng, F., Wang, F., Ingoglia, F., van den Akker, F., Borriello, F., Vizeacoumar, F. J., Luh, F., Buckner, F. S., Vizeacoumar, F. S., Bdira, F. B., Svensson, F., Rodriguez, G. M., Bognár, G., Lembo, G., Zhang, G., Dempsey, G., Eitzen, G., Mayer, G., Greene, G. L., Garcia, G. A., Lukacs, G. L., Prikler, G., Parico, G. C. G., Colotti, G., De Keulenaer, G., Cortopassi, G., Roti, G., Girolimetti, G., Fiermonte, G., Gasparre, G., Leuzzi, G., Dahal, G., Michlewski, G., Conn, G. L., Stuchbury, G. D., Bowman, G. R., Popowicz, G. M., Veit, G., de Souza, G. E., Akk, G., Caljon, G., Alvarez, G., Rucinski, G., Lee, G., Cildir, G., Li, H., Breton, H. E., Jafar-Nejad, H., Zhou, H., Moore, H. P., Tilford, H., Yuan, H., Shim, H., Wulff, H., Hoppe, H., Chaytow, H., Tam, H. K., Van Remmen, H., Xu, H., Debonsi, H. M., Lieberman, H. B., Jung, H., Fan, H. Y., Feng, H., Zhou, H., Kim, H. J., Greig, I. R., Caliandro, I., Corvo, I., Arozarena, I., Mungrue, I. N., Verhamme, I. M., Qureshi, I. A., Lotsaris, I., Cakir, I., Perry, J. J. P., Kwiatkowski, J., Boorman, J., Ferreira, J., Fries, J., Kratz, J. M., Miner, J., Siqueira-Neto, J. L., Granneman, J. G., Ng, J., Shorter, J., Voss, J. H., Gebauer, J. M., Chuah, J., Mousa, J. J., Maynes, J. T., Evans, J. D., Dickhout, J., MacKeigan, J. P., Jossart, J. N., Zhou, J., Lin, J., Xu, J., Wang, J., Zhu, J., Liao, J., Xu, J., Zhao, J., Lin, J., Lee, J., Reis, J., Stetefeld, J., Bruning, J. B., Bruning, J. B., Coles, J. G., Tanner, J. J., Pascal, J. M., So, J., Pederick, J. L., Costoya, J. A., Rayman, J. B., Maciag, J. J., Nasburg, J. A., Gruber, J. J., Finkelstein, J. M., Watkins, J., Rodríguez-Frade, J. M., Arias, J. A. S., Lasarte, J. J., Oyarzabal, J., Milosavljevic, J., Cools, J., Lescar, J., Bogomolovas, J., Wang, J., Kee, J. M., Kee, J. M., Liao, J., Sistla, J. C., Abrahão, J. S., Sishtla, K., Francisco, K. R., Hansen, K. B., Molyneaux, K. A., Cunningham, K. A., Martin, K. R., Gadar, K., Ojo, K. K., Wong, K. S., Wentworth, K. L., Lai, K., Lobb, K. A., Hopkins, K. M., Parang, K., Machaca, K., Pham, K., Ghilarducci, K., Sugamori, K. S., McManus, K. J., Musta, K., Faller, K. M. E., Nagamori, K., Mostert, K. J., Korotkov, K. V., Liu, K., Smith, K. S., Sarosiek, K., Rohde, K. H., Kim, K. K., Lee, K. H., Pusztai, L., Lehtiö, L., Haupt, L. M., Cowen, L. E., Byrne, L. J., Su, L., Wert-Lamas, L., Puchades-Carrasco, L., Chen, L., Malkas, L. H., Zhuo, L., Hedstrom, L., Hedstrom, L., Walensky, L. D., Antonelli, L., Iommarini, L., Whitesell, L., Randall, L. M., Fathallah, M. D., Nagai, M. H., Kilkenny, M. L., Ben-Johny, M., Lussier, M. P., Windisch, M. P., Lolicato, M., Lolli, M. L., Vleminckx, M., Caroleo, M. C., Macias, M. J., Valli, M., Barghash, M. M., Mellado, M., Tye, M. A., Wilson, M. A., Hannink, M., Ashton, M. R., Cerna, M. V. C. D., Giorgis, M., Safo, M. K., Maurice, M. S., McDowell, M. A., Pasquali, M., Mehedi, M., Serafim, M. S. M., Soellner, M. B., Alteen, M. G., Champion, M. M., Skorodinsky, M., O’Mara, M. L., Bedi, M., Rizzi, M., Levin, M., Mowat, M., Jackson, M. R., Paige, M., Al-Yozbaki, M., Giardini, M. A., Maksimainen, M. M., De Luise, M., Hussain, M. S., Christodoulides, M., Stec, N., Zelinskaya, N., Van Pelt, N., Merrill, N. M., Singh, N., Kootstra, N. A., Singh, N., Gandhi, N. S., Chan, N. L., Trinh, N. M., Schneider, N. O., Matovic, N., Horstmann, N., Longo, N., Bharambe, N., Rouzbeh, N., Mahmoodi, N., Gumede, N. J., Anastasio, N. C., Khalaf, N. B., Rabal, O., Kandror, O., Escaffre, O., Silvennoinen, O., Bishop, O. T., Iglesias, P., Sobrado, P., Chuong, P., O’Connell, P., Martin-Malpartida, P., Mellor, P., Fish, P. V., Moreira, P. O. L., Zhou, P., Liu, P., Liu, P., Wu, P., Agogo-Mawuli, P., Jones, P. L., Ngoi, P., Toogood, P., Ip, P., von Hundelshausen, P., Lee, P. H., Rowswell-Turner, R. B., Balaña-Fouce, R., Rocha, R. E. O., Guido, R. V. C., Ferreira, R. S., Agrawal, R. K., Harijan, R. K., Ramachandran, R., Verma, R., Singh, R. K., Tiwari, R. K., Mazitschek, R., Koppisetti, R. K., Dame, R. T., Douville, R. N., Austin, R. C., Taylor, R. E., Moore, R. G., Ebright, R. H., Angell, R. M., Yan, R., Kejriwal, R., Batey, R. A., Blelloch, R., Vandenberg, R. J., Hickey, R. J., Kelm, R. J., Lake, R. J., Bradley, R. K., Blumenthal, R. M., Solano, R., Gierse, R. M., Viola, R. E., McCarthy, R. R., Reguera, R. M., Uribe, R. V., do Monte-Neto, R. L., Gorgoglione, R., Cullinane, R. T., Katyal, S., Hossain, S., Phadke, S., Shelburne, S. A., Geden, S. E., Johannsen, S., Wazir, S., Legare, S., Landfear, S. M., Radhakrishnan, S. K., Ammendola, S., Dzhumaev, S., Seo, S. Y., Li, S., Zhou, S., Chu, S., Chauhan, S., Maruta, S., Ashkar, S. R., Shyng, S. L., Conticello, S. G., Buroni, S., Garavaglia, S., White, S. J., Zhu, S., Tsimbalyuk, S., Chadni, S. H., Byun, S. Y., Park, S., Xu, S. Q., Banerjee, S., Zahler, S., Espinoza, S., Gustincich, S., Sainas, S., Celano, S. L., Capuzzi, S. J., Waggoner, S. N., Poirier, S., Olson, S. H., Marx, S. O., Van Doren, S. R., Sarilla, S., Brady-Kalnay, S. M., Dallman, S., Azeem, S. M., Teramoto, T., Mehlman, T., Swart, T., Abaffy, T., Akopian, T., Haikarainen, T., Moreda, T. L., Ikegami, T., Teixeira, T. R., Jayasinghe, T. D., Gillingwater, T. H., Kampourakis, T., Richardson, T. I., Herdendorf, T. J., Kotzé, T. J., O’Meara, T. R., Corson, T. W., Hermle, T., Ogunwa, T. H., Lan, T., Su, T., Banjo, T., O’Mara, T. A., Chou, T., Chou, T. F., Baumann, U., Desai, U. R., Pai, V. P., Thai, V. C., Tandon, V., Banerji, V., Robinson, V. L., Gunasekharan, V., Namasivayam, V., Segers, V. F. M., Maranda, V., Dolce, V., Maltarollo, V. G., Scoffone, V. C., Woods, V. A., Ronchi, V. P., Van Hung Le, V., Clayton, W. B., Lowther, W. T., Houry, W. A., Li, W., Tang, W., Zhang, W., Van Voorhis, W. C., Donaldson, W. A., Hahn, W. C., Kerr, W. G., Gerwick, W. H., Bradshaw, W. J., Foong, W. E., Blanchet, X., Wu, X., Lu, X., Qi, X., Xu, X., Yu, X., Qin, X., Wang, X., Yuan, X., Zhang, X., Zhang, Y. J., Hu, Y., Aldhamen, Y. A., Chen, Y., Li, Y., Sun, Y., Zhu, Y., Gupta, Y. K., Pérez-Pertejo, Y., Li, Y., Tang, Y., He, Y., Tse-Dinh, Y. C., Sidorova, Y. A., Yen, Y., Li, Y., Frangos, Z. J., Chung, Z., Su, Z., Wang, Z., Zhang, Z., Liu, Z., Inde, Z., Artía, Z. & Heifets, A., Dec 2024, In: Scientific reports. 14, 1, 7526.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

An orally available compound suppresses glucagon hypersecretion and normalizes hyperglycemia in type 1 diabetes

Asadi, F., Gunawardana, S. C., Dolle, R. E. & Piston, D. W., Jan 2024, In: JCI Insight. 9, 2, e172626.

Research output: Contribution to journal › Article › peer-review

Open Access

Architecture of the bacteriophage lambda tail

Wang, C., Duan, J., Gu, Z., Ge, X., Zeng, J. & Wang, J., Jan 4 2024, In: Structure. 32, 1, p. 35-46.e3

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Bifunctional Peptide Nanofibrils for Targeted Protein Degradation

Lin, Z., Garcia, B. A. & Lv, D., Jan 15 2024, In: Angewandte Chemie - International Edition. 63, 3, e202316581.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants

Ghahremani, S., Kanwal, A., Pettinato, A., Ladha, F., Legere, N., Thakar, K., Zhu, Y., Tjong, H., Wilderman, A., Stump, W. T., Greenberg, L., Greenberg, M. J., Cotney, J., Wei, C. L. & Hinson, J. T., Apr 16 2024, In: Circulation. 149, 16, p. 1285-1297 13 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Cutting Edge: The Tetraspanin CD53 Promotes CXCR4 Signaling and Bone Marrow Homing in B Cells

Chakraborty, M., Greenberg, Z. J., Dong, Q., Roundy, N., Bednarski, J. J., Paracatu, L. C., Duncavage, E., Li, W. & Schuettpelz, L. G., Apr 1 2024, In: Journal of Immunology. 212, 7, p. 1075-1080 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Direct prediction of intrinsically disordered protein conformational properties from sequence

Lotthammer, J. M., Ginell, G. M., Griffith, D., Emenecker, R. J. & Holehouse, A. S., Mar 2024, In: Nature Methods. 21, 3, p. 465-476 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections

Maddirala, A. R., Tamadonfar, K., Pinkner, J. S., Sanick, D., Hultgren, S. J. & Janetka, J. W., Mar 14 2024, In: Journal of Medicinal Chemistry. 67, 5, p. 3668-3678 11 p.

Research output: Contribution to journal › Article › peer-review

Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

Jankowski, M. S., Griffith, D., Shastry, D. G., Pelham, J. F., Ginell, G. M., Thomas, J., Karande, P., Holehouse, A. S. & Hurley, J. M., Dec 2024, In: Nature communications. 15, 1, 3523.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity

Fazio, N. T., Mersch, K. N., Hao, L. & Lohman, T. M., Jan 15 2024, In: Journal of Molecular Biology. 436, 2, 168381.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Efficacy of host cell serine protease inhibitor MM3122 against SARS-CoV-2 for treatment and prevention of COVID-19

Boon, A. C. M., Bricker, T. L., Fritch, E. J., Leist, S. R., Gully, K., Baric, R. S., Graham, R. L., Troan, B. V., Mahoney, M. & Janetka, J. W., May 2024, In: Journal of virology. 98, 5

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Extracellular domain mutations of the EGF receptor differentially modulate high-affinity and low-affinity responses to EGF receptor ligands

Macdonald-Obermann, J. L. & Pike, L. J., Mar 2024, In: Journal of Biological Chemistry. 300, 3, 105763.

Research output: Contribution to journal › Article › peer-review

Open Access

FLT3 tyrosine kinase inhibition modulates PRC2 and promotes differentiation in acute myeloid leukemia

Sung, P. J., Selvam, M., Riedel, S. S., Xie, H. M., Bryant, K., Manning, B., Wertheim, G. B., Kulej, K., Pham, L., Bowman, R. L., Peresie, J., Nemeth, M. J., Levine, R. L., Garcia, B. A., Meyer, S. E., Sidoli, S., Bernt, K. M. & Carroll, M., Feb 2024, In: Leukemia. 38, 2, p. 291-301 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

G Protein Activation Occurs via a Largely Universal Mechanism

Vithani, N., Todd, T. D., Singh, S., Trent, T., Blumer, K. J. & Bowman, G. R., Apr 18 2024, In: Journal of Physical Chemistry B. 128, 15, p. 3554-3562 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells

Leszczynska, K. B., Freitas-Huhtamäki, A., Jayaprakash, C., Dzwigonska, M., Vitorino, F. N. L., Horth, C., Wojnicki, K., Gielniewski, B., Szadkowska, P., Kaza, B., Nazarian, J., Ciolkowski, M. K., Trubicka, J., Grajkowska, W., Garcia, B. A., Majewski, J., Kaminska, B. & Mieczkowski, J., Feb 27 2024, In: Cell Reports. 43, 2, 113707.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Helicity of a tardigrade disordered protein contributes to its protective function during desiccation

Biswas, S., Gollub, E., Yu, F., Ginell, G., Holehouse, A., Sukenik, S. & Boothby, T. C., Feb 2024, In: Protein Science. 33, 2, e4872.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Hepsin promotes breast tumor growth signaling via the TGFβ-EGFR axis

Belitškin, D., Munne, P., Pant, S. M., Anttila, J. M., Suleymanova, I., Belitškina, K., Kirchhofer, D., Janetka, J., Käsper, T., Jalil, S., Pouwels, J., Tervonen, T. A. & Klefström, J., Mar 2024, In: Molecular Oncology. 18, 3, p. 547-561 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Fernandez-Rojas, M., Fuller, C. N., Tose, L. V., Willetts, M., Park, M. A., Bhanu, N. V., Garcia, B. A. & Fernandez-Lima, F., 2024, In: Journal of Visualized Experiments. 2024, 203, e65589.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Human PLCG2 haploinsufficiency results in a novel natural killer cell immunodeficiency

Alinger, J. B., Mace, E. M., Porter, J. R., Mah-Som, A. Y., Daugherty, A. L., Li, S., Throm, A. A., Pingel, J. T., Saucier, N., Yao, A., Chinn, I. K., Lupski, J. R., Ehlayel, M., Keller, M., Bowman, G. R., Cooper, M. A., Orange, J. S. & French, A. R., Jan 2024, In: Journal of Allergy and Clinical Immunology. 153, 1, p. 216-229 14 p.

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Identification of plant transcriptional activation domains

Morffy, N., Van den Broeck, L., Miller, C., Emenecker, R. J., Bryant, J. A., Lee, T. M., Sageman-Furnas, K., Wilkinson, E. G., Pathak, S., Kotha, S. R., Lam, A., Mahatma, S., Pande, V., Waoo, A., Wright, R. C., Holehouse, A. S., Staller, M. V., Sozzani, R. & Strader, L. C., Aug 1 2024, In: Nature. 632, 8023, p. 166-173 8 p.

Research output: Contribution to journal › Article › peer-review

Improved detection of DNA replication fork-associated proteins

Rivard, R. S., Chang, Y. C., Ragland, R. L., Thu, Y. M., Kassab, M., Mandal, R. S., Van Riper, S. K., Kulej, K., Higgins, L. A., Markowski, T. M., Shang, D., Hedberg, J., Erber, L., Garcia, B., Chen, Y., Bielinsky, A. K. & Brown, E. J., May 28 2024, In: Cell Reports. 43, 5, 114178.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Inhibition of autocrine HGF maturation overcomes cetuximab resistance in colorectal cancer

Jones, V. T., Graves-Deal, R., Cao, Z., Bogatcheva, G., Ramirez, M. A., Harmych, S. J., Higginbotham, J. N., Sharma, V., Damalanka, V. C., Wahoski, C. C., Joshi, N., Irudayam, M. J., Roland, J. T., Ayers, G. D., Liu, Q., Coffey, R. J., Janetka, J. W. & Singh, B., Dec 2024, In: Cellular and Molecular Life Sciences. 81, 1, 28.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development

Baeza, J., Coons, B. E., Lin, Z., Riley, J., Mendoza, M., Peranteau, W. H. & Garcia, B. A., Feb 26 2024, In: Cell Reports Methods. 4, 2, 100713.

Research output: Contribution to journal › Article › peer-review

Open Access

Labile assembly of a tardigrade protein induces biostasis

Sanchez-Martinez, S., Nguyen, K., Biswas, S., Nicholson, V., Romanyuk, A. V., Ramirez, J., Kc, S., Akter, A., Childs, C., Meese, E. K., Usher, E. T., Ginell, G. M., Yu, F., Gollub, E., Malferrari, M., Francia, F., Venturoli, G., Martin, E. W., Caporaletti, F. & Giubertoni, G. & 5 others, Woutersen, S., Sukenik, S., Woolfson, D. N., Holehouse, A. S. & Boothby, T. C., Apr 2024, In: Protein Science. 33, 4, e4941.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Longitudinal modeling of human neuronal aging reveals the contribution of the RCAN1–TFEB pathway to Huntington’s disease neurodegeneration

Lee, S. W., Oh, Y. M., Victor, M. B., Yang, Y., Chen, S., Strunilin, I., Dahiya, S., Dolle, R. E., Pak, S. C., Silverman, G. A., Perlmutter, D. H. & Yoo, A. S., Jan 2024, In: Nature Aging. 4, 1, p. 95-109 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices

Dai, J., Ma, M., Niu, Q., Eisert, R. J., Wang, X., Das, P., Lechtreck, K. F., Dutcher, S. K., Zhang, R. & Brown, A., Apr 11 2024, In: Cell. 187, 8, p. 1907-1921.e16

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Mechanism-Based Macrocyclic Inhibitors of Serine Proteases

Damalanka, V. C., Banas, V., De Bona, P., Kashipathy, M. M., Battaile, K., Lovell, S. & Janetka, J. W., Mar 28 2024, In: Journal of Medicinal Chemistry. 67, 6, p. 4833-4854 22 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Mycobacterium tuberculosis Ku Stimulates Multi-round DNA Unwinding by UvrD1 Monomers

Chadda, A., Kozlov, A. G., Nguyen, B., Lohman, T. M. & Galburt, E. A., Jan 15 2024, In: Journal of Molecular Biology. 436, 2, 168367.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Neuroactive steroid effects on autophagy in a human embryonic kidney 293 (HEK) cell model

Salvatore, S. V., Ilagan, M. X. G., Shu, H., Lambert, P. M., Benz, A., Qian, M., Covey, D. F., Zorumski, C. F. & Mennerick, S., Dec 2024, In: Scientific reports. 14, 1, 1042.

Research output: Contribution to journal › Article › peer-review

Open Access

Phase transition of GvpU regulates gas vesicle clustering in bacteria

Li, Z., Shen, Q., Usher, E. T., Anderson, A. P., Iburg, M., Lin, R., Zimmer, B., Meyer, M. D., Holehouse, A. S., You, L., Chilkoti, A., Dai, Y. & Lu, G. J., 2024, (Accepted/In press) In: Nature microbiology.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production

Grams, N., Charman, M., Halko, E., Lauman, R., Garcia, B. A. & Weitzman, M. D., Jan 16 2024, In: EMBO Journal. 43, 2, p. 277-303 27 p.

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Open Access

1 Scopus citations

Regulation of Absorption and Emission in a Protein/Fluorophore Complex

Santos, E. M., Chandra, I., Assar, Z., Sheng, W., Ghanbarpour, A., Bingham, C., Vasileiou, C., Geiger, J. H. & Borhan, B., Aug 16 2024, In: ACS Chemical Biology. 19, 8, p. 1725-1732 8 p.

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Open Access

ROR2/Wnt5a Signaling Regulates Directional Cell Migration and Early Tumor Cell Invasion in Ovarian Cancer

Grither, W. R., Baker, B., Morikis, V. A., Ilagan, M. X. G., Fuh, K. C. & Longmore, G. D., May 1 2024, In: Molecular Cancer Research. 22, 5, p. 495-507 13 p.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Rrm3 and Pif1 division of labor during replication through leading and lagging strand G-quadruplex

Varon, M., Dovrat, D., Heuzé, J., Tsirkas, I., Singh, S. P., Pasero, P., Galletto, R. & Aharoni, A., Feb 28 2024, In: Nucleic acids research. 52, 4, p. 1753-1762 10 p.

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Open Access

3 Scopus citations

Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction

Obermann, R., Yemane, B., Jarvis, C., Franco, F. M., Kyriukha, Y., Nolan, W., Gohara, B., Krezel, A. M., Wildman, S. A. & Janetka, J. W., Apr 16 2024, In: ChemMedChem. 19, 8, e202300648.

Research output: Contribution to journal › Article › peer-review

Structural basis of pH-dependent activation in a CLC transporter

Fortea, E., Lee, S., Chadda, R., Argyros, Y., Sandal, P., Mahoney-Kruszka, R., Ciftci, H. D., Falzone, M. E., Huysmans, G., Robertson, J. L., Boudker, O. & Accardi, A., Apr 2024, In: Nature Structural and Molecular Biology. 31, 4, p. 644-656 13 p.

Research output: Contribution to journal › Article › peer-review

Structural biases in disordered proteins are prevalent in the cell

Moses, D., Guadalupe, K., Yu, F., Flores, E., Perez, A. R., McAnelly, R., Shamoon, N. M., Kaur, G., Cuevas-Zepeda, E., Merg, A. D., Martin, E. W., Holehouse, A. S. & Sukenik, S., Feb 2024, In: Nature Structural and Molecular Biology. 31, 2, p. 283-292 10 p.

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Open Access

8 Scopus citations

Structural insights into vesicular monoamine storage and drug interactions

Ye, J., Chen, H., Wang, K., Wang, Y., Ammerman, A., Awasthi, S., Xu, J., Liu, B. & Li, W., May 2 2024, In: Nature. 629, 8010, p. 235-243 9 p.

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Open Access

1 Scopus citations

Subunit Communication within Dimeric SF1 DNA Helicases

Nguyen, B., Hsieh, J., Fischer, C. J. & Lohman, T. M., Jun 1 2024, In: Journal of Molecular Biology. 436, 11, 168578.

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Open Access

1 Scopus citations

TGF-β controls alveolar type 1 epithelial cell plasticity and alveolar matrisome gene transcription in mice

Callaway, D. A., Penkala, I. J., Zhou, S., Knowlton, J. J., Cardenas-Diaz, F., Babu, A., Morley, M. P., Lopes, M., Garcia, B. A. & Morrisey, E. E., Mar 15 2024, In: Journal of Clinical Investigation. 134, 6, e172095.

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Open Access

1 Scopus citations

The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA

Cubuk, J., Alston, J. J., Incicco, J. J., Holehouse, A. S., Hall, K., Stuchell-Brereton, M. D. & Soranno, A., Mar 21 2024, In: Nucleic acids research. 52, 5, p. 2609-2624 16 p.

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Open Access

5 Scopus citations

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

Frisbie, V. S., Hashimoto, H., Xie, Y., De Luna Vitorino, F. N., Baeza, J., Nguyen, T., Yuan, Z., Kiselar, J., Garcia, B. A. & Debler, E. W., Dec 2024, In: Nature communications. 15, 1, 2467.

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Open Access

Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin

Mahoney, M. W., Helander, J., Kooner, A. S., Norman, M., Damalanka, V. C., De Bona, P., Kasperkiewicz, P., Rut, W., Poreba, M., Kashipathy, M. M., Battaile, K. P., Lovell, S., O'Donoghue, A. J., Craik, C. S., Drag, M. & Janetka, J. W., Aug 2024, In: Protein Science. 33, 8, e5110.

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Acetyl-methyllysine marks chromatin at active transcription start sites

Lu-Culligan, W. J., Connor, L. J., Xie, Y., Ekundayo, B. E., Rose, B. T., Machyna, M., Pintado-Urbanc, A. P., Zimmer, J. T., Vock, I. W., Bhanu, N. V., King, M. C., Garcia, B. A., Bleichert, F. & Simon, M. D., Oct 5 2023, In: Nature. 622, 7981, p. 173-179 7 p.

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Open Access

7 Scopus citations

A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation

Ghanbarpour, A., Cohen, S. E., Fei, X., Kinman, L. F., Bell, T. A., Zhang, J. J., Baker, T. A., Davis, J. H. & Sauer, R. T., Dec 2023, In: Nature communications. 14, 1, 7281.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

A DNA damage–induced phosphorylation circuit enhances Mec1^ATR Ddc2^ATRIP recruitment to Replication Protein A

Yates, L. A., Tannous, E. A., Morgan, R. M., Burgers, P. M. & Zhang, X., 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 14, e2300150120.

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Open Access

6 Scopus citations

A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy

Townley, B. A., Buerer, L., Tsao, N., Bacolla, A., Mansoori, F., Rusanov, T., Clark, N., Goodarzi, N., Schmidt, N., Srivatsan, S. N., Sun, H., Sample, R. A., Brickner, J. R., McDonald, D., Tsai, M. S., Walter, M. J., Wozniak, D. F., Holehouse, A. S., Pena, V. & Tainer, J. A. & 2 others, Fairbrother, W. G. & Mosammaparast, N., Jul 6 2023, In: Molecular cell. 83, 13, p. 2258-2275.e11

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Open Access

2 Scopus citations

Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA

Shinn, M. K., Chaturvedi, S. K., Kozlov, A. G. & Lohman, T. M., Mar 21 2023, In: Nucleic acids research. 51, 5, p. 2284-2297 14 p.

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Open Access

5 Scopus citations

Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression

Agosto, L. M., Mallory, M. J., Ferretti, M. B., Blake, D., Krick, K. S., Gazzara, M. R., Garcia, B. A. & Lynch, K. W., Mar 28 2023, In: Cell Reports. 42, 3, 112273.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications

Searfoss, R. M., Karki, R., Lin, Z., Robison, F. & Garcia, B. A., Nov 1 2023, In: Journal of the American Society for Mass Spectrometry. 34, 11, p. 2508-2517 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Department of Biochemistry & Molecular Biophysics

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