Recent Publications

Alpha Raj Mekapogu, Zhihong Xu, Srinivasa Pothula, Chamini Perera, Tony Pang, S M Zahid Hosen, Vishnu Damalanka, James Janetka, David Goldstein, Romano Pirola, Jeremy Wilson & Minoti Apte (2023). “HGF/c-Met pathway inhibition combined with chemotherapy increases cytotoxic T-cell infiltration and inhibits pancreatic tumour growth and metastasis” Cancer Lett. 2023 Aug 1:568:216286. doi: 10.1016/j.canlet.2023.216286. Epub 2023 Jun 22. (Abstract)

Denis Belitškin, Pauliina Munne, Shishir M Pant, Johanna M Anttila, Ilida Suleymanova, Kati Belitškina, Daniel Kirchhofer, James Janetka, Taivo Käsper, Sami Jalil, Jeroen Pouwels, Topi A Tervonen & Juha Klefström (2024). “Hepsin promotes breast tumor growth signaling via the TGFβ-EGFR axis” Mol Oncol. 2024 Mar;18(3):547-561. doi: 10.1002/1878-0261.13545. Epub 2023 Nov 13. (Abstract)

Vivian Truong Jones, Ramona Graves-Deal, Zheng Cao, Galina Bogatcheva, Marisol A Ramirez, Sarah J Harmych, James N Higginbotham, Vineeta Sharma, Vishnu C Damalanka, Claudia C Wahoski, Neeraj Joshi, Maria Johnson Irudayam, Joseph T Roland, Gregory D Ayers, Qi Liu, Robert J Coffey, James W Janetka & Bhuminder Singh (2024). “Inhibition of autocrine HGF maturation overcomes cetuximab resistance in colorectal cancer” Cell Mol Life Sci. 2024 Jan 12;81(1):28. doi: 10.1007/s00018-023-05071-5. (Abstract)

Robert Obermann, Bereket Yemane, Cassie Jarvis, Francisco M Franco, Yevhenii Kyriukha, William Nolan, Beth Gohara, Andrzej M Krezel, Scott A Wildman & James W Janetka (2024). “Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction” ChemMedChem. 2024 Feb 1:e202300648. doi: 10.1002/cmdc.202300648. Online ahead of print. (Abstract)

Amarendar Reddy Maddirala, Kevin Tamadonfar, Jerome S Pinkner, Denise Sanick, Scott J Hultgren & James W Janetka (2024). “Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections” J Med Chem. 2024 Mar 14;67(5):3668-3678. doi: 10.1021/acs.jmedchem.3c02128. Epub 2024 Feb 3. (Abstract)

Vishnu C Damalanka, Victoria Banas, Paolo De Bona, Maithri M Kashipathy, Kevin Battaile, Scott Lovell & James W Janetka (2024). “Mechanism-Based Macrocyclic Inhibitors of Serine Proteases” J Med Chem2024 Mar 28;67(6):4833-4854. doi: 10.1021/acs.jmedchem.3c02388. Epub 2024 Mar 13. (Abstract)

Adrianus C. M. Boon, Traci L. Bricker, Ethan J. Fritch, Sarah R. Leist, Kendra Gully, Ralph S. Baric, Rachel L. Graham, Brigid V. Troan, Matthew Mahoney  & James W. Janetka (2024). “Efficacy of host cell serine protease inhibitor MM3122 against SARS-CoV-2 for treatment and prevention of COVID-19.” J Virol. 2024 Apr;9. doi:10.1128/jvi.01903-23 (Abstract)

Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard Börner, Felix Erichson, Achillefs N. Kapanidis, Harold D. Kim, Marcia Levitus, Timothy M. Lohman, Abhishek Mazumder, David S. Rueda, Fabio D. Steffen, Thorben Cordes, Steven W. Magennis, & Eitan Lerner (2023). “A new twist on PIFE: photoisomerisation-related fluorescence enhancement” ArXiv. 2023 Jul 10;arXiv:2302.12455v2. (Abstract)

Min Kyung Shinn, Sumit K. Chaturvedi, Alexander G. Kozlov, & Timothy M. Lohman (2023). “Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA” Nucleic Acids Res. 2023 Mar 21;51(5):2284-2297. doi: 10.1093/nar/gkad084. (Abstract)

Zev J. Greenberg, Darlene Monlish, Luana Chiquetto Paracatu, Qian Dong, Michael P. Rettig, Nate Dee Roundy, Rofaida Gaballa, Weikai Li, Wei Yang, Cliff J. Luke, & Laura Schuettpelz (2022). “The tetraspanin CD53 protects stressed hematopoietic stem cells via promotion of DREAM complex- mediated quiescence” Blood. 2022 Dec 21;blood.2022016929. doi: 10.1182/blood.2022016929. Online ahead of print. (Abstract)

Garrett M. Ginell & Alex S. Holehouse (2022). “An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates” Methods Mol Biol. 2023;2563:95-116. doi: 10.1007/978-1-0716-2663-4_4. (Abstract)

Nicolás S. González-Foutel, Juliana Glavina, Wade M. Borcherds, Matías Safranchik, Susana Barrera-Vilarmau, Amin Sagar, Alejandro Estaña, Amelie Barozet, Nicolás A. Garrone, Gregorio Fernandez-Ballester, Clara Blanes-Mira, Ignacio E. Sánchez, Gonzalo de Prat-Gay, Juan Cortés, Pau Bernadó, Rohit V. Pappu, Alex S. Holehouse, Gary W. Daughdrill, & Lucía B. Chemes (2022). “Conformational buffering underlies functional selection in intrinsically disordered protein regions” Nat Struct Mol Biol. 2022 Aug;29(8):781-790. doi: 10.1038/s41594-022-00811-w. Epub 2022 Aug 10. (Abstract)

Liana Beld, Hyeim Jung, Christina A. Bulman, Bruce A. Rosa, Peter U. Fischer, James W. Janetka, Sara Lustigman, Judy A. Sakanari, and Makedonka Mitreva (2022). “Aspartyl Protease Inhibitors as Anti-Filarial Drugs” Pathogens. 2022 Jun 18;11(6):707. doi: 10.3390/pathogens11060707. (Abstract)

Alexander G. Kozlov, Xian Cheng, Hongshan Zhang, Min Kyung Shinn, Elizabeth Weiland, Binh Nguyen, Irina A. Shkel, Emily Zytkiewicz, Ilya J. Finkelstein, M. Thomas Record Jr., & Timothy M. Lohman (2022). “How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein” J Mol Biol. 2022 Mar 26;434(9):167562. doi: 10.1016/j.jmb.2022.167562. Online ahead of print.

Jie Sun, Weikai Li, & Michael L. Gross (2022). “Advances in mass spectrometry-based footprinting of membrane proteins” Proteomics. 2022 Apr;22(8):e2100222. doi: 10.1002/pmic.202100222. (Abstract)

Upasana L. Mallimadugula & Eric A. Galburt (2022). “Parallel path mechanisms lead to nonmonotonic force-velocity curves and an optimum load for molecular motor function” Phys Rev E. 2022 Mar;105(3-1):034405. doi: 10.1103/PhysRevE.105.034405. (Abstract)

Shixuan Liu, Shuang Li, Andrzej M. Krezel, & Weikai Li (2022). “Stabilization and structure determination of integral membrane proteins by termini restraining” Nat Protoc. 2022 Jan 17. doi: 10.1038/s41596-021-00656-5. Online ahead of print. (Abstract)

Jie Sun, Xiaoran Roger Liu, Shuang Li, Peng He, Weikai Li, & Michael L. Gross (2021). “Nanoparticles and photochemistry for native-like transmembrane protein footprinting” Nat Commun. 2021 Dec 14;12(1):7270. doi: 10.1038/s41467-021-27588-8. (Abstract)

Vishnu C. Damalanka, Jorine J. L. P. Voss, Matthew W. Mahoney, Tina Primeau, Shunqiang Li, Lidija Klampfer, & James W. Janetka (2021). “Macrocyclic Inhibitors of HGF-Activating Serine Proteases Overcome Resistance to Receptor Tyrosine Kinase Inhibitors and Block Lung Cancer Progression” J Med Chem. 2021 Dec 13. doi: 10.1021/acs.jmedchem.1c01671. Online ahead of print. (Abstract)

Maya Topf, Edina Rosta, Gregory R. Bowman, & Massimiliano Bonomi (2021). “Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function” Front Mol Biosci. 2021 Nov 29;8:799406. doi: 10.3389/fmolb.2021.799406. eCollection 2021. (Abstract)

Matthew Mahoney, Vishnu C. Damalanka, Michael A. Tartell, Dong Hee Chung, André Luiz Lourenco, Dustin Pwee, Anne E. Mayer Bridwell, Markus Hoffmann, Jorine Voss, Partha Karmakar, Nurit Azouz, Andrea M. Klingler, Paul W. Rothlauf, Cassandra E. Thompson, Melody Lee, Lidija Klampfer, Christina Stallings, Marc E. Rothenberg, Stefan Pöhlmann, Sean P. Whelan, Anthony J. O’Donoghue, Charles S. Craik, & James W. Janetka (2021). “A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells” Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):e2108728118. doi: 10.1073/pnas.2108728118. (Abstract)

Samantha K. Barrick & Michael J. Greenberg (2021). “Cardiac myosin contraction and mechanotransduction in health and disease” J Biol Chem. 2021 Nov;297(5):101297. doi: 10.1016/j.jbc.2021.101297. Epub 2021 Oct 9. (Abstract)

Benjamin C. Stark, Yuanyuan Gao, Diane S. Sepich, Lakyn Belk, Matthew A. Culver, Bo Hu, Marlene Mekel, Wyndham Ferris, Jimann Shin, Lilianna Solnica-Krezel, Fang Lin, & John A. Cooper (2021). “CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish” Dev Biol. 2022 Jan;481:148-159. doi: 10.1016/j.ydbio.2021.09.008. Epub 2021 Sep 30. (Abstract)

Chia-Chen Liu, Melissa E. Murray, Xia Li, Na Zhao, Na Wang, Michael G. Heckman, Francis Shue, Yuka Martens, Yonghe Li, Ana-Caroline Raulin, Cassandra L. Rosenberg, Sydney V. Doss, Jing Zhao, Melissa C. Wren, Lin Jia, Yingxue Ren, Tadafumi C. Ikezu, Wenyan Lu, Yuan Fu, Thomas Caulfield, Zachary A. Trottier, Joshua Knight, Yixing Chen, Cynthia Linares, Xue Wang, Aishe Kurti, Yan W. Asmann, Zbigniew K. Wszolek, Glenn E. Smith, Prashanthi Vemuri, Kejal Kantarci, David S. Knopman, Val J. Lowe, Clifford R. Jack Jr., Joseph E. Parisi, Tanis J. Ferman, Bradley F. Boeve, Neill R. Graff-Radford, Ronald C. Petersen, Steven G. Younkin, John D. Fryer, Hu Wang, Xianlin Han, Carl Frieden, Dennis W. Dickson, Owen A. Ross, & Guojun Bu (2021). “APOE3-Jacksonville (V236E) variant reduces self-aggregation and risk of dementia” Sci Transl Med. 2021 Sep 29;13(613):eabc9375. doi: 10.1126/scitranslmed.abc9375. Epub 2021 Sep 29. (Abstract)

Daniel Griffith & Alex S. Holehouse (2021). “PARROT is a flexible recurrent neural network framework for analysis of large protein datasets” Elife. 2021 Sep 17;10:e70576. doi: 10.7554/eLife.70576. (Abstract)