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  1. 1.   Distinct allosteric networks in CDK4 and CDK6 in the cell cycle and in drug resistance
  2. Zhang,Wengang; Bradburn, Devin; Heidebrink, Gretchen; Liu, Yonglan; Jang,Hyunbum; Nussinov,Ruth; Kõivomägi, Mardo
  3. Journal of Molecular Biology. 2025, Mar 31; 169121.
  1. 2.   ShiftScan: A tool for rapid analysis of high-throughput differential scanning fluorimetry data and compound prioritization
  2. Waterworth, Samantha C; Shenoy, Shilpa R; Sharma, Nirmala D; Wolcott,Chris; Donohue,Duncan; O'Keefe,Barry; Beutler,John
  3. Protein Science : a publication of the Protein Society. 2025, Mar; 34(3): e70055.
  1. 3.   Multi-objective latent space optimization of generative molecular design models
  2. Abeer, A N M Nafiz; Urban, Nathan M; Weil,Michael; Alexander, Francis J; Yoon, Byung-Jun
  3. Patterns (New York, N.Y.). 2024, Oct 11; 5(10): 101042.
  1. 4.   Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries
  2. Song, Robert X; Nicklaus,Marc; Tarasova,Nadya
  3. Journal of Computer-Aided Molecular Design. 2024, May 16; 38(1): 22.
  1. 5.   Slower CDK4 and faster CDK2 activation in the cell cycle
  2. Zhang,Wengang; Liu,Yonglan; Jang,Hyunbum; Nussinov,Ruth
  3. Structure (London, England : 1993). 2024, Apr 23;
  1. 6.   A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening
  2. Vasanthakumari, Priyanka; Zhu, Yitan; Brettin, Thomas; Partin, Alexander; Shukla, Maulik; Xia, Fangfang; Narykov, Oleksandr; Weil,Michael; Stevens, Rick L
  3. Cancers. 2024, Jan 26; 16(3):
  1. 7.   DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
  2. Balius,Trent; Tan, Y Stanley; Chakrabarti,Mayukh
  3. Journal of Computational Chemistry. 2023, Sep 25;
  1. 8.   Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction
  2. Fan, Ya Ju; Allen, Jonathan E; McLoughlin, Kevin S; Shi, Da; Bennion, Brian J; Zhang, Xiaohua; Lightstone, Felice C
  3. Artificial Intelligence Chemistry. 2023, Jun; 1(1):
  1. 9.   Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target
  2. Olenginski, Lukasz T; Kasprzak, Wojciech K; Attionu, Solomon K; Shapiro, Bruce A; Dayie, Theodore K
  3. Molecules (Basel, Switzerland). 2023, Feb 14; 28(4):
  1. 10.   Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design
  2. Shaw,Gary; Fan,Lixin; Cherry,Scott; Shi,Genbin; Tropea, Joseph E; Ji,Xinhua
  3. Current Research in Structural Biology. 2023, Jan 30; 5: 100095.
  1. 11.   Virtual screening for small-molecule pathway regulators by image-profile matching
  2. Rohban, Mohammad H; Fuller, Ashley M; Tan, Ceryl; Goldstein, Jonathan T; Syangtan, Deepsing; Gutnick, Amos; DeVine, Ann; Nijsure, Madhura P; Rigby,Megan; Sacher, Joshua R; Corsello, Steven M; Peppler, Grace B; Bogaczynska, Marta; Boghossian, Andrew; Ciotti, Gabrielle E; Hands, Allison T; Mekareeya, Aroonroj; Doan, Minh; Gale, Jennifer P; Derynck, Rik; Turbyville,Tommy; Boerckel, Joel D; Singh, Shantanu; Kiessling, Laura L; Schwarz, Thomas L; Varelas, Xaralabos; Wagner, Florence F; Kafri, Ran; Eisinger-Mathason, T S Karin; Carpenter, Anne E
  3. Cell Systems. 2022, Sep 01; 13(9): 724-736.e9.
  1. 12.   Target 2035-update on the quest for a probe for every protein
  2. Mueller, Susanne; Ackloo, Suzanne; Al Chawaf, Arij; Al-Lazikani, Bissan; Antolin, Albert; Baell, Jonathan B.; Beck, Hartmut; Beedie, Shaunna; Betz, Ulrich A. K.; Bezerra, Gustavo Arruda; Brennan, Paul E.; Brown, David; Brown, Peter J.; Bullock, Alex N.; Carter, Adrian J.; Chaikuad, Apirat; Chaineau, Mathilde; Ciulli, Alessio; Collins, Ian; Dreher, Jan; Drewry, David; Edfeldt, Kristina; Edwards, Aled M.; Egner, Ursula; Frye, Stephen; Fuchs, Stephen M.; Hall, Matthew D.; Hartung, Ingo; Hillisch, Alexander; Hitchcock, Stephen H.; Homan, Evert; Kannan, Natarajan; Kiefer, James R.; Knapp, Stefan; Kostic, Milka; Kubicek, Stefan; Leach, Andrew R.; Lindemann, Sven; Marsden, Brian D.; Matsui, Hisanori; Meier,Jordan; Merk, Daniel; Michel, Maurice; Morgan, Maxwell R.; Mueller-Fahrnow, Anke; Owen, Dafydd R.; Perry, Benjamin G.; Rosenberg, Saul H.; Saikatendu, Kumar Singh; Schapira, Matthieu; Scholten, Cora; Sharma, Sujata; Simeonov, Anton; Sundstrom, Michael; Superti-Furga, Giulio; Todd, Matthew H.; Tredup, Claudia; Vedadi, Masoud; von Delft, Frank; Willson, Timothy M.; Winter, Georg E.; Workman, Paul; Arrowsmith, Cheryl H.
  3. RSC Medicinal Chemistry . 2022, Jan 27; 13(1): 13-21.
  1. 13.   Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma
  2. Lu, Xiuxiu; Sabbasani, Venkata R.; Osei-Amponsa, Vasty; Evans, Christine N.; King, Julianna C.; Tarasov, Sergey G.; Dyba, Marzena; Das, Sudipto; Chan, King C.; Schwieters, Charles D.; Choudhari, Sulbha; Fromont, Caroline; Zhao, Yongmei; Tran, Bao; Chen, Xiang; Matsuo, Hiroshi; Andresson, Thorkell; Chari, Raj; Swenson, Rolf E.; Tarasova, Nadya I.; Walters, Kylie J.
  3. Nature Communications. 2021, Dec 16; 12(1):
  1. 14.   Mechanism of activation and the rewired network: New drug design concepts
  2. Nussinov,Ruth; Zhang,Mingzhen; Maloney, Ryan; Tsai,Chung-Jung; Yavuz, Bengi Ruken; Tuncbag, Nurcan; Jang, Hyunbum
  3. Medicinal research reviews. 2021, Oct 25; 0198-6325:
  1. 15.   Comparative microsomal proteomics of a model lung cancer cell line NCI-H23 reveals distinct differences between molecular profiles of 3D and 2D cultured cells
  2. Kaczmarczyk,Jan; Roberts,Rhonda; Luke,Brian; Chan,King; Van Wagoner, Carly M; Felder, Robin A; Saul, Richard G; Simona, Colantonio; Blonder,Josip
  3. Oncotarget. 2021, Sep 28; 12(20): 2022-2038.
  1. 16.   Proteogenomic characterization of pancreatic ductal adenocarcinoma
  2. Cao, Liwei; Huang, Chen; Zhou, Daniel Cui; Hu, Yingwei; Lih, T. Mamie; Savage, Sara R.; Krug, Karsten; Clark, David J.; Schnaubelt, Michael; Chen, Lijun; Leprevost, Felipe da Veiga; Eguez, Rodrigo Vargas; Yang, Weiming; Pan, Jianbo; Wen, Bo; Dou, Yongchao; Jiang, Wen; Liao, Yuxing; Shi, Zhiao; Terekhanova, Nadezhda; Cao, Song; Lu, Rita Jui-Hsien; Li, Yize; Liu, Ruiyang; Zhu, Houxiang; Ronning, Peter; Wu, Yige; Wyczalkowski, Matthew A.; Easwaran, Hariharan; Danilova, Ludmila; Mer, Arvind Singh; Yoo, Seungyeul; Wang, Joshua M.; Liu, Wenke; Haibe-Kains, Benjamin; Thiagarajan,Mathangi; Jewell, Scott D.; Hostetter, Galen; Newton, Chelsea J.; Li, Qing Kay; Roehr, Michael H.; Fenyo, David; Wang, Pei; Nesvizhskii, Alexey; Mani, D. R.; Omenn, Gilbert S.; Boja, Emily S.; Mesri, Mehdi; Robles, Ana; Rodriguez, Henry; Bathe, Oliver F.; Chan, Daniel W.; Hruban, Ralph H.; Ding, Li; Zhang, Bing; Zhang, Hui
  3. Cell. 2021, Sep 16; 184(19): 5031-5052.e26.
  1. 17.   Drugging multiple same-allele driver mutations in cancer
  2. Nussinov,Ruth; Zhang,Mingzhen; Maloney,Ryan; Jang, Hyunbum
  3. Expert Opinion on Drug Discovery. 2021, Aug; 16(8): 823-828.
  1. 18.   Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident
  2. Morton, Lindsay M.; Karyadi, Danielle M.; Stewart, Chip; Bogdanova, Tetiana; Dawson, Eric T.; Steinberg,Mia; Dai, Jieqiong; Hartley, Stephen W.; Schonfeld, Sara J.; Sampson, Joshua N.; Maruvka, Yosef E.; Kapoor,Vidushi; Ramsden, Dale A.; Carvajal-Garcia, Juan; Perou, Charles M.; Parker, Joel S.; Krznaric, Marko; Yeager,Meredith; Boland,Joseph; Hutchinson,Amy; Hicks,Belynda; Dagnall,Casey; Gastier-Foster, Julie M.; Bowen, Jay; Lee, Olivia; Machiela, Mitchell J.; Cahoon, Elizabeth K.; Brenner, Alina; Mabuchi, Kiyohiko; Drozdovitch, Vladimir; Masiuk, Sergii; Chepurny, Mykola; Zurnadzhy, Liudmyla Yu; Hatch, Maureen; de Gonzalez, Amy Berrington; Thomas, Gerry A.; Tronko, Mykola D.; Getz, Gad; Chanock, Stephen J.
  3. Science (New York, N.Y.). 2021, May 14; 372(6543): 705-+.
  1. 19.   MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
  2. Cai, Tian; Lim, Hansaim; Abbu, Kyra Alyssa; Qiu, Yue; Nussinov,Ruth; Xie, Lei
  3. Journal of Chemical Information and Modeling. 2021, Apr 26; 61(4): 1570-1582.
  1. 20.   Proteogenomic and metabolomic characterization of human glioblastoma
  2. Wang, Liang-Bo; Karpova, Alla; Gritsenko, Marina A.; Kyle, Jennifer E.; Cao, Song; Li, Yize; Rykunov, Dmitry; Colaprico, Antonio; Rothstein, Joseph H.; Hong, Runyu; Stathias, Vasileios; Cornwell, MacIntosh; Petralia, Francesca; Wu, Yige; Reva, Boris; Krug, Karsten; Pugliese, Pietro; Kawaler, Emily; Olsen, Lindsey K.; Liang, Wen-Wei; Song, Xiaoyu; Dou, Yongchao; Wendl, Michael C.; Caravan, Wagma; Liu, Wenke; Zhou, Daniel Cui; Ji, Jiayi; Tsai, Chia-Feng; Petyuk, Vladislav A.; Moon, Jamie; Ma, Weiping; Chu, Rosalie K.; Weitz, Karl K.; Moore, Ronald J.; Monroe, Matthew E.; Zhao, Rui; Yang, Xiaolu; Yoo, Seungyeul; Krek, Azra; Demopoulos, Alexis; Zhu, Houxiang; Wyczalkowski, Matthew A.; McMichael, Joshua F.; Henderson, Brittany L.; Lindgren, Caleb M.; Boekweg, Hannah; Lu, Shuangjia; Baral, Jessika; Yao, Lijun; Stratton, Kelly G.; Bramer, Lisa M.; Zink, Erika; Couvillion, Sneha P.; Bloodsworth, Kent J.; Satpathy, Shankha; Sieh, Weiva; Boca, Simina M.; Schurer, Stephan; Chen, Feng; Wiznerowicz, Maciej; Ketchum, Karen A.; Boja, Emily S.; Kinsinger, Christopher R.; Robles, Ana; Hiltke, Tara; Thiagarajan,Mathangi; Nesvizhskii, Alexey; Zhang, Bing; Mani, D. R.; Ceccarelli, Michele; Chen, Xi S.; Cottingham, Sandra L.; Li, Qing Kay; Kim, Albert H.; Fenyo, David; Ruggles, Kelly; Rodriguez, Henry; Mesri, Mehdi; Payne, Samuel H.; Resnick, Adam C.; Wang, Pei; Smith, Richard D.; Iavarone, Antonio; Chheda, Milan G.; Barnholtz-Sloan, Jill S.; Rodland, Karin D.; Liu, Tao; Ding, Li
  3. Cancer Cell. 2021, Apr 12; 39(4): 509-528.e20.
  1. 21.   A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome
  2. Mun, Seyoung; Kim, Songmi; Lee, Wooseok; Kang, Keunsoo; Meyer,Thomas; Han, Bok-Ghee; Han, Kyudong; Kim, Heui-Soo
  3. Experimental and Molecular Medicine. 2021, Apr; 53(4): 615-630.
  1. 22.   Tumor aggressiveness is independent of radiation quality in murine hepatocellular carcinoma and mammary tumor models
  2. Udho, Eshwar B.; Huebner, Shane M.; Albrecht, Dawn M.; Matkowskyj, Kristina A.; Clipson, Linda; Hedican, Catigan A.; Koth, Rachel; Snow, Santina M.; Eberhardt, Emily L.; Miller, Devon; Van Doorn, Rachel; Gjyzeli, Genti; Spengler, Erin K.; Storts, Douglas R.; Thamm, Douglas H.; Edmondson,Elijah; Weil, Michael M.; Halberg, Richard B.; Bacher, Jeffery W.
  3. International Journal of Radiation Biology. 2021, Mar 31; 97(8): 1140-1151.
  1. 23.   Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
  2. Huang, Chen; Chen, Lijun; Savage, Sara R.; Eguez, Rodrigo Vargas; Dou, Yongchao; Li, Yize; Leprevost, Felipe da Veiga; Jaehnig, Eric J.; Lei, Jonathan T.; Wen, Bo; Schnaubelt, Michael; Krug, Karsten; Song, Xiaoyu; Cieslik, Marcin; Chang, Hui-Yin; Wyczalkowski, Matthew A.; Li, Kai; Colaprico, Antonio; Li, Qing Kay; Clark, David J.; Hu, Yingwei; Cao, Liwei; Pan, Jianbo; Wang, Yuefan; Cho, Kyung-Cho; Shi, Zhiao; Liao, Yuxing; Jiang, Wen; Anurag, Meenakshi; Ji, Jiayi; Yoo, Seungyeul; Zhou, Daniel Cui; Liang, Wen-Wei; Wendl, Michael; Vats, Pankaj; Carr, Steven A.; Mani, D. R.; Zhang, Zhen; Qian, Jiang; Chen, Xi S.; Pico, Alexander R.; Wang, Pei; Chinnaiyan, Arul M.; Ketchum, Karen A.; Kinsinger, Christopher R.; Robles, Ana; An, Eunkyung; Hiltke, Tara; Mesri, Mehdi; Thiagarajan,Mathangi; Weaver, Alissa M.; Sikora, Andrew G.; Lubinski, Jan; Wierzbicka, Malgorzata; Wiznerowicz, Maciej; Satpathy, Shankha; Gillette, Michael A.; Miles, George; Ellis, Matthew J.; Omenn, Gilbert S.; Rodriguez, Henry; Boja, Emily S.; Dhanasekaran, Saravana M.; Ding, Li; Nesvizhskii, Alexey; El-Naggar, Adel K.; Chan, Daniel W.; Zhang, Hui; Zhang, Bing
  3. Cancer Cell. 2021, Mar 8; 39(3): 361-379.
  1. 24.   Crystallographic models of SARS-CoV-2 3CL(pro): in-death assessment of structure quality and validation
  2. Jaskolski, Mariusz; Dauter, Zbigniew; Shabalin, Ivan G.; Gilski, Miroslaw; Brzezinski, Dariusz; Kowiel, Marcin; Rupp, Bernhard; Wlodawer,Alexander
  3. IUCrJ. 2021, Feb 9; 8(Pt 2): 238-256.
  1. 25.   Predicting Volume of Distribution in Humans: Performance of in silico Methods for A Large Set of Structurally Diverse Clinical Compounds
  2. Murad, Neha; Pasikanti, Kishore K; Madej,Benjamin; Minnich, Amanda; McComas, Juliet M; Crouch, Sabrinia; Polli, Joseph W; Weber, Andrew D
  3. Drug metabolism and disposition: the biological fate of chemicals. 2021, Feb 1; 49: 169-178.
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