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  1. 1.   Duplicate entries in the Protein Data Bank: how to detect and handle them
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Jaskolski, Mariusz; Jiang, Ziqiu; Jeffcott, William; Anosova, Olga; Kurlin, Vitaliy
  3. Acta Crystallographica. Section D, Structural Biology. 2025, Apr 01;
  1. 2.   The human oral microbiome and risk of colorectal cancer within three prospective cohort studies in the United States
  2. Vogtmann, Emily; Yano, Yukiko; Zouiouich, Semi; Hua,Xing; Wan, Yunhu; Purandare, Vaishnavi; Li, Shilan; Dagnall,Casey; Jones, Kristine; Hicks,Belynda; Hutchinson,Amy; Caporaso, J Gregory; Wheeler, William; Huang, Wen-Yi; Freedman, Neal D; Sandler, Dale P; Beane Freeman, Laura E; Liao, Linda M; Gail, Mitchell H; Shi, Jianxin; Abnet, Christian C; Sinha, Rashmi
  3. Cancer. 2025, Mar 15; 131(6): e35802.
  1. 3.   Waterless structures in the Protein Data Bank
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Loch, Joanna I; Brzezinski, Dariusz; Gilski, Miroslaw; Jaskolski, Mariusz
  3. IUCrJ. 2024, Nov 01;
  1. 4.   Longitudinal analysis of the lung proteome reveals persistent repair months after mild to moderate COVID-19
  2. Kanth, Shreya M; Huapaya, Julio A; Gairhe, Salina; Wang, Honghui; Tian, Xin; Demirkale, Cumhur Y; Hou, Chunyan; Ma, Junfeng; Kuhns,Doug; Fink,Dani; Malayeri, Ashkan; Turkbey, Evrim; Harmon, Stephanie A; Chen, Marcus Y; Regenold, David; Lynch, Nicolas F; Ramelli, Sabrina; Li, Willy; Krack, Janell; Kuruppu, Janaki; Lionakis, Michail S; Strich, Jeffrey R; Davey, Richard; Childs, Richard; Chertow, Daniel S; Kovacs, Joseph A; Parizi, Parizad Torabi-; Suffredini, Anthony F
  3. Cell Reports. Medicine. 2024, Jul 16; 5(7): 101642.
  1. 5.   Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus
  2. Lyons,Erica; Watson,Daniel; Alodadi,Mohammad; Haugabook, Sharie J; Tawa, Gregory J; Hannah-Shmouni, Fady; Porter, Forbes D; Collins, Jack R; Ottinger, Elizabeth A; Mudunuri,Uma
  3. BMC Genomics. 2023, Aug 16; 24(1): 460.
  1. 6.   Proteogenomic data and resources for pan-cancer analysis
  2. Li, Yize; Dou, Yongchao; Da Veiga Leprevost, Felipe; Geffen, Yifat; Calinawan, Anna P; Aguet, François; Akiyama, Yo; Anand, Shankara; Birger, Chet; Cao, Song; Chaudhary, Rekha; Chilappagari, Padmini; Cieslik, Marcin; Colaprico, Antonio; Zhou, Daniel Cui; Day, Corbin; Domagalski, Marcin J; Esai Selvan, Myvizhi; Fenyö, David; Foltz, Steven M; Francis, Alicia; Gonzalez-Robles, Tania; Gümüs, Zeynep H; Heiman, David; Holck, Michael; Hong, Runyu; Hu, Yingwei; Jaehnig, Eric J; Ji, Jiayi; Jiang, Wen; Katsnelson, Lizabeth; Ketchum, Karen A; Klein, Robert J; Lei, Jonathan T; Liang, Wen-Wei; Liao, Yuxing; Lindgren, Caleb M; Ma, Weiping; Ma, Lei; MacCoss, Michael J; Martins Rodrigues, Fernanda; McKerrow, Wilson; Nguyen, Ngoc; Oldroyd, Robert; Pilozzi, Alexander; Pugliese, Pietro; Reva, Boris; Rudnick, Paul; Ruggles, Kelly V; Rykunov, Dmitry; Savage, Sara R; Schnaubelt, Michael; Schraink, Tobias; Shi, Zhiao; Singhal, Deepak; Song, Xiaoyu; Storrs, Erik; Terekhanova, Nadezhda V; Thangudu, Ratna R; Thiagarajan,Mathangi; Wang, Liang-Bo; Wang, Joshua M; Wang, Ying; Wen, Bo; Wu, Yige; Wyczalkowski, Matthew A; Xin, Yi; Yao, Lijun; Yi, Xinpei; Zhang, Hui; Zhang, Qing; Zuhl, Maya; Getz, Gad; Ding, Li; Nesvizhskii, Alexey I; Wang, Pei; Robles, Ana I; Zhang, Bing; Payne, Samuel H
  3. Cancer Cell. 2023, Aug 14; (8): 1397-1406.
  1. 7.   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. 8.   Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset
  2. Conrad, Ryan; Narayan,Kedar
  3. Cell Systems. 2023, Jan 18; 14(1): 58-71.e5.
  1. 9.   Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States
  2. Kassaye, Seble G; Grossman, Zehava; Vengurlekar, Priyanka; Chai, William; Wallace, Megan; Rhee, Soo-Yon; Meyer, William A; Kaufman, Harvey W; Castel, Amanda; Jordan, Jeanne; Crandall, Keith A; Kang, Alisa; Kumar, Princy; Katzenstein, David A; Shafer, Robert W; Maldarelli,Frank
  3. Viruses. 2022, Dec 25; 15(1):
  1. 10.   Real-World Studies Link Nonsteroidal Anti-inflammatory Drug Use to Improved Overall Lung Cancer Survival
  2. Roszik, Jason; Lee, J Jack; Wu, Yi-Hung; Liu,Xi; Kawakami, Masanori; Kurie, Jonathan M; Belouali, Anas; Boca, Simina M; Gupta, Samir; Beckman, Robert A; Madhavan, Subha; Dmitrovsky,Ethan
  3. Cancer Research Communications. 2022, Jul; 2(7): 590-601.
  1. 11.   CAR T cells targeting tumor-associated exons of glypican 2 regress neuroblastoma in mice
  2. Li, Nan; Torres, Madeline B.; Spetz, Madeline R.; Wang, Ruixue; Peng, Luyi; Tian, Meijie; Dower, Christopher M.; Nguyen, Rosa; Sun, Ming; Tai, Chin-Hsien; de Val, Natalia; Cachau,Raul; Wu, Xiaolin; Hewitt, Stephen M.; Kaplan, Rosandra N.; Khan, Javed; St Croix,Brad; Thiele, Carol J.; Ho, Mitchell
  3. Cell reports. Medicine. 2021, Jun 15; 2(6):
  1. 12.   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. 13.   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. 14.   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. 15.   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. 16.   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. 17.   Celebrating the 75th birthday of Professor Wladek Minor, one of the most accomplished Polish-American structural biologists
  2. Jaskolski, Mariusz; Wlodawer,Alexander; Dauter, Zbigniew; Shabalin, Ivan; Chruszcz, Maksymilian
  3. Acta Biochimica Polonica. 2021, Jan 21; 68(1): 1-4.
  1. 18.   Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment
  2. Wheeler, David A; Takebe, Naoko; Hinoue, Toshinori; Hoadley, Katherine A; Cardenas, Maria F; Hamilton, Alina M; Laird, Peter W; Wang, Linghua; Johnson, Adrienne; Dewal, Ninad; Miller, Vincent; Piñeyro, David; Castro de Moura, Manuel; Esteller, Manel; Shen, Hui; Zenklusen, Jean Claude; Tarnuzzer, Roy; McShane, Lisa M; Tricoli, James V; Williams, Paul M; Lubensky, Irina; O'Sullivan-Coyne, Geraldine; Kohn, Elise C; Little, Richard F; White, Jeffrey; Malik, Shakun; Harris, Lyndsay; Weil, Carol; Chen, Alice P; Karlovich,Chris; Rodgers, Brian; Shankar, Lalitha; Jacobs, Paula; Nolan, Tracy; Hu, Jianhong; Muzny, Donna M; Doddapaneni, Harshavardhan; Korchina, Viktoriya; Gastier-Foster, Julie; Bowen, Jay; Leraas, Kristen; Edmondson,Elijah; Doroshow, James H; Conley, Barbara A; Ivy, S Percy; Staudt, Louis M
  3. Cancer Cell. 2021, Jan 11; 39(1): 38-53.e7.
  1. 19.   A network-based deep learning methodology for stratification of tumor mutations
  2. Liu, Chuang; Han, Zhen; Zhang, Zi-Ke; Nussinov,Ruth; Cheng, Feixiong
  3. Bioinformatics. 2021, Jan 08; 37(1): 82-88.
  1. 20.   Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery
  2. Hinkson, Izumi V; Madej,Benjamin; Stahlberg,Eric
  3. Frontiers in pharmacology. 2020, Jun 30; 11: 770.
  1. 21.   Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank
  2. Wlodawer,Alexander; Dauter,Zbigniew; Shabalin, Ivan; Gilski, Miroslaw; Brzezinski, Dariusz; Kowiel, Marcin; Minor, Wladek; Rupp, Bernhard; Jaskolski, Mariusz
  3. The FEBS journal. 2020, JUN 24;
  1. 22.   Network-based Prediction of Drug-Target Interactions using an Arbitrary-Order Proximity Embedded Deep Forest
  2. Zeng, Xiangxiang; Zhu, Siyi; Hou, Yuan; Zhang, Pengyue; Li, Lang; Li, Jing; Huang, L Frank; Lewis, Stephen J; Nussinov,Ruth; Cheng, Feixiong
  3. Bioinformatics (Oxford, England). 2020, MAY 1; 36(9): 2805-2812.
  1. 23.   Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2
  2. Dhaked,Devendra Kumar; Ihlenfeldt, Wolf-Dietrich; Patel,Hitesh; Delannee,Victorien; Nicklaus,Marc
  3. JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2020, Mar 23; 60(3): 1253-1275.
  1. 24.   Target identification among known drugs by deep learning from heterogeneous networks
  2. Zeng, Xiangxiang; Zhu, Siyi; Lu, Weiqiang; Liu, Zehui; Huang, Jin; Zhou, Yadi; Fang, Jiansong; Huang, Yin; Guo, Huimin; Li, Lang; Trapp, Bruce D.; Nussinov,Ruth; Eng, Charis; Loscalzo, Joseph; Cheng, Feixiong
  3. CHEMICAL SCIENCE. 2020, Feb 21; 11(7): 1775-1797.
  1. 25.   Estimating associations between antidepressant use and incident mild cognitive impairment in older adults with depression
  2. Han, Fang; Bonnett,Tyler; Brenowitz, Willa D; Teylan, Merilee A; Besser, Lilah M; Chen, Yen-Chi; Chan, Gary; Cao, Ke-Gang; Gao, Ying; Zhou, Xiao-Hua
  3. PloS one. 2020, JAN 17; 15(1): e0227924.
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