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  1. 1.   Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics
  2. Lu,Xiuxiu; Sabbasani, Venkata R; Walters,Kylie; Swenson, Rolf E; Walters,Kylie
  3. The Journal of Biological Chemistry. 2025, Apr 18; 108520.
  1. 2.   Discovery of potent and selective PROTACs for the protein kinase LZK for the treatment of head and neck cancer
  2. Katerji,Meghri; Bergman, Knickole L; Lindberg, Eric; Rubin,Maxine; Funk, Amy L; Woodroofe, Carolyn C; Nyswaner, Katherine; Karpinska, Kamila; Serwa, Remigiusz; Marusiak, Anna; Swenson, Rolf E; Brognard,John
  3. The Journal of Biological Chemistry. 2025, Mar 27; 108452.
  1. 3.   Humoral Immunity Profiling to Pandemic and Bat-Derived Coronavirus Variants: A Geographical Comparison
  2. Fathi, Parinaz; Alfonso, Andrea Lucia; Yek, Christina; Putman, Zoe; Drew,Matt; Esposito,Dom; Zaidi, Irfan; Chea, Sophana; Ly, Sokna; Sath, Rathanak; Lon, Chanthap; Chea, Huch; Leang, Rithea; Huy, Rekol; Ly, Sovann; Seng, Heng; Tan, Chee Wah; Zhu, Feng; Wang, Lin-Fa; Oliveira, Fabiano; Sadtler, Kaitlyn; Manning, Jessica
  3. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 2024, Oct 29; e2403503.
  1. 4.   Multi-scale signaling and tumor evolution in high-grade gliomas
  2. Liu, Jingxian; Cao, Song; Imbach, Kathleen J; Gritsenko, Marina A; Lih, Tung-Shing M; Kyle, Jennifer E; Yaron-Barir, Tomer M; Binder, Zev A; Li, Yize; Strunilin, Ilya; Wang, Yi-Ting; Tsai, Chia-Feng; Ma, Weiping; Chen, Lijun; Clark, Natalie M; Shinkle, Andrew; Naser Al Deen, Nataly; Caravan, Wagma; Houston, Andrew; Simin, Faria Anjum; Wyczalkowski, Matthew A; Wang, Liang-Bo; Storrs, Erik; Chen, Siqi; Illindala, Ritvik; Li, Yuping D; Jayasinghe, Reyka G; Rykunov, Dmitry; Cottingham, Sandra L; Chu, Rosalie K; Weitz, Karl K; Moore, Ronald J; Sagendorf, Tyler; Petyuk, Vladislav A; Nestor, Michael; Bramer, Lisa M; Stratton, Kelly G; Schepmoes, Athena A; Couvillion, Sneha P; Eder, Josie; Kim, Young-Mo; Gao, Yuqian; Fillmore, Thomas L; Zhao, Rui; Monroe, Matthew E; Southard-Smith, Austin N; Li, Yang E; Jui-Hsien Lu, Rita; Johnson, Jared L; Wiznerowicz, Maciej; Hostetter, Galen; Newton, Chelsea J; Ketchum, Karen A; Thangudu, Ratna R; Barnholtz-Sloan, Jill S; Wang, Pei; Fenyö, David; An, Eunkyung; Thiagarajan,Mathangi; Robles, Ana I; Mani, D R; Smith, Richard D; Porta-Pardo, Eduard; Cantley, Lewis C; Iavarone, Antonio; Chen, Feng; Mesri, Mehdi; Nasrallah, MacLean P; Zhang, Hui; Resnick, Adam C; Chheda, Milan G; Rodland, Karin D; Liu, Tao; Ding, Li
  3. Cancer Cell. 2024, Jul 08; 42(7): 1217-1238.e19.
  1. 5.   The Degradation of Botulinum Neurotoxin Light Chains Using PROTACs
  2. Tsai,Yien Che; Kozar, Loren; Mawi, Zo P; Ichtchenko, Konstantin; Shoemaker, Charles B; McNutt, Patrick M; Weissman,Allan
  3. International Journal of Molecular Sciences. 2024, Jul 08; 25(13):
  1. 6.   Comprehensive proteogenomic characterization of rare kidney tumors
  2. Li, Ginny Xiaohe; Chen, Lijun; Hsiao, Yi; Mannan, Rahul; Zhang, Yuping; Luo, Jie; Petralia, Francesca; Cho, Hanbyul; Hosseini, Noshad; Leprevost, Felipe da Veiga; Calinawan, Anna; Li, Yize; Anand, Shankara; Dagar, Aniket; Geffen, Yifat; Kumar-Sinha, Chandan; Chugh, Seema; Le, Anne; Ponce, Sean; Guo, Shenghao; Zhang, Cissy; Schnaubelt, Michael; Al Deen, Nataly Naser; Chen, Feng; Caravan, Wagma; Houston, Andrew; Hopkins, Alex; Newton, Chelsea J; Wang, Xiaoming; Polasky, Daniel A; Haynes, Sarah; Yu, Fengchao; Jing, Xiaojun; Chen, Siqi; Robles, Ana I; Mesri, Mehdi; Thiagarajan,Mathangi; An, Eunkyung; Getz, Gad A; Linehan, W Marston; Hostetter, Galen; Jewell, Scott D; Chan, Daniel W; Wang, Pei; Omenn, Gilbert S; Mehra, Rohit; Ricketts, Christopher J; Ding, Li; Chinnaiyan, Arul M; Cieslik, Marcin P; Dhanasekaran, Saravana M; Zhang, Hui; Nesvizhskii, Alexey I
  3. Cell Reports. Medicine. 2024, May 21; 5(5): 101547.
  1. 7.   Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
  2. Savage, Sara R; Wang, Yuefan; Chen, Lijun; Jewell, Scott; Newton, Chelsea; Dou, Yongchao; Li, Qing Kay; Bathe, Oliver F; Robles, Ana I; Omenn, Gilbert S; Thiagarajan,Mathangi; Zhang, Hui; Hostetter, Galen; Zhang, Bing
  3. Clinical Proteomics. 2024, Jan 30; 21(1): 7.
  1. 8.   Tools and tactics to define specificity of metabolic chemical reporters
  2. Mukherjee, Mana Mohan; Bond, Michelle R; Abramowitz, Lara K; Biesbrock, Devin; Woodroofe, Carolyn C; Kim, Eun Ju; Swenson, Rolf E; Hanover, John A
  3. Frontiers in Molecular Biosciences. 2023, Dec 7; 10: 1286690.
  1. 9.   Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing
  2. Craig, Amanda J; Silveira, Maruhen A Datsch; Ma, Lichun; Revsine, Mahler; Wang, Limin; Heinrich, Sophia; Rae, Zachary; Ruchinskas, Allison; Dadkhah,Kimia; Do, Whitney; Behrens, Shay; Mehrabadi, Farid R; Dominguez, Dana A; Forgues, Marshonna; Budhu, Anuradha; Chaisaingmongkol, Jittiporn; Hernandez, Jonathan M; Davis, Jeremy L; Tran,Bao; Marquardt, Jens U; Ruchirawat, Mathuros; Kelly, Michael; Greten, Tim F; Wang, Xin W
  3. Cell Reports. 2023, Nov 17; 42(11): 113446.
  1. 10.   PIM1 targeted degradation prevents the emergence of chemoresistance in prostate cancer
  2. Torres-Ayuso, Pedro; Katerji,Meghri; Mehlich, Dawid; Lookingbill, Sophia A; Sabbasani, Venkata R; Liou, Hope; Casillas, Andrea L; Chauhan, Shailender S; Serwa, Remigiusz; Rubin,Maxine; Marusiak, Anna A; Swenson, Rolf E; Warfel, Noel A; Brognard,John
  3. Cell Chemical Biology. 2023, Nov 16;
  1. 11.   Methotrexate-based PROTACs as DHFR-specific chemical probes
  2. Rana, Sandeep; Dranchak, Patricia; Dahlin, Jayme L; Lamy, Laurence; Li,Wenqing; Oliphant, Erin; Shrimp, Jonathan H; Rajacharya, Girish H; Tharakan, Ravi; Holland, David O; Whitten, Apryl S; Wilson, Kelli M; Singh, Pankaj K; Durum,Scott; Tao, Dingyin; Rai, Ganesha; Inglese, James
  3. Cell Chemical Biology. 2023, Oct 17;
  1. 12.   Proteogenomic insights suggest druggable pathways in endometrial carcinoma
  2. Dou, Yongchao; Katsnelson, Lizabeth; Gritsenko, Marina A; Hu, Yingwei; Reva, Boris; Hong, Runyu; Wang, Yi-Ting; Kolodziejczak, Iga; Lu, Rita Jui-Hsien; Tsai, Chia-Feng; Bu, Wen; Liu, Wenke; Guo, Xiaofang; An, Eunkyung; Arend, Rebecca C; Bavarva, Jasmin; Chen, Lijun; Chu, Rosalie K; Czekanski, Andrzej; Davoli, Teresa; Demicco, Elizabeth G; DeLair, Deborah; Devereaux, Kelly; Dhanasekaran, Saravana M; Dottino, Peter; Dover, Bailee; Fillmore, Thomas L; Foxall, McKenzie; Hermann, Catherine E; Hiltke, Tara; Hostetter, Galen; Jedryka, Marcin; Jewell, Scott D; Johnson, Isabelle; Kahn, Andrea G; Ku, Amy T; Kumar-Sinha, Chandan; Kurzawa, Pawel; Lazar, Alexander J; Lazcano, Rossana; Lei, Jonathan T; Li, Yi; Liao, Yuxing; Lih, Tung-Shing M; Lin, Tai-Tu; Martignetti, John A; Masand, Ramya P; Matkowski, Rafal; McKerrow, Wilson; Mesri, Mehdi; Monroe, Matthew E; Moon, Jamie; Moore, Ronald J; Nestor, Michael D; Newton, Chelsea; Omelchenko, Tatiana; Omenn, Gilbert S; Payne, Samuel H; Petyuk, Vladislav A; Robles, Ana I; Rodriguez, Henry; Ruggles, Kelly V; Rykunov, Dmitry; Savage, Sara R; Schepmoes, Athena A; Shi, Tujin; Shi, Zhiao; Tan, Jimin; Taylor, Mason; Thiagarajan,Mathangi; Wang, Joshua M; Weitz, Karl K; Wen, Bo; Williams, C M; Wu, Yige; Wyczalkowski, Matthew A; Yi, Xinpei; Zhang, Xu; Zhao, Rui; Mutch, David; Chinnaiyan, Arul M; Smith, Richard D; Nesvizhskii, Alexey I; Wang, Pei; Wiznerowicz, Maciej; Ding, Li; Mani, D R; Zhang, Hui; Anderson, Matthew L; Rodland, Karin D; Zhang, Bing; Liu, Tao; Fenyö, David
  3. Cancer Cell. 2023, Sep 11; 41(9): 1586-1605.e15.
  1. 13.   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. 14.   Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
  2. Geffen, Yifat; Anand, Shankara; Akiyama, Yo; Yaron, Tomer M; Song, Yizhe; Johnson, Jared L; Govindan, Akshay; Babur, Özgün; Li, Yize; Huntsman, Emily; Wang, Liang-Bo; Birger, Chet; Heiman, David I; Zhang, Qing; Miller, Mendy; Maruvka, Yosef E; Haradhvala, Nicholas J; Calinawan, Anna; Belkin, Saveliy; Kerelsky, Alexander; Clauser, Karl R; Krug, Karsten; Satpathy, Shankha; Payne, Samuel H; Mani, D R; Gillette, Michael A; Dhanasekaran, Saravana M; Thiagarajan,Mathangi; Mesri, Mehdi; Rodriguez, Henry; Robles, Ana I; Carr, Steven A; Lazar, Alexander J; Aguet, François; Cantley, Lewis C; Ding, Li; Getz, Gad
  3. Cell. 2023, Aug 09;
  1. 15.   De Novo Design of a Versatile Peptide-Based Coating to Impart Targeted Functionality at the Surface of Native Polystyrene
  2. Yamada, Yuji; Anderson,Caleb; Schneider,Joel
  3. ACS Applied Materials & Interfaces. 2023, Jun 05; 15(23): 27560-27567.
  1. 16.   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. 17.   Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
  2. Li, Yize; Lih, Tung-Shing M; Dhanasekaran, Saravana M; Mannan, Rahul; Chen, Lijun; Cieslik, Marcin; Wu, Yige; Lu, Rita Jiu-Hsien; Clark, David J; Kolodziejczak, Iga; Hong, Runyu; Chen, Siqi; Zhao, Yanyan; Chugh, Seema; Caravan, Wagma; Naser Al Deen, Nataly; Hosseini, Noshad; Newton, Chelsea J; Krug, Karsten; Xu, Yuanwei; Cho, Kyung-Cho; Hu, Yingwei; Zhang, Yuping; Kumar-Sinha, Chandan; Ma, Weiping; Calinawan, Anna; Wyczalkowski, Matthew A; Wendl, Michael C; Wang, Yuefan; Guo, Shenghao; Zhang, Cissy; Le, Anne; Dagar, Aniket; Hopkins, Alex; Cho, Hanbyul; Leprevost, Felipe da Veiga; Jing, Xiaojun; Teo, Guo Ci; Liu, Wenke; Reimers, Melissa A; Pachynski, Russell; Lazar, Alexander J; Chinnaiyan, Arul M; Van Tine, Brian A; Zhang, Bing; Rodland, Karin D; Getz, Gad; Mani, D R; Wang, Pei; Chen, Feng; Hostetter, Galen; Thiagarajan,Mathangi; Linehan, W Marston; Fenyö, David; Jewell, Scott D; Omenn, Gilbert S; Mehra, Rohit; Wiznerowicz, Maciej; Robles, Ana I; Mesri, Mehdi; Hiltke, Tara; An, Eunkyung; Rodriguez, Henry; Chan, Daniel W; Ricketts, Christopher J; Nesvizhskii, Alexey I; Zhang, Hui; Ding, Li
  3. Cancer Cell. 2023, Jan 9; 41(1): 139-163.
  1. 18.   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. 19.   Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma
  2. Li, Qing Kay; Hu, Yingwei; Chen, Lijun; Schnaubelt, Michael; Cui Zhou, Daniel; Li, Yize; Lu, Rita Jui-Hsien; Thiagarajan,Mathangi; Hostetter, Galen; Newton, Chelsea J; Jewell, Scott D; Omenn, Gil; Robles, Ana I; Mesri, Mehdi; Bathe, Oliver F; Zhang, Bing; Ding, Li; Hruban, Ralph H; Chan, Daniel W; Zhang, Hui
  3. Clinical proteomics. 2022, Oct 20; 19(1): 36.
  1. 20.   Immune correlates of HIV-1 reservoir cell decline in early-treated infants
  2. Hartana, Ciputra Adijaya; Garcia-Broncano, Pilar; Rassadkina, Yelizaveta; Lian, Xiaodong; Jiang, Chenyang; Einkauf, Kevin B; Maswabi, Kenneth; Ajibola, Gbolahan; Moyo, Sikhulile; Mohammed, Terence; Maphorisa, Comfort; Makhema, Joseph; Yuki,Yuko; Martin,Pat; Bennett, Kara; Jean-Philippe, Patrick; Viard,Mathias; Hughes, Michael D; Powis, Kathleen M; Carrington,Mary; Lockman, Shahin; Gao, Ce; Yu, Xu G; Kuritzkes, Daniel R; Shapiro, Roger; Lichterfeld, Mathias
  3. Cell Reports. 2022, Jul 19; 40(3): 111126.
  1. 21.   Heterobifunctional molecules tackle targeted protein dephosphorylation
  2. Sibley, Christopher D; Schneekloth, John S
  3. Trends in Pharmacological Sciences. 2022, Jan 28;
  1. 22.   Refining the N-Termini of the SARS-CoV-2 Spike Protein and Its Discrete Receptor-Binding Domain
  2. D'Ippolito,Robert; Drew,Matt; Mehalko,Jennifer; Snead,Kelly; Wall,Vanessa; Putman,Zoe; Esposito,Dom; Dehart,Caroline
  3. Journal of proteome research. 2021, Sep 3; 20: 4427-4434.
  1. 23.   A proteogenomic portrait of lung squamous cell carcinoma
  2. Satpathy, Shankha; Krug, Karsten; Jean Beltran, Pierre M; Savage, Sara R; Petralia, Francesca; Kumar-Sinha, Chandan; Dou, Yongchao; Reva, Boris; Kane, M Harry; Avanessian, Shayan C; Vasaikar, Suhas V; Krek, Azra; Lei, Jonathan T; Jaehnig, Eric J; Omelchenko, Tatiana; Geffen, Yifat; Bergstrom, Erik J; Stathias, Vasileios; Christianson, Karen E; Heiman, David I; Cieslik, Marcin P; Cao, Song; Song, Xiaoyu; Ji, Jiayi; Liu, Wenke; Li, Kai; Wen, Bo; Li, Yize; Gümüs, Zeynep H; Selvan, Myvizhi Esai; Soundararajan, Rama; Visal, Tanvi H; Raso, Maria G; Parra, Edwin Roger; Babur, Özgün; Vats, Pankaj; Anand, Shankara; Schraink, Tobias; Cornwell, MacIntosh; Rodrigues, Fernanda Martins; Zhu, Houxiang; Mo, Chia-Kuei; Zhang, Yuping; da Veiga Leprevost, Felipe; Huang, Chen; Chinnaiyan, Arul M; Wyczalkowski, Matthew A; Omenn, Gilbert S; Newton, Chelsea J; Schurer, Stephan; Ruggles, Kelly V; Fenyö, David; Jewell, Scott D; Thiagarajan,Mathangi; Mesri, Mehdi; Rodriguez, Henry; Mani, Sendurai A; Udeshi, Namrata D; Getz, Gad; Suh,James; Li, Qing Kay; Hostetter, Galen; Paik, Paul K; Dhanasekaran, Saravana M; Govindan, Ramaswamy; Ding, Li; Robles, Ana I; Clauser, Karl R; Nesvizhskii, Alexey I; Wang, Pei; Carr, Steven A; Zhang, Bing; Mani, D R; Gillette, Michael A
  3. Cell. 2021, Aug 05; 184(16): 4348-4371.e40.
  1. 24.   Roseabol A, a New Peptaibol from the Fungus Clonostachys rosea
  2. Kim, Chang-Kwon; Haugh Krumpe,Lauren; Smith,Emily; Henrich,Curtis; Brownell, Isaac; Wendt, Karen L.; Cichewicz, Robert H.; O'Keefe,Barry; Gustafson,Kirk
  3. Molecules (Basel, Switzerland). 2021, Jun; 26(12):
  1. 25.   CENP-A overexpression promotes aneuploidy with karyotypic heterogeneity
  2. Shrestha, Roshan L.; Rossi, Austin; Wangsa, Darawalee; Hogan, Ann K.; Zaldana, Kimberly S.; Suva, Evelyn; Chung, Yang Jo; Sanders,Chelsea; Difilippantonio,Simone; Karpova, Tatiana S.; Karim,Baktiar; Foltz, Daniel R.; Fachinetti, Daniele; Aplan, Peter D.; Ried, Thomas; Basrai, Munira A.
  3. The Journal of Cell Biology. 2021, Feb 23; 220(4):
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