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  1. 1.   Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting
  2. Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard,Yvonne; Partin, Alexander; Xia, Fangfang; Shukla, Maulik; Vasanthakumari, Priyanka; Doroshow, James H; Stevens, Rick L
  3. Briefings in Bioinformatics. 2025, Mar 04; 26(2):
  1. 2.   Gene Co-Expression Network Analysis Associated with Endometrial Cancer Tumorigenesis and Survival Outcomes
  2. Clark, Alexis J; Singh, Rajesh; Leonis, Regina L; Stahlberg, Eric A; Clark, Zachary S; Lillard, James W
  3. International Journal of Molecular Sciences. 2024, Nov 18; 25(22):
  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.   Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer's disease
  2. Qiu, Yunguang; Hou, Yuan; Gohel, Dhruv; Zhou, Yadi; Xu, Jielin; Bykova, Marina; Yang, Yuxin; Leverenz, James B; Pieper, Andrew A; Nussinov,Ruth; Caldwell, Jessica Z K; Brown, J Mark; Cheng, Feixiong
  3. Cell Reports. 2024, Apr 21; 43(5): 114128.
  1. 5.   Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients
  2. Radtke, Andrea J; Postovalova, Ekaterina; Varlamova, Arina; Bagaev, Alexander; Sorokina, Maria; Kudryashova, Olga; Meerson, Mark; Polyakova, Margarita; Galkin, Ilia; Svekolkin, Viktor; Isaev, Sergey; Wiebe, Daniil; Sharun, Anna; Sarachakov, Alexander; Perelman, Grigory; Lozinsky, Yaroslav; Yaniv, Ziv; Lowekamp, Bradley C; Speranza, Emily; Yao, Li; Pittaluga, Stefania; Shaffer, Arthur L; Jonigk, Danny; Phelan, James D; Davies-Hill, Theresa; Huang, Da Wei; Ovcharov, Pavel; Nomie, Krystle; Nuzhdina, Ekaterina; Kotlov, Nikita; Ataullakhanov, Ravshan; Fowler, Nathan; Kelly,Michael; Muppidi, Jagan; Davis, Jeremy L; Hernandez, Jonathan M; Wilson, Wyndham H; Jaffe, Elaine S; Staudt, Louis M; Roschewski, Mark; Germain, Ronald N
  3. Cancer Cell. 2024, Feb 21; 42
  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.   The trajectory patterns of single HIV-1 virus-like particle in live CD4 cells: A real time three-dimensional multi-resolution microscopy study using encapsulated nonblinking giant quantum dot
  2. Li, Wei-You; Yin, Shuhui; Huang, Szu-Wei; Yang, Ming-Hui; Chen, Patricia Mt; Wu, Shang-Rung; Welsher, Kevin; Yang, Haw; Arthur Chen, Yi-Ming
  3. Journal of Microbiology, Immunology, and Infection = Wei mian yu gan ran za zhi. 2022, Aug 28;
  1. 8.   Design and implementation of an international, multi-arm, multi-stage platform master protocol for trials of novel SARS-CoV-2 antiviral agents: Therapeutics for Inpatients with COVID-19 (TICO/ACTIV-3)
  2. Murray, Daniel D.; Babiker, Abdel G.; Baker, Jason; Barkauskas, Christina E.; Brown, Samuel M.; Chang, Christina C.; Davey, Victoria J.; Gelijns, Annetine C.; Ginde, Adit A.; Grund, Birgit; Higgs, Elizabeth; Hudson, Fleur; Kan, Virginia L.; Lane, H. Clifford; Murray, Thomas A.; Paredes, Roger; Parmar, Mahesh K. B.; Pett, Sarah; Phillips, Andrew N.; Polizzotto, Mark N.; Reilly, Cavan; Sandkovsky, Uriel; Sharma, Shweta; Teitelbaum,Marc; Thompson, B. Taylor; Young, Barnaby E.; Neaton, James D.; Lundgren, Jens D.
  3. Clinical Trials. 2021, Oct 10;
  1. 9.   Potential of substituted quinazolines to interact with multiple targets in the treatment of cancer
  2. Choudhary, Shruti; Doshi, Arpit; Luckett-Chastain, Lerin; Ihnat, Michael; Hamel,Ernest; Mooberry, Susan L.; Gangjee, Aleem
  3. Bioogranic & Medicinal Chemistry. 2021, Apr 1; 35
  1. 10.   Combined multi-band decoupling in biomolecular NMR spectroscopy
  2. Anklin, Clemens; Byrd, R. Andrew
  3. Journal of Biomolecular NMR . 2021, Mar; 75(2-3): 89-95.
  1. 11.   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. 12.   Novel Opportunity to Reverse Antibiotic Resistance: To Explore Traditional Chinese Medicine With Potential Activity Against Antibiotics-Resistance Bacteria
  2. Su, Ting; Qiu, Ye; Hua, Xuesi; Ye, Bi; Luo, Haoming; Liu, Da; Qu, Peng; Qiu, Zhidong
  3. Frontiers in microbiology. 2020, DEC 22; 11
  1. 13.   Three-Color Imaging Enables Simultaneous Screening of Multiple RNA Targets on Small Molecule Microarrays
  2. Jordan,Deondre; Yang,Mo; Schneekloth,Jay
  3. Current protocols in chemical biology. 2020, Dec; 12(4): e87.
  1. 14.   Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions
  2. Weckworth, Julie K; Davis, Brian W; Roelke-Parker,Melody; Wilkes, Rebecca P; Packer, Craig; Eblate, Ernest; Schwartz, Michael K; Mills, L Scott
  3. Pathogens (Basel, Switzerland). 2020, NOV; 9(11): E872.
  1. 15.   Multi-omics: Differential expression of IFN-? results in distinctive mechanistic features linking chronic inflammation, gut dysbiosis, and autoimmune diseases
  2. Bae,Heekyong; Leung, Patrick S C; Hodge, Deborah L; Fenimore,John; Jeon, Seon-Min; Thovarai,Vishal; Dzutsev,Amiran; Welcher, Andrew A; Boedigheimer, Michael; Damore, Michael A; Choi, Myung-Sook; Fravell, Richard A; Trinchieri,Giorgio; Gershwin, M Eric; Young,Howard
  3. Journal of autoimmunity. 2020, JUL; 111: 102436.
  1. 16.   AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
  2. Bhattacharya, Tanmoy; Brettin, Thomas; Doroshow, James H.; Evrard,Yvonne; Greenspan, Emily J.; Gryshuk, Amy L.; Hoang, Thuc T.; Lauzon, Carolyn B. Vea; Nissley,Dwight; Penberthy, Lynne; Stahlberg,Eric; Stevens, Rick; Streitz, Fred; Tourassi, Georgia; Xia, Fangfang; Zaki,George
  3. Frontiers in oncology. 2019, Oct 2; 9
  1. 17.   Evaluating the size criterion for PI-RADSv2 category 5 upgrade: is 15 mm the best threshold?
  2. An, Julie Y; Harmon, Stephanie; Mehralivand, Sherif; Czarniecki, Marcin; Smith, Clayton P; Peretti, Julie A; Wood, Bradford J; Pinto, Peter A; Choyke, Peter L; Shih, Joanna H; Turkbey, Baris
  3. Abdominal radiology (New York). 2018, Dec; 43(12): 3436-3444.
  1. 18.   Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET
  2. Huang, F.; Ma, Z.; Pollan, S.; Yuan, X.; Swartwood, S.; Gertych, A.; Rodriguez, M.; Mallick, J.; Bhele, S.; Guindi, M.; Dhall, D.; Walts, A. E.; Bose, S.; de Peralta Venturina, M.; Marchevsky, A. M.; Luthringer, D. J.; Feller, S. M.; Berman, B.; Freeman, M. R.; Alvord, W. G.; Vande Woude, G.; Amin, M. B.; Knudsen, B. S.
  3. The journal of pathology. Clinical research. 2016, Oct; 2(4): 210-222.
  1. 19.   Inhibition of multi-drug resistant HIV-1 reverse transcriptase by nucleoside beta-triphosphates
  2. Dash, C.; Ahmadibeni, Y.; Hanley, M. J.; Pandhare, J.; Gotte, M.; Le Grice, S. F. J.; Parang, K.
  3. Bioorganic & Medicinal Chemistry Letters. 2011, Jun; 21(12): 3519-3522.
  1. 20.   Documenting the location of systematic transrectal ultrasound-guided prostate biopsies: correlation with multi-parametric MRI
  2. Turkbey, B.; Xu, S.; Kruecker, J.; Locklin, J.; Pang, Y. X.; Shah, V.; Bernardo, M.; Baccala, A.; Rastinehad, A.; Benjamin, C.; Merino, M. J.; Wood, B. J.; Choyke, P. L.; Pinto, P. A.
  3. Cancer Imaging. 2011, Mar; 11(1): 31-36.
  1. 21.   Nanotechnology-Based Cancer Therapeutics-Promise and Challenge-Lessons Learned Through the NCI Alliance for Nanotechnology in Cancer
  2. Farrell, D.; Ptak, K.; Panaro, N. J.; Grodzinski, P.
  3. Pharmaceutical Research. 2011, Feb; 28(2): 273-278.
  1. 22.   Functional studies of host-specific ephrin-B ligands as Henipavirus receptors
  2. Bossart, K. N.; Tachedjian, M.; McEachern, J. A.; Crameri, G.; Zhu, Z. Y.; Dimitrov, D. S.; Broder, C. C.; Wang, L. F.
  3. Virology. 2008 372(2): 357-371.
  1. 23.   HIV-1 protease variants from 100-fold drug resistant clinical isolates: expression, purification, and crystallization
  2. Vickrey, J. F.; Logsdon, B. C.; Proteasa, G.; Palmer, S.; Winters, M. A.; Merigan, T. C.; Kovari, L. C.
  3. Protein Expression and Purification. 2003 28(1): 165-172.
  1. 24.   A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations
  2. Ivanic, J.; Ruedenberg, K.
  3. Journal of Computational Chemistry. 2003 24(10): 1250-1262.
  1. 25.   Renal transplant patients show variations in their self- reactive repertoires: a serial study
  2. Portugal, K.; Dozmorov, I.; Sidorov, I.; Marrero, I.; Fonseca, J. A.; Spadafora-Ferreira, M.; Kalil, J.; Coelho, V.
  3. International Immunology. 2001 13(6): 747-755.
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