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  1. 1.   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. 2.   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. 3.   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. 4.   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. 5.   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. 6.   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. 7.   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. 8.   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. 9.   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.
  1. 10.   Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities
  2. Vasaikar, Suhas; Huang, Chen; Wang, Xiaojing; Petyuk, Vladislav A.; Savage, Sara R.; Wen, Bo; Dou, Yongchao; Zhang, Yun; Shi, Zhiao; Arshad, Osama A.; Gritsenko, Marina A.; Zimmerman, Lisa J.; McDermott, Jason E.; Clauss, Therese R.; Moore, Ronald J.; Zhao, Rui; Monroe, Matthew E.; Wang, Yi-Ting; Chambers, Matthew C.; Slebos, Robbert J. C.; Lau, Ken S.; Mo, Qianxing; Ding, Li; Ellis, Matthew; Thiagarajan,Mathangi; Kinsinger, Christopher R.; Rodriguez, Henry; Smith, Richard D.; Rodland, Karin D.; Liebler, Daniel C.; Liu, Tao; Zhang, Bing; Ellis, Matthew J. C.; Bavarva, Jasmin; Borucki, Melissa; Elburn, Kimberly; Hannick, Linda; Vatanian, Negin; Payne, Samuel H.; Carr, Steven A.; Clauser, Karl R.; Gillette, Michael A.; Kuhn, Eric; Mani, D. R.; Cai, Shuang; Ketchum, Karen A.; Thangudu, Ratna R.; Whiteley, Gordon A.; Paulovich, Amanda; Whiteaker, Jeff; Edward, Nathan J.; Madhavan, Subha; McGarvey, Peter B.; Chan, Daniel W.; Shih, Ie-Ming; Zhang, Hui; Zhang, Zhen; Zhu, Heng; Skates, Steven J.; White, Forest M.; Mertins, Philip; Pandey, Akhilesh; Slebos, Robert J. C.; Boja, Emily; Hiltke, Tara; Kinsinger, Christopher R.; Mesri, Mehdi; Rivers, Robert C.; Stein, Stephen E.; Fenyo, David; Ruggles, Kelly; Levine, Douglas A.; Oberti, Mauricio; Rudnick, Paul A.; Snyder, Michael; Tabb, David L.; Zhao, Yingming; Chen, Xian; Ransohoff, David F.; Hoofnagle, Andrew; Sanders, Melinda E.; Wang, Yue; Davies, Sherri R.; Townsend, R. Reid; Watson, Mark
  3. CELL. 2019, May 2; 177(4): 1035-1049.e19.
  1. 11.   A close look onto structural models and primary ligands of metallo-beta-plactamases
  2. Raczynska, Joanna E.; Shabalin, Ivan G.; Minor, Wladek; Wlodawer,Alexander; Jaskolski, Mariusz
  3. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy. 2018, Sep; 40: 1-12.
  1. 12.   Chemoinformatics at the CADD Group of the National Cancer Institute
  2. Peach,Megan; Nicklaus,Marc
  3. Applied Chemoinformatics: Achievements and Future Opportunities. 2018; 385-393.
  1. 13.   Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations
  2. Karcher, Sandra; Willighagen, Egon L.; Rumble, John; Ehrhart, Friederike; Evelo, Chris T.; Fritts, Martin; Gaheen, Sharon; Harper, Stacey L.; Hoover, Mark D.; Jeliazkova, Nina; Lewinski, Nastassja; Robinson, Richard L. Marchese; Mills, Karmann C.; Mustad, Axel P.; Thomas, Dennis G.; Tsiliki, Georgia; Hendren, Christine Ogilvie
  3. NanoImpact. 2018, Jan; 9: 85-101.
  1. 14.   Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
  2. Tuncbag, N.; Keskin, O.; Nussinov, R.; Gursoy, A.
  3. Proteins-Structure Function and Bioinformatics. 2012, Apr; 80(4): 1239-1249.
  1. 15.   PDB Ligand Conformational Energies Calculated Quantum-Mechanically
  2. Sitzmann, M.; Weidlich, I. E.; Filippov, I. V.; Liao, C.; Peach, M. L.; Ihlenfeldt, W. D.; Karki, R. G.; Borodina, Y. V.; Cachau, R. E.; Nicklaus, M. C.
  3. Journal of Chemical Information and Modeling. 2012, Mar; 52(3): 739-756.
  1. 16.   GWASdb: a database for human genetic variants identified by genome-wide association studies
  2. Li, M. L. J.; Wang, P. W.; Liu, X. R.; Lim, E. L.; Wang, Z. Y.; Yeager, M.; Wong, M. P.; Sham, P. C.; Chanock, S. J.; Wang, J. W.
  3. Nucleic Acids Research. 2012, Jan; 40(D1): D1047-D1054.
  1. 17.   Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
  2. Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O.
  3. Nature Protocols. 2011, Sep; 6(9): 1341-1354.
  1. 18.   Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement
  2. Cohen-Gihon, I.; Sharan, R.; Nussinov, R.
  3. Physical Biology. 2011, Jun; 8(3): 9.
  1. 19.   Evolution of domain promiscuity in eukaryotic genomes-a perspective from the inferred ancestral domain architectures
  2. Cohen-Gihon, I.; Fong, J. H.; Sharan, R.; Nussinov, R.; Przytycka, T. M.; Panchenko, A. R.
  3. Molecular Biosystems. 2011, Mar 1; 7(3): 784-792.
  1. 20.   Genetic Associations of Variants in Genes Encoding HIV-Dependency Factors Required for HIV-1 Infection
  2. Chinn, L. W.; Tang, M. Z.; Kessing, B. D.; Lautenberger, J. A.; Troyer, J. L.; Malasky, M. J.; McIntosh, C.; Kirk, G. D.; Wolinsky, S. M.; Buchbinder, S. P.; Gomperts, E. D.; Goedert, J. J.; O'Brien, S. J.
  3. Journal of Infectious Diseases. 2010, Dec; 202(12): 1836-1845.
  1. 21.   Unmet challenges of structural genomics
  2. Chruszcz, M.; Domagalski, M.; Osinski, T.; Wlodawer, A.; Minor, W.
  3. Current Opinion in Structural Biology. 2010, Oct; 20(5): 587-597.
  1. 22.   Gene duplications in prokaryotes can be associated with environmental adaptation
  2. Bratlie, M. S.; Johansen, J.; Sherman, B. T.; Huang, D. W.; Lempicki, R. A.; Drablos, F.
  3. Bmc Genomics. 2010, Oct; 11: 17.
  1. 23.   CCRXP: exploring clusters of conserved residues in protein structures
  2. Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2010, Jul; 38: W398-W401.
  1. 24.   Tautomerism in large databases
  2. Sitzmann, M.; Ihlenfeldt, W. D.; Nicklaus, M. C.
  3. Journal of Computer-Aided Molecular Design. 2010, Jun; 24(6-7): 521-551.
  1. 25.   mRNA and microRNA Expression Profiles of the NCI-60 Integrated with Drug Activities
  2. Liu, H. F.; D'Andrade, P.; Fulmer-Smentek, S.; Lorenzi, P.; Kohn, K. W.; Weinstein, J. N.; Pommier, Y.; Reinhold, W. C.
  3. Molecular Cancer Therapeutics. 2010, May; 9(5): 1080-1091.
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