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  1. 1.   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. 2.   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. 3.   Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline
  2. Ward, Henry N.; Aregger,Michael; Gonatopoulos Pournatzis,Thomas; Billmann, Maximilian; Ohsumi, Toshiro K.; Brown, Kevin R.; Blencowe, Benjamin J.; Moffat, Jason; Myers, Chad L.
  3. Nature protocols. 2021, Oct; 16(10): 4766-4798.
  1. 4.   An Integrated Epigenomic and Transcriptomic Map of Mouse and Human aß T Cell Development
  2. Chopp, Laura B; Gopalan, Vishaka; Ciucci, Thomas; Ruchinskas,Allison; Rae, Zachary; Lagarde, Manon; Gao, Yayi; Li, Caiyi; Bosticardo, Marita; Pala, Francesca; Livak, Ferenc; Kelly,Michael; Hannenhalli, Sridhar; Bosselut, Rémy
  3. Immunity. 2020, Dec 15; 53(6): 1182-1201.e8.
  1. 5.   Computational network biology: Data, models, and applications
  2. Liu, Chuang; Ma, Yifang; Zhao, Jing; Nussinov,Ruth; Zhang, Yi-Cheng; Cheng, Feixiong; Zhang, Zi-Ke
  3. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS. 2020, MAR 3; 846: 1-66.
  1. 6.   Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology
  2. Turner, Oliver C; Aeffner, Famke; Bangari, Dinesh S; High, Wanda; Knight, Brian; Forest, Tom; Cossic, Brieuc; Himmel, Lauren E; Rudmann, Daniel G; Bawa, Bhupinder; Muthuswamy, Anantharaman; Aina, Olulanu H; Edmondson,Elijah; Saravanan, Chandrassegar; Brown, Danielle L; Sing, Tobias; Sebastian, Manu M
  3. Toxicologic pathology. 2019, Oct 23; 192623319881401.
  1. 7.   Transmission Dynamics of HIV Subtype A in Tel Aviv, Israel: Implications for HIV Spread and Eradication
  2. Grossman,Zehava; Avidor, Boaz; Girshengoren, Shirley; Katchman, Eugene; Maldarelli,Frank; Turner, Dan
  3. Open forum infectious diseases. 2019, Jul; 6(7): pii: ofz304..
  1. 8.   A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution
  2. Shelley, Mee Y.; SeIvan, Myvizhi Esai; Zhao, Jun; Babin, Volodymyr; Liao, Chenyi; Li, Jianing; Shelley, John C.
  3. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2017, Aug; 13(8): 3881-3897.
  1. 9.   Bridging epigenetics and metabolism: role of non-essential amino acids
  2. Phang, J. M.; Liu, W.; Hancock, C.
  3. Epigenetics. 2013, Mar; 8(3): 231-6.
  1. 10.   Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways
  2. Nussinov, R.
  3. British Journal of Pharmacology. 2012, Apr; 165(7): 2110-2112.
  1. 11.   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. 12.   Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review
  2. Csermely, P.; Sandhu, K. S.; Hazai, E.; Hoksza, Z.; Kiss, H. J. M.; Miozzo, F.; Veres, D. V.; Piazza, F.; Nussinov, R.
  3. Current Protein & Peptide Science. 2012, Feb; 13(1): 19-33.
  1. 13.   Controlled biodegradation of Self-assembling beta-hairpin Peptide hydrogels by proteolysis with matrix metalloproteinase-13
  2. Giano, M. C.; Pochan, D. J.; Schneider, J. P.
  3. Biomaterials. 2011, Sep; 32(27): 6471-6477.
  1. 14.   Isolated and Skeptical: Social Engagement and Trust in Information Sources Among Smokers
  2. Rutten, L. J. F.; Blake, K.; Hesse, B. W.; Ackerson, L. K.
  3. Journal of Cancer Education. 2011, Sep; 26(3): 465-473.
  1. 15.   Enhanced Mechanical Rigidity of Hydrogels Formed from Enantiomeric Peptide Assemblies
  2. Nagy, K. J.; Giano, M. C.; Jin, A.; Pochan, D. J.; Schneider, J. P.
  3. Journal of the American Chemical Society. 2011, Sep; 133(38): 14975-14977.
  1. 16.   A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
  2. Luna, A.; Karac, E. I.; Sunshine, M.; Chang, L.; Nussinov, R.; Aladjem, M. I.; Kohn, K. W.
  3. Bmc Bioinformatics. 2011, May; 12: 13.
  1. 17.   Comparison of Strong Cation Exchange and SDS-PAGE Fractionation for Analysis of Multiprotein Complexes
  2. Das, S.; Bosley, A. D.; Ye, X. Y.; Chan, K. C.; Chu, I.; Green, J. E.; Issaq, H. J.; Veenstra, T. D.; Andresson, T.
  3. Journal of Proteome Research. 2010, Dec; 9(12): 6696-6704.
  1. 18.   Tumor antigen analysis in neuroblastoma by serological interrogation of bioinformatic data
  2. Kohler, M. E.; Johnson, B. D.; Palen, K.; Chen, Q. R.; Khan, J.; Orentas, R. J.
  3. Cancer Science. 2010, Nov; 101(11): 2316-2324.
  1. 19.   Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
  2. Csermely, P.; Palotai, R.; Nussinov, R.
  3. Trends in Biochemical Sciences. 2010, Oct; 35(10): 539-546.
  1. 20.   The molecular pathology of cancer
  2. Harris, T. J. R.; McCormick, F.
  3. Nature Reviews Clinical Oncology. 2010, May; 7(5): 251-265.
  1. 21.   Hematopoietic Immortalizing Function of the NKL-Subclass Homeobox Gene TLX1
  2. Renn, L. A. Z.; Hawley, T. S.; Burkett, S.; Ramezani, A.; Riz, I.; Adlers, R. L.; Hickstein, D. D.; Hawley, R. G.
  3. Genes Chromosomes & Cancer. 2010, Feb; 49(2): 119-131.
  1. 22.   Energetic determinants of protein binding specificity: Insights into protein interaction networks
  2. Carbonell, P.; Nussinov, R.; del Sol, A.
  3. Proteomics. 2009 9(7): 1744-1753.
  1. 23.   Improving clinical research and cancer care delivery in community settings: evaluating the NCI community cancer centers program
  2. Clauser, S. B.; Johnson, M. R.; O'Brien, D. M.; Beveridge, J. M.; Fennell, M. L.; Kaluzny, A. D.
  3. Implementation Science. 2009 4 AR 63
  1. 24.   Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms
  2. Tsai, C. J.; del Sol, A.; Nussinov, R.
  3. Molecular Biosystems. 2009 5(3): 207-216.
  1. 25.   microRNA Profiling Identifies Cancer-Specific and Prognostic Signatures in Pediatric Malignancies
  2. Wei, J. S.; Johansson, P.; Chen, Q. R.; Song, Y. K.; Durinck, S.; Wen, X. Y.; Cheuk, A.; Smith, M. A.; Houghton, P.; Morton, C.; Khan, J.
  3. Clinical Cancer Research. 2009 15(17): 5560-5568.
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