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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.   Gene network landscape of mouse splenocytes reveals integrin complex as the A151 ODN-responsive hub molecule in the immune transcriptome
  2. Yazar, Volkan; Yilmaz, Ismail Cem; Bulbul, Artun; Klinman, Dennis M; Gursel, Ihsan
  3. Molecular Therapy. Nucleic Acids. 2023, Mar 14; 31: 553-565.
  1. 3.   Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
  2. Xu, Junlin; Xu, Jielin; Meng, Yajie; Lu, Changcheng; Cai, Lijun; Zeng, Xiangxiang; Nussinov,Ruth; Cheng, Feixiong
  3. Cell Reports Methods. 2023, Jan 23; 3(1): 100382.
  1. 4.   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. 5.   Mechanism of activation and the rewired network: New drug design concepts
  2. Nussinov,Ruth; Zhang,Mingzhen; Maloney, Ryan; Tsai,Chung-Jung; Yavuz, Bengi Ruken; Tuncbag, Nurcan; Jang, Hyunbum
  3. Medicinal research reviews. 2021, Oct 25; 0198-6325:
  1. 6.   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. 7.   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. 8.   Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing
  2. Fang, Jiansong; Pieper, Andrew A.; Nussinov,Ruth; Lee, Garam; Bekris, Lynn; Leverenz, James B.; Cummings, Jeffrey; Cheng, Feixiong
  3. Medicinal research reviews. 2020, NOV; 40(6): 2386-2426.
  1. 9.   Promoting evidence-based practices for breast cancer care through web-based collaborative learning
  2. Cira,Mishka; Tesfay, R; Zujewski, J A; Sinulingga, D T; Aung, S; Mwakatobe, K; Lasebikan, N; Nkegoum, B; Duncan, K; Dvaladze, A
  3. Journal of cancer policy. 2020, Sep; 25: pii: 100242.
  1. 10.   Predicting RNA SHAPE scores with deep learning
  2. Bliss, Noah; Bindewald,Eckart; Shapiro,Bruce
  3. RNA biology. 2020, JUN 1; 1-7.
  1. 11.   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. 12.   Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry
  2. Guven Maiorov,Emine; Tsai,Chung-Jung; Nussinov,Ruth
  3. Frontiers in oncology. 2019, Nov 15; 9: 1236.
  1. 13.   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. 14.   High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
  2. Johnston, Michael J.; Nikolic, Ana; Ninkovic, Nicoletta; Guilhamon, Paul; Cavalli, Florence M. G.; Seaman,Steven; Zemp, Franz J.; Lee, John; Abdelkareem, Aly; Ellestad, Katrina; Murison, Alex; Kushida, Michelle M.; Coutinho, Fiona J.; Ma, Yussanne; Mungall, Andrew J.; Moore, Richard; Marra, Marco A.; Taylor, Michael D.; Dirks, Peter B.; Pugh, Trevor J.; Morrissy, Sorana; St Croix,Brad; Mahoney, Douglas J.; Lupien, Mathieu; Gallo, Marco
  3. GENOME RESEARCH. 2019, AUG; 29(8): 1211-1222.
  1. 15.   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. 16.   Allostery in Its Many Disguises: From Theory to Applications
  2. Wodak, Shoshana J.; Paci, Emanuele; Dokholyan, Nikolay; Berezovsky, Igor N.; Horovitz, Amnon; Li, Jing; Hilser, Vincent J.; Behar, Ivet; Karanicolas, John; Stock, Gerhard; Hamm, Peter; Stote, Roland H.; Eberhardt, Jerome; Chebaro, Yassmine; Dejaegere, Annick; Cecchini, Marco; Changeux, Jean-Pierre; Bolhuis, Peter G.; Vreede, Jocelyne; Faccioli, Pietro; Orioli, Simone; Ravasio, Riccardo; Yen, Le; Brito, Carolina; Wyart, Matthieu; Gkeka, Paraskevi; Rivalta, Ivan; Palermo, Giulia; Mccammon, J. Andrew; Panecka-Hofman, Joanna; Wade, Rebecca C.; Di Pizio, Antonella; Niv, Masha Y.; Nussinov,Ruth; Tsai,Chung-Jung; Jang,Hyunbum; Padhorny, Dzmitry; Kozakov, Dima; Mcleish, Tom
  3. Structure (London, England : 1993). 2019, Apr 2; 27(4): 566-578.
  1. 17.   Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer
  2. Guven-Maiorov, Emine; Tsai, Chung-Jung; Ma, Buyong; Nussinov, Ruth
  3. Journal of molecular biology. 2017, Dec 8; 429(24): 3925-3941.
  1. 18.   Triggered Formation of Anionic Hydrogels from Self-Assembling Acidic Peptide Amphiphiles
  2. Sinthuvanich, Chomdao; Nagy-Smith, Katelyn J.; Walsh, Scott; Schneider, Joel
  3. Macromolecules. 2017, Aug 08; 50(15): 5643-5651.
  1. 19.   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. 20.   Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains.
  2. Zhao, Jun; Nussinov, Ruth; Ma, Buyong
  3. Protein engineering, design & selection: PEDS. 2017, Jan; 30(1): 67-76.
  1. 21.   Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
  2. Kim, Taejin; Kasprzak, Wojciech; Shapiro, Bruce
  3. Methods in molecular biology (Clifton, N.J.). 2017 1632: 33-64.
  1. 22.   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. 23.   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. 24.   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. 25.   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.
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