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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.   Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage ? and Its Host, Escherichia coli
  2. Thomason,Lynn; Court,Don
  3. PHAGE (New Rochelle, N.Y.). 2022, Sep 01; 3(3): 153-164.
  1. 6.   QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
  2. Mehta, Raghav; Filos, Angelos; Baid, Ujjwal; Sako, Chiharu; McKinley, Richard; Rebsamen, Michael; Dätwyler, Katrin; Meier, Raphael; Radojewski, Piotr; Murugesan, Gowtham Krishnan; Nalawade, Sahil; Ganesh, Chandan; Wagner, Ben; Yu, Fang F; Fei, Baowei; Madhuranthakam, Ananth J; Maldjian, Joseph A; Daza, Laura; Gómez, Catalina; Arbeláez, Pablo; Dai, Chengliang; Wang, Shuo; Reynaud, Hadrien; Mo, Yuanhan; Angelini, Elsa; Guo, Yike; Bai, Wenjia; Banerjee, Subhashis; Pei, Linmin; Ak, Murat; Rosas-González, Sarahi; Zemmoura, Ilyess; Tauber, Clovis; Vu, Minh H; Nyholm, Tufve; Löfstedt, Tommy; Ballestar, Laura Mora; Vilaplana, Veronica; McHugh, Hugh; Maso Talou, Gonzalo; Wang, Alan; Patel, Jay; Chang, Ken; Hoebel, Katharina; Gidwani, Mishka; Arun, Nishanth; Gupta, Sharut; Aggarwal, Mehak; Singh, Praveer; Gerstner, Elizabeth R; Kalpathy-Cramer, Jayashree; Boutry, Nicolas; Huard, Alexis; Vidyaratne, Lasitha; Rahman, Md Monibor; Iftekharuddin, Khan M; Chazalon, Joseph; Puybareau, Elodie; Tochon, Guillaume; Ma, Jun; Cabezas, Mariano; Llado, Xavier; Oliver, Arnau; Valencia, Liliana; Valverde, Sergi; Amian, Mehdi; Soltaninejad, Mohammadreza; Myronenko, Andriy; Hatamizadeh, Ali; Feng, Xue; Dou, Quan; Tustison, Nicholas; Meyer, Craig; Shah, Nisarg A; Talbar, Sanjay; Weber, Marc-André; Mahajan, Abhishek; Jakab, Andras; Wiest, Roland; Fathallah-Shaykh, Hassan M; Nazeri, Arash; Milchenko, Mikhail; Marcus, Daniel; Kotrotsou, Aikaterini; Colen, Rivka; Freymann,John; Kirby,Justin; Davatzikos, Christos; Menze, Bjoern; Bakas, Spyridon; Gal, Yarin; Arbel, Tal
  3. The journal of Machine Learning for Biomedical Imaging. 2022, Aug; 2022
  1. 7.   QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
  2. Mehta, Raghav; Filos, Angelos; Baid, Ujjwal; Sako, Chiharu; McKinley, Richard; Rebsamen, Michael; Dätwyler, Katrin; Meier, Raphael; Radojewski, Piotr; Murugesan, Gowtham Krishnan; Nalawade, Sahil; Ganesh, Chandan; Wagner, Ben; Yu, Fang F; Fei, Baowei; Madhuranthakam, Ananth J; Maldjian, Joseph A; Daza, Laura; Gómez, Catalina; Arbeláez, Pablo; Dai, Chengliang; Wang, Shuo; Reynaud, Hadrien; Mo, Yuanhan; Angelini, Elsa; Guo, Yike; Bai, Wenjia; Banerjee, Subhashis; Pei, Linmin; Ak, Murat; Rosas-González, Sarahi; Zemmoura, Ilyess; Tauber, Clovis; Vu, Minh H; Nyholm, Tufve; Löfstedt, Tommy; Ballestar, Laura Mora; Vilaplana, Veronica; McHugh, Hugh; Maso Talou, Gonzalo; Wang, Alan; Patel, Jay; Chang, Ken; Hoebel, Katharina; Gidwani, Mishka; Arun, Nishanth; Gupta, Sharut; Aggarwal, Mehak; Singh, Praveer; Gerstner, Elizabeth R; Kalpathy-Cramer, Jayashree; Boutry, Nicolas; Huard, Alexis; Vidyaratne, Lasitha; Rahman, Md Monibor; Iftekharuddin, Khan M; Chazalon, Joseph; Puybareau, Elodie; Tochon, Guillaume; Ma, Jun; Cabezas, Mariano; Llado, Xavier; Oliver, Arnau; Valencia, Liliana; Valverde, Sergi; Amian, Mehdi; Soltaninejad, Mohammadreza; Myronenko, Andriy; Hatamizadeh, Ali; Feng, Xue; Dou, Quan; Tustison, Nicholas; Meyer, Craig; Shah, Nisarg A; Talbar, Sanjay; Weber, Marc-André; Mahajan, Abhishek; Jakab, Andras; Wiest, Roland; Fathallah-Shaykh, Hassan M; Nazeri, Arash; Milchenko, Mikhail; Marcus, Daniel; Kotrotsou, Aikaterini; Colen, Rivka; Freymann,John; Kirby,Justin; Davatzikos, Christos; Menze, Bjoern; Bakas, Spyridon; Gal, Yarin; Arbel, Tal
  3. The Journal of Machine Learning for Biomedical Imaging. 2022, Aug; 2022
  1. 8.   Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis
  2. Dharavath,Sudhaker; Shaw,Gary; Ji,Xinhua
  3. RNA Biology. 2022, Jan; 19(1): 908-915.
  1. 9.   A Pilot Study of Dynamic 18F-DCFPyL PET/CT Imaging of Prostate Adenocarcinoma in High-Risk Primary Prostate Cancer Patients
  2. Lu, Michelle; Lindenberg, Liza; Mena, Esther; Turkbey, Baris; Seidel,Jurgen; Ton, Anita; McKinney, Yolanda; Eclarinal, Philip; Merino, Maria; Pinto, Peter; Choyke, Peter; Adler,Stephen
  3. Molecular Imaging and Biology. 2021, Nov 01;
  1. 10.   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. 11.   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. 12.   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. 13.   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. 14.   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. 15.   Predicting RNA SHAPE scores with deep learning
  2. Bliss, Noah; Bindewald,Eckart; Shapiro,Bruce
  3. RNA biology. 2020, JUN 1; 1-7.
  1. 16.   Dynamic F-18-DCFPyL PET/CT imaging of biopsy-proven high-risk primary prostate cancer patients
  2. Lu, Michelle; Adler,Stephen; Lindenberg, Maria Liza; Mena, Esther; Turkbey, Ismail; Seidel, Jurgen; Choyke, Peter
  3. JOURNAL OF NUCLEAR MEDICINE. 2020, MAY 1; 61(Supp.1):
  1. 17.   Dynamic F-18-DCFPyL PET/CT imaging of biopsy-proven high-risk primary prostate cancer patients
  2. Lu, Michelle; Adler,Stephen; Lindenberg, Maria Liza; Mena, Esther; Turkbey, Ismail; Seidel, Jurgen; Choyke, Peter
  3. JOURNAL OF NUCLEAR MEDICINE. 2020, MAY 1; 61(1Supp. ):
  1. 18.   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. 19.   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. 20.   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. 21.   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. 22.   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. 23.   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. 24.   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. 25.   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.
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