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  1. 1.   Development of a multiassay algorithm (MAA) to identify recent HIV infection in newly diagnosed individuals in Indonesia
  2. Wulan, Wahyu Nawang; Yunihastuti, Evy; Arlinda, Dona; Merati, Tuti Parwati; Wisaksana, Rudi; Lokida, Dewi; Grossman, Zehava; Huik, Kristi; Lau,Chuen-Yen; Susanto, Nugroho Harry; Kosasih, Herman; Aman, Abu Tholib; Ang, Sunarto; Evalina, Rita; Ayu Yuli Gayatri, Anak Agung; Hayuningsih, Chakrawati; Indrati, Agnes Rengga; Kumalawati, July; Mutiawati, Vivi Keumala; Realino Nara, Mario Bernardinus; Nurulita, Asvin; Rahmawati, Rahmawati; Rusli, Adria; Rusli, Musofa; Sari, Dewi Yennita; Sembiring, Justina; Udji Sofro, Muchlis Achsan; Susanti, Wiwi Endang; Tandraeliene, Janice; Tanzil, Fransisca Lianiwati; Neal, Aaron; Karyana, Muhammad; Sudarmono, Pratiwi; Maldarelli, Frank
  3. iScience. 2023, Oct 20; 26(10): 107986.
  1. 2.   Automated Computational Detection, Quantitation, and Mapping of Mitosis in Whole-Slide Images for Clinically Actionable Surgical Pathology Decision Support
  2. Puri, Munish; Hoover, Shelley B; Hewitt, Stephen M; Wei,Bih; Adissu, Hibret Amare; Halsey, Charles H C; Beck, Jessica; Bradley, Charles; Cramer, Sarah D; Durham, Amy C; Esplin, D Glen; Frank, Chad; Lyle, L Tiffany; McGill, Lawrence D; Sánchez, Melissa D; Schaffer, Paula A; Traslavina, Ryan P; Buza, Elizabeth; Yang, Howard H; Lee, Maxwell P; Dwyer, Jennifer E; Simpson, R Mark
  3. Journal of pathology informatics. 2019, Feb; 10: 4.
  1. 3.   Can computer-aided diagnosis assist in the identification of prostate cancer on prostate MRI? a multi-center, multi-reader investigation
  2. Gaur, Sonia; Lay, Nathan; Harmon,Stephanie; Doddakashi, Sreya; Mehralivand, Sherif; Argun, Burak; Barrett, Tristan; Bednarova, Sandra; Girometti, Rossanno; Karaarslan, Ercan; Kural, Ali Riza; Oto, Aytekin; Purysko, Andrei S; Antic, Tatjana; Magi-Galluzzi, Cristina; Saglican, Yesim; Sioletic, Stefano; Warren, Anne Y; Bittencourt, Leonardo; Fütterer, Jurgen J; Gupta, Rajan T; Kabakus, Ismail; Law, Yan Mee; Margolis, Daniel J; Shebel, Haytham; Westphalen, Antonio C; Wood, Bradford J; Pinto, Peter A; Shih, Joanna H; Choyke, Peter L; Summers, Ronald M; Turkbey, Baris
  3. Oncotarget. 2018, Sep 18; 9(73): 33804-33817.
  1. 4.   LUNGx Challenge for computerized lung nodule classification.
  2. Armato, Samuel G; Drukker, Karen; Li, Feng; Hadjiiski, Lubomir; Tourassi, Georgia D; Engelmann, Roger M; Giger, Maryellen L; Redmond, George; Farahani, Keyvan; Kirby, Justin S; Clarke, Laurence P
  3. Journal of medical imaging (Bellingham, Wash.). 2016, Oct; 3(4): 044506.
  1. 5.   MPGAfold in dengue secondary structure prediction
  2. Kasprzak, W. K.; Shapiro, B. A.
  3. Methods in molecular biology (Clifton, N.J.). 2014, 20-Feb; 1138: 199-224.
  1. 6.   Segmentation and quantitative analysis of individual cells in developmental tissues
  2. Nandy, K.; Kim, J.; McCullough, D. P.; McAuliffe, M.; Meaburn, K. J.; Yamaguchi, T. P.; Gudla, P. R.; Lockett, S. J.
  3. Methods in molecular biology (Clifton, N.J.). 2014 1092: 235-53.
  1. 7.   Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape
  2. Lee, J. S.; Ruell, E. W.; Boydston, E. E.; Lyren, L. M.; Alonso, R. S.; Troyer, J. L.; Crooks, K. R.; Vande Woude, S.
  3. Molecular Ecology. 2012, Apr; 21(7): 1617-1631.
  1. 8.   A method for correlating in vivo prostate magnetic resonance imaging and histopathology using individualized magnetic resonance-based molds
  2. Shah, V.; Pohida, T.; Turkbey, B.; Mani, H.; Merino, M.; Pinto, P. A.; Choyke, P.; Bernardo, M.
  3. The Review of scientific instruments. 2009, Oct; 80(10): 104301.
  1. 9.   IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
  2. Cer, R. Z.; Mudunuri, U.; Stephens, R.; Lebeda, F. J.
  3. Nucleic Acids Research. 2009 37(Web Server issue): W441-W445.
  1. 10.   Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation
  2. Feng, H. Q.; Jenkins, L.; Durell, S. R.; Hayashi, R.; Mazur, S. J.; Cherry, S.; Tropea, J. E.; Miller, M.; Wlodawer, A.; Appella, E.; Bai, Y.
  3. Structure. 2009 17(2): 202-210.
  1. 11.   Computer Simulated Screening of Dentin Bonding Primer Monomers Through Analysis of Their Chemical Functions and Their Spatial 3D Alignment
  2. Vaidyanathan, J.; Vaidlyanathan, T. K.; Ravich, ran
  3. Journal of Biomedical Materials Research Part B-applied Biomaterials. 2009 88B(2): 447-457.
  1. 12.   The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics
  2. Antunes, A.; Troyer, J. L.; Roelke, M. E.; Pecon-Slattery, J.; Packer, C.; Winterbach, C.; Winterbach, H.; Hemson, G.; Frank, L.; Stander, P.; Siefert, L.; Driciru, M.; Funston, P. J.; Alexander, K. A.; Prager, K. C.; Mills, G.; Wildt, D.; Bush, M.
  3. Plos Genetics. 2008 4(11):
  1. 13.   Estimation of the bottleneck size in Florida panthers
  2. Culver, M.; Hedrick, P. W.; Murphy, K.; O'Brien, S.; Hornocker, M. G.
  3. Animal Conservation. 2008 11(2): 104-110.
  1. 14.   Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design
  2. Liu, J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2008 105(3): 901-906.
  1. 15.   Internet resources integrating many small-molecule databases
  2. Sitzmann, M.; Filippov, I. V.; Nicklaus, M. C.
  3. SAR and QSAR in Environmental Research. 2008 19(1-2): 1-9.
  1. 16.   Virtual screening application of a model of full-length HIV-1 integrase complexed with viral DNA
  2. Liao, C. Z.; Karki, R. G.; March, C.; Pommier, Y.; Nicklaus, M. C.
  3. Bioorganic & Medicinal Chemistry Letters. 2007, Oct; 17(19): 5361-5365.
  1. 17.   Coarse-grained representation of beta-helical protein building blocks
  2. Curco, D.; Nussinov, R.; Aleman, C.
  3. Journal of Physical Chemistry B. 2007, Sep; 111(35): 10538-10549.
  1. 18.   Bridging the gap in RNA structure prediction
  2. Shapiro, B. A.; Yingling, Y. G.; Kasprzak, W.; Bindewald, E.
  3. Current Opinion in Structural Biology. 2007, Apr; 17(2): 157-165.
  1. 19.   Characterization and comparison of galactomannan enzyme immunoassay and quantitative real-time PCR assay for detection of Aspergillus fumigatus in bronchoalveolar lavage fluid from experimental invasive pulmonary aspergillosis
  2. Francesconi, A.; Kasai, M.; Petraitiene, R.; Petraitis, V.; Kelaher, A. M.; Schaufele, R.; Hope, W. W.; Shea, Y. R.; Bacher, J.; Walsh, T. J.
  3. Journal of Clinical Microbiology. 2006, Jul; 44(7): 2475-2480.
  1. 20.   De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs
  2. Haspel, N.; Zanuy, D.; Aleman, C.; Wolfson, H.; Nussinov, R.
  3. Structure. 2006, Jul; 14(7): 1137-1148.
  1. 21.   Computational intelligence, bioinformatics and computational biology: A brief overview of methods, problems and perspectives
  2. Kasabov, N.; Sidorov, I. A.; Dimitrov, D. S.
  3. Journal of Computational and Theoretical Nanoscience. 2005, DEC; 2(4): 473-491.
  1. 22.   Qualitative assessment Of IC50 values of inhibitors of the neuronal nicotinic acetylcholine receptor using a single chromatographic experiment and multivariate cluster analysis
  2. Jozwiak, K.; Moaddel, R.; Yamaguchi, R.; Ravichandran, S.; Collins, J. R.; Wainer, I. W
  3. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences. 2005, MAY 5; 819(1): 169-174.
  1. 23.   Structural and functional analysis of the RNA transport element, a member of an extensive family present in the mouse genome
  2. Smulevitch, S.; Michalowski, D.; Zolotukhin, A. S.; Schneider, R.; Bear, J.; Roth, P.; Pavlakis, G. N.; Felber, B. K.
  3. Journal of Virology. 2005, FEB; 79(4): 2356-2365.
  1. 24.   Discovery of protein substructures in EM maps
  2. Lasker, K.; Dror, O.; Nussinov, R.; Wolfson, H.
  3. Algorithms in bioinformatics. 2005; 3692 : 423-434.
  1. 25.   MAPPIS: Multiple 3D alignment of protein-protein interfaces
  2. Shulman-Peleg, A.; Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Computational Life Sciences. 2005; 3695 : 91-103.
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