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  1. 1.   Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
  2. Talsania,Keyur; Shen,Tsai-Wei; Chen, Xiongfong; Jaeger, Erich; Li, Zhipan; Chen, Zhong; Chen, Wanqiu; Tran,Bao; Kusko, Rebecca; Wang, Limin; Pang, Andy Wing Chun; Yang, Zhaowei; Choudhari, Sulbha; Colgan, Michael; Fang, Li Tai; Carroll, Andrew; Shetty,Jyoti; Kriga,Yuliya; German,Oksana; Smirnova,Tatyana; Liu, Tiantain; Li, Jing; Kellman, Ben; Hong, Karl; Hastie, Alex R; Natarajan, Aparna; Moshrefi, Ali; Granat, Anastasiya; Truong, Tiffany; Bombardi, Robin; Mankinen, Veronnica; Meerzaman, Daoud; Mason, Christopher E; Collins, Jack; Stahlberg, Eric; Xiao, Chunlin; Wang, Charles; Xiao, Wenming; Zhao,Yongmei
  3. Genome Biology. 2022, Dec 13; 23(1): 255.
  1. 2.   Elevated basal serum tryptase: disease distribution and variability in a regional health system
  2. Waters, Aubri M; Park, Hyun J; Weskamp, Andrew L; Mateja,Allyson; Kachur, Megan E; Lyons, Jonathan J; Rosen, Benjamin J; Boggs, Nathan A
  3. The Journal of Allergy and Clinical Immunology. 2022, Jan 12; 10(9): 2424.
  1. 3.   A practical guide to large-scale docking
  2. Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun; Webb, Chase M.; Stein, Reed M.; Fink, Elissa A.; Balius,Trent; Carlsson, Jens; Irwin, John J.; Shoichet, Brian K.
  3. Nature protocols. 2021, Oct; 16(10): 4799-4832.
  1. 4.   SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach
  2. Wang,Mingyi; Luo,Wen; Jones,Kristine; Bian, Xiaopeng; Williams,Russell; Higson,Herbert; Wu,Dongjing; Hicks,Belynda; Yeager,Meredith; Zhu,Bin
  3. Scientific reports. 2020, Jul 30; 10(1): 12898.
  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.   Multistrand RNA Secondary Structure Prediction and Nanostructure Design Including Pseudoknots
  2. Bindewald, E.; Afonin, K.; Jaeger, L.; Shapiro, B. A.
  3. Acs Nano. 2011, Dec; 5(12): 9542-9551.
  1. 7.   SymmRef: A flexible refinement method for symmetric multimers
  2. Mashiach-Farkash, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2011, Sep; 79(9): 2607-2623.
  1. 8.   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. 9.   Identification of Cis-Acting Elements in the 3 '-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication
  2. Manzano, M.; Reichert, E. D.; Polo, S.; Falgout, B.; Kasprzak, W.; Shapiro, B. A.; Padmanabhan, R.
  3. Journal of Biological Chemistry. 2011, Jun; 286(25): 22521-22534.
  1. 10.   CyloFold: secondary structure prediction including pseudoknots
  2. Bindewald, E.; Kluth, T.; Shapiro, B. A.
  3. Nucleic Acids Research. 2010, Jul; 38: W368-W372.
  1. 11.   FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking
  2. Mashiach, E.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2010, Jul; 38: W457-W461.
  1. 12.   Feature Identification via a Combined ICA-Wavelet Method for Image Information Mining
  2. Shah, V. P.; Younan, N. H.; Durbha, S. S.; King, R. L.
  3. Ieee Geoscience and Remote Sensing Letters. 2010, Jan; 7(1): 18-22.
  1. 13.   An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells
  2. Shiao, Y. H.; Lupascu, S. T.; Gu, Y. D.; Kasprzak, W.; Hwang, C. J.; Fields, J. R.; Leighty, R. M.; Quinones, O.; Shapiro, B. A.; Alvord, W. G.; Anderson, L. M.
  3. Plos One. 2009, Oct; 4(10): 11.
  1. 14.   Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications
  2. Dror, O.; Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.; Wolfson, H. J.
  3. Journal of Chemical Information and Modeling. 2009 49(10): 2333-2343.
  1. 15.   The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels
  2. Linnstaedt, S. D.; Kasprzak, W. K.; Shapiro, B. A.; Casey, J. L.
  3. Rna-a Publication of the Rna Society. 2009 15(6): 1177-1187.
  1. 16.   Asymmetric synthesis of 2,3-dihydro-2-arylquinazolin-4-ones: Methodology and application to a potent fluorescent tubulin inhibitor with anticancer activity
  2. Chinigo, G. M.; Paige, M.; Grindrod, S.; Hamel, E.; Dakshanamurthy, S.; Chruszcz, M.; Minor, W.; Brown, M. L.
  3. Journal of Medicinal Chemistry. 2008 51(15): 4620-4631.
  1. 17.   Statistical Resolution of Ambiguous HLA Typing Data
  2. Listgarten, J.; Brumme, Z.; Kadie, C.; Gao, X. J.; Walker, B.; Carrington, M.; Goulder, P.; Heckerman, D.
  3. Plos Computational Biology. 2008 4(2):
  1. 18.   FireDock: a web server for fast interaction refinement in molecular docking
  2. Mashiach, E.; Schneidman-Duhovny, D.; Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2008 36: W229-W232.
  1. 19.   Structural domains within the 3 ' untranslated region of Turnip crinkle virus
  2. McCormack, J. C.; Yuan, X. F.; Yingling, Y. G.; Kasprzak, W.; Zamora, R. E.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2008 82(17): 8706-8720.
  1. 20.   FireDock: Fast interaction refinement in molecular docking
  2. Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Oct; 69(1): 139-159.
  1. 21.   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. 22.   Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm
  2. Shapiro, B. A.; Kasprzak, W.; Grunewald, C.; Aman, J.
  3. Journal of Molecular Graphics & Modelling. 2006, Dec; 25(4): 514-531.
  1. 23.   A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis
  2. Zhang, J. C.; Zhang, G. H.; Guo, R.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2006, Sep; 80(18): 9181-9191.
  1. 24.   A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
  2. Wainreb, G.; Haspel, N.; Wolfson, H. J.; Nussinov, R.
  3. Bioinformatics. 2006, Jun; 22(11): 1343-1352.
  1. 25.   Assessment of in vitro and in vivo activities in the National Cancer Institute's anticancer screen with respect to chemical structure, target specificity, and mechanism of action
  2. Huang, R. L.; Wallqvist, A.; Covell, D. G.
  3. Journal of Medicinal Chemistry. 2006, Mar; 49(6): 1964-1979.
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