Publications

N.B.: BK stands for Bala Krishnamoorthy.

  1. BK and Alex Tropsha. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics, 19, 12, 2003, 1540–1548.   Preprint, code, and supplementary material.
  2. BK, J. Scott Provan, and Alex Tropsha. A topological characterization of protein structure. In Biocomputing, the proceedings of the Conference on Data Mining in Biomedicine held at the University of Florida 2004; edited by Panos M. Paradalos, Vladimir Boginski, and Alkis Vazacapoulos, Springer, 2005 (accepted), ISBN: 0-387-69318-1. Preprint.
  3. Christopher Deutsch and BK. Four-body scoring function for mutagenesis. Bioinformatics, 23, 22, 2007, 3009–3015. Preprint, dataset, and code.
  4. Bounds on the size of branch-and-bound proofs for integer knapsacks. Operations Research Letters, 36, 1, 2008, 19–25. Preprint.
  5. BK and Gábor Pataki. Column basis reduction and decomposable knapsack problems. Discrete Optimization, 6, 3, 2009, 242–270.   arXiv:0807.1317
  6. Tamal Dey, Anil Hirani, and BK. Optimal homologous cycles, total unimodularity, and linear programming. In Proceedings of 42nd ACM Annual Symposium on Theory of Computing (STOC) 2010, 221–230.   arXiv:1001.0338.
  7. Ye Tian, Christopher Deutsch, and BK. Optimized scoring function for solubility mutagenesis. Algorithms for Molecular Biology, 5, 33, 2010. Preprint, dataset, and code.
  8. Svetlana Lockwood, BK, and Ping Ye. Neighborhood properties are significant determinants of temperature sensitive mutants. PLoS ONE, 6, 12, 2011, e28507. (open access)
  9. Tamal Dey, Anil Hirani, and BK. Optimal homologous cycles, total unimodularity, and linear programming. SIAM Journal on Computing, 40, 4, 2011, 1026–1040. This is the expanded version, with some new results, of the STOC 2010 paper listed above. arXiv:1001.0338.
  10. Bethany Suderman, BK, and Anita Vasavada. Neck muscle paths and moment arms are significantly affected by wrapping surface parameters. Computer Methods in Biomechanics and Biomedical Engineering, 15, 7, 2012, 735–744.   Preprint.
  11. BK, William Webb, and Nathan Moyer. Lattice-based algorithms for number partitioning in the hard phase. Discrete Optimization, 9, 3, 2012, 159–171. (open access)   OO Preprint.
  12. Johannes Elferich, Danielle Williamson, BK, and Ujwal Shinde. Propeptides of eukaryotic proteases encode histidines to exploit organelle pH for regulation. The FASEB Journal, 27, 8, 2013, 2939–2945. Preprint.
  13. Sharif Ibrahim, BK, and Kevin Vixie. Simplicial flat norm with scale. Journal of Computational Geometry, 4, 1, 2013, 133–159. (open access)   arxiv:1105.5104.
  14. Tamal Dey, Anil Hirani, BK, and Gavin Smith. Edge contractions and Simplicial Homology. Submitted, 2013. arXiv:1304.0664.
  15. BK, Brian Bay, and Robert Hart. Bone Mineral Density and Donor Age are Not Predictive of Allograft Bone Mechanical Strength. Journal of Orthopaedic Research, 32, 10, 2014, 1271–1276. (open access)   Preprint.
  16. Nathan Hamlin, BK, and William Webb. A knapsack-like code using recurrence sequence representations. The Fibonacci Quarterly, 53, 1, 2015, 24–33. arXiv:1503.04238.
  17. Svetlana Lockwood and BK. Topological Features in Cancer Gene Expression Data. In Proceedings of the Pacific Symposium on Biocomputing (PSB 2015), 20, 108–119, 2015. Preprint: arXiv:1410.3198.
  18. BK and Gavin Smith. Non Total-Unimodularity Neutralized Simplicial Complexes. Discrete Applied Mathematics, 240, 11, 2018, 44–62 (published online Feb 2016). arxiv:1304.4985.
  19. Sharif Ibrahim, BK, and Kevin Vixie. Flat Norm Decomposition of Integral Currents. Journal of Computational Geometry, 7, 1, 2016, 285–307. (open access)   arXiv:1411.0882.
  20. BK. Thinner is not always better: Cascade knapsack problems. Operations Research Letters, 45, 1, 2017, 77–83.   Preprint and instances.
  21. Sabina Blizzard, BK, Matthew Shinseki, Marcel Betsch, and Jung Yoo. The magnitude of angular and translational displacement of dens fractures is dependent on the sagittal alignment of the cervical spine rather than the force of injury. The Spine Journal, 17, 12, 2017, 1859–1865.   Preprint.
  22. Philip Behrend and BK. Considerations for waste gasification as an alternative to landfilling in Washington state using decision analysis and optimization. Sustainable Production and Consumption, 12, 2017, 170–179.   Preprint.
  23. Dayton Opel, Benjamin Rapone, BK, Jung Yoo, and James Meeker. Race and gender influence management of humerus shaft fractures. Journal of Orthopaedics, 15, 2, 2018, 540–544.   Preprint.
  24. Methun Kamruzzaman, Ananth Kalyanaraman, BK, and Patrick S. Schnable. Toward a scalable exploratory framework for complex high-dimensional phenomics data. Under review, submitted in 2017.   arXiv:1707.04362.
  25. Ananth Kalyanaraman, Methun Kamruzzaman, and BK. Interesting paths in the Mapper. Under review, submitted in 2017.   arXiv:1712.10197.
  26. Yunfeng Hu, Matthew Hudelson, BK, Altaa Tumurbaatar, and Kevin Vixie. Median shapes. Under review, 2018.   arXiv:1802.04968.
  27. Marcel Betsch, Sabina Blizzard, BK, and Jung Yoo. Association between cervical spine degeneration and the presence of dens fractures. Under review, 2018.   Preprint.
  28. Methun Kamruzzaman, Ananth Kalyanaraman, and BK. Detecting divergent subpopulations in phenomics data using interesting flares. Under review, 2018.   Preprint.