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.   Web page, with 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.
  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.   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.
  13. Sharif Ibrahim, BK, and Kevin Vixie. Simplicial flat norm with scale. Journal of Computational Geometry, 4, 1, 2013, 133–159.   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, 2014.   Preprint.
  16. Nathan Hamlin, BK, and William Webb. A knapsack-like code using recurrence sequence representations. The Fibonacci Quarterly, 53, 1, 2015, 24–33. Preprint.
  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. NTU Neutralized Simplicial Complexes. Discrete Applied Mathematics, to appear (accepted Dec 2015). arxiv:1304.4985.
  19. Sharif Ibrahim, BK, and Kevin Vixie. Flat Norm Decomposition of Integral Currents. Under review, 2015. Preprint: arXiv:1411.0882.
  20. BK. Thinner is not better: Cascade knapsack problems. Under review, 2015. Preprint, talk, and instances.
  21. Jung Yoo, Sabina Blizzard, BK, Matthew Shinseki, and Marcel Betsch. The Influence of Cervical Sagittal Plane Alignment on Displacement of Dens Fractures. Under review, 2015.
  22. Dayton Opel, Benjamin Rapone, BK, Jung Yoo, and James Meeker. Disparities in orthopaedic care: race and gender influence management of humerus shaft fractures. Under review, 2015.