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. Detecting divergent subpopulations in phenomics data using interesting flares. In the Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '18), 155–164, 2018, Preprint.
  25. Marcel Betsch, Sabina Blizzard, BK, and Jung Yoo. Association between cervical spine degeneration and the presence of dens fractures. Zeitschrift fur Orthopadie und Unfallchirurgie, 158, 01, 46–50, 2020 (published online Apr 9, 2019).   Preprint.
  26. Kaniz Madhobi, Methun Kamruzzaman, Ananth Kalyanaraman, Eric Lofgren, Rebekah Moehring, BK. A visual analytics framework for analysis of patient trajectories. In the Proceedings of the 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '19), 2019. Preprint.
    → A shorter version of the above paper is accepted to the ACM SIGKDD Workshop titled epiDAMIK: Epidemiology meets Data Mining and Knowledge discovery, 2019.
  27. Yunfeng Hu, Matthew Hudelson, BK, Altaa Tumurbaatar, and Kevin Vixie. Median shapes.   Journal of Computational Geometry, 10, 1, 2019, 322–388. arXiv:1802.04968.
  28. Methun Kamruzzaman, Ananth Kalyanaraman, BK, Stefan Hey, and Patrick S. Schnable. Hyppo-X: A scalable exploratory framework for analyzing complex phenomics data. IEEE Transactions on Computational Biology and Bioinformatics, 2019.   DOI:10.1109/TCBB.2019.2947500.   arXiv:1707.04362.
  29. Ananth Kalyanaraman, Methun Kamruzzaman, and BK. Interesting paths in the mapper complex.   Journal of Computational Geometry, 10, 1, 2019, 500–531. arXiv:1712.10197.
  30. Prashant Gupta, BK, and Gregory Dreifus. Continuous toolpath planning in a graphical framework for sparse infill additive manufacturing. Computer-Aided Design, 127, 2020, 102880. Issue on papers accepted to Solid and Physical Modeling (SPM 2020). Preprint: arXiv:1908.07452.
  31. Enrique Alvarado, Zhu Liu, Michael Servis, BK, and Aurora Clark. A geometric measure theory approach to identify complex structural features of soft matter surfaces. Journal of Chemical Theory and Computation, 16, 7, 2020, 4579–4587. Preprint: ChemRxiv.
  32. Prashant Gupta and BK. Euler transformation of polyhedral complexes. International Journal of Computational Geometry & Applications (IJCGA), 30, 03n04, 2020, 183–211. arXiv:1812.02412.
  33. Yunfeng Hu, Phonemany Ounkham, Ondrej Marsalek, Thomas Markland, BK, and Aurora Clark. Persistent homology metrics reveal quantum fluctuations and reactive atoms in path integral dynamics. Frontiers in Chemistry, 9. 2021. Preprint: ChemRxiv.
  34. Joshua Mirth, Yanqin Zhai, Johnathan Bush, Enrique Alvarado, Howie Jordan, Mark Heim, BK, Markus Pflaum, Aurora Clark, Y Z, and Henry Adams. Representations of energy landscapes by sublevelset persistent homology: An example with n-alkanes. The Journal of Chemical Physics, 154, 11, 2021, p114114. Preprint: arXiv:2011.00918.
  35. Youjia Zhou, Methun Kamruzzaman, Patrick Schnable, BK, Ananth Kalyanaraman, and Bei Wang. Pheno-Mapper: An interactive toolbox for the visual exploration of phenomics data. In the Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '21), Article 20, 2021, 1–10. Preprint: arXiv:2106.13397.
  36. Enrique Alvarado, BK, and Kevin Vixie. The maximum distance problem and minimal spanning trees. International Journal of Analysis and Applications, 19, 5, 2021, 633–659. Preprint: arXiv:2004.07323.
  37. Prashant Gupta, Yiran Guo, Narasimha Boddeti, and BK. SFCDecomp: Multicriteria optimized tool path planning in 3D printing using space-filling curve based domain decomposition. International Journal of Computational Geometry & Applications (IJCGA), 31, 04, 2021, 193–220. Preprint: arXiv:2109.01769.
  38. Youjia Zhou, Nathaniel Saul, Ilkin Safarli, BK, and Bei Wang. Stitch Fix for Mapper and Topological Gains. Research In Computational Topology 2, 2022, 265–294. Preprint: arXiv: 2105.01961.
  39. Hung Le, Sushant Kumar, Nathan May, Ernesto Martinez-Baez, Ravishankar Sundararaman, BK, and Aurora Clark. Behavior of linear and nonlinear dimensionality reduction for collective variable identification of small molecule solution-phase reactions. Journal of Chemical Theory and Computation", 18, 3, 2022, 1286–1296 2022. Preprint: ChemRXiv.
  40. Dustin Arendt, Matthew Broussard, BK, and Nathaniel Saul. Steinhaus filtration and stable paths in the Mapper. Submitted, 2021. arXiv:1906.08256.
  41. Krishnamurthy Dvijotham, BK, Yunqi Luo, and Benjamin Rapone. Robust feasibility of systems of quadratic equations using topological degree theory. Submitted, 2021. Preprint: arXiv:1907.12206.
  42. Matthew Broussard, BK, David Makin, Dale Willits. Extracting insights on use of force by police in encounters through topological data analysis of body-worn camera video datasets. Submitted, 2021. Preprint.
  43. Methun Kamruzzaman, Matthew Bielskas, BK, Achla Marathe, Anil Vullikanti, and Ananth Kalyanaraman. Navigating the COVID-19 Data Landscape: Automated Hypothesis Generation using Topological Data Analysis. Submitted, 2021. Preprint: ResearchSquare.
  44. Matthew Broussard and BK. A tight max-flow min-cut duality theorem for non-linear multicommodity flows. Submitted, 2021. Preprint: arXiv:2107.04252.
  45. Enrique Alvarado, BK, and Kevin Vixie. Geometry of a Set and its Random covers. Submitted, 2021. Preprint: arXiv:2112.14979.
  46. David Makin, Guangzhen Wu, Matthew Broussard, and BK. Predicting Police Integrity: An Application of Support Vector Machines (SVM) to The Police Integrity Instrument. Submitted, 2022. Preprint.