Publications

 Molecular biophysics

  1. A. Ramanathan, A.J. Savol, V. Burger, C.S. Chennubhotla, P.K. Agarwal, Protein conformational populations and functionally relevant sub-states. ACS Accounts of Chemical Research (2014). 47 (1): 149-156. [Link]
  2. H. Bilheux, J. Katsaras, C. B. Stanley, A. Ramanathan, D.A.A. Myles, M. Cekanova, Multi-scale applications of neutron scattering and imaging, 4th Annual Bio-Medical Science and Engineering Center Conference, Oak Ridge, TN (2014). [Link]
  3. J. B. Castro, A. Ramanathan, C.S. Chennubhotla, Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization. PLoS ONE (2013). 8 (9): e73289. [Link]
  4. S.S. Hampton, S. Alam, P.F. Crozier, A. Ramanathan and P.K. Agarwal, Performance modeling of microsecond scale biological molecular dynamics simulations on heterogeneous architecturesConcurrency and Computation: Practice and Experience [accepted]. [Link] [Abstract]
  5. A. Ramanathan, A.J. Savol, P.K. Agarwal, C.S. Chennubhotla, Event detection and sub-state discovery from bio-molecular simulations using higher-order statistics: Application to enzyme Adenylate kinase. Proteins: Structure, Function and Bioinformatics (2012). 80 (11): 2536-2551. [Link] [Abstract]
  6. A. Ramanathan, A.J. Savol, V. Burger, S.P. Quinn, P.K. Agarwal, C.S. Chennubhotla, Statistical inference techniques for big data problems in molecular biophysics. In the proceedings of the Workshop on BigLearn (2012), Neural Information Processing Systems (NIPS), Lake Tahoe, CA. [Link] [Abstract]
  7. V. Burger, A. Ramanathan, A.J. Savol, C.B. Stanley, P.K. Agarwal, C.S. Chennubhotla, Quasi-harmonic analysis reveals intermediate states in he nuclear co-activator binding domain ensemble. Proceedings of the Pacific Symposium on Bio-computing (2012).  17: 70-81. [Link] [Abstract]
  8. A.J. Savol, V. Burger, P.K. Agarwal, A. Ramanathan* and C.S. Chennubhotla*, QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitinBioinformatics. (2011). Vol. 27 (13): i52-i60. (2012) [Link] [Abstract]
  9. A.J. Savol, V. Burger, P.K. Agarwal, A. Ramanathan*, C.S. Chennubhotla*, QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB’11), Vienna, Austria. (*co-corresponding authors) [Acceptance rate: 48/258 = 18.6%] [Link] [Abstract]
  10. A. Ramanathan and P.K. AgarwalEvolutionary linkage between enzyme fold, flexibility and functionPLoS Biology (2011). Vol. 9 (11): e1001193. [Highlighted as cover article]  [Link] [Abstract]
  11. N. S. Razavian, S. Moitra, H. Kamisetty, A. Ramanathan, C.J. Langmead, Time-Varying Gaussian Graphical Models of Molecular Dynamics DataProceedings of 3DSIG 2010 Structural Bioinformatics and Computational Biophysics 2010, Boston, MA[Link] [Abstract]
  12. A. RamanathanJ.-O. Yoo and C.J. Langmead, On-the-fly identification of conformational sub-states from molecular dynamics simulationsJournal of Chemical Theory and Computation. (2011). Vol. 7 (3): 778-789. Impact factor: 5.14 (2010)
  13. A. RamanathanA.J. Savol, C.J. Langmead, P.K. Agarwal and C.S. ChennubhotlaDiscovering conformational sub-states relevant to protein functionPLoS One (2010). Vol. 6 (1): e15827. [Link] [Abstract]
  14. H. KamisettyA. RamanathanC. Bailey-Kellogg and C. J. LangmeadAccounting for conformational entropy in protein-protein interactionsProteins: Structure, Function & Bioinformatics (2010). Vol. 72 (2): 444-462. [Link] [Abstract]
  15. A. Ramanathan, P. K. Agarwal, M.G. Kurnikova, and C. J. LangmeadAn online approach for mining collective behaviors from molecular dynamics simulationsJournal of Computational Biology. (2010). Vol. 17 (3): 309-324. [Invited submission] [Link] [Abstract]
  16. A. Ramanathanand Chritopher J. Langmead, Dynamic Invariants in Protein Folding Pathways Revealed by Tensor Analysis, Computational Systems Biology (CSB) 2009, Stanford, CA. [Link] [Abstract]
  17. A. RamanathanPratul K. Agarwal, Maria G. Kurnikova, and Christopher J. LangmeadAn online approach for mining collective behaviors from molecular dynamics simulations, Research in Computational Molecular Biology (RECOMB) 2009, Tuscon, AZ. [Acceptance rate: 37/166 = 22%] [Link] [Abstract]
  18. A. Ramanathan and P.K. Agarwal, Computational identification of slow conformational fluctuations in proteinsJ. Phys. Chem. B. (2009). Vol. 113 (52): 16669-16680. [Highlighted as Cover article] [Link] [Abstract]
  19. A. RamanathanT. Mamonova, M. Madrid and M. G. Kurnikova, Subdomain Motions of HIV-1 Reverse Transcriptase Investigated by Long-Scale Molecular DynamicsTERAGRID Conference 2008, Arlington. [Link] [Abstract]

Technical Reports

  1. A. Ramanathan, Internal Dynamics and Energetics during Enzyme Catalysis, Ph.D. Thesis, CMU-CB-10-102. [2010] [Link] [Abstract]
  2. N.S. Razavian, S. Moitra, H. Kamisetty, A. Ramanathan and C.J. Langmead, Time-varying Gaussian graphical models of molecular dynamics data. CMU-CS-10-119. [2010] [Link] [Abstract]
  3. J. O. Yoo, A. Ramanathan, C.J. Langmead, PyTensor: A Python based Tensor Library. CMU-CS-10-102. [2010] [Link] [Abstract]
  4. A. Ramanathan, P.K. Agarwal and C.J. Langmead, Using Tensor Analysis to Characterize Contact-Map Dynamics of Proteins. CMU-CS-08-108. [2008] [Link] [Abstract]

Public health dynamics

  1. A. Ramanathan*, L. L. Pullum, T. C. Hobson, C. A. Steed, S. P. Quinn, C. S. Chennubhotla, S. Valkova, ORBiT: Oak Ridge Bio-surveillance Toolkit for public health dynamics. BMC Bioinformatics (2015) [Accepted]  [Link] [Abstract]
  2. A. Ramanathan*, L. L. Pullum, T. C. Hobson, C. A. Steed, S. P. Quinn, C. S. Chennubhotla, S. Valkova, Discovering multi-scale co-occurrence patterns of asthma and flu using Oak Ridge Bio-surveillance Toolkit. Frontiers in Public Health (2015) Special Issue on Advances in Information Sciences for Disease Surveillance. [invited submission].  [Link] [Abstract]
  3. A. Ramanathan, L.L. Pullum, T.C. Hobson, S.P. Quinn, C. S. Chennubhotla, S. Valkova, Discovering disease co-occurrence patterns from electronic healthcare reimbursement claims, Workshop on Big Data Analytic Technology for Bioinformatics and Health Informatics (KDDBHI) as part of Knowledge Discovery and Data mining (ACM SIG-KDD 2014), New York, Aug 2014. [Link] [Abstract]
  4. L. L. Pullum, A. Ramanathan, Scalable machine learning for public health surveillance, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS),  Florida, Aug 2014.
  5. F. Hussain, A. Ramanathan, L. L. Pullum, S. K. Jha, EpiSpec: A formal specification language for parameterized agent-based models against epidemiological ground truth2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS),  Florida, Aug 2014. [Link]
  6. Chad A. Steed, T. E. Potok, L.L. Pullum, A. Ramanathan, G. Shipman, P.E. Thornton, Extreme Scale Visual Anlaytics, 4th SupercomputingWorkshop on Petascale (Big) Data Analytics: Challenges and Opportunities, Denver, Colorado, 2013. [Link]
  7. A. Ramanathan*, T. Parker, L.L. Pullum, C.A. Steed, S.P. Quinn, C.S. Chennubhotla, Oak Ridge Bio-surveillance Toolkit (ORBiT): integrating big data analytics with visual analytics for public health dynamics , Workshop on Public Health’s Wicked Problems: Can Visual Analytics Save Lives?, IEEE Conference on Visual Analytics (VAST), Atlanta, 2013.  [Link] [Abstract]
  8. A. Ramanathan*, T. Parker, L.L. Pullum, C.A. Steed, S.P. Quinn, C.S. Chennubhotla, Integrating heterogeneous healthcare datasets and visual analytics for disease bio-surveillance and dynamics, 4th Workshop on Integrative Text and Visual Analytics, IEEE Conference on Visual Analytics (VAST), Atlanta, 2013. [Link] [Abstract]
  9. Sumit K. Jha , A. Ramanathan*, Uncertainty quantification of epidemiological models, Workshop on Verification and Validation of Epidemiological models (VVEM’12) 2012 ASE Conference on Biomedical Computing, Washington, DC.  [Link] [Abstract]
  10. A. Ramanathan*, C. A. Steed, L. L. Pullum, Verification of compartmental epidemiological models using metamorphic testing, model checking and visual analytics, Workshop on Verification and Validation of Epidemiological models (VVEM’12) 2012 ASE Conference on Biomedical Computing, Washington, DC.  [Link] [Abstract]
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