Publications

 Molecular biophysics

30          Wilson, B. A., Ramanathan, A. & Lopez, C. F. Cardiolipin-dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations. Biophysics Journal, [accepted] (2019).

29          Romero, R.et al. Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning. Proceedings of the National Academy of Sciences USA 116, 5086-5095 (2019).

28          Demerdash, O. N.et al. Using small-angle scattering data and parametric machine learning to optimize forcefield parameters for intrinsically disordered proteins. Frontiers in Molecular Biosciences 6, 64 (2019). [accepted]

27        Parvatikar, A., Vacaliuc, G. S., Ramanathan, A. & Chennubhotla, S. C. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations. Biophysical journal 114, 2040-2043 (2018).

26        Haider, S.et al.Holliday Junctions Formed from Human Telomeric DNA. Journal of the American Chemical Society 140, 15366-15374 (2018).

25        Duff Jr, M. R.et al.Modulating enzyme activity by altering protein dynamics with solvent. Biochemistry 57, 4263-4275 (2018).

24        Bhowmik, D., Gao, S., Young, M. T. & Ramanathan, A. Deep clustering of protein folding simulations. BMC bioinformatics 19, 484 (2018).

23        Ban, D., Iconaru, L. I., Ramanathan, A., Zuo, J. & Kriwacki, R. W. A small molecule causes a population shift in the conformational landscape of an intrinsically disordered protein. Journal of the American Chemical Society 139, 13692-13700 (2017).

22        Mei, Y.et al.Conformational flexibility enables the function of a BECN1 region essential for starvation-mediated autophagy. Biochemistry 55, 1945-1958 (2016).

21        Mansouri, A. L.et al.Folding propensity of intrinsically disordered proteins by osmotic stress. Molecular BioSystems 12, 3695-3701 (2016).

20        Agarwal, P. K., Doucet, N., Chennubhotla, C., Ramanathan, A. & Narayanan, C. in Methods in enzymology 578    273-297 (Academic Press, 2016).

19        Sinha, S.et al.Order-to-Disorder Transitions in BECN1 Regulate Autophagy. The FASEB Journal 29, 712.716 (2015).

18        Iconaru, L. I.et al.Discovery of Small Molecules that Inhibit the Disordered Protein, p27 Kip1. Scientific reports 5, 15686 (2015).

17        Bogdan, P., Majumder, T., Ramanathan, A. & Xue, Y. in Proceedings of the 9th International Symposium on Networks-on-Chip.  27 (ACM).

16        Castro, J., Quinn, S., Ramanathan, A. & Chennubhotla, C. Categorical, low-dimensional decomposition of human odor space with non-negative matrix factorization. Flavour 3, P3 (2014).

15        Bilheux, H.et al.in Proceedings of the 2014 Biomedical Sciences and Engineering Conference.  1-4 (IEEE).

14        Ramanathan, A., Savol, A., Burger, V., Chennubhotla, C. S. & Agarwal, P. K. Protein conformational populations and functionally relevant substates. Accounts of chemical research 47, 149-156 (2013).

13        Castro, J. B., Ramanathan, A. & Chennubhotla, C. S. Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization. PloS one 8, e73289 (2013).

12        Ramanathan, A., Savol, A. J., Agarwal, P. K. & Chennubhotla, C. S. Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase. Proteins: Structure, Function, and Bioinformatics 80, 2536-2551 (2012).

11        Ramanathan, A.et al.in Neural Information Processing Systems: Workshop on Big Learning.

10        Burger, V. M.et al.in Biocomputing 2012     70-81 (2012).

9        Savol, A. J., Burger, V. M., Agarwal, P. K., Ramanathan, A. & Chennubhotla, C. S. QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. Bioinformatics 27, i52-i60 (2011).

8        Ramanathan, A., Yoo, J. O. & Langmead, C. J. On-the-fly identification of conformational substates from molecular dynamics simulations. Journal of Chemical Theory and Computation 7, 778-789 (2011).

7        Ramanathan, A., Savol, A. J., Langmead, C. J., Agarwal, P. K. & Chennubhotla, C. S. Discovering conformational sub-states relevant to protein function. PLoS ONE 6, e15827 (2011).

6        Ramanathan, A. & Agarwal, P. K. Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis. PLoS Biology 9, e1001193 (2011).

5        Kamisetty, H., Ramanathan, A., Bailey‐Kellogg, C. & Langmead, C. J. Accounting for conformational entropy in predicting binding free energies of protein‐protein interactions. Proteins: Structure, Function, and Bioinformatics 79, 444-462 (2011).

4        Yoo, J. O., Ramanathan, A. & Langmead, C. J. Pytensor: A python based tensor library. (Technical Report CMU-CS-10-102, Carnegie Mellon University, 2010. 4.4, 2010).

3        Ramanathan, A., Agarwal, P. K., Kurnikova, M. G. & Langmead, C. J. An online approach for mining collective behaviors from molecular dynamics simulations. Journal of Computational Biology 17, 309-324 (2010).

2        Ramanathan, A., Agarwal, P. K., Kurnikova, M. & Langmead, C. J. in Annual International Conference on Research in Computational Molecular Biology.  138-154 (Springer, Berlin, Heidelberg).

1        Ramanathan, A. & Agarwal, P. K. Computational identification of slow conformational fluctuations in proteins. Journal of Physical Chemistry B113, 16669–16680 (2009).

Public health dynamics

18          Zhang, Y., Ramanathan, A., Vullikanti, A., Pullum, L. & Prakash, B. A. Data-driven efficient network and surveillance-based immunization. Knowledge and Information Systems, 1-27 (2019).

17        Zhang, Y., Ramanathan, A., Vullikanti, A., Pullum, L. & Prakash, B. A. in 2017 IEEE International Conference on Data Mining (ICDM).  615-624 (IEEE).

16        Özmen, Ö., Pullum, L. L., Ramanathan, A. & Nutaro, J. J. Augmenting epidemiological models with point-of-care diagnostics data. PloS one11, e0153769 (2016).

15        Özmen, Ö., Nutaro, J. J., Pullum, L. L. & Ramanathan, A. Analyzing the impact of modeling choices and assumptions in compartmental epidemiological models. Simulation92, 459-472 (2016).

14        Margevicius, K. J.et al.The Biosurveillance Analytics Resource Directory (BARD): facilitating the use of epidemiological models for infectious disease surveillance. PloS one11, e0146600 (2016).

13        Pullum, L. L., Ramanathan, A. & Hobson, T. C. Sequential Pattern Mining of Electronic Healthcare Reimbursement Claims: Experiences and Challenges in Uncovering How Patients are Treated by Physicians. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2015).

12        Jha, S. K., Pullum, L. L. & Ramanathan, A. Integrating Symbolic and Statistical Methods for Testing Intelligent Systems Applications to Machine Learning and Computer Vision. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2016).

11        Ramanathan, A.et al.ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics. BMC bioinformatics16, S4 (2015).

10        Ramanathan, A.et al.Discovering Multi-Scale Co-Occurrence Patterns of Asthma and Influenza with Oak Ridge Bio-Surveillance Toolkit. Frontiers in public health3, 182 (2015).

9        Malhotra, K., Hobson, T. C., Valkova, S., Pullum, L. L. & Ramanathan, A. in 2015 IEEE International Conference on Big Data (Big Data).  2670-2679 (IEEE).

8        Ramanathan, A.et al.Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement Claims Data. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2014).

7        Pullum, L. L. & Ramanathan, A. in 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).  1-1 (IEEE).

6        Pullum, L. & Ramanathan, A. ORBiT-The Oak Ridge Biosurveillance Toolkit. Online journal of public health informatics 6(2014).

5        Ramanathan, A.et al.in 3rd IEEE Workshop on Visual Text Analytics.

4        Ramanathan, A.et al.Oak Ridge Bio-surveillance Toolkit (ORBiT): Integrating Big-Data Analytics with Visual Analysis for Public Health Dynamics. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2013).

3        Hussain, F., Ramanathan, A., Pullum, L. L. & Jha, S. K. in 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).  1-6 (IEEE).

2        Ramanathan, A., Pullum, L., Steed, C., Quinn, S. & Chennubhotla, C. in IEEE VAST Workshop on Public Health’s Wicked Problems: Can InfoVis Save Lives.

1        Steed, C. A.et al.in The 4th Workshop on Petascale (Big) Data Analytics at SuperComputing.

Machine Learning

13        Young, M. T., Hinkle, J., Ramanathan, A. & Kannan, R. in 2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD). 339-347 (IEEE).

12         Yoon, H.-J., Ramanathan, A., Alamudun, F. & Tourassi, G. in 14th International Workshop on Breast Imaging (IWBI 2018).  107181H (International Society for Optics and Photonics).

11        Qiu, J. X.et al.Scalable deep text comprehension for Cancer surveillance on high-performance computing. BMC bioinformatics19, 488 (2018).

10        Pullum, L. L., Steed, C. A., Jha, S. K. & Ramanathan, A. Mathematically Rigorous Verification & Validation of Scientific Machine Learning. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2018).

9        Gao, S., Ramanathan, A. & Tourassi, G. Hierarchical convolutional attention networks for text classification. (Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States), 2018).

8        Ramanathan, A.et al.in 2017 Tenth International Conference on Contemporary Computing (IC3).  1-6 (IEEE).

7        Raj, S., Pullum, L., Ramanathan, A. & Jha, S. K. in International Symposium on Foundations and Practice of Security.  277-292 (Springer, Cham).

6        Raj, S., Jha, S. K., Ramanathan, A. & Pullum, L. L. in 2017 International Conference on Embedded Software (EMSOFT).  1-2 (IEEE).

5        Raj, S., Jha, S., Pullum, L. L. & Ramanathan, A. Statistical Hypothesis Testing using CNN Features for Synthesis of Adversarial Counterexamples to Human and Object Detection Vision Systems. ORNL TR6, 17 (2017).

4        Yoon, H.-J., Ramanathan, A. & Tourassi, G. in INNS Conference on Big Data.  195-204 (Springer, Cham).

3        Vazhkudai, S. S.et al.in 2016 IEEE International Conference on Big Data (Big Data).  3052-3061 (IEEE).

2        Ramanathan, A., Pullum, L. L., Hussain, F., Chakrabarty, D. & Jha, S. K. in 2016 Design, Automation & Test in Europe Conference & Exhibition (DATE). 786-791 (IEEE).

1        Jha, S. K. & Ramanathan, A. in 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).  80-85 (IEEE).

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