Bioimage Analysis, Computer Vision & Machine Learning

• Quantifying intra-tumor heterogeneity.
  Spagnolo, D. et al.
  Manuscript in review, 2015.
• Automated identification of abnormal respiratory ciliary motion in nasal biopsies.
  Quinn S, Zahid M, Durkin J, Francis R, Lo C, Chennubhotla CS.
  Science Translational Medicine. 05 Aug 2015. Vol. 7, Issue 299, pp. 299ra124. doi: 10.1126/scitranslmed.aaa1233
  News Media: UPMC, UGA
• Automated epithelial nuclei segmentation algorithm to aid detection of precancerous alterations in non-dysplastic Barrett’s esophagus tissue.
  Burger V, Uttam S, Bista R, Staton K, Sepulveda A, Davison J, Hartman D, Liu Y, Chennubhotla CS. 2014
• Spectral clustering strategies for heterogeneous disease expression data.
  Huang GT, Cunningham K, Benos PV, Chennubhotla CS.
  Pacific Symposium on Biocomputing (PSB). 2013:212-223 PMID: 23424126
• Novel use of differential image velocity invariants to categorize ciliary motion defects.
  Quinn S, Francis R, Lo C, Chennubhotla CS.
  Proceedings of the Biomedical Science and Engineering Conference (BSEC) 2011.
• Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps.
  Burger V, Chennubhotla CS.
  Biopolymers. 2012 Sep;97(9):732-41. doi: 10.1002/bip.22041. PMID: 22696408
• Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.
  Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN.
  BMC Bioinformatics. 2006 Oct 28;7:478. PMID: 17069658
• Hierarchical eigensolver for transition matrices in spectral methods.
  Chennubhotla C, Jepson A.
  Advances in Neural Information Processing Systems (NIPS) 17, 2005, 273:280, MIT Press, Cambridge MA.
• Spectral embedding and min-cut for image segmentation.
  Estrada F, Jepson A, Chennubhotla C.
  British Machine Vision Conference (BMVC), Cambridge UK, 2004, 34.1:34.10.
• EigenCuts: Half-lives of eigenflows for spectral clustering.
  Chennubhotla C, Jepson A.
  Advances in Neural Information Processing Systems (NIPS) 15, 2003, 689:696, MIT Press, Cambridge MA.
• Sparse-PCA: Extracting multi-scale structure from data.
  Chennubhotla C, Jepson A.
  Eighth IEEE International Conference on Computer Vision (ICCV) 2001, v1, 641:647. doi: 10.1109/ICCV.2001.937579

Biophysics

• Approximating frustration scores in complex networks via perturbed Laplacian spectra.
  Savol A, Chennubhotla CS.
  Physical Review E., Accepted, 2015
• Quantifying the sources of kinetic frustration in folding simulations of small proteins.
  Savol A, Chennubhotla CS.
  Journal of Chemical Theory and Computation. 2014 doi: 10.1021/ct500361w PMID: 25136267
• Evol and ProDy for bridging protein sequence evolution and structural dynamics.
  Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla CS, Lezon T, Bahar I
  Bioinformatics. 2014 doi: 10.1093/bioinformatics/btu336 PMID: 24849577
• Protein conformational populations and functionally relevant sub-states.
  Ramanathan A, Savol A, Burger V, Chennubhotla CS*, Agarwal P*
  Accounts of Chemical Research. 2013 doi: 10.1021/ar400084s PMID: 23988159
• Statistical inference for big-data problems in molecular biophysics.
  Ramanathan A, Savol A, Burger V, Quinn S, Agarwal PK, Chennubhotla CS.
  NIPS2012 Workshop on Parallel and Large-Scale Machine Learning. 2012
• Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase.
  Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS.
  Proteins. 2012 Nov;80(11):2536-51. doi: 10.1002/prot.24135. Epub 2012 Aug 8. PMID: 22733562
• Quasi-anharmonic analysis reveals intermediate states in the nuclear co-activator receptor binding domain ensemble.
  Burger VM, Ramanathan A, Savol AJ, Stanley CB, Agarwal PK, Chennubhotla CS.
  Pac Symp Biocomput. 2012:70-81. PMID: 22174264
• QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin.
  Savol AJ, Burger VM, Agarwal PK, Ramanathan A, Chennubhotla CS.
  Bioinformatics. 2011 Jul 1;27(13):i52-60. doi: 10.1093/bioinformatics/btr248. PMID: 21685101
• Discovering conformational sub-states relevant to protein function.
  Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS.
  PLoS One. 2011 Jan 28;6(1):e15827. doi: 10.1371/journal.pone.0015827. PMID: 21297978
• Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.
  Chennubhotla C, Yang Z, Bahar I.
  Mol Biosyst. 2008 Apr;4(4):287-92. doi: 10.1039/b717819k. Epub 2008 Feb 20. PMID: 18354781
• Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation.
  Bahar I, Chennubhotla C, Tobi D.
  Curr Opin Struct Biol. 2007 Dec;17(6):633-40. Epub 2007 Nov 19. Review. PMID: 18024008
• Signal propagation in proteins and relation to equilibrium fluctuations.
  Chennubhotla C, Bahar I.
  PLoS Comput Biol. 2007 Sep;3(9):1716-26. Erratum in: PLoS Comput Biol. 2007 Oct 12;3(10):2043. PMID: 17892319
• Markov methods for hierarchical coarse-graining of large protein dynamics.
  Chennubhotla C, Bahar I.
  J Comput Biol. 2007 Jul-Aug;14(6):765-76. PMID: 17691893
• Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
  Eyal E, Chennubhotla C, Yang LW, Bahar I.
  Bioinformatics. 2007 Jul 1;23(13):i175-84. PMID: 17646294
• Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.
  Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I.
  Structure. 2007 Jun;15(6):741-9. PMID: 17562320
• Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.
  Chennubhotla C, Bahar I.
  Mol Syst Biol. 2006;2:36. Epub 2006 Jul 4. PMID:16820777
• Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.
  Chennubhotla C, Rader AJ, Yang LW, Bahar I.
  Phys Biol. 2005 Nov 9;2(4):S173-80. PMID: 16280623

Olfaction

• Designing a physicochemical descriptor based metric for categorizing odors.
  Quinn S, Ramanathan A, Castro J, Chennubhotla CS.
  Revised manuscript in review. 2015
• Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization.
  Castro J, Ramanathan A, Chennubhotla CS.
  PLoS One. 2013 8(9): e73289 8(9): doi:10.1371/journal.pone.0073289. PMID: 24058466
  News Media: NBC News, LA Times, Times London, The Independent London, BBC, CBC As it happens

Others

• Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge Bio-surveillance Toolkit.
  Ramanathan A, Pullum L, Hobson T, Stahl C, Steed C, Quinn S, Chennubhotla CS.
  Accepted,  Frontiers in Public Health, Section Infectious Diseases. 2015
• Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement
  Claims Data.
  Ramanathan A, Pullum L, Hobson T, Quinn S, Chennubhotla C, Valkova S.
  KDDBHI 2014: Big Data Analytic Technology for Bioinformatics and Health Informatics
• ORBiT: Oak Ridge Bio-surveillance Toolkit for Public Health.
  Ramanathan A, Pullum L, Hobson T, Steed C, Quinn S, Chennubhotla CS.
  BMC Bioinformatics, Accepted. 2014
• Modeling boundary conditions for balanced proliferation in metastatic latency.
  Taylor D, Wells J, Savol A, Chennubhotla CS, Wells A.
  Clinical Cancer Research. 2013 19(5):1063-70. doi: 10.1158/1078-0432.CCR-12-3180. 2013 PMID: 23329811