- 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.
- 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
- 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
- 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.
- Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement
Claims Data.
Ramanathan A, Pullum L, Hobson T, Quinn S, Chennubhotla C, Valkova S.
- 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