Finding structurally consistent motion correspondences. - David W. Jacobs; Chakra Chennubhotla 001 (ICPR (1), 1994)

Sparse PCA: Extracting Multi-scale Structure from Data. - Chakra Chennubhotla 001; Allan D. Jepson (ICCV, 2001)

Robust Contrast-Invariant EigenDetection. - Chakra Chennubhotla 001; Allan D. Jepson; John Midgley (ICPR (2), 2002)

Half-Lives of EigenFlows for Spectral Clustering. - Chakra Chennubhotla 001; Allan D. Jepson (NIPS, 2002)

Spectral clustering of protein sequences. - Alberto Paccanaro; Chakra Chennubhotla 001; James A. Casbon; Mansoor A. S. Saqi (IJCNN, 2003)

Markov Analysis of Protein Sequence Similarities. - Chakra Chennubhotla 001; Alberto Paccanaro (WIRN, 2003)

Spectral Embedding and Min Cut for Image Segmentation. - Francisco J. Estrada; Allan D. Jepson; Chakra Chennubhotla 001 (BMVC, 2004)

Perceptual Distance Normalization for Appearance Detection. - Chakra Chennubhotla 001; Allan D. Jepson (ICPR (2), 2004)

Hierarchical Eigensolver for Transition Matrices in Spectral Methods. - Chakra Chennubhotla 001; Allan D. Jepson (NIPS, 2004)

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. - Illés J. Farkas; Chuang Wu; Chakra Chennubhotla 001; Ivet Bahar; Zoltán N. Oltvai (BMC Bioinform., 2006)

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. - Eran Eyal; Chakra Chennubhotla 001; Lee-Wei Yang; Ivet Bahar (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. - Chakra Chennubhotla 001; Ivet Bahar (J. Comput. Biol., 2007)

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. - Chakra Chennubhotla 001; Ivet Bahar (PLoS Comput. Biol., 2007)

Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. - Chakra Chennubhotla 001; Ivet Bahar (PLoS Comput. Biol., 2007)

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. - Andrej J. Savol; Virginia M. Burger; Pratul K. Agarwal; Arvind Ramanathan; Chakra S. Chennubhotla (Bioinform., 2011)

Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble. - Virginia M. Burger; Arvind Ramanathan; Andrej J. Savol; Christopher B. Stanley; Pratul K. Agarwal; Chakra S. Chennubhotla (Pacific Symposium on Biocomputing, 2012)

Spectral Clustering Strategies for Heterogeneous Disease Data. - Grace T. Huang; Kathryn I. Cunningham; Panayiotis V. Benos; Chakra S. Chennubhotla (Pacific Symposium on Biocomputing, 2013)

Evol and ProDy for bridging protein sequence evolution and structural dynamics. - Ahmet Bakan; Anindita Dutta; Wenzhi Mao; Ying Liu; Chakra Chennubhotla 001; Timothy R. Lezon; Ivet Bahar (Bioinform., 2014)

ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics. - Arvind Ramanathan; Laura L. Pullum; Tanner C. Hobson; Chad A. Steed; Shannon P. Quinn; Chakra S. Chennubhotla; Silvia Valkova (BMC Bioinform., 2015)

Architectural patterns for differential diagnosis of proliferative breast lesions from histopathological images. - Luong Nguyen; Akif Burak Tosun; Jeffrey L. Fine; D. Lansing Taylor; S. Chakra Chennubhotla (ISBI, 2017)

Histological Detection of High-Risk Benign Breast Lesions from Whole Slide Images. - Akif Burak Tosun; Luong Nguyen; Nathan Ong; Olga Navolotskaia; Gloria Carter; Jeffrey L. Fine; D. Lansing Taylor; S. Chakra Chennubhotla (MICCAI (2), 2017)

Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images. - Luong Nguyen; Akif Burak Tosun; Jeffrey L. Fine; Adrian V. Lee; D. Lansing Taylor; S. Chakra Chennubhotla (IEEE Trans. Medical Imaging, 2017)

Dynamic Social Network Modeling of Diffuse Subcellular Morphologies. - Andrew Durden; Allyson T. Loy; Barbara Reaves; Mojtaba Sedigh Fazli; Abigail Courtney; Frederick D. Quinn; S. Chakra Chennubhotla; Shannon P. Quinn (SciPy, 2018)

Stacked Neural Networks for end-to-end ciliary motion analysis. - Charles Lu 001; Maurice Marx; Maliha Zahid; Cecilia W. Lo; Chakra Chennubhotla 001; Shannon P. Quinn (CoRR, 2018)

Classifying Nuclei Shape Heterogeneity in Breast Tumors with Skeletons. - Brian Falkenstein; Adriana Kovashka; Seong Jae Hwang; S. Chakra Chennubhotla (ECCV Workshops (1), 2020)

Modeling Histological Patterns for Differential Diagnosis of Atypical Breast Lesions. - Akash Parvatikar; Om Choudhary; Arvind Ramanathan; Olga Navolotskaia; Gloria Carter; Akif Burak Tosun; Jeffrey L. Fine; S. Chakra Chennubhotla (MICCAI (5), 2020)

Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology. - Marcus Hill; Mojtaba Sedigh Fazli; Rachel Mattson; Meekail Zain; Andrew Durden; Allyson T. Loy; Barbara Reaves; Abigail Courtney; Frederick D. Quinn; S. Chakra Chennubhotla; Shannon P. Quinn (SciPy, 2020)

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. - Arvind Ramanathan; Heng Ma; Akash Parvatikar; S. Chakra Chennubhotla (CoRR, 2020)

OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks. - Mojtaba Sedigh Fazli; Marcus Hill; Andrew Durden; Rachel Mattson; Allyson T. Loy; Barbara Reaves; Abigail Courtney; Frederick D. Quinn; Chakra Chennubhotla 001; Shannon Quinn (J. Open Source Softw., 2020)

HistoMapr™: An Explainable AI (xAI) Platform for Computational Pathology Solutions. - Akif Burak Tosun; Filippo Pullara; Michael J. Becich; D. Lansing Taylor; S. Chakra Chennubhotla; Jeffrey L. Fine (AI and ML for Digital Pathology, 2020)

Prototypical Models for Classifying High-Risk Atypical Breast Lesions. - Akash Parvatikar; Om Choudhary; Arvind Ramanathan; Rebekah Jenkins; Olga Navolotskaia; Gloria Carter; Akif Burak Tosun; Jeffrey L. Fine; S. Chakra Chennubhotla (MICCAI (8), 2021)

Classification of Diffuse Subcellular Morphologies. - Neelima Pulagam; Marcus Hill; Mojtaba Sedigh Fazli; Rachel Mattson; Meekail Zain; Andrew Durden; Frederick D. Quinn; S. Chakra Chennubhotla; Shannon P. Quinn (SciPy, 2021)

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. - Anda Trifan; Defne Gorgun; Michael Salim; Zongyi Li; Alexander Brace; Maxim Zvyagin; Heng Ma; Austin Clyde; David Clark; David J. Hardy; Tom Burnley; Lei Huang 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)