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ORCIDS. Chakra Chennubhotla
Person information
- affiliation: SpIntellx Inc., Pittsburgh, PA, USA
- affiliation: University of Pittsburgh, Department of Computational and Systems Biology, Pittsburgh, PA, USA
- affiliation (former): University of Toronto, ON, Canada
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2020 – today
- 2023
[j11]Abigail C. Dommer, Lorenzo Casalino
, Fiona L. Kearns, Mia A. Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'Connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas F. Miller III, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro:
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37(1): 28-44 (2023)- 2022
- [j10]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, John D. McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Tom Gibbs, James C. Phillips, S. Chakra Chennubhotla, Ian T. Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, Arvind Ramanathan:
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. Int. J. High Perform. Comput. Appl. 36(5-6): 603-623 (2022) - 2021
- [c20]Akash Parvatikar, Om Choudhary, Arvind Ramanathan, Rebekah Jenkins, Olga Navolotskaia, Gloria Carter, Akif Burak Tosun, Jeffrey L. Fine, S. Chakra Chennubhotla:
Prototypical Models for Classifying High-Risk Atypical Breast Lesions. MICCAI (8) 2021: 143-152 - [c19]Neelima Pulagam, Marcus Hill, Mojtaba Sedigh Fazli, Rachel Mattson, Meekail Zain, Andrew Durden, Frederick D. Quinn, S. Chakra Chennubhotla, Shannon P. Quinn:
Classification of Diffuse Subcellular Morphologies. SciPy 2021: 115-122 - 2020
- [j9]Mojtaba Sedigh Fazli, Marcus Hill, Andrew Durden, Rachel Mattson, Allyson T. Loy, Barbara Reaves, Abigail Courtney, Frederick D. Quinn, Chakra Chennubhotla, Shannon Quinn:
OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks. J. Open Source Softw. 5(47): 1983 (2020) - [c18]Brian Falkenstein, Adriana Kovashka, Seong Jae Hwang, S. Chakra Chennubhotla:
Classifying Nuclei Shape Heterogeneity in Breast Tumors with Skeletons. ECCV Workshops (1) 2020: 310-323 - [c17]Akash Parvatikar, Om Choudhary, Arvind Ramanathan, Olga Navolotskaia, Gloria Carter, Akif Burak Tosun, Jeffrey L. Fine, S. Chakra Chennubhotla:
Modeling Histological Patterns for Differential Diagnosis of Atypical Breast Lesions. MICCAI (5) 2020: 550-560 - [c16]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:
Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology. SciPy 2020: 91-97 - [p1]Akif Burak Tosun, Filippo Pullara, Michael J. Becich, D. Lansing Taylor, S. Chakra Chennubhotla, Jeffrey L. Fine:
HistoMapr™: An Explainable AI (xAI) Platform for Computational Pathology Solutions. AI and ML for Digital Pathology 2020: 204-227 - [i2]Arvind Ramanathan, Heng Ma, Akash Parvatikar, S. Chakra Chennubhotla:
Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. CoRR abs/2012.00885 (2020)
2010 – 2019
- 2018
- [c15]Andrew Durden, Allyson T. Loy, Barbara Reaves, Mojtaba Sedigh Fazli, Abigail Courtney, Frederick D. Quinn, S. Chakra Chennubhotla, Shannon P. Quinn:
Dynamic Social Network Modeling of Diffuse Subcellular Morphologies. SciPy 2018: 1-7 - [i1]Charles Lu, Maurice Marx, Maliha Zahid, Cecilia W. Lo, Chakra Chennubhotla, Shannon P. Quinn:
Stacked Neural Networks for end-to-end ciliary motion analysis. CoRR abs/1803.07534 (2018) - 2017
- [j8]Luong Nguyen, Akif Burak Tosun, Jeffrey L. Fine, Adrian V. Lee, D. Lansing Taylor, S. Chakra Chennubhotla:
Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images. IEEE Trans. Medical Imaging 36(7): 1522-1532 (2017) - [c14]Luong Nguyen, Akif Burak Tosun, Jeffrey L. Fine, D. Lansing Taylor, S. Chakra Chennubhotla:
Architectural patterns for differential diagnosis of proliferative breast lesions from histopathological images. ISBI 2017: 152-155 - [c13]Akif Burak Tosun, Luong Nguyen, Nathan Ong, Olga Navolotskaia, Gloria Carter, Jeffrey L. Fine, D. Lansing Taylor, S. Chakra Chennubhotla:
Histological Detection of High-Risk Benign Breast Lesions from Whole Slide Images. MICCAI (2) 2017: 144-152 - 2015
- [j7]Arvind Ramanathan, Laura L. Pullum, Tanner C. Hobson, Chad A. Steed, Shannon P. Quinn, Chakra S. Chennubhotla, Silvia Valkova:
ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics. BMC Bioinform. 16(S17): S4 (2015) - 2014
- [j6]Ahmet Bakan, Anindita Dutta, Wenzhi Mao, Ying Liu, Chakra Chennubhotla, Timothy R. Lezon, Ivet Bahar:
Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinform. 30(18): 2681-2683 (2014) - 2013
- [c12]Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla:
Spectral Clustering Strategies for Heterogeneous Disease Data. Pacific Symposium on Biocomputing 2013: 212-223 - 2012
- [c11]Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanley, Pratul K. Agarwal, Chakra S. Chennubhotla:
Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble. Pacific Symposium on Biocomputing 2012: 70-81 - 2011
- [j5]Andrej J. Savol, Virginia M. Burger, Pratul K. Agarwal, Arvind Ramanathan, Chakra S. Chennubhotla:
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. Bioinform. 27(13): 52-60 (2011)
2000 – 2009
- 2007
- [j4]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. J. Comput. Biol. 14(6): 765-776 (2007) - [j3]Chakra Chennubhotla, Ivet Bahar:
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(9) (2007) - [j2]Chakra Chennubhotla, Ivet Bahar:
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(10) (2007) - [c10]Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar:
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. ISMB/ECCB (Supplement of Bioinformatics) 2007: 175-184 - 2006
- [j1]Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai:
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinform. 7: 478 (2006) - [c9]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB 2006: 379-393 - 2004
- [c8]Francisco J. Estrada, Allan D. Jepson, Chakra Chennubhotla:
Spectral Embedding and Min Cut for Image Segmentation. BMVC 2004: 1-10 - [c7]Chakra Chennubhotla, Allan D. Jepson:
Perceptual Distance Normalization for Appearance Detection. ICPR (2) 2004: 23-27 - [c6]Chakra Chennubhotla, Allan D. Jepson:
Hierarchical Eigensolver for Transition Matrices in Spectral Methods. NIPS 2004: 273-280 - 2003
- [c5]Chakra Chennubhotla, Alberto Paccanaro:
Markov Analysis of Protein Sequence Similarities. WIRN 2003: 278-286 - 2002
- [c4]Chakra Chennubhotla, Allan D. Jepson, John Midgley:
Robust Contrast-Invariant EigenDetection. ICPR (2) 2002: 745-748 - [c3]Chakra Chennubhotla, Allan D. Jepson:
Half-Lives of EigenFlows for Spectral Clustering. NIPS 2002: 689-696 - 2001
- [c2]Chakra Chennubhotla, Allan D. Jepson:
Sparse PCA: Extracting Multi-scale Structure from Data. ICCV 2001: 641-647
1990 – 1999
- 1994
- [c1]David W. Jacobs, Chakra Chennubhotla:
Finding structurally consistent motion correspondences. ICPR (1) 1994: 650-653
Coauthor Index
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