Publications

Journals, Conferences and Workshops

Evolutionary immunotherapy in NSCLC: An integrated approach

Prabhakaran S, Bursell TM, Luddy K, Pineiro J, Bravo R, West J, Johnson M, Robertson-Tessi M, Beg AA, Gray JE, Antonia S, Gatenby RA, Anderson AR.

Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Research: 84(3). 2024 view pdf
Spatial analysis of recurrent glioblastoma reveals perivascular niche organization

Ugoma Onubogu, Chandler D. Gatenbee, Sandhya Prabhakaran, Kelsey Wolfe, Benjamin Oakes, Roberto Salatino, Rachael Vaubel, Oszkar Szentirmai, Alexander R.A. Anderson, Michalina Janiszewska

Under Review, 2024.
Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma

Zuzanna Nowicka, Frederika Rentzeperis, Richard Beck, Vural Tagal, Ana M Forero Pinto, Elisa Scanu, Thomas Veith, Jackson Cole, Didem Ilter, William Dominguez Viqueira, Jamie K Teer, Konstantin Maksin, Stefano Pasetto, Mahmoud A Abdalah, Giada Fiandaca, Sandhya Prabhakaran, Andrew Schultz, Maureiq Ojwang, Jill S Barnholtz-Sloan, Farinhas M Joaquim, Ana P Gomes, Parag Katira, Noemi Andor

bioRxiv, 2023. view pdf
Addressing persistent challenges in digital image analysis of cancerous tissues

Sandhya Prabhakaran*, Clarence Yapp*, Gregory J Baker, Johanna Beyer, Young Hwan Chang, Allison L Creason, Robert Krueger, Jeremy Muhlich, Nathan Heath Patterson, Kevin Sidak, Damir Sudar, Adam J Taylor, Luke Ternes, Jakob Troidl, Xie Yubin, Artem Sokolov, Darren R Tyson, Participants of the Cell Imaging Hackathon 2022.

bioRxiv, 2023. view pdf
VALIS: Virtual Alignment of pathoLogy Image Series

Chandler D. Gatenbee, Ann-Marie Baker, Sandhya Prabhakaran, Robbert J. C. Slebos, Gunjan Mandal, Eoghan Mulholland, Simon Leedham, Jose R. Conejo-Garcia, Christine H. Chung, Mark Robertson-Tessi, Trevor A. Graham, Alexander R.A. Anderson.

Nature Communications, 2023

In: Proceedings of the 114th Annual Meeting of the American Association for Cancer Research; 2023 April 14-19; Orlando, FL. Philadelphia (PA): AACR; 2023. Abstract nr 6614. view site

bioRxiv, 2021. view pdf
Spatial transcriptomic driven mechanistic model to investigate and predict pathogenesis of oligodendroglioma

Sandhya Prabhakaran*, Heyrim Cho*, Maximilian Strobl, Russell Rockne, Alexander R.A. Anderson.

In: Proceedings of the 114th Annual Meeting of the American Association for Cancer Research; 2023 April 14-19; Orlando, FL. Philadelphia (PA): AACR; 2023. Abstract nr 6614. view site
Autocrine signaling extends PD-L1 expression in NSCLC following an active immune response

Taylor M. Bursell*, Sandhya Prabhakaran*, Kimberly Luddy, Julian Pineriro, Rafael Bravo, Jeffrey West, Mark Robertson-Tessi, Amer Beg, Jhanelle Gray, Scott Antonia, Robert Gatenby, Alexander R.A. Anderson.

In: Proceedings of the 114th Annual Meeting of the American Association for Cancer Research; 2023 April 14-19; Orlando, FL. Philadelphia (PA): AACR; 2023. Abstract nr 124. view site
PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects

Inês G. Gonçalves, David A. Hormuth II, Sandhya Prabhakaran, Caleb M. Phillips, José Manuel García-Aznar.

Gigabyte, 2023 view site

bioRxiv, 2022 view site
Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response

Sandhya Prabhakaran, Chandler Gatenbee, Mark Robertson-Tessi, Amer A. Beg, Jhanelle Gray, Scott Antonia, Robert A. Gatenby, Alexander R. A. Anderson.

bioRxiv, 2022 view site
Developing tools for analyzing and viewing multiplexed images

Sandhya Prabhakaran, Chandler Gatenbee, Alexander R. A. Anderson.

Cell Patterns 2022 view pdf

A 'People of Data' article featuring the Anderson lab
Mistic: an open-source multiplexed image t-SNE viewer

Sandhya Prabhakaran, Chandler Gatenbee, Mark Robertson-Tessi, Jeffrey West, Amer A. Beg, Jhanelle Gray,Scott Antonia, Robert A. Gatenby, Alexander R. A. Anderson.

Cell Patterns 2022 view pdf

bioRxiv, 2021. view pdf

Mistic on the Mathematical Oncology blog Visit Site

Mistic is highlighted on Bokeh's User Showcase Visit Site

Moffitt news release on Mistic Visit Site

Inside Precision Medicine featuring Mistic Visit Site

Medical Xpress featuring Mistic Visit Site
Sparcle: assigning transcripts to cells in multiplexed images

Sandhya Prabhakaran

Bioinformatics Advances 2022. view pdf
Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response [abstract]

Sandhya Prabhakaran, Chandler Gatenbee, Mark Robertson-Tessi, Amer A. Beg, Jhanelle Gray, Scott Antonia, Robert A. Gatenby, Alexander R. A. Anderson

Proceedings of the 112th Annual Meeting of the American Association for Cancer Research; 2022 Apr 8–13; New Orleans. Louisiana: AACR; 2022. Abstract nr 5037. 2022. view site
Ovarian Cancer Immunogenicity is Governed by a Narrow Subset of Progenitor Tissue-Resident Memory T-Cells

Anadon, Carmen M. and Yu, Xiaoqing and Biswas, Subir and Chaurio, Ricardo A. and Hanggi, Kay and Martin, Alexandra and Payne, Kyle K. and Mandal, Gunjan and Innamarato, Pasquale P. and Harro, Carly M. and Mine, Jessica A. and Sprenger, Kimberly B. and Powers, John J. and Costich, Tara L. and Perez, Bradford A. and Gatenbee, Chandler D. and Prabhakaran, Sandhya and Marchion, Douglas and Heemskerk, Mirjam HM and Curiel, Tyler J. and Anderson, Alexander R.A. and Wenham, Robert M. and Rodriguez, Paulo C. and Conejo-Garcia, Jose R.

Cancer Cell 2022.
IgA-dominated humoral immune responses govern patients’ outcome in endometrial cancer

Gunjan Mandal, Subir Biswas, Carmen Anadon Galindo, Xiaoqing Yu, Chandler Gatenbee, Sandhya Prabhakaran, Kyle Payne, Ricardo Chaurio, Alexandra Martin, Patrick Innamarato, Carlos Morán-Segura, John Powers, Carly Harro, Jessica Mine, Kristen Rigolizzo, Kimberly Sprenger, Xuefeng Wang, Tyler Curiel, Paulo Rodriguez, Alexander R.A. Anderson, Ozlen Saglam, and José Conejo-Garcia

Cancer Research, 2022. view site
Bayesian Clustering For HIV1 Protease Inhibitor Contact Maps

Sandhya Prabhakaran and Julia E. Vogt.

Artificial Intelligence in Medicine (AIME), Springer Lecture Notes in Artificial Intelligence, 2019. Visit Site
A Nonparametric Multi-view Model for Estimating Cell Type-Specific Gene Regulatory Networks

Cassandra Burdziak, Elham Azizi, Sandhya Prabhakaran, Dana Pe'er.

arXiv:1902.08138 in stat.ML, 2019. view pdf
A Bayesian Model for Overlapping Clusters from Distance Data

Sandhya Prabhakaran, Severin Kasser, Sven Wellmann and Julia E. Vogt.

Spotlight, ALL OF BAYESIAN NONPARAMETRICS, BNP@Neurips, 2018. view pdf
Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment

Elham Azizi*, Ambrose J. Carr*, George Plitas*, Andrew E. Cornish*, Catherine Konopacki, Sandhya Prabhakaran, Juozas Nainys, Kenmin Wu, Vaidotas Kiseliovas, Manu Setty, Kristy Choi, Phuong Dao, Linas Mazutis, Alexander Y. Rudensky, Dana Pe'er. bioRxiv, 2017.view pdf, Cell 174(5): 1293-1308, 2018. view pdf

(*Authors contributed equally)
Bayesian Inference for Single-cell Clustering and Imputing

Elham Azizi*, Sandhya Prabhakaran*, Ambrose Carr, Dana Peer. Genomics and Computational Biology, 2017.view pdf

(*Authors contributed equally)
Tensor decomposition for single-cell RNA-seq data

Kristy Choi*, Ambrose J Carr*, Sandhya Prabhakaran and Dana Pe'er.
(*Authors contributed equally)
Practical Bayesian Nonparametrics Workshop, BNP@Neurips, 2016. view pdf
Bayesian Nonparametric Extensions to the K-mer Motif Multinomial Mixture Model

Brian Trippe and Sandhya Prabhakaran. Practical Bayesian Nonparametrics Workshop, BNP@Neurips, 2016. view pdf
K-mer Motif Multinomial Mixtures

Brian L Trippe, Sandhya Prabhakaran, Harmen Bussemaker.
bioRxiv:096735, 2016.view pdf
Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data

Sandhya Prabhakaran*, Elham Azizi*, Ambrose Carr, Dana Peer. The 33rd International Conference on Machine Learning (ICML’16), pages 1070 --1079, 2016.view pdf view supplementary

(*Authors contributed equally)
Probabilistic Clustering of Time-Evolving Distance Data

Julia E. Vogt, Marius Kloft, Stefan Stark, Sudhir Raman, Sandhya Prabhakaran, Volker Roth, Gunnar Rätsch. Machine Learning Journal, 2015,view pdf
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Francesca Di Giallonardo, Armin Töpfer, Melanie Rey, Sandhya Prabhakaran, Yannick Duport, Christine Leemann, Stefan Schmutz et al. Nucleic Acid Research (NAR) 42, no. 14, 2014. view pdf
HIV Haplotype Inference using a propagating Dirichlet Process Mixture Model

Sandhya Prabhakaran, Melanie Rey, Osvaldo Zagordi, Niko Beerenwinkel and Volker Roth. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), volume 11, no.1, 2014. view pdf -- An extended abstract was presented at the Machine Learning in Computational Biology (MLCB) Workshop, NIPS 2010
Recovering networks from distance data

Sandhya Prabhakaran, David Adametz, Karin J. Metzner, Alexander Boehm and Volker Roth. Machine Learning Journal, volume 92:2-3, pages 251--283, 2013. view pdf -- A conference proceeding has appeared here: Asian Conference of Machine Learning (ACML'12), Journal of Machine Learning Research Workshop and Conference Proceedings, volume 25, pages 349--364, 2012.
view pdf Best Student Paper award
Probabilistic Inference of Viral Quasispecies Subject to Recombination

Armin Toepfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin and Niko Beerenwinkel. Journal of Computational Biology (JCB), volume 20:2, pages 113--123, 2013. view pdf -- A conference proceeding has appeared here: The 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB'12), pages 342--354, 2012. view pdf
Automatic Model Selection in Archetype Analysis

Sandhya Prabhakaran, Sudhir Raman, Julia E. Vogt and Volker Roth. 34th German Conference on Pattern Recognition (DAGM/OAGM), volume 7476 of Lecture Notes in Computer Science, page 458--467, 2012.
view pdf
The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data

Julia E. Vogt, Sandhya Prabhakaran, Thomas J. Fuchs and Volker Roth. The 27th International Conference on Machine Learning (ICML'10), pages 1111--1118, 2010. view pdf Best Paper award runner-up
Converting z/OS assembler code to COBOL

Sandhya Prabhakaran IBM developerworks, 2007. Visit Site

Book Chapter

Structure Preserving Embedding of Dissimilarity Data

Volker Roth, Thomas J. Fuchs, Julia E. Vogt, Sandhya Prabhakaran and Joachim M. Buhmann. Similarity-Based Pattern Analysis and Recognition, Advances in Computer Vision and Pattern Recognition series, Springer London, pages 157–177, 2013. view pdf

Theses

Machine Learning Methods for HIV/AIDS Diagnostics and Therapy Planning, Doctoral Thesis, 2014. view pdf
Multi-scale, Reactive Motion Planning with Deformable Linear Objects, Masters Thesis, 2008. view pdf

Intellectual Property (IP) Disclosure

Data Transfer from JCL to COBOL

Padmaraj Meethal and Sandhya Prabhakaran, IBM Software Laboratories.
Disclosure number: IPCOM000167543D, 2008 Visit Site

Publications

Journals, Conferences and Workshops

Evolutionary immunotherapy in NSCLC: An integrated approach

Spatial analysis of recurrent glioblastoma reveals perivascular niche organization

Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma

Addressing persistent challenges in digital image analysis of cancerous tissues

VALIS: Virtual Alignment of pathoLogy Image Series

Spatial transcriptomic driven mechanistic model to investigate and predict pathogenesis of oligodendroglioma

Autocrine signaling extends PD-L1 expression in NSCLC following an active immune response

PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects

Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response

Developing tools for analyzing and viewing multiplexed images

Mistic: an open-source multiplexed image t-SNE viewer

Sparcle: assigning transcripts to cells in multiplexed images

Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response [abstract]

Ovarian Cancer Immunogenicity is Governed by a Narrow Subset of Progenitor Tissue-Resident Memory T-Cells

IgA-dominated humoral immune responses govern patients’ outcome in endometrial cancer

Bayesian Clustering For HIV1 Protease Inhibitor Contact Maps

A Nonparametric Multi-view Model for Estimating Cell Type-Specific Gene Regulatory Networks

A Bayesian Model for Overlapping Clusters from Distance Data

Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment

Bayesian Inference for Single-cell Clustering and Imputing

Tensor decomposition for single-cell RNA-seq data

Bayesian Nonparametric Extensions to the K-mer Motif Multinomial Mixture Model

K-mer Motif Multinomial Mixtures

Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data

Probabilistic Clustering of Time-Evolving Distance Data

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

HIV Haplotype Inference using a propagating Dirichlet Process Mixture Model

Recovering networks from distance data

Probabilistic Inference of Viral Quasispecies Subject to Recombination

Automatic Model Selection in Archetype Analysis

The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data

Converting z/OS assembler code to COBOL

Book Chapter

Structure Preserving Embedding of Dissimilarity Data

Theses

Intellectual Property (IP) Disclosure

Data Transfer from JCL to COBOL