Search Results - "Prabhakaran, Sandhya"

Probabilistic inference of viral quasispecies subject to recombination by Töpfer, Armin, Zagordi, Osvaldo, Prabhakaran, Sandhya, Roth, Volker, Halperin, Eran, Beerenwinkel, Niko

“…RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination…”
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Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations by Giallonardo, Francesca Di, Töpfer, Armin, Rey, Melanie, Prabhakaran, Sandhya, Duport, Yannick, Leemann, Christine, Schmutz, Stefan, Campbell, Nottania K, Joos, Beda, Lecca, Maria Rita, Patrignani, Andrea, Däumer, Martin, Beisel, Christian, Rusert, Peter, Trkola, Alexandra, Günthard, Huldrych F, Roth, Volker, Beerenwinkel, Niko, Metzner, Karin J

“…Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently…”
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Virtual alignment of pathology image series for multi-gigapixel whole slide images by Gatenbee, Chandler D., Baker, Ann-Marie, Prabhakaran, Sandhya, Swinyard, Ottilie, Slebos, Robbert J. C., Mandal, Gunjan, Mulholland, Eoghan, Andor, Noemi, Marusyk, Andriy, Leedham, Simon, Conejo-Garcia, Jose R., Chung, Christine H., Robertson-Tessi, Mark, Graham, Trevor A., Anderson, Alexander R. A.

“…Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and…”
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PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects by Gonçalves, Inês G, Hormuth, 2nd, David A, Prabhakaran, Sandhya, Phillips, Caleb M, García-Aznar, José Manuel

“…models of biological systems are usually very complex and rely on a large number of parameters describing physical and biological properties that require…”
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Sparcle: assigning transcripts to cells in multiplexed images by Prabhakaran, Sandhya

“…Imaging-based spatial transcriptomics has the power to reveal patterns of single-cell gene expression by detecting mRNA transcripts as individually resolved…”
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Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment by Azizi, Elham, Carr, Ambrose J., Plitas, George, Cornish, Andrew E., Konopacki, Catherine, Prabhakaran, Sandhya, Nainys, Juozas, Wu, Kenmin, Kiseliovas, Vaidotas, Setty, Manu, Choi, Kristy, Fromme, Rachel M., Dao, Phuong, McKenney, Peter T., Wasti, Ruby C., Kadaveru, Krishna, Mazutis, Linas, Rudensky, Alexander Y., Pe’er, Dana

“…Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response…”
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Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells by Anadon, Carmen M., Yu, Xiaoqing, Hänggi, Kay, Biswas, Subir, Chaurio, Ricardo A., Martin, Alexandra, Payne, Kyle K., Mandal, Gunjan, Innamarato, Patrick, Harro, Carly M., Mine, Jessica A., Sprenger, Kimberly B., Cortina, Carla, Powers, John J., Costich, Tara Lee, Perez, Bradford A., Gatenbee, Chandler D., Prabhakaran, Sandhya, Marchion, Douglas, Heemskerk, Mirjam H.M., Curiel, Tyler J., Anderson, Alexander R., Wenham, Robert M., Rodriguez, Paulo C., Conejo-Garcia, Jose R.

“…Despite repeated associations between T cell infiltration and outcome, human ovarian cancer remains poorly responsive to immunotherapy. We report that the…”
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IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer by Mandal, Gunjan, Biswas, Subir, Anadon, Carmen M, Yu, Xiaoqing, Gatenbee, Chandler D, Prabhakaran, Sandhya, Payne, Kyle K, Chaurio, Ricardo A, Martin, Alexandra, Innamarato, Patrick, Moran, Carlos, Powers, John J, Harro, Carly M, Mine, Jessica A, Sprenger, Kimberly B, Rigolizzo, Kristen E, Wang, Xuefeng, Curiel, Tyler J, Rodriguez, Paulo C, Anderson, Alexander R, Saglam, Ozlen, Conejo-Garcia, Jose R

“…Recent studies suggest that B cells could play an important role in the tumor microenvironment. However, the role of humoral responses in endometrial cancer…”
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HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model by Prabhakaran, Sandhya, Rey, Melanie, Zagordi, Osvaldo, Beerenwinkel, Niko, Roth, Volker

“…This paper presents a new computational technique for the identification of HIV haplotypes. HIV tends to generate many potentially drug-resistant mutants…”
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Abstract 2078: VALIS: Virtual Alignment of pathoLogy Image Series for multi-gigapixel whole slide images by Gatenbee, Chandler Dean, Baker, Ann-Marie, Prabhakaran, Sandhya, Robertson-Tessi, Mark, Graham, Trevor, Anderson, Alexander R.

“…Abstract Interest in spatial omics is on the rise, but generation of highly multiplexed images used in many spatial analyses remains challenging, due to cost,…”
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Abstract 6614: Spatial transcriptomic driven mechanistic model to investigate and predict pathogenesis of oligodendroglioma by Prabhakaran, Sandhya, Cho, Heyrim, Strobl, Maximilian, Rockne, Russell, Anderson, Alexander R.

“…Abstract Rationale: Oligodendrogliomas represent the second most common glioma in adults after glioblastoma. Recent studies conjecture that oligodendrocyte…”
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Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T-cells by Galindo, Carmen Maria Anadon, Yu, Xiaoqing, Hanggi, kay, Biswas, Subir, Chaurio, Ricardo, Mandal, Gunjan, Martin, Alexandra, Payne, Kyle K, Innamarato, Pasquale P, Harro, Carly M, Mine, Jessica, Sprenger, Kimberly, Cortina, Carla, Powers, John J, Perez, Bradford A, Gatenbee, Chandler D, Prabhakaran, Sandhya, Marchion, Douglas, Heemskerk, Mirjam H, Curiel, Tyler J, Anderson, Alexander R.A., Wenham, Robert M, Rodriguez, Paulo C, Conejo-Garcia, Jose R

“…Abstract Despite repeated associations between T-cell infiltration and patient outcome, human ovarian cancer remains poorly responsive to immunotherapy. We…”
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Spontaneous class-switched antibody responses at endometrial cancer tumor bed drives superior patients’ outcome by MANDAL, GUNJAN, Biswas, Subir, Anadon, Carmen M, Yu, Xiaoqing, Gatenbee, Chandler D, Prabhakaran, Sandhya, Payne, Kyle K, Chaurio, Ricardo A, Martin, Alexandra, Innamarato, Patrick, Moran, Carlos, Powers, John J, Harro, Carly M, Mine, Jessica A, Sprenger, Kimberly B, Rigolizzo, Kristen E, Wang, Xuefeng, Curiel, Tyler J, Rodriguez, Paulo C, Anderson, Alexander R.A., Saglam, Ozlen, Conejo-Garcia, Jose R

“…Abstract The role of humoral responses in endometrial cancer remains insufficiently investigated. Using a cohort of 107 patients with different histological…”
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Developing tools for analyzing and viewing multiplexed images by Prabhakaran, Sandhya, Gatenbee, Chandler, Anderson, Alexander R A

“…Dr. Prabhakaran and Dr Gatenbee are research scientists in Anderson's lab and have developed Mistic, a publicly available tool that simultaneously views…”
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Abstract C035: Spatially limited stroma-mediated resistance potentiates targeted therapy resistance through an integration of multiple juxtacrine and paracrine mechanisms by Desai, Bina, Miti, Tatiana, Prabhakaran, Sandhya, Miroshnychenko, Daria, Henry, Menkara, Marusyk, Viktoriya, Gatenbee, Chandler, Bui, Marilyn, Scott, Jacob, Altrock, Philipp M., Haura, Eric, Anderson, Alexander R.A., Basanta, David, Marusyk, Andriy

“…Abstract Despite the ability to induce strong clinical responses, therapies that target mutational drivers of oncogenic signaling are not curative in advanced…”
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Abstract 5037: Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response by Prabhakaran, Sandhya, Gatenbee, Chandler, Robertson-Tessi, Mark, Beg, Amer A., Gray, Jhanelle, Antonia, Scott, Gatenby, Robert A., Anderson, Alexander R.

“…Abstract Rationale: Examination of multiplexed images of tissues has recently emerged as a routine clinical procedure for cancer diagnosis and prognosis. The…”
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Abstract B020: Distinct spatiotemporal tumor-immune ecologies enable disease prediction in NSCLC patients by Prabhakaran, Sandhya, Gatenbee, Chandler, Robertson-Tessi, Mark, Beg, Amer A., Gray, Jhanelle, Antonia, Scott, Gatenby, Robert A., Anderson, Alexander R.A.

“…Abstract Purpose of study: Non-small cell lung cancer (NSCLC) is the most common and fatal of cancers. In this work, we examine multiplexed images of NSCLC…”
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Abstract 124: Autocrine signaling extends PD-L1 expression in NSCLC following an active immune response by Bursell, Taylor M., Prabhakaran, Sandhya, Luddy, Kimberly, Pineriro, Julian, Bravo, Rafael, West, Jeffrey, Robertson-Tessi, Mark, Beg, Aner, Gray, Jhanelle, Antonia, Scott, Gatenby, Robert, Anderson, Alexander

“…Abstract Checkpoint inhibitors disrupting the PD-1/PD-L1 axis are used in multiple cancer subtypes. However, not all patients respond, and predictive…”
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Spatial analysis of recurrent glioblastoma reveals perivascular niche organization by Onubogu, Ugoma, Gatenbee, Chandler D, Prabhakaran, Sandhya, Wolfe, Kelsey L, Oakes, Benjamin, Salatino, Roberto, Vaubel, Rachael, Szentirmai, Oszkar, Anderson, Alexander Ra, Janiszewska, Michalina

“…Tumor evolution is driven by genetic variation; however, it is the tumor microenvironment (TME) that provides the selective pressure contributing to evolution…”
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Abstract A021: Evolutionary immunotherapy in NSCLC: An integrated approach by Prabhakaran, Sandhya, Bursell, Taylor M., Luddy, Kimberly, Pineiro, Julian, Bravo, Rafael, West, Jeffrey, Johnson, Megan, Robertson-Tessi, Mark, Beg, Amer A., Gray, Jhanelle E., Antonia, Scott, Gatenby, Robert A., Anderson, Alexander R. A.

“…Abstract Purpose: Our study examines tumor growth dynamics and immunosuppression under the presence of immune attack to identify optimal immune pulsing…”
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