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Spatial proteomics and transcriptomics reveal early immune cell organization in human pancreatic intraepithelial neoplasia

Cancer Research
2024 | Journal article
Contributors: Lyman, Melissa R.; Mitchell, Jacob T.; Kagohara, Luciane T.; Huff, Amanda L.; Haldar, Daniel; Shin, Sarah; Guinn, Samantha; Barrett, Benjamin; Longway, Gabriella; Hernandez, Alexei et al.
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Data from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Data Table 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Equations from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Figures from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Movie 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Movie 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Movie 3 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Movie 4 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Table 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-09-27 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Data from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

Cancer Research
2024-08-15 | Journal article
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Data Table 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Data Table 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Equations from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Equations from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Figures from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Figures from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Supplementary Movie 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 3 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 3 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 4 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Movie 4 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Table 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
Source: check_circle
Crossref

Supplementary Table 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

2024-08-15 | Preprint
Contributors: Shuming Zhang; Atul Deshpande; Babita K. Verma; Hanwen Wang; Haoyang Mi; Long Yuan; Won Jin Ho; Elizabeth M. Jaffee; Qingfeng Zhu; Robert A. Anders et al.
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Crossref

Virtual patient analysis identifies strategies to improve the performance of predictive biomarkers for PD-1 blockade

2024-05-21 | Preprint
Contributors: Theinmozhi Arulraj; Hanwen Wang; Atul Deshpande; Ravi Varadhan; Leisha A. Emens; Elizabeth M. Jaffee; Elana J. Fertig; Cesar A. Santa-Maria; Aleksander S. Popel
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Crossref

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

BioRxiv
2023 | Journal article
Contributors: Zhang, Shuming; Deshpande, Atul; Verma, Babita K.; Wang, Hanwen; Mi, Haoyang; Yuan, Long; Ho, Won Jin; Jaffee, Elizabeth M.; Zhu, Qingfeng; Anders, Robert A et al.
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Web of Science Researcher Profile Sync

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

bioRxiv
2023 | Other
EID:

2-s2.0-85150949797

Part of ISSN: 26928205
Contributors: Zhang, S.; Yuan, L.; Danilova, L.; Mo, G.; Zhu, Q.; Deshpande, A.; Bell, A.T.F.; Elisseeff, J.; Popel, A.S.; Anders, R.A. et al.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

Genome Medicine
2023 | Journal article
EID:

2-s2.0-85171580414

Part of ISSN: 1756994X
Contributors: Zhang, S.; Yuan, L.; Danilova, L.; Mo, G.; Zhu, Q.; Deshpande, A.; Bell, A.T.F.; Elisseeff, J.; Popel, A.S.; Anders, R.A. et al.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces (vol 14, pg 285, 2023)

Cell Systems
2023 | Journal article
Contributors: Deshpande, Atul; Loth, Melanie; Sidiropoulos, Dimitrios N.; Zhang, Shuming; Yuan, Long; Bell, Alexander T. F.; Zhu, Qingfeng; Ho, Won Jin; Santa-Maria, Cesar; Gilkes, Daniele M. et al.
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Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

2023-09-17 | Preprint
Contributors: Jeanette A.I. Johnson; Genevieve L. Stein-O’Brien; Max Booth; Randy Heiland; Furkan Kurtoglu; Daniel R. Bergman; Elmar Bucher; Atul Deshpande; André Forjaz; Michael Getz et al.
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Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Cell Systems
2023-04 | Journal article
Contributors: Atul Deshpande; Melanie Loth; Dimitrios N. Sidiropoulos; Shuming Zhang; Long Yuan; Alexander T.F. Bell; Qingfeng Zhu; Won Jin Ho; Cesar Santa-Maria; Daniele M. Gilkes et al.
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IMAGING MASS CYTOMETRY IDENTIFIES NOVEL NATURAL KILLER CELL INTERACTIONS IN THE PANCREATIC DUCTAL ADENOCARCINOMA TUMOR MICROENVIRONMENT

Journal for ImmunoTherapy of Cancer
2022 | Journal article
Contributors: Malchiodi, Zoe; Peran, Ivana; Fertig, Elana; Ho, Won Jin; Suter, Robert; Danilova, Ludmila; Deshpande, Atul; Jablonski, Sandra; Weiner, Louis
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Network inference with Granger causality ensembles on single-cell transcriptomics

Cell Reports
2022 | Journal article
EID:

2-s2.0-85124179734

Part of ISSN: 22111247
Contributors: Deshpande, A.; Chu, L.-F.; Stewart, R.; Gitter, A.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

bioRxiv
2022 | Other
EID:

2-s2.0-85143916629

Part of ISSN: 26928205
Contributors: Bell, A.T.F.; Mitchell, J.T.; Kiemen, A.L.; Fujikura, K.; Fedor, H.; Gambichler, B.; Deshpande, A.; Wu, P.-H.; Sidiropoulos, D.N.; Erbe, R. et al.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

Uncovering the spatial landscape of tumor-immune interactions using latent spaces from spatial transcriptomics

Cancer Research
2022 | Journal article
Contributors: Deshpande, Atul; Loth, Melanie; Sidiropoulos, Dimitrios; Zhu, QingFeng; Stein-O'Brien, Genevieve; Rao, NIkhil; Uytingco, Cedric; Williams, Stephen; Santa-Maria, Cesar; Gilkes, Daniele M. et al.
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Web of Science Researcher Profile Sync

Generating colorblind-friendly scatter plots for single-cell data

eLife
2022-12-16 | Journal article
Contributors: Tejas Guha; Elana J Fertig; Atul Deshpande
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Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

2022-06-02 | Preprint
Contributors: Atul Deshpande; Melanie Loth; Dimitrios N. Sidiropoulos; Shuming Zhang; Long Yuan; Alexander Bell; Qingfeng Zhu; Won Jin Ho; Cesar Santa-Maria; Daniele Gilkes et al.
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Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology
2021 | Journal article
EID:

2-s2.0-85112128617

Part of ISSN: 1474760X 14747596
Contributors: Lê Cao, K.-A.; Abadi, A.J.; Davis-Marcisak, E.F.; Hsu, L.; Arora, A.; Coullomb, A.; Deshpande, A.; Feng, Y.; Jeganathan, P.; Loth, M. et al.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

Community-wide hackathons to identify central themes in single-cell multi-omics (vol 22, 220, 2021)

Genome Biology
2021 | Journal article
Contributors: Cao, Kim-Anh Le; Abadi, Al J.; Davis-Marcisak, Emily F.; Hsu, Lauren; Arora, Arshi; Coullomb, Alexis; Deshpande, Atul; Feng, Yuzhou; Jeganathan, Pratheepa; Loth, Melanie et al.
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Web of Science Researcher Profile Sync

From bench to bedside: Single-cell analysis for cancer immunotherapy

Cancer Cell
2021 | Journal article
EID:

2-s2.0-85111883273

Part of ISSN: 18783686 15356108
Contributors: Davis-Marcisak, E.F.; Deshpande, A.; Stein-O'Brien, G.L.; Ho, W.J.; Laheru, D.; Jaffee, E.M.; Fertig, E.J.; Kagohara, L.T.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

Imaging mass cytometry reveals key spatial features among immune cells in hepatocellular carcinomas treated with neoadjuvant cabozantinib and nivolumab

Cancer Research
2021 | Journal article
Contributors: Zhang, Shu; Zhu, Qingfeng; Gross, Nicole; Charmsaz, Soren; Deshpande, Atul; Xavier, Stephanie; Mohan, Aditya; Leatherman, James; Mo, Guanglan; Durham, Jennifer et al.
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Neoadjuvant cabozantinib and nivolumab convert locally advanced hepatocellular carcinoma into resectable disease with enhanced antitumor immunity

Nature Cancer
2021 | Journal article
EID:

2-s2.0-85111622429

Part of ISSN: 26621347
Contributors: Ho, W.J.; Zhu, Q.; Durham, J.; Popovic, A.; Xavier, S.; Leatherman, J.; Mohan, A.; Mo, G.; Zhang, S.; Gross, N. et al.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

scatterHatch: an R/Bioconductor package for generating colorblind-friendly scatter plots for single-cell data

2021-10-07 | Preprint
Contributors: Tejas Guha; Elana Fertig; Atul Deshpande
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Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response

ImmunoInformatics
2021-07-24 | Journal article
Contributors: Shuming Zhang; Chang Gong; Alvaro Ruiz-Martinez; Hanwen Wang; Emily Davis-Marcisak; Atul Deshpande; Aleksander S. Popel; Elana J. Fertig
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Dimensions

On simultaneous long-short stock trading controllers with cross-coupling

arXiv
2020 | Other
EID:

2-s2.0-85169273463

Part of ISSN: 23318422
Contributors: Deshpande, A.; Gubner, J.A.; Ross Barmish, B.
Source: Self-asserted source
Atul Deshpande via Scopus - Elsevier

On Simultaneous Long-Short Stock Trading Controllers with Cross-Coupling

ArXiv
2020 | Journal article
Contributors: Deshpande, Atul; A Gubner, John; Ross Barmish, B.
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Peer review (3 reviews for 2 publications/grants)

Review activity for Cell systems. (1)
Review activity for ImmunoInformatics. (2)