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13 research outcomes, page 1 of 2
  • publication . Preprint . Part of book or chapter of book . 2020
    Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation.
    Open Access English
    Authors:
    Saad Nadeem; Travis J. Hollmann; Allen Tannenbaum;
    doi: 10.1007/978-3-030-59722-1_35
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Glymphatic function in a ... (5R01AG048769-04)

    Variations in hematoxylin and eosin (H&E) stained images (due to clinical lab protocols, scanners, etc) directly impact the quality and accuracy of clinical diagnosis, and hence it is important to control for these variations for a reliable diagnosis. In this work, we p...

  • publication . Preprint . 2019
    A Novel Integrative Multiomics Method Reveals a Hypoxia-Related Subgroup of Breast Cancer with Significantly Decreased Survival
    Open Access English
    Authors:
    Joseph O. Deasy; Maryam Pouryahya; Jung Hun Oh; Allen Tannenbaum; Allen Tannenbaum; Zehor Belkhatir; James C. Mathews; Pedram Javanmard;
    doi: 10.1101/558700
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | MOUSE GENETICS (2P30CA008748-43)

    <jats:title>Abstract</jats:title><jats:p>The remarkable growth of multi-platform genomic profiles has led to the multiomics data integration challenge. The effective integration of such data provides a comprehensive view of the molecular complexity of cancer tumors and ...

  • publication . Other literature type . Preprint . 2019
    Network-based clustering for drug sensitivity prediction in cancer cell lines
    Open Access
    Authors:
    James C. Mathews; Joseph O. Deasy; Caroline Moosmüller; Caroline Moosmüller; Maryam Pouryahya; Jung Hun Oh; Zehor Belkhatir; Allen Tannenbaum; Allen Tannenbaum;
    doi: 10.1101/764043
    Publisher: bioRxiv
    Project: NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | MOUSE GENETICS (2P30CA008748-43)

    <jats:title>Abstract</jats:title><jats:p>The study of large-scale pharmacogenomics provides an unprecedented opportunity to develop computational models that can accurately predict large cohorts of cell lines and drugs. In this work, we present a novel method for predic...

  • publication . Preprint . Article . 2020
    Fractional SIR Epidemiological Models.
    Open Access
    Authors:
    Taghvaei, Amirhossein; Georgiou, Tryphon T.; Norton, Larry; Tannenbaum, Allen R;
    doi: 10.1101/2020.04.28.20083865 , 10.1038/s41598-020-77849-7
    pmc: PMC7705759 ,
    View all 6 identifiers
    Publisher: Cold Spring Harbor Laboratory
    Project: NSF | Collaborative Research: D... (1807664), NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | MOUSE GENETICS (2P30CA008748-43)

    Author(s): Taghvaei, Amirhossein; Georgiou, Tryphon T; Norton, Larry; Tannenbaum, Allen R | Abstract: The purpose of this work is to make a case for epidemiological models with fractional exponent in the contribution of sub-populations to the transmission rate. More spe...

  • publication . Preprint . 2019
    Probabilistic Kernel Support Vector Machines
    Open Access English
    Authors:
    Chen, Yongxin; Georgiou, Tryphon T.; Tannenbaum, Allen R.;
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NSF | Collaborative Research: D... (1807664), NSF | EAGER: Real-Time: Search ... (1839441), NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | Dose-distribution radiomi... (5R01CA198121-02)

    Comment: 6 pages, 6 figures

  • publication . Preprint . Other literature type . 2019
    Optimal Mass Transport Kinetic Modeling for Head and Neck DCE-MRI: Initial Analysis
    Open Access
    Authors:
    Nancy Y. Lee; Eve LoCastro; Allen Tannenbaum; Amita Shukla-Dave; Saad Nadeem; Joseph O. Deasy; Rena Elkin; Ramesh Paudyal; Vaios Hatzoglou;
    doi: 10.1101/612770 , 10.1002/mrm.27897
    pmc: PMC6716991
    View all 4 identifiers
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | Dose-distribution radiomi... (5R01CA198121-02)

    <jats:title>Abstract</jats:title><jats:p>Current state-of-the-art models for estimating the pharmacokinetic parameters do not account for intervoxel movement of the contrast agent (CA). We introduce an optimal mass transport (OMT) formulation that naturally handles inte...

  • publication . Other literature type . Preprint . 2020
    Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53
    Open Access
    Authors:
    Joseph O. Deasy; Zehor Belkhatir; Mahdi Kooshkbaghi; Ioannis G. Kevrekidis; Maryam Pouryahya; Caroline Moosmueller; Jose Reyes; Christopher J Tralie; Allen Tannenbaum;
    doi: 10.1101/2020.02.04.933192
    Publisher: bioRxiv
    Project: NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | MOUSE GENETICS (2P30CA008748-43)

    <jats:title>Abstract</jats:title><jats:p>In this paper, we analyze the dynamical behavior of the tumor suppressor protein p53, an essential player in the cellular stress response, which prevents a cell from dividing if severe DNA damage is present. When this response sy...

  • publication . Part of book or chapter of book . Preprint . 2019
    Fisher-Rao Regularized Transport Analysis of the Glymphatic System and Waste Drainage
    Open Access
    Authors:
    Saad Nadeem; Rena Elkin; Helene Benveniste; Hedok Lee; Allen Tannenbaum;
    doi: 10.1007/978-3-030-59728-3_56
    Publisher: Springer International Publishing
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Glymphatic function in a ... (5R01AG048769-04), NIH | Dose-distribution radiomi... (5R01CA198121-02)

    Comment: To appear in MICCAI 2020

  • publication . Other literature type . Article . Preprint . 2019
    Topological Data Analysis of PAM50 and 21-Gene Breast Cancer Assays
    Open Access
    Authors:
    Maryam Pouryahya; Joseph O. Deasy; James C. Mathews; Allen Tannenbaum; Arnold J. Levine; Saad Nadeem;
    doi: 10.1038/s41523-019-0124-8 , 10.1101/480723
    pmc: PMC6733897
    View all 4 identifiers
    Publisher: Springer Science and Business Media LLC
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Glymphatic function in a ... (5R01AG048769-04)

    This study uses new techniques of topological data analysis to demonstrate the relationship between breast cancer assays and important biological modules. Specifically, we map the landscape of breast tumor molecular states and integrate the information provided by the P...

  • publication . Preprint . Other literature type . Article . 2019
    Network Curvature as a Hallmark of Brain Structural Connectivity
    Open Access
    Authors:
    Allen Tannenbaum; Yongxin Chen; Christophe Lenglet; Hamza Farooq; Tryphon T. Georgiou;
    doi: 10.1101/162875 , 10.1038/s41467-019-12915-x
    pmc: PMC6821808
    View all 4 identifiers
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | SILICON GRAPHICS PRISM EX... (1S10RR023043-01), NSF | Theory and Techniques for... (1509387), NIH | Neuroimaging Analysis Cen... (5P41EB015902-20), NIH | Center for Functional Ima... (5P41EB015896-18), NIH | A Storage Area Network fo... (1S10RR023401-01A2), NIH | FUNCTIONAL MRI INFORMATIC... (5P41RR013218-09), NIH | NMR Imaging and Spectrosc... (4P41EB015894-24), NIH | Computeserver Structural ... (1S10RR019307-01), NIH | Core 3 - Institutional Ce... (5P30NS076408-02), NIH | MOUSE GENETICS (2P30CA008748-43),...

    Although brain functionality is often remarkably robust to lesions and other insults, it may be fragile when these take place in specific locations. Previous attempts to quantify robustness and fragility sought to understand how the functional connectivity of brain netw...

13 research outcomes, page 1 of 2