Selected publications

Full list on google scholar.

2025

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    Decomposing patient heterogeneity of single-cell cancer data by cross-attention neural networks
    Sishir Subedi and Yongjin P Park
    In Review, 2025
    url Code
    python deep learning transformers latent space decomposition

2024

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    A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
    Sishir Subedi, Tomokazu S Sumida, and Yongjin P Park
    Life Science Alliance, 2024
    url Code
    c++ python variational inference Bayesian non-linear model

2023

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    Single-cell pair-wise relationships untangled by composite embedding model
    Sishir Subedi and Yongjin P Park
    Iscience, 2023
    url Code
    python deep-learning embedded model

2021

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    Sequence analysis of 20,453 severe acute respiratory syndrome coronavirus 2 genomes from the Houston metropolitan area identifies the emergence and widespread distribution of multiple isolates of all major variants of concern
    S Wesley Long, Randall J Olsen, Paul A Christensen, and 8 more authors
    The American journal of pathology, 2021
    url
    python bioinfo-toolkit COVID-19 surveillance
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    Implementing flowdensity for automated analysis of bone marrow lymphocyte population
    Ghazaleh Eskandari, Sishir Subedi, Paul Christensen, and 3 more authors
    Journal of Pathology Informatics, 2021
    url Code
    python R flow cytometry
  3. germlinevariants.png
    Identifying possible germline variants from tumor-only sequencing of hematological malignancies
    Jianming Shao, Sishir Subedi, Kristi Pepper, and 6 more authors
    Leukemia & Lymphoma, 2021
    url
    python bioinfo-toolkit genomic variant analysis

2020

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    Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data
    Paul A Christensen, Sishir Subedi, Kristi Pepper, and 5 more authors
    JAMIA open, 2020
    url Code
    java python bioinfo-toolkit system design
  2. cellcycle.png
    Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria
    Aditya C. Bandekar, Sishir Subedi, Thomas R. Ioerger, and 1 more author
    Current Biology, 2020
    url Code
    python R cell-cycle analysis

2018

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    Predicting all-Cause 30-Day ICU Readmissions Using Robust Feature Selection
    Arash Pakbin, Parvez Rafi, and Sishir Subedi
    TAMU CSE, 2018
    url Code
    python electronic health record (EHR)

2015

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    A System for the Analysis of EEG Data and Brain State Modeling
    S Subedi, Y Li, C Early, and 5 more authors
    Emerging trends in Computing,Elsevier/MK, 2015
    url Code
    R human-machine interface (HMI)