Bioinformatics Application and Development

Trupti Joshi Lab

Research Interests

The Joshi lab has expertise in the areas of bioinformatics and its application to biomedical sciences, plants sciences, animal sciences, and health informatics fields. The lab has three key research pillars:

  • Multiomics Informatics Data Analytics and Framework Development
  • Multiomics Informatics Method Development
  • Multiomics Data Integration Tool Development

PRINCIPAL INVESTIGATOR

Trupti Joshi

email

Research Interests

The Joshi lab has expertise in the areas of bioinformatics and its application to biomedical sciences, plants sciences, animal sciences, and health informatics fields. The lab has three key research pillars:

  • Multiomics Informatics Data Analytics and Framework Development
  • Multiomics Informatics Method Development
  • Multiomics Data Integration Tool Development

More about Trupti Joshi


ABOUT THE LAB

The lab currently focuses on:

    1. Building knowledge base frameworks such as SoyKB and KBCommons for genomics and multiomics data integration in agricultural and biomedical domains.

    1. Development of data analytics pipelines using HPC and cloud based resources (PGen, SnakyVC).

    1. Multiomics data integration methods and tools development (Allele Catalog, GenVarX, SNPViz).

    1. Deep learning (G2PDeep, IRnet) and machine learning methods development for phenotype predictions and biomarker identification.

    1. Computational algorithm development for in silico hypothesis generation (IMPRes).

    1. Application of translational bioinformatics techniques towards advances in precision medicine, precision agriculture, and genomic epidemiology (Covid Portal).

Examples of our research:

Web-based Frameworks and Portal Development

Knowledge Base Commons (KBCommons): https://kbcommons.org

Soybean Knowledge Base (SoyKB): https://soykb.org

Covid Genomic Epidemiology: https://dataportals.missouri.edu/SARSCoV2 and https://kbcommons.org/system/browse/msphl/index/SARSCoV2

Web-based Tools Development Within KBCommons and SoyKB

Allele Catalog: Tool for new allele discovery using large scale genomics variations SNPs/Indels and phenotypic data.

GenVarX: Tool for uncovering regulatory and structural changes using large scale genomics variations SNPs/Indels and phenotypic data.

SNPViz: Tool for causative genes discovery to further assist GWAS using large-scale genomics variations data.

MADis: Tool for mutative allele discovery composed of multiple mutative allele position combinations.

Computational Methods Development

G2PDeep (Deep learning method for phenotype prediction)

IMPRes (Integrative Multiomics Pathway Resolution)

IRnet (Immunotherapy Response Prediction)

CrossMP (Single cell cross-modality prediction between scRNAseq and scATACseq)

LAB MEMBERS

Research Topics

  • Animal science

  • Applied computing

  • Artificial intelligence

  • Autoimmune disease mechanisms

  • Biomedical informatics

  • Cancer immunotherapy

  • Chronic inflammatory diseases and immune responses

  • Crop improvement and agricultural sustainability

  • Data management

  • Deep learning and AI for biological data

  • Drug delivery and therapeutic development

  • Fatty acid biosynthesis

  • Genomic tools and systems biology

  • Global warming effects on crops

  • Host-pathogen interactions

  • Immunotherapies and immune system regulation

  • Machine learning

  • Metabolic pathway engineering

  • Metabolic pathways and mechanisms

  • Multi-omics and bioinformatics tools

  • Multi-stress plant responses

  • Neurodegeneration and neuromuscular diseases

  • Nitrogen fixation in soybeans

  • Plant immunity and stress responses

  • Plant-microbe interactions

  • Reactive Oxygen Species (ROS) signaling

  • Single-cell genomics

  • Software engineering

  • Spatial transcriptomics

  • Translational bioinformatics

  • Vaccine development

  • Virus pathogenesis and transmission

In The News

April 28, 2025

Behind the cell structures of childhood sleep disruption

How high-performance computing connects brain differences to apnea Adobe Stock image By Sophie Rentschler | Bond LSC  A good night’s rest lays the foundation for your daily performance but when a child’s body hampers airflow, that can lead to cognitive problems in their waking lives.  One recent Mizzou study looks at healthy neurological processes and how this differs for patients with obstructive sleep apnea. The study collected a wealth of patient information that can be utilized to help clinicians give a diagnosis quicker in the future.   Yen On Chan,…

Nov. 30, 2018

#IAmScience Trupti Joshi

By Erica Overfelt | Bond LSC Juggling research, teaching, collaborative meetings, grant writing, and training postdocs and students is no problem for Trupti Joshi. That array of responsibilities is just part of the job for a Bond LSC researcher focused on bioinformatics, an area that connects so many types of science by collecting and analyzing genetic data. “Bioinformatics is a very interdisciplinary science that marries the wet and the dry labs,” Joshi said. “It applies software tools and computational techniques from computer science, engineering, mathematics and statistics towards efficient ways to analyze, integrate and mine large-scale genomics and…

Aug. 18, 2017

Drowning in Data

New web-based framework helps scientists analyze and integrate data By Emily Kummerfeld | Bond LSC Large-scale data analysis on computers is not exactly what comes to mind when thinking about biological research. But these days, the potential benefit of work done in the lab or the field depends on them. That’s because often research doesn’t focus on a single biological process, but must be viewed within the context of other processes. Known as multi-omics, this particular field of study seeks to draw a clearer picture of dynamic biological interactions from gigantic amounts of data. But, how exactly can scientists suitably…