Systems Biology/Bioinformatics

Systems Biology/Bioinformatics


My lab is interested in utilizing cellular, molecular, and genomics based approaches to understanding human lung diseases.  We incorporate techniques such as gene sequencing, human cell culture, PCR and enzymatic assays to help us uncover important cell signaling pathways.  Our strategy is to combine sophisticated computational analysis, machine learning and physiology along with hypothesis-driven laboratory experiments to elucidate disease pathogenesis.

human buccal mucosa

Freshly cultured human buccal mucosa epithelial cells from anonymous donor (Healthy).  Epithelial tissues are widespread throughout the body. They form the covering of all body surfaces, line body cavities and hollow organs, and are the major tissue in glands. They perform a variety of functions that include protection, secretion, absorption, excretion, filtration, diffusion, and sensory reception.  

Current Projects

Project 1- Characterization of the diversity of the Immune Repertoire in Acute Respiratory Distress Syndrome

  • The immune system is the body's defense against infectious organisms and other invaders. 
  • Through a series of steps called the immune response, the immune system attacks organisms and substances that invade body systems and cause disease.
  • The immune system is made up of a network of cells, tissues, and organs that work together to protect the body. 
  • T Cells have become the focus of intense research using novel sequencing technology known as immune receptor sequencing.
  • Diverse lymphocyte repertoires can be analyzed by high throughput sequencing.
  • High throughput repertoire sequencing has applications in basic and clinical immunology.

Project 2- Machine Learning using genomics data

ARDS genomics

Project 3- Basic studies into Human lung diseases (focusing on the cellular and molecular mechanisms)

The effects of vaping nicotine on the physioological homeostasis of the human epithelium

Epithelial cells exposed to nicotine

Software and database resources developed by our lab-

ARDS-DB: Acute Respiratory Distress Syndrome Research Database of Genes:

Machine Learning:


Summer workshop series for student research training

Introduction of Systems Biology and Bioinformatics- part 1

Introduction of Systems Biology and Bioinformatics- part 2

Introduction of Systems Biology and Bioinformatics- part 3

Active Research Grants and Funding-

ARDS private fund research grant to I.Toby

Women in Immune Driven Medicine, Adaptive Biotechnologies, PI: Inimary Toby

Marcus Fund for Research, University of Dallas

Active Research Collaborative Agreements-

Penn State University College of Medicine, Lab of Dr Joanna Floros

National Institute of Health-National Heart, Lung and Blood Institute, BioLINCC

BioLINCC: Biologic Specimen and Data Repository Information Coordinating Center - Web Access to NHLBI Biospecimens and Data

Recent Scientific Publications (past 5 years)

Editorial: Unleashing Innovation on Precision Public Health-Highlights From the MCBIOS and MAQC 2021 Joint Conference. Homayouni R, Hong H, Manda P, Nanduri B, Toby IT . Front Artif Intell. 2022 Feb 25;5:859700. doi: 10.3389/frai.2022.859700. eCollection 2022. PMID: 35280236 

A Data Report on the Curation and Development of a Database of Genes for Acute Respiratory Distress Syndrome. Quintanilla E, Diwa K, Nguyen A, Vu L, Toby IT . Front Genet. 2021 Dec 9;12:750568. doi: 10.3389/fgene.2021.750568. eCollection 2021. PMID: 34956316 

Identification of potential antiviral compounds against SARS-CoV-2 structural and non structural protein targets: A pharmacoinformatics study of the CAS COVID-19 dataset. García R, Hussain A, Koduru P, Atis M, Wilson K, Park JY, Toby I , Diwa K, Vu L, Ho S, Adnan F, Nguyen A, Cox A, Kirtek T, García P, Li Y, Jones H, Shi G, Green A, Rosenbaum D. Comput Biol Med. 2021 Jun;133:104364. doi: 10.1016/j.compbiomed.2021.104364. Epub 2021 Apr 19. PMID: 33895457 

Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Wren JD, Doerkson RJ, Toby IT , Nanduri B, Homayouni R, Manda P, Thakkar S. BMC Bioinformatics. 2019 Mar 14;20(Suppl 2):95. doi: 10.1186/s12859-019-2618-7. PMID: 30871470 

Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue. Ostmeyer J, Christley S, Toby IT , Cowell LG. Cancer Res. 2019 Apr 1;79(7):1671-1680. doi: 10.1158/0008-5472.CAN-18-2292. Epub 2019 Jan 8. PMID: 30622114 

  VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT , Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG. Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018. PMID: 29867956 

Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. Wren JD, Dozmorov MG, Toby I , Nanduri B, Homayouni R, Manda P, Thakkar S. BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):498. doi:10.1186/s12859-017-1887-2. PMID: 29297277 

  VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.  Christley S, Levin MK, Toby IT , Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z. PMID: 29020925 

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. Ostmeyer J, Christley S, Rounds WH, Toby I , Greenberg BM, Monson NL, Cowell LG. BMC Bioinformatics. 2017 Sep 7;18(1):401. doi: 10.1186/s12859-017-1814-6. PMID: 28882107 

Additional scientific publications

Lab Members

A full list of lab alumni, research interns and present research students can be accessed below: