College of Medicine
University of Nebraska Medical Center
University of Nebraska Medical Center

Publications

Full list of publications -  NCBI

Selected Lab publications in the last 5 years (*denotes trainees from Guda Lab)

  1. *Patel JC, *Veerappa A, Guda C. An explainable-AI framework reveals novel lncRNAs specific for breast cancer subtypes. Frontiers in Bioinformatics (In press)
  2. *Jagadesan S, Guda C. (2026) VST-DAVis: Browser-based R Shiny Application for Visium HD Spatial Transcriptomics Data Analysis and Visualization Bioinformatics Advances, 2026, 6:vbag007. PMID: 41640624. PMCID: PMC12866912.
  3. *Veerappa A, *Patel JC, *Shakyawar S, *Jagadesan S, Guda C. (2025) – scAED: A framework for mapping the enhancer state at single-cell resolution Briefings in Bioinformatics, 26(6):bbaf646. PMID: 41359545; PMCID: PMC12684730
  4. *Jagadesan S, Guda C. (2025) ScRDAVis: A Comprehensive R Shiny Application for Single-Cell Transcriptome Data Analysis and Visualization. PLoS Computational Biology, 21(11):e1013721, PMID: 41231930; PMCID: PMC12626302.
  5. *Patel JC, *Shakyawar SK, *Sethi A, Guda C. (2025) GAIN-BRCA: A graphical explainable AI-net framework for breast cancer subtype classification using multiomics data. Bioinformatics Advances 2025, 5:vbaf116. PMID: 40496492. PMCID: PMC12151285
  6. *Jagadesan S, Guda C. (2025) MetaDAVis: An R shiny application for metagenomic data analysis and visualization. PLOSONE, 20(4):e0319949. PMID: 40193328. PMCID: PMC11975103.
  7. *Nagarajan N, Guda C. (2024) Identification of potential inhibitors for drug-resistant EGFR mutations in non-small cell lung cancer using whole exome sequencing data Frontiers in Pharmacology, 2024 Jul 25;15:1428158. PMID: 39130636 PMCID: PMC11310931.
  8. *Veerappa A#, Rowley MJ#, Maggio A, Beaudry L, Hawkins D, Kim A, *Sethi S, Sorgen PL, Guda C. (2024) CloudATAC: A cloud-based interactive pipeline for the analysis of pooled-cell and single-cell ATAC-seq data. Briefings in Bioinformatics 2024 Jul 23;25(Supplement_1):bbae090. doi: 10.1093/bib/bbae090. PMID: 39041910 PMCID: PMC11264300.
  9. *Sethi S, *Shakyawar SK, Reddy AS, *Patel J, Guda C. (2024) A Machine Learning Model for Prediction of COVID-19 Severity using RNA-seq, Clinical and Co-morbidity Data, Diagnostics, 14:1284. PMID: 38928699. PMCID: PMC11202902.
  10. *Veerappa A, Guda C. (2024) Coordination among frequent variants impart substance use susceptibility and pathogenesis. Frontiers in Neuroscience, 18:1332419. PMID: 38660223. PMCID: PMC11041639
  11. *Shakyawar SK, Sajja BR, *Patel JC, Guda C. (2024) iCluF: An unsupervised iterative cluster fusion method for disease subtyping using multiomics data. Bioinformatics Advances, 2024, 4:vbar015 PMID: 38698887. PMCID: PMC11063539.
  12. *Pandey S, *Avuthu N, Guda C. (2023) StrainIQ: A novel n-gram-based method for taxonomic profiling of human microbiota at the strain level. Genes, 14:1647. PMID: 37628698. PMCID: PMC10454763
  13. *Jagadesan S, Mondal P, Carlson M, Guda C. (2023) Identification of best-fit animal model to study the human diseases: using a bioinformatics approach. Biomedicines, 11:2197. PMID: 37626695. PMCID: PMC10452283
  14. *Vellichirammal NN, *Yuande T, *Peng X, Eudy JD, Shats O, Kelly D, Desler M, Cowan K, Guda C. (2023) The mutational landscape of a US Midwestern breast cancer cohort reveals subtype-specific cancer drivers and prognostic markers. Human Genomics, 17:64. PMID: 37454130; PMCID: PMC10349437
  15. *Southekal S, *Mishra NK, *Shakyawar S, Prachi B, Elkholy A, Manne U, Guda C. (2023) Survival analysis and molecular subtyping of osteosarcoma reveals prognostic genes in key canonical pathways. Cancers, 15:2134. PMID: 37046795; PMCID: PMC10093233
  16. *Vellichirammal N, *Albahrani A, Guda C. (2022) Fusion gene recurrence in non-small cell lung cancers and its association with cigarette smoke exposure Translational Lung Cancer Research, 11:2022-2039. PMID: 36386463
  17. *Shakyawar S, *Siddesh S, Guda C. (2022) mintRULS: Prediction of miRNA-Targets interactions using regularized least square method. Genes 13:1528. PMID: 36140696. PMCID: PMC9498445.
  18. *Tan YD, Guda C. (2022) NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data. Scientific Reports. 12:12833. doi: 10.1038/s41598-022-15762-x. PMID: 35896555, PMCID: PMC9329447
  19. *Avuthu N, Guda C. (2022) Meta-analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer Microbiology Spectrum 2022:e0001322. PMID: 35766483; PMCID: PMC9431300.
  20. *Veerappa A, Pendyala G, Guda C. (2021) A systems omics-based approach to decode substance use disorders and neuroadaptations, Neuroscience and Biobehavioral Reviews, 130:61-80. PMID: 34411560. PMCID: PMC8511293.
  21. *Shakyawar SK, *Pandey S, Harvey DJ, Bousfield G, Guda C. FGDB: Database of follicle stimulating hormone glycans (2021) Comput Struct Biotechnol J. 19:1635-1640. PMID: 33897975; PMCID: PMC8050109.
  22. *Southekal S, *Mishra NK, Guda C. (2021) Pan-cancer analysis of human kinome gene expression and promoter DNA methylation identifies prognostic biomarkers in multiple cancers. Cancers 13:1189. PMID: 33801837; PMCID: PMC8001681.
  23. *Vellichirammal NN, Guda C. (2021) A compiled dataset of pathways associated with fusion genes identified in pediatric cancers. Data in Brief, 35:106780. PMID: 33553527; PMCID: PMC7848762.