Chittibabu (Babu) Guda, PhD

Professor & Chief Bioinformatics and Research Computing Officer

   

Department of Genetics, Cell Biology and Anatomy
985805 Nebraska Medical Center
Omaha, NE 68198-5805

402-559-5954
Email
Lab Website


Education:

PhD, Molecular Biology, Auburn University, 1997
Post-doc, Computational Biology, University of California at San Diego, 2001

Academic Appointments:
Director, Bioinformatics and Systems Biology Core Facility, UNMC
Director, Bioinformatics and Systems Biology Doctoral Program, UNMC

Research:
Our laboratory nurtures a wide range of research projects related to Genomics, Bioinformatics, Systems Biology and Personal Medicine.  The major research projects in my laboratory can be grouped into three broad areas:  (i) Development of novel algorithms for analyzing different types of biomolecular data, followed by experimental validation and development of software and web application tools; (ii) Building data analysis pipelines for processing a variety of high-throughput ‘omics’ datasets (ExomeSeq, RNASeq, ChIPseq, methylation data, miRNA arrays and proteomics data); and (iii) cancer genomics projects that involve integrative data analysis of molecular data across large populations, identification of molecular subtypes of cancers and functional characterization of genes and gene products identified from these studies.  Some of the current research projects in my lab include analysis of breast, pancreatic and glioblastoma cancer genomics data obtained from The Cancer Genome Atlas (TCGA) project, development of novel tools for detecting fusion genes and tumor heterogeneity, and metagenomic profiling of human microbiomes.  For more details on specific research projects, please visit our laboratory webpage.

Our laboratory also manages the Bioinformatics and Systems Biology Core Facility at UNMC.  The Core provides services on a pay-per-use basis to over 60 independent investigators, most of whom are NIH funded.  Click here for more details on the type of services offered through the core.  The Core is also a part of several collaborative projects on campus that include supporting the Data Coordination Center for National NeuroAIDS Consortium and Bioinformatics Core for the INBRE network.

I serve on the advisory board for Worlds of Connections, an NIH-funded project which promotes understanding of network science among members of underrepresented minority communities to support diversity in bio-behavioral and biomedical careers.  To learn more, visit http://worldsofconnections.com/

Publications listed in PubMed

Publications:
  1. Shakyawar SK, Pandey S, Harvey DJ, Bousfield G, Guda C. FGDB: Database of follicle stimulating hormone glycans. Comput Struct Biotechnol J., (2021) 19:1635-1640 [PubMed]
  2. Southekal S, Mishra NK, Guda C. Pan-cancer analysis of human kinome gene expression and promoter DNA methylation identifies prognostic biomarkers in multiple cancers.  Cancers, (2021) 13:1189 [PubMed]
  3. Vellichirammal NN, Guda C. A compiled dataset of molecular pathways associated with fusion genes identified in pediatric cancers. Data in Brief, (2021) 35:106780 [PubMed]
  4. Jagadeesan S, Ahmad R, Avuthu N, Singh AP, Guda C. Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn’s Disease. Frontiers in Medicine, Gastroenterology, (2020) 7:606298 [PubMed]
  5. Vellichirammal NN, Chaturvedi N, Joshi SS, Coulter DW, Guda C. Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Letters, (2020) 499:24-38 [PubMed]
  6. Shakyawar S, Sethi S, Southekal S, Mishra NK, Guda C. Big data analytics for modeling COVID-19 and comorbidities: An unmet need. In Computational Intelligence Techniques for Combating COVID-19, Springer Book Chapter,(Eds. Kautish S, Peng S, Obaid A.) (2020)
  7. Mishra NK, Meng N, Guda C. Identification of prognostic markers in cholangiocarcinoma using altered DNA methylation and gene expression profiles. Frontiers in Genetics, (2020) 11:522125 [PedMed]
  8. Mishra NK, Siddesh S, Guda C. (2019) Survival analysis of multi-omics data identifies potential prognostic markers of pancreatic ductal adenocarcinoma.  Frontiers in Genetics. DOI: 10.3389/fgene.2019.00624. [PubMed]
  9. Cornish A, Roychoudhury S, Sarma K, Pramanik S, Bhakat K, Dudley A, Guda C. Red Panda: a novel method for detecting variants in single-cell RNA sequencing. BMC Genomics Supplement,(2020) 21(Suppl 11):830 [PubMed]
  10. Mishra NK, Southekal S, Guda C. Prognostic value of biomarkers in the tumor microenvironment of pancreatic ductal adenocarcinoma. Annals of Translational Medicine, (2020) 8(10):615 [PubMed]
  11. Tan Y, Xiao P, Guda C. In-depth Mendelian randomization analysis of causal factors for coronary artery disease. Scientific Reports(2020) 10(1):9208. [PubMed]
  12. Vellichirammal NN, Albahrani A, Banwait JK, Mishra NK, Li Y, Roychoudhury S, King MJ, Mirza S, Bhakat KK, Band V, Joshi SS, Guda C. Pan-cancer analysis reveals the diverse landscape of novel sense and antisense fusion transcripts. Molecular Therapy Nucleic Acids, (2020) 19:1379-1398. [PubMed]
  13. Vellichirammal NN, Albahrani A, Li Y, Guda C (2020). Identification of fusion transcripts from unaligned RNA-seq reads using ChimeRScope. Methods in Molecular Biology. DOI: 10.1007/978-1-4939-9904-0_2. [PubMed]
  14. Cserhati M, Peng X, Guda C. K-mer based motif analysis in insect species across Anopheles, Drosophila and Glossina genera and its application to species classification. Computational and Mathematical Models in Medicine, (2019) doi:10.1155/2019/4259479. [PubMed]
  15. Mishra NK, Siddesh S, Guda C. Survival analysis of multi-omics data identifies potential prognostic markers of pancreatic ductal adenocarcinoma. Frontiers in Genetics, (2019) doi:10.3389/fgene.2019.00624. [PubMed]
  16. Wipfler K, Cornish A, Guda C. (2018) Comparative molecular characterization of typical and exceptional responders in Glioblastoma. Oncotarget. doi: 10.18632/oncotarget.25420 [PubMed]
  17. Cserhati M, Mooter ME, Peterson L, Wicks B, Pauley M and Guda C. (2018) Motifome comparison between modern human, Neanderthal and Denisova. BMC Genomics. doi: 10.1186/s12864-018-4710-1. [PubMed]
  18. Mishra N, Guda C. (2017) Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer., Oncotarget, 8:28990-29012. [PubMed]
  19. Negi SK, Guda C. (2017) Global gene expression profiling of healthy human brain and its application in studying neurological disorders, Scientific Reports, 7:897 [PubMed]
  20. Li Y, Heavican TB, Vellichirammal NN, Iqbal J, Guda C. (2017) ChimeRScope: a novel alignment-free algorithm for fusion gene prediction using paired-end RNA-Seq data, Nucleic Acids Res. 45:e120. [PubMed]
  21. Wang X, Guda C. (2016) Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets. Medicine (Baltimore). Jul;95(30):e4321. doi: 10.1097/MD.0000000000004321. [PubMed].
  22. Vural S, Wang X, Guda C. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. BMC Systems Biology [PubMed].