PROFESSOR, DIRECTOR OF BIOINFORMATICS AND SYSTEMS BIOLOGY CORE
Ph. D. in Molecular Biology, Auburn University, 1997
Post-doc training in Computational Biology
University of California at San Diego, 2001
Research - Overall Goals:
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.
Selected Recent Publications:
- 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].
- Zhang W, Klinkebiel D, Barger CJ, Pandey S, Guda C, Lui S, Miller A, Akers SN, Odunsi K, Karpf AR. () Global DNA hypomethylation in epithelial ovarian cancer: passive demethylation and association with genomic instability (Submitted).
- Stauch KL, Villeneuve LM, Purnell, PR, Pandey S, Guda C, and Fox HS. Genetic ablation of the Parkinson’s disease-related proteins, PINK1, DJ-1, and Parkin, result in common synaptic mitochondrial alterations in the striatum early during disease progression. (Submitted).
- Vural S, Wang X, Guda C. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. BMC Systems Biology (Accepted).
- Zhao Z, Jin VX, Huang Y, Guda C, Ruan J. (2015) Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Res Int. 2015:725491. doi: 10.1155/2015/725491 [PubMed].
- Massilamany C, Mohammed A, Loy JD, Purvis T, Krishnan B, Basavalingappa RH, Kelley CM, Guda C, Barletta RG, Moriyama EN, Smith TPL, Reddy J. Genome sequence analysis and characterization of Bacillus infantis NRRL B-14911 that can induce myocarditis in A/J mice. BMC Genomics (Accepted)
- Cserhati M, Pandey S, Beaudoin J J, Baccaglini, L, Guda C, Fox H S. (2015) The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies. Database: Jul 30;2015:bav074. doi: 10.1093/database/bav074. [PubMed].
- Shen R, Wang, X, Guda C. (2015) Mining functional subgraphs from cancer protein-protein interaction networks. BioMed Research International, Suppl 3:S2. doi: 10.1186/1752-0509-6-S3-S2. [PubMed].
- Lakshmanan I, Seshacharyulu P, Haridas D, Rachagani S, Gupta S, Joshi S, Guda C, Jain M, Ganti AK, Ponnusamy, MP and Batra, SK. (2015) Novel HER3/MUC4 oncogenic signaling aggravates the tumorigenic phenotypes of pancreatic cancer cells. Oncotarget, Aug 28;6(25):21085-99. [PubMed].
- Li Y, Wang X, Vural S, Cowan KH, Guda C. (2015) Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers. PLoS ONE, 10(3):e0119383 [PubMed].
- Mohammed A, Guda C. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. BMC Genomics (In press).
- Cornish A, Guda C. A comparison of variant calling pipelines using Genome-in-a-Bottle as a reference. BioMed Research International (2015). [Hindawi]
- Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C. LocSigDB: A database of experimental and predicted protein localization signals. Database (2015). [PubMed]
- Shen R, Guda C. (2014) Applied graph-mining algorithms to study biomolecular interaction networks. BioMed Research International. (In press)
- Goonesekhere N, Wang X, Ludwig L, Guda C. (2014) A meta analysis of pancreatic microarray datasets yields new targets as cancer genes and biomarkers. PLoS ONE (In press)
- Wang X, Guda C. (2014) Computational analysis of transcriptional circuitries in human embryonic stem cells reveals multiple and independent networks. BioMed Research International. 2014;2014:725780. [PubMed]
- Srinivasan SM, Guda C. (2013) MetaID: A novel method for identification and quantification of metagenomic samples. BMC Genomics, [PubMed]
- Read BA, Kegel J, … Emiliana huxleyi Annotation Consortium (Guda C.) … Grigoriev IV (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-213.[PubMed]
- Guda C. (2013) Bioinformatic methods and resources for neuroscience research. In: Current Laboratory Methods in Neuroscience Research, Xiong H and Gendelman HE Eds. Springer publishing (In press)
- Ozturk F, Li Y, Zhu X, Guda C, Nawshad A. (2013) Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFbeta3-knockout mice alleles: RNA-Seq analysis of TGFbeta3 Mice. BMC Genomics, 14:113. [PubMed]
- Srinivasan SM, Vural S, King BR, Guda C. (2013) Mining for class-specific motifs in protein sequence classification. BMC Bioinformatics, 14:96. [PubMed]
- King BR, Vural S, Pandey S, Barteau A, Guda C. (2012) ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes. BMC Research Notes, 5:351.[PubMed]
- Mohibi S, Gurumurthy CB, Nag A, Wang J, Mirza S, Mian Y, Quinn M, Katafiasz B, Eudy J, Pandey S, Guda C, Naramura M, Band H, Band V. (2012) Mammalian alteration/deficiency in activation 3 (Ada3) is essential for embryonic development and cell cycle progression. J Biol Chem., 287:29442-56. [PubMed]
- Shen R, Gooneshkere NCW, Guda C. (2012) Mining functional subgraphs from cancer protein-protein interaction networks. BMC Systems Biology, 6:S2
- Gu, SQ, Bakthavachalu B, Han J, Patil D, Otsuka Y, Guda C, Schoenberg DR. (2012) Identification of the human PMR1 mRNA endonuclease as an alternatively processed product of the gene for peroxidasin-like protein. RNA 18:1186-1196.[PubMed]
- Zhu X, Ozturk F, Pandey S, Guda C, Nowshad A. (2012) Implications of TGF-B on transcriptome and cellular biofunctions of palatal mesenchyme. Frontiers in Physiology, 3:1-22. [PubMed]
- Mukherjee A, Reisdorph N, Guda C, Pandey S, Roy SK. (2012) Changes in ovarian protein expression during primordial follicle formation in the hamster. Molecular and Cellular Endocrinology, 348:87-94. [PubMed].