PROFESSOR, CHIEF BIOINFORMATICS & RESEARCH COMPUTING OFFICER, 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.
Publications from the last 5 years:
- Wipfler K, Cornish A, Guda C. (2018) Comparative molecular characterization of typical and exceptional responders in Glioblastoma Oncotarget (In press)
- Cserhati M, Mooter ME, Peterson L, Wicks B, Pauley M and Guda C. (2018) Motifome comparison between modern human, Neanderthal and Denisova. BMC Genomics (In press)
- Luan H, Mohapatra B, Bielecki T, Mushtaq I, Mirza S, Bailey T, Clubb R, An W, Ahmed D, Ansari R, Storck M, Mishra NK, Guda C, Sheinin Y, Meza J, Raja S, Rakha E, Band V, Band H. (2018) Loss of the nuclear pool of ubiquitin ligase CHIP/STUB1 in breast cancer unleashes the MZF1-cathepsin pro-oncogenic program. Cancer Research doi: 10.1158/0008-5472.CAN-16-2140. [PubMed]
- Lopez W, Page AM, Carlson DJ, Ericson BL, Cserhati MF, Guda C, Carlson KA. (2018) Analysis of immune-related genes during Nora virus infection of Drosophila melanogaster using next-generation sequencing. AIMS Microbiology, 4:123-139. [PubMed]
- Talbott H, Hou X, Qiu F, Zhang P, Guda C, Yu F, Cushman RA, Wood JR, Wang C, Cupp AS, Davis JS. (2017) Transcriptomic and Bioinformatics Analysis of Short Prostaglandin F2 alpha Time-course in Bovine Corpus Luteum. Data in Brief 14:695-706.[PubMed]
- Talbott H, Hou X, Qiu F, Zhang P, Guda C, Yu F, Cushman RA, Wood JR, Wang C, Cupp AS, Davis JS. (2017) Early transcriptome responses of the bovine midcycle corpus luteum to prostaglandin F2α include cytokine signaling. Molecular and Cellular Endocrinology, 452:93-109.[PubMed]
- Mishra N, Guda C. (2017) Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer., Oncotarget, 8:28990-29012. [PubMed]
- 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]
- 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]
- Massilamany C, Nandakumar R, Madayiputhiya, Pandey S, Guda C, Reddy J. Gender-differences in the expression of proteins in autoreactive T cells specific to central nervous system myelin proteolipid protein (2017) Journal of Autoimmune Diseases, 3 (1) 30
- Stauch KL, Villeneuve LM, Purnell, PR, Pandey S, Guda C, and Fox HS. (2016) SWATH-MS proteome profiling data comparison of DJ-1, Parkin, and PINK1 knockout rat striatal mitochondria. Data in Brief, 9:589-593 [PubMed]
- 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].
- Vural S, Wang X, Guda C. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. BMC Systems Biology [PubMed].
- 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 [PubMed]
- 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. [PubMed].
- 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. [PubMed]
- 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 [PubMed]
- 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
- 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]