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. 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 (in press)
  2. Jang HS, Noh MR, Jung EM, Kim WY, Guda C, Foster KW, Oupicky D, Ferrer FA, Padanilam BJ. Proximal tubule cyclophilin D regulates fatty acid oxidation in cisplatin-induced acute kidney injury. Kidney International, DOI.
  3. Bahado-Singh R, Vishweswaraiah S, Aydas B, Mishra NK, Yilmaz A, Guda C, Radhakrishna U. Artificial intelligence analysis of Newborn Leucocyte epigenomic markers for the Prediction of Autism, Brain Research, 1724:146457.[PubMed]
  4. Mishra NK, Siddesh S, Guda C. (2019) Survival analysis of multi-omics data identifies potential prognostic markers of pancreatic ductal adenocarcinoma. Frontiers in Genetics (in press)
  5. Vellichirammal NN, Albahrani A, Li Y, Guda C (2019). Identification of fusion transcripts from unaligned RNA-seq reads using ChimeRScope. Methods in Molecular Biology (in press)
  6. Bahado-Singh R, Vishweswaraiah S, Aydas B, Mishra NK, Guda C, Radhakrishna U. (2019) Deep Learning/ Artificial Intelligence and the Epigenomic Prediction of Cerebral Palsy. Int. J. Molecular Sciences, 20:E2075. [PubMed]
  7. Moore D, Meays BM, Madduri LSV, Shahjin F, Chand S, Niu M, Albahrani A, Guda C, Pendyala G, Fox HS, and Yelamanchili SV. (2019) Downregulation of an evolutionary young miR-1290 in an iPSC derived neural stem cell model of autism spectrum disorder. Stem Cells Int. 2019 May 2;2019:8710180. doi: 10.1155/2019/8710180. [PubMed]
  8. Vishweswaraiah S, Swierkowska J, Ratnamala U, Mishra NK, Guda C, Johar KR, Mrugacz M, Karolak JA, Gajecka M, Radhakrishna U. (2019) Epigenetically dysregulated genes and pathways implicated in the pathogenesis of non-syndromic high myopia. Scientific Reports, 9:4145, PMID: 30858441. [PubMed]
  9. Bahado-Singh R, Vishweswaraiah S, Veerappa AM, Mishra NK, Guda C, Radhakrishna U. (2019) Placental DNA methylation changes for the detection of Tetralogy of Fallot (TOF) Ultrasound in Obstetrics and Gynecology. doi: 10.1002/uog.20292.  [PubMed]
  10. Bahado-Singh R, Albayrak S Zafra R, Baraa A, Veerappa AV, Mahishi D, Saiyed NM, *Mishra NK, Guda C, Ali-Fehmi R, Radhakrishna U. Placental epigenetics for evaluation of fetal congenital heart defects: Ventricular septal defect (VSD). PLoS One, 14:e0200229, PMID: 30897084 [PubMed]
  11. Heithoff AJ, Totusek SA, Le D, Barwick L, Gensler G, Franklin DR, Dye AC, Pandey S, Sherman S, Guda C, Fox HS. (2019) The integrated national neuroAIDS tissue consortium (NNTC) database: A rich platform for neuroHIV research. Database doi: 10.1093/database/bay134. PMID: 30624650. [PubMed]
  12. Radhakrishna U, Veerappa AV, Vishweswaraiah S, Zafra R, Albayrak S, Sitharam PH, Saiyed NM, Mishra NK, Guda C, Bahado-Singh R. Cord blood DNA epigenetic variations and signaling pathway genes associated 1 with Tetralogy of Fallot (TOF). PLoS One, 13:e0203893 [PubMed]
  13. Roy S, Bag AK, Dutta S, Polavaram NS, Islam R, Schellenburg S, Banwait JK, Guda C, Ran S, Hollingsworth MA, Singh RK, Talmadge JE, Muders MH, Batra SK, Datta K. (2018) Macrophage-derived Neuropilin-2 exhibits novel tumor-promoting functions. Cancer Research, 78:5600-5617 [PubMed]
  14. Wipfler K, Cornish A, Guda C. (2018) Comparative molecular characterization of typical and exceptional responders in Glioblastoma. Oncotarget. doi: 10.18632/oncotarget.25420 [PubMed]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Mishra N, Guda C. (2017) Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer., Oncotarget, 8:28990-29012. [PubMed]
  21. 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]
  22. 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]
  23. 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. DOI: 10.21767/2471-8513.100030. [iMedPub]
  24. 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]
  25. 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].
  26. Vural S, Wang X, Guda C. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. BMC Systems Biology [PubMed].
  27. 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].
  28. 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]
  29. 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].
  30. 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].
  31. 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].
  32. 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].
  33. Mohammed A, Guda C. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. BMC Genomics. [PubMed].
  34. Cornish A, Guda C. A comparison of variant calling pipelines using Genome-in-a-Bottle as a reference. BioMed Research International (2015). [Hindawi]
  35. Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C. LocSigDB: A database of experimental and predicted protein localization signals. Database (2015). [PubMed]
  36. Shen R, Guda C. (2014) Applied graph-mining algorithms to study biomolecular interaction networks. BioMed Research International. [PubMed]
  37. 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]
  38. 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]