• My research interests include

    • Investigate the molecular mechanisms involved in prostate, breast, lung, colon, bladder cancer, other solid tumors and lymphoma development and progression using integrative genomic, proteomic and systems biology approach. Therapeutic targeting.
    • Develop user-friendly web based cancer data portals, which allows access to publicly available cancer omics data and facilitates integrative analysis. Primary target users would be cancer researchers with minimum or no programming knowledge.
    • Implement machine learning (ML) approaches on genomics, transcriptomics or proteomic data to identify risk gene signatures or prognostic biomarkers.
    • Collaborative research and Team Science approach. I have collaborated with over 25 research groups within and outside UAB since joining UAB in 2016.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2022 19S Proteasome Subunits as Oncogenes and Prognostic Biomarkers in FLT3-Mutated Acute Myeloid Leukemia (AML)International Journal of Molecular Sciences.  23. 2022
    2022 Author Correction: Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways (Nature Communications, (2022), 13, 1, (2669), 10.1038/s41467-022-30342-3)Nature Communications.  13. 2022
    2022 Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathwaysNature Communications.  13. 2022
    2022 19S Proteasome Subunits As Oncogenes and Prognostic Biomarkers in FLT3-Mutated Acute Myeloid Leukemia (AML)Blood.  140:3381-3382. 2022
    2022 ARID1A-deficient bladder cancer is dependent on PI3K signaling and sensitive to EZH2 and PI3K inhibitorsJCI Insight.  7. 2022
    2022 RNA splicing: a dual-edged sword for hepatocellular carcinoma.Medical Oncology.  39:173. 2022
    2022 Reducing regorafenib toxicity by combining with dual JAK-HDAC inhibitor in colorectal cancer.Journal of Clinical Oncology.  40:e15597-e15597. 2022
    2022 Distinct Gene Expression Profiles of Matched Primary and Metastatic Triple-Negative Breast CancersCancers.  14. 2022
    2022 DCZ0415, a small-molecule inhibitor targeting TRIP13, inhibits EMT and metastasis via inactivation of the FGFR4/STAT3 axis and the Wnt/β-catenin pathway in colorectal cancerMolecular Oncology.  16:1728-1745. 2022
    2022 UALCAN: An update to the integrated cancer data analysis platformNeoplasia.  25:18-27. 2022
    2022 Abstract P2-12-24: Exosomal metabolic signatures are associated with differential response to neoadjuvant chemotherapy in patients with breast cancerCancer Research.  82:p2-12-24-p2-12-24. 2022
    2022 Abstract P3-09-14: Whole exome sequencing of matched primary and metastatic triple-negative breast cancer samplesCancer Research.  82:p3-09-14-p3-09-14. 2022
    2022 Global molecular alterations involving recurrence or progression of pediatric brain tumorsNeoplasia.  24:22-33. 2022
    2021 The TGF-β/HDAC7 axis suppresses TCA cycle metabolism in renal cancerJCI Insight.  6. 2021
    2021 Abstract LB245: TRIM29 mediates metastasis though hypoxia-regulated proteins in microsatellite-stable and p53-mutated colorectal cancersCancer Research.  81:lb245-lb245. 2021
    2021 Mass-spectrometry-based proteomic correlates of grade and stage reveal pathways and kinases associated with aggressive human cancersOncogene.  40:2081-2095. 2021
    2021 Subcellular localization of EZH2 phosphorylated at T367 stratifies metaplastic breast carcinoma subtypesBreast Cancer.  28:496-505. 2021
    2021 TGF-β signaling suppresses TCA cycle metabolism in renal cancer 2021
    2021 ARID1A-mutant and deficient bladder cancer is sensitive to EZH2 pharmacologic inhibition 2021
    2021 Alterations in the Ca2+ toolkit in oesophageal adenocarcinoma.Exploration of Targeted Anti-tumor Therapy.  2:543-575. 2021
    2020 TRIP13 promotes metastasis of colorectal cancer regardless of p53 and microsatellite instability statusMolecular Oncology.  14:3007-3029. 2020
    2020 MicroRNA-mediated inflammation and coagulation effects in rats exposed to an inhaled analog of sulfur mustardAnnals of the New York Academy of Sciences.  1479:148-158. 2020
    2020 Abstract 2012: Recurrent rearrangements of NAALADL2 in prostate, breast, cervical, head and neck and lung squamous cell carcinomaCancer Research.  80:2012-2012. 2020
    2020 PGC1α suppresses kidney cancer progression by inhibiting collagen-induced SNAIL expressionMatrix Biology.  89:43-58. 2020
    2020 Comparative transcriptome analyses reveal genes associated with SARS-CoV-2 infection of human lung epithelial cells 2020
    2020 PRDM16 suppresses HIF-targeted gene expression in kidney cancerJournal of Experimental Medicine.  217. 2020
    2020 Therapeutically actionable PAK4 is amplified, overexpressed, and involved in bladder cancer progressionOncogene.  39:4077-4091. 2020
    2020 Fermentable fibers induce rapid macro- And micronutrient depletion in Toll-like receptor 5-deficient mice 2020
    2020 PAICS, a purine nucleotide metabolic enzyme, is involved in tumor growth and the metastasis of colorectal cancerCancers.  12. 2020
    2019 Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancersNature Communications.  10. 2019
    2019 Pseudogene Associated Recurrent Gene Fusion in Prostate CancerNeoplasia.  21:989-1002. 2019
    2019 Successful Derivation of an Induced Pluripotent Stem Cell Line from a Genetically Nonpermissive Enhanced Green Fluorescent Protein-Transgenic FVB/N Mouse Strain.Cellular Reprogramming.  21:270-284. 2019
    2019 Therapeutically actionable PAK4 is amplified, overexpressed and involved in bladder cancer progression 2019
    2019 Abstract 2481: Developing analysis platform for pan-cancer study of DNA methylation, mirna and lncrna expression based on tumor subtypes using TCGA dataCancer Research.  79:2481-2481. 2019
    2019 Abstract 5247: Overexpression of methylenetetrahydrofolate dehydrogenase 1 like (MTHFD1L) in bladder cancer: A potential therapeutic targetCancer Research.  79:5247-5247. 2019
    2019 Abstract LB-247: 9cis-retinoic UAB30 inhibits UVB-induced pro-inflammatory cytokines/chemokines signaling via targeting Bromodomain-4Cancer Research.  79:lb-247-lb-247. 2019
    2019 Large-scale profiling of serum metabolites in African American and European American patients with bladder cancer reveals metabolic pathways associated with patient survivalCancer.  125:921-932. 2019
    2019 Inhibition of Hedgehog signaling reprograms the dysfunctional immune microenvironment in breast cancerOncoImmunology.  8. 2019
    2019 Ferritin light chain confers protection against sepsis-induced inflammation and organ injuryFrontiers in Immunology.  10. 2019
    2019 Integrative epigenetic and gene expression analysis of renal tumor progression to metastasisMolecular Cancer Research.  17:84-96. 2019
    2018 A Role for De Novo Purine Metabolic Enzyme PAICS in Bladder Cancer ProgressionNeoplasia.  20:894-904. 2018
    2018 Gene Expression Profiling of Advanced Penile Squamous Cell Carcinoma Receiving Cisplatin-based Chemotherapy Improves Prognostication and Identifies Potential Therapeutic TargetsEuropean urology focus.  4:733-736. 2018
    2018 Abstract 3495: Trip13, a target of miR192, facilitates colorectal cancer progression through WNT/β-catenin signalingCancer Research.  78:3495-3495. 2018
    2018 Abstract 4043: A novel role for Hedgehog signaling in macrophage-mediated immune evasionCancer Research.  78:4043-4043. 2018
    2018 miR-34a regulates expression of the stathmin-1 oncoprotein and prostate cancer progressionMolecular Cancer Research.  16:1125-1137. 2018
    2018 214 High fat diet accelerates UVB-induced development of basal cell and squamous cell carcinoma in Ptch+/-/SKH-1 miceJournal of Investigative Dermatology.  138:s36. 2018
    2018 Chemotherapy induces secretion of exosomes loaded with heparanase that degrades extracellular matrix and impacts tumor and host cell behaviorMatrix Biology.  65:104-118. 2018
    2018 RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer.Journal of Oncology.  2018:2439527. 2018
    2017 UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival AnalysesNeoplasia.  19:649-658. 2017
    2017 Abstract 475: Role of microRNA-34a in regulating oncoprotein STMN1Cancer Research.  77:475-475. 2017
    2017 Chondroitin sulfate proteoglycan serglycin influences protein cargo loading and functions of tumor-derived exosomesOncotarget.  8:73723-73732. 2017
    2016 MicroRNA-101 regulated transcriptional modulator SUB1 plays a role in prostate cancerOncogene.  35:6330-6340. 2016
    2016 Multiplatform comprehensive kinase analysis of muscle-invasive bladder cancer (MIBC) to identify potentially actionable therapeutic targets.Journal of Clinical Oncology.  34:e16014-e16014. 2016
    2013 TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.BMC Genomics.  14:922. 2013
    2010 A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis databaseBMC Genomics.  11. 2010


    Year Title Altmetric
    2015 Alignment Free Frequency Based Distance Measures for Promoter Sequence Comparison.  183-193. 2015

    Research Overview

  • Bioinformatics
    Biological databases
    Machine learning
  • Education And Training

  • Doctor of Philosophy in Bioinformatics, Manipal University 2014
  • Master's Level Degree in Bioinformatics, Kuvempu University 2007
  • Bachelor's Level Degree in Biotechnology, Kuvempu University 2005
  • Full Name

  • Darshan Shimoga Chandrashekar