Akshay Bhat

Cancer Bioinformatician

Akshay joined The University of Sheffield in October 2023 as a cancer bioinformatician at the Bioinformatics Core

Academic Experience

2023 -… Cancer Bioinformatician, Sheffield Bioinformatics Core, The University of Sheffield.

2021 - 2023: LIMS Manager, Center of Covid-19 Research Facility (CRUSH), University of Glasgow.

2019 – 2021: Bioinformatics Postdoctoral Fellow, Livestrong Cancer Institutes, University of Austin at Texas.

2016 – 2018: Mitacs Elevate Postdoctoral Fellow, University of British Columbia, Vancouver Prostate Center and GenomeDX Biosciences.

2013 – 2016: PhD (Marie Curie Fellow - Multi-Omics, Bioinformatics and Bladder Cancer) Charite Medical University - Berlin, Biomedical Research Foundation Association Athens (BRFAA), Mosaiques Diagnositics GmBH - Hannover, Germany, emergentech Bioengineering GmBH - Vienna, Austria, University of Glasgow, University of Systems Biology - Ireland and INSERM - Toulouse, France

2010 – 2012: MRes. (Bioinformatics) University of Glasgow

2005 – 2010: Bachelors of Engineering (BE - Biotechnology) The Oxford University of Technology - Bangalore, India

Industrial Experience

2013 - 2016: Bladder Multi-Omics Bioinformatician - Mosaiques Diagnostics GmBH, Hannover, Germany 2018 - 2020: Research Analyst and Visiting Faculty - Proteomics Facility, Indian Institute of Technology - Bombay and University of Mumbai

2021 - 2022: CTO, GeneBox Pvt Ltd. and SpeedGaze Technologies, Mumbai, India


I joined the Sheffield Bioinformatics Core in October 2023 after completing a position as a laboratory informatics systems (LIMS) manager at the CVR-CRUSH (COVID-19 Drug-Screening and Resistance Hub), University of Glasgow. Prior to this position, I was a bioinformatics scientific advisor (CTO) for commercial entities named the Gene Box and SpeedGaze technologies solution Pvt Ltd. (Mumbai). I completed two postdoctoral fellowship at the Dell Medical Center – UT Austin, Texas, USA and Vancouver Prostate Center - Canada before taking up a position as a visiting faculty for bioinformatics at the University of Mumbai and Indian Institute of Technology - Bombay. Earlier to this position, I was a Marie Curie early-stage researcher (PhD.) at the Charite University Berlin and Mosaiques Diagnositics GmBH - Germany in a bladder cancer project entitled Bladder Cancer Molecular Medicine (BCMolMed). The project emphasized on a multidisciplinary approach in discovering bladder cancer biomarkers and included biotech industries, universities, and academic research centers across the European Union and North America.

In the Mitacs Elevate/BCMolMed fellowships, my tasks involved the bioinformatics modelling of genomics, transcriptomics and proteomics changes in bladder cancer invasion patients treated with neoadjuvant chemotherapy. I am proficient in using statistical software R-bioconductor, bio-python packages and network modelling tools from Cytoscape to integrate protein-interaction networks, gene-regulatory data and pathway enrichment databases for defining relevant biological processes in bladder cancer invasion. In addition, I have also used large scale public databases like TCGA, AACR GENIE, CPTAC, ProteomeXchange, GEO, SRA-EBI and ENCODE in order to download, analyse and validate bladder, prostate, breast and colorectal cancer data. I have experience in handling and analyzing omics data sets from DNA/RNA sequencing (including CNV), gene expression microarrays, single-cell RNA-seq and mass-spectrometry profiles. My research as a cancer bioinformatician at the Sheffield University is to integrate -omics techniques with tissue imaging by using machine-learning and deep-neural networks algorithms to predict resistance to therapy in diseased patients and distinguish drug-responsive patients based on gene regulatory networks. In order to assimilate this knowledge, I had opportunities to attend courses, workshops and conferences held by EMBL, Heidelberg, Germany, and Marie-Curie training programs within the last years.


Selected Publications

  1. Xu Hua, Robert Marick, Yongsheng Li, Sairahul Pentaparthi, Daniel McGrail, Raymond Zou, Li Guo, Aditya Shrawat, Kara Cirillo, Qing Li, Akshay Bhat and S. Stephen Yi. mGI-map: Landscape of microRNA regulatory network architecture and functional rerouting in cancer - CAN-20-0371R1 – Jan 14th 2022.

  2. Akshay Bhat, Anna Capasso, Jeanne Kowalski-Muegge, Omar Hamdani, S. Gail Eckhardt, William Matsui, Carla Van Den Berg, Stephen Song Yi - Proteogenomic Analysis Reveals Distinct Functional Characterization of Left- and Right-Sided Colorectal Cancer - under co-author revision, Journal of Clinical Research in Oncology

  3. Xu Hua, Yongsheng Li, Li Guo, Min Xu, Dan Qi, Jason H. Huang, Akshay Bhat, Yunyun Zhou, Erxi Wu, and S. Stephen Yi - Systematic characterization of somatic mutation-mediated microRNA regulatory network perturbations - bioRxiv preprint, 2020 doi: https://doi.org/10.1101/2020.06.02.128777

  4. Junqing Wang, Xiuquan Wang, Akshay Bhat, Yixin Chen, Keli Xu, Yin-yuan Mo, S. Stephen Yi, Yunyun Zhou - Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma - Front. Genet., 15 July 2020

  5. Akihiro Goriki; Roland Seiler; Alexander W. Wyatt; Alberto Contreras-Sanz; Akshay Bhat; Akio Matsubara; Tetsutaro Hayashi; Peter C. Black. Unravelling disparate roles of NOTCH in bladder cancer. Nature Reviews. Urology Jun 2018, 15(6):345-357

  6. Jason A. Efstathiou, Ewan Gibb, David Tomoaki Miyamoto, Chin-Lee Wu, Michael Drumm, Jonathan Lehrer, Hussam Al-Deen Ashab, Nicholas Erho, Marguerite du Plessis, Kaye Ong, Akshay Bhat, Kent William Mouw, Elai Davicioni, William U. Shipley. Subtyping muscle-invasive bladder cancer to assess clinical response to trimodality therapy. Meeting Abstract - 2017 Genitourinary Cancers Symposium

  7. Akshay Bhat, Marika Mokou, Jerome Zoidakis, Antonia Vlahou, Harald Mischak, Vera Jankowski. BcCluster: A bladder cancer knowledgebase at its molecular level. Bl Cancer. 2016; 2(1): 65–76.

  8. Akshay Bhat, Vera Jankowski, Antonia Vlahou, Harald Mischak, Jerome Zoidakis. Comparison of ClueGO and IMPALA for integrated pathway enrichment analysis. J J Bioinform Proteom. 2016, 1(1): 002.

  9. Esther Nkuipou-Kenfack, Akshay Bhat, Vera Jankowski, Julie Klein, William Mullen, Antonia Vlahou, Thomas Koeck, Mohammed Dakna, Joost P. Schanstra, Petra Zürbig, Andreas Pich, Harald Mischak. Identification of urinary age-specific peptides in a healthy population. Oncotarget. 2015 Oct 27; 6(33): 34106–34117.

  10. Akshay Bhat, Andreas Heinzel, Bernd Mayer, Paul Perco, Irmgard Mühlberger, Holger Husi, Axel S. Merseburger, Joost P Schanstra, Jerome Zoidakis, Antonia Vlahou, Harald Mischak, Vera Jankowski. Protein Interactome for Muscle Invasive Bladder Cancer.PLoS One. 2015 Jan 8;10(1):e0116404.

  11. Akshay Bhat, Mohammed Dakna and Harald Mischak. Integrating Proteomics Profiling Data Sets – A Network Perspective. Methods Mol Biol. 2015; 1243:237-53.

  12. Maria Frantzi, Akshay Bhat, Agnieszka Latosinska. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. ClinTransl Med. 2014 Mar 29; 3(1):7

  13. Akshay Bhat, Vinay Sridhar, Hemanth Kumar K and Abhilash M. (2010) Novel Nuclear Receptor Super Family Database. International Journal of Pharmaceutical Sciences and Research.Vol.1 (10):41- 49