Avinash Ghanate Email & Phone Number

London, United Kingdom

As part of the Bioinformatics and Biostatistics facility, we collaborate with various research groups across institute for supporting the analysis of their genomic/transcriptomic data. This requires involvement right from the project/experimental design inception until the final results for publications exploring various experiment centric analytical possibilities. I have taken up projects involving bulkRNAseq analysis from cell based assay to complex epidemiological studies with clinical… Show more As part of the Bioinformatics and Biostatistics facility, we collaborate with various research groups across institute for supporting the analysis of their genomic/transcriptomic data. This requires involvement right from the project/experimental design inception until the final results for publications exploring various experiment centric analytical possibilities. I have taken up projects involving bulkRNAseq analysis from cell based assay to complex epidemiological studies with clinical data. I also worked on a very interesting ChIPseq project analysis involving eSPAN technology for regulatory genomic characterisation. Additionally in this role, I was involved predominantly on single-cell RNAseq data analysis with key focus on data integration, clustering, differential gene express analysis, RNA velocity analysis, cell annotation and also Immune receptor clonal repertoire analysis. Show less

London, England, United Kingdom

This role as a postdoctoral training fellow at the Francis Crick Institute(London) involved application of modern machine learning methods on mass spectrometryimaging data to study heterogeneous breast cancer metabolism. Considering the large-scaleof the data and noisy nature, it required careful pre-processing followed by hyphenated datareduction/clustering methods either adapted from RNAseq data analysis workflow or tailoredspecifically. As the role was part of a CRUK… Show more This role as a postdoctoral training fellow at the Francis Crick Institute(London) involved application of modern machine learning methods on mass spectrometryimaging data to study heterogeneous breast cancer metabolism. Considering the large-scaleof the data and noisy nature, it required careful pre-processing followed by hyphenated datareduction/clustering methods either adapted from RNAseq data analysis workflow or tailoredspecifically. As the role was part of a CRUK grand challenge project, I was also fortunatelyable to closely interact with different domain data analysis experts from various esteemedinstitutes, such as Imperial College London and National Physics Laboratory. This helped usoptimize the data analysis pipeline which is efficiently being used by the consortium’s reserachmembers. Show less

Primarily I was involved in supporting setting up the data analysis workflow, analysis strategy and also building data analysis software to improve productivity and throughout.I have continued to provide consultancy support where required.

Pune Area, India

Short title: High-Throughput Analysis Tools for Mass Spectrometry-Based Data QuantitationMy research area interest is in developing quantitative workflows/ data analysis methods to facilitate quantitative analysis using High-Resolution Mass Spectrometry in tandem with MALDI-HRMS (Matrix Assisted Laser Desorption / Ionization) and/or LC-HRMS (Liquid Chromatography).In last few decades, MALDI MS has opened lot many avenues for analysis of small molecules, mostly biomolecules related… Show more Short title: High-Throughput Analysis Tools for Mass Spectrometry-Based Data QuantitationMy research area interest is in developing quantitative workflows/ data analysis methods to facilitate quantitative analysis using High-Resolution Mass Spectrometry in tandem with MALDI-HRMS (Matrix Assisted Laser Desorption / Ionization) and/or LC-HRMS (Liquid Chromatography).In last few decades, MALDI MS has opened lot many avenues for analysis of small molecules, mostly biomolecules related to metabolomics, drug analysis, and therapeutics. Not only this, the high throughput attained by MALDI is unparalleled. But along with these advantages, MALDI technique is also burdened with many disadvantages like lack of reproducibility and matrix interference.We have developed command-line tools and UI based software for HRMS data processing and quantitative analysis of metabolites. Validation of these tools was showcased using in-house experimental data for cancer metabolites, clinical biomarkers from biofluids and food contaminant analysis. Using metabolic profiles for cancer cells, context-specific genome-scale metabolic models were developed that were used to develop clinical treatment strategies following constraint-based linear optimization modeling approaches, such as Flux Balance Analysis (FBA), Synthetic lethal analysis etc. Show less

Pune Area, India

Short title: Understanding transcription kinetics with the help of deterministic and stochastic modelingI have worked on understanding gene regulatory pathways which operated in stochastic limits, using Gillespie's stochastic simulation algorithm. In principle, most of the crucial gene regulatory mechanisms, which decide cellular fate, acts under the control of molecules which are released/ exists at very low concentration levels. Because of this limitation, a skewed population… Show more Short title: Understanding transcription kinetics with the help of deterministic and stochastic modelingI have worked on understanding gene regulatory pathways which operated in stochastic limits, using Gillespie's stochastic simulation algorithm. In principle, most of the crucial gene regulatory mechanisms, which decide cellular fate, acts under the control of molecules which are released/ exists at very low concentration levels. Because of this limitation, a skewed population differentiation is resulted showing multimodality. Though such multi-modality is beneficial in terms of adapting to the changing environment and for better sustainability, they could also lead to deleterious effects in certain conditions. For understanding such transition, stochastic simulation algorithms are used which takes into consideration of natural randomness in the system. But these algorithms are computationally very expensive.We have explored different strategies to reduce the computational efforts using approximations and system reductions along with understanding the outcomes of such model alterations. Show less

Mumbai Area, India

Short title: Development and evaluation of various multivariate tools for discrimination of Raman Spectroscopic models in multi-cancer scenarioI have made use of different Multivariate Statistical Algorithms for understanding diagnostic and prognostic capabilities of Raman spectroscopy.Raman spectroscopy holds the capability of providing functional group characterization without or with minimal damage to cellular structures and because of this it can be used for noninvasive in-vivo… Show more Short title: Development and evaluation of various multivariate tools for discrimination of Raman Spectroscopic models in multi-cancer scenarioI have made use of different Multivariate Statistical Algorithms for understanding diagnostic and prognostic capabilities of Raman spectroscopy.Raman spectroscopy holds the capability of providing functional group characterization without or with minimal damage to cellular structures and because of this it can be used for noninvasive in-vivo studies without the need of surgery. This opens doors in the diagnostic analysis using Raman spectroscopy with minimal preparation and improved sensitivity.We have shown this diagnostic capability of Raman spectroscopy for various cancer tissues. In this study, we have studied different multivariate statistical tools for chemometric analysis, and have measured their up and down features. By developing a software interface for the pre-processing and diagnostic analysis with Raman spectroscopy, we have shown improved analysis time and sensitivity of the analysis. Not only diagnostics but we were able to show prognostic profiles of cancer signature marks. Show less

Pune Area, India

Short title: Integrative analysis of gene expression profiles in human ovarian epithelial cancer for identification of prognostic gene signature markersIdentified gene signature markers responsible for regulating transformation of normal ovarian epithelial cells into cancerous cells following data mining from publicly available microarray gene expression data. Validation of identified list of gene signatures using in-house ovarian adenocarcinoma cell line.

Doctor Of Philosophy - Phd, Biology/Biological Sciences, General

Master Of Technology (M.Tech.), Biotechnology And Bioinformatics, O

Master Of Science (M.Sc.), Biotechnology And Bioinformatics, A

Higher Secondary Education