Research Interests

Bioinformatics, DataScience, Machine and Deep Learning, DevOps.

I read about what I code. I work across a wide variety of topics which includes bioinformatics, data science, machine and deep learning and devops. I work on the analysis of the genomics and the transcriptomics datasets from the plant, bacterial and fungal genomes. I specializes in analyzing the illumina (Miseq, NextSeq, NovaSeq) and long read sequencing such as the PacBio or the Oxford Nanopore sequencing. I also work on the analysis of the metagenomes and the meta-transcriptomes. I apply data science approaches, machine learning approaches to learn from the data. I have established independent computing cluster and also specific blades in my previous positions. I am skilled in both pbs and slurm based high performance computing clusters, devops management and uses git, docker and kubernetes for container orchestration. I program across Python, R, Shell, NuShell, Hashicorp, Ruby, Awk, Crystal. Shiny interface for python and R. Shell and NuShell for datascience, bioinformatics and high performance clusters. Ruby for DevOps plus other programming objects and classes. Getting along with Ruby on Rails and Crystal and Django in Python for front end development.

Education

2006 – 2009          PhD, JNV University

2005                        Master of Sc. (Biotechnology, First position), MGIAS, University of Rajasthan, Jaipur, India.

2003                        Bachelor of Sc.(Biotechnology) – LMCST, Jai Narian Vyas University, India

Research/Teaching 

2024: Academic Staff Member, University of Potsdam, Germany.

2022-2023: Self-employed Bioinformatics, DataScience, Machine and Deep Learning, DevOPs.

July 2017- Dec 2021: Postdoctoral Researcher, Finnish Museum of Natural History (Botany), Finland.

Aug 2016-Jan 2017: University Fellow, University of Connecticut, Storrs, USA.

Sept 2014-Sept 2016: Research Fellow, University of Technology Sydney, Australia.

Sept 2011-Sept 2014: CoCoPro, Fondazione Edmund Mach, IASMA, Italy.

Dec 2010-Aug 2011: Visiting Post-doc Researcher, Huazhong Agricultural University, China.

2006-2009: PhD Candidate, Jai Narian Vyas University (JNVU), India.

2005-2006: Adjunct Lecturer (Biotechnology), MGIAS (University Affiliated college), India

Fellowships and Travel Grants

2014-2016: UTS Internal Start-up Grant ($20K) Project Role: Principal Investigator.

2015-2016: KARORA: Graphic driven platform independent proteomics workflow for spectral libraries (2016) University of Technology Sydney ($15K) Project Role: Principal Investigator.

2012-2014: Awarded CoCoPro Fellowship for “Developing NGS tools and techniques for large scale methods implementation in transcriptomics and genomics.

2011-2012: Awarded EU Postdoctoral Fellowship (BIOMASFOR) “Enhancing biomass potential for European forest using NGS technologies”.

2012: Awarded travel grant by European Conference on Computation Biology, Swiss Institute of Bioinformatics (ECCB, 2012) for presenting FungPROTDB: Database of protein homo-repeats in fungal proteomes and secretomes.

2010-2011: Chinese Fellowship “Developing transcriptomics tools for Disopyros kaki”.

2011: Awarded Prestigious DS Kothari Post-Doctoral Fellowship by Department of Science and Technology, Government of India (Award Number BL/10/0057) on Identification of potential stress related microRNAs in Wheat and Pennisetum. Project Role: Principal Investigator.

2006-2009: Awarded University Research Fellowship on Doctoral Dissertation, Computational Mining of Phyto-Diversity Resources of Rajasthan and Analysis of Simple Sequence Repeats (SSR’s), Biotechnology Centre, Jai Narian Vyas University, India.

2009: “Molecular Characterization and Prediction of Interspecies Diversity in Acacia’s for Sustainable Rehabilitation through Agroforestry”- F7(7)/DST/SP/2009/343-355. Funding: State Department of Science and Technology, Rajasthan, India. Project Role: Principal Investigator.

2008: Molecular Characterization of the Prosopis cineraria: A sustainable move towards conservation of Biodiversity of Arid Regions”- P35/DST/2008/2227. Funding: State Department of Science and Technology, Rajasthan, India. Project Role: Principal Investigator.

Publications

Gagnon E, Hilgenhof R, Orejuela A, McDonnell A, Sablok G, Aubriot X, Giacomin L, Gouvêa Y, Bohs L, Dodsworth S, Martine C, Poczai P, Knapp S, Särkinen T (2020) 

Phylogenomic data reveal hard polytomies across the backbone of the large genus Solanum (Solanaceae)

American Journal of Botany 109:580-601