Kumar Saurabh Singh

Kumar Saurabh Singh

Assistant Professor

Maastricht University

About

The rapid advancement of high-throughput omics technologies has revolutionized our understanding of plant-specific pathways that lead to traits useful for the society. As vast amounts of omics data become available, computational methods have taken center stage in decoding the complex pathways and their regulatory mechanisms. The field is now moving towards a more holistic integration of genomics, transcriptomics, metabolomics, proteomics, and metagenomics spurred by technological innovations that enable untargeted pathway discovery. My research focuses on the synergistic potential of integrating multiple omics datasets and explores how the interplay of gene regulatory networks and temporal data can unravel the complex interactions within these pathways.
Interests
  • Integrative -omics
  • Bioinformatics
  • Gene regulatory networks
  • Biotic interactions and co-evolution
Education
  • PhD in Bioinformatics, 2014

    University of Camerino Italy

  • MSc. in Bioinformatics, 2008

    Nottingham Trent University UK

  • BSc in Biotechnology, 2006

    University of Pune India

Research

Wageningen University and Utrecht University, the Netherlands

In this postdoctoral position, together with the WUR Bioinformatics group (Prof. Marnix Medema), Plant-Microbe interaction group (Prof. Saskia Van Wees/Prof. Corné Pieterse) at Utrecht University and Microbial Sciences group, Institute of Biology, Leiden University (Prof. Gilles van Wezel and Dr. Somayah Elsayed), I explored and implemented innovative -omics integration strategies to map genes and their expression patterns to metabolites that play key roles in host-microbe interactions. We developed a method that integrates metabolomics and transcriptomics data and predicts putative reactions that represent either complete or partial steps of biosyntehtic pathways. This method represents a significant advancement towards obtaining a holistic view of plant metabolism and thus providing researchers, across disciplines, with a powerful tool to unravel complex metabolic routes and generate actionable hypotheses for further investigations.

Rothamsted Research & University of Exeter, UK

My postdoctoral work at the University of Exeter and Rothamsted Research are mainly driven by key questions in resistance evolution of insect-pests to natural and synthetic insecticides. I used genome-wide investigations and computational approaches to answer such questions, ensuring these are relevant to a broad scientific community.
  1. Our work on brownplanthoppers in elucidating the role of the cytochrome P450 CYP6ER1 in resistance to neonicotinoid insecticides provided a novel example of gene duplication and neofunctionalization leading to resistance development in this species. Brown planthopper is the most devastating pest of south-east Asia and the findings of this study have helped in building suitable IPM strategies.
  2. Transcriptional plasticity of phytophagous generalist pests has always puzzled researchers. To further explore this, I have assembled the genome of a glasshouse whitefly, Trialeurodes vaporariorum, and helped perform transcriptomics in order to identify differences in expression of key genes on challenging host-plants. The findings in this work provide further insights in the ability of generalist pests to effectively reprogram genes expression during host-shift and the potential implication of transcriptional plasticity on their sensitivity to synthetic insecticides.
  3. My primary research has exploited cutting edge bioinformatics approaches to consistently progress beyond the state of the art. I have developed a novel software pipeline to electronically extend partial gene transcriptsup to full gene lengths, using raw RNA-seq data. This has helped characterize the correct number of genes, from different families, responsible for detoxifying allelochemicals in one of the solitary red mason bees.
  4. I also assembled the first genome sequence of a solitary bee Osmia bicornis and together with a PhD student showed that it lacks the CYP9Q subfamily of CYP450s but, despite this, it exhibits low acute toxicity to the neonicotinoid thiacloprid. Functional studies revealed that a P450 within the CYP9BU subfamily, with recent shared ancestry to the Apidae CYP9Q subfamily, metabolises thiacloprid in vitro and confers tolerancein vivo. This study is the landmark discovery of inherent tolerance of thiacloprid in solitary bees and can be leveraged to avoid negative pesticide impacts on these important pollinators.
  5. My most impactful academic output has been the work on aphid, Myzus persicae, and its host-shift to tobacco. In this work I used transcriptomics and genomics approaches to identify molecular signatures and genomic rearrangements that shape host mediated resistance evolution in aphids. My contribution in this work has laid the foundation of further experimental work that has provided key insights into the evolutionary processes facilitating insect adaptation to a novel host plant. Importantly, all genomic resources, along with four insect genomes and software developed by me, are used by many groups, extending beyond my field of expertise, to explore new and exciting avenues in molecular and evolutionary biology.

Experience

 
 
 
 
 
Assistant Professor
Aug 2024 – Present Brightsland Future Farming Institute, Venlo, the Netherlands
Plant Genome Bioinformatics
 
 
 
 
 
Postdoctoral researcher
May 2021 – Jun 2024 Wageningen and Utrecht, the Netherlands
Plant-microbe interaction using Multi-Omics
 
 
 
 
 
Postdoctoral researcher (Bass lab)
Jan 2016 – Mar 2021 Penryn Campus, Penryn Cornwall UK
Insect pests resistance evolution and Insect genomics
 
 
 
 
 
Postdoctoral Bioinformatics Scientist
Nov 2014 – Dec 2015 Harpenden, Hertfordshire UK
Bee Toxicogenomics - Genomics and Transcriptomics
 
 
 
 
 
EU FP7 Research Scholar
May 2011 – Oct 2014 Camerino Italy
Data analysis, algorithm development and web development
 
 
 
 
 
Bioinformatics Scientist
May 2008 – Jan 2011 Palo Alto CA USA
Domain expert Primer Premier, AlleleID, Primer Plex, Beacon Designer, Array Designer

Contact

  • Innovalaan 1, Venlo, Maastricht University 5928 SX
  • Brightlands Future Farming Institute
  • Mon-Wed-Thu-Fri 9.00 to 17:00
  • Book an appointment
  • DM Me