Sandeep Kumar Kushwaha

My primary interest lies in exploring the applied aspects of bioinformatics in plant science. Basically, I am applying bioinformatics approaches coupled with genomics and transcriptomics approaches to understand genetic and genomic mechanism related to plant infection, metabolism and environmental stress. Currently, I am engaged in developing method to capture plant resistance genes at large scale.

Research projects
2016-2017: Computational Infrastructure: To drive the plant breeding education and research front at SLU, Kungliga Fysiografiska Sällskapets, (applicant)

2016-2018: The microbiome of the invasive pest Drosophila suzukii and its impact on the fly’s sexual com­mu­nication, behavior and reproduction, Crafoord foundation (co-applicant)

2016-2018: Transcriptional regulation of oil in wheat, Crafoord fundation, (co-applicant).

2017-2018: Molecular Biology to Support Oat Breeding for Seed Development and Oil Storage, Kungliga Fysiografiska Sällskapets, (applicant)

2018-2020: Resistance Gene Array” a targeted approach for capturing of plant resistance genes, FORMAS, (co-applicant)

2018-2019:Targeted transcriptomics approach for the capturing of plant resistance genes at large scale Kungliga Fysiografiska Sällskapets, (applicant)

Developed Tools/software:

PINAT1.0: protein interaction network analysis tool

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction.

Education / Academic experience:

Postdoc, Plant Breeding, SLU Alnarp, Sweden (Aug 2015- March 2018)

Research Engineer,Plant Protection, SLU Alnarp, Sweden, (July 2014 - July 2015)

Postdoc, Department of Biology, Lund University, Lund Sweden, (Jan 2012-June 2014)

Ph.D., MANIT, Bhopal, M.P., India, (2012)

M.Phil. APS University, M.P., India, (2007)

Masters in Bioinformatics, University of Allahabad, U.P. India, (2005)

Bachelors in Biology, University of Allahabad, U.P., India, (2002)

Ramesh R Vetukuri, Sucheta Tripathy, C Malar, Arijit Panda, Sandeep K Kushwaha, Aakash Chawade, Erik Andreasson, Laura J Grenville-Briggs, Stephen C Whisson, 2018. Draft genome sequence for the tree pathogen Phytophthora plurivora, Genome biology and evolution.

Ramesh Raju Vetukuri, Sandeep Kushwaha, Diya Sen, Stephen C Whisson, Kurt Lamour, Laura Grenville-Briggs., 2018. Genome sequence resource for the oomycete taro pathogen Phytophthora colocasiae.Molecular Plant-Microbe Interactions.

Lokeshwaran Manoharan, Sandeep K. Kushwaha, Dag Ahrén, Katarina Hedlund, Agricultural land use determines functional genetic diversity of soil microbial communities, In Soil Biology and Biochemistry, Volume 115, 2017, Pages 423-432,

Grenville-Briggs LJ, Kushwaha SK, Chawdae A., Vetukuri RR,. 2017.Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).Genomics Data : 10.1016/j.gdata.2017.05.010

Kunwar Paritosh, Sandeep K Kushwaha, Monika Yadav, Nidhi Pareek, Aakash Chawade, Vivekanand Vivekanand., 2017.Food waste to energy: an overview of sustainable approaches for food waste management and nutrient recycling.BioMed Research International, hindwai

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ. 2017. Draft genome sequence of the mycoparasitic oomycete Pythium periplocum strain CBS 532.74. Genome Announc 5:e00057-17.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ. 2017. Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum strain CBS 530.74 .Genome Announc 5:e00156-17.

Vetukuri RR, Kushwaha SK, Vetukuri RR, Kurt H Lamour Grenville-Briggs LJ. 2017. Draft genome of the oomycete taro pathogen Phytophthora colocasiae, strain 7290, Data in Brief

Per Hofvander, Till Ischebeck, Helle Turesson, Sandeep K Kushwaha, Ivo Feussner, Anders S Carlsson, Mariette Andersson., 2016. Potato tuber expression of Arabidopsis WRINKLED1 increase triacylglycerol and membrane lipids while affecting central carbohydrate metabolism., Plant biotechnology journal

Amit Roy, WB Walker III, H Vogel, SK Kushwaha, Sophie Chattington, MC Larsson, P Anderson, DG Heckel, Fredrik Schlyter.,2016, Data set for diet specific differential gene expression analysis in three Spodoptera moths., Data in brief

Kushwaha, Sandeep K, Chauhan, Pallavi, Hedlund, Katarina, Ahrén ,Dag. 2015. NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. Bioinformatics. 2016 Apr 15;32(8):1223-5.

Manoharan, Lokeshwaran, Kushwaha, Sandeep K, Hedlund, Katarina, Ahrén ,Dag. 2015. Captured metagenomics: large-scale targeting of genes based on ‘sequence capture’ reveals functional diversity in soils. DNA Res. 2015 Dec;22(6):451-60. doi: 10.1093/dnares/dsv026

Kushwaha, Sandeep K, Manoharan, Lokeshwaran, Meerupati, Tejashwari, Hedlund, Katarina, Ahrén, Dag. 2015. MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinformatics. 2015 Feb 28; 16:65 doi: 10.1186/s12859-015-0501-8.

Kushwaha,  S. Shakya,  M. (2009).  PINAT1.0: protein interaction network analysis tool  Bioinformation, 3 (10),  pp.419-421.