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Aakash Chawade

Aakash Chawade
I am an Associate Professor (Docent) at the Department of Plant Breeding at SLU. The overall research goal of my lab is to understand genetic, molecular and physiological mechanisms underlying biotic and abiotic stresses in wheat. Ongoing research projects are focused on wheat disease resistance mechanisms, plant microbe interactions, high-throughput phenotyping and machine learning.

Teaching

Lectures in plant breeding, bioinformatics, basic statistics and high-throughput phenotyping in undergraduate, MSc and Phd courses at SLU.

Research

The focus of my lab is to identify key resistance genes for yellow rust, Fusarium head blight and Septoria tritici blotch resistance in wheat. By SNP genotyping, next generation sequencing and proteomics, we aim to identify molecular mechanisms underlying resistance to these diseases in wheat. We also integrate high-throughput phenotyping and machine learning. These techniques generate large amount of data requiring software pipelines for efficient data processing and analysis. Thus, we are also developing open source software for efficient data analysis. We work in close collaboration with stakeholders.

Current lab members:

  • Dhananjay Kumar (PostDoc)
  • Firuz Odilbekov (PostDoc)
  • Alexander Koc (Phd student)
  • Chiara Delvento (Master thesis student)
  • Behnaz Sirooeinejad (visiting Phd student)

Previous lab members:

Rita Armoniené (PostDoc)

Alexander Koc (MSc thesis student)

Salvatore Caruso (Erasmus exchange student)

Ongoing projects:

  • Developing data analysis pipeline for high-throughput plant phenotyping
  • Developing computational approaches for integrated analysis of transriptomics, proteomics and genomics data to identify dominant patterns and understand biological mechanisms.
  • Identifying molecular mechanisms underlying resistance to Septoria tritici blotch and yellow rust in wheat
  • Identifying novel quantitative trait loci (QTL) and SNP markers in wheat
  • Project leader of the BalticWheat network comprising of researchers from 10 organizations in 7 countries with focus on sustainable wheat production in the Baltic region. Project homepage

Open Source software:

1. Specalyzer: An online tool for interactive analysis of phenomics data: http://www.specalyzer.org

2. Delexplorer: An online tool for interactive analysis of omics data. http://www.delexplorer.org

3. Normalyzer: An online tool for rapid evaluation of normalization methods for omics datasets: http://quantitativeproteomics.org/normalyzer

4. Dinosaur: An open source peptide MS feature detector: https://github.com/fickludd/dinosaur

5. NormalyzerDE: Online tool for normalization of omics data. http://quantitativeproteomics.org/normalyzerde

Research Funding (current & previous):
Carl Tryggers Foundation, Crafoord Foundation, Einar & Inga Nilsson foundation, Jordbruksverket (Swedish Board of Agriculture), Lantmännen research foundation, Nilsson-Ehle Foundation, Partnerskap Alnarp, PlantLink, SLU, STINT, Swedish Institute.

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ResearchGate

Background

Education / Academic experience:

  • Researcher (2014-2016), Lund University
  • Post Doc in computational proteomics (2012-2014), Lund University
  • PhD in Biology (2006-2011), University of Gothenburg
  • Masters in Bioinformatics (2003-2005), University of Skövde
  • BSc in Genetics, Microbiology, Chemistry (1997-2000), Osmania University, India

Supervision

Main supervisor to:

1. Alexander Koc. PhD student at the Department of Plant Breeding, SLU, 2018 – 2022. Assistant supervisors: Prof. Rodomiro Ortiz and Dr. Kristiina Himanen (Helsinki University). 

Assistant Supervisor to the following doctoral students:

1.      Catja Selga. PhD student at the Department of Plant Breeding, SLU, 2016 – 2019. Main supervisor Prof. Rodomiro Ortiz, Assistant supervisors are Dr. Mariette Andersson, Dr. Aakash Chawade.

2.      Jakob Wilfors. PhD student at the Department of Immunotechnology, Lund University, 2016 – 2019. Main Supervisor Docent. Fredrik Levander, Lund University. Assistant supervisors are Dr. Aakash Chawade and Prof. Erik Andreasson.

Supervised several MSc thesis students.

Selected publications

2018

Koc, A., Henriksson, T., & Chawade, A. (2018). Specalyzer — an interactive online tool to analyze spectral reflectance measurements. PeerJ, 6(e5031), 1–14. https://doi.org/10.7717/peerj.5031

Odilbekov, F., Armoniené, R., Henriksson, T., & Chawade, A. (2018). Proximal Phenotyping and Machine Learning Methods to Identify Septoria Tritici Blotch Disease Symptoms in Wheat. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00685

Armoniené, R., Odilbekov, F., Vivekanand, V., & Chawade, A. (2018). Affordable Imaging Lab for Noninvasive Analysis of Biomass and Early Vigour in Cereal Crops. BioMed Research International, 2018, 23–26. https://doi.org/10.1155/2018/5713158

Chawade, A., et. al. (2018). A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region. Physiologia Plantarum. https://doi.org/10.1111/ppl.12726

Willforss, J., Chawade, A., & Levander, F. (2018). NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis. Journal of Proteome Research, acs.jproteome.8b00523. https://doi.org/10.1021/acs.jproteome.8b00523

Eriksson, D., Ammann, K., Chassy, B., & Chawade, A. (2018). Comments on two recent publications on GM maize and Roundup. Scientific Reports, 8(1), 13338. https://doi.org/10.1038/s41598-018-30440-7

Vetukuri, R. R., Tripathy, S., Malar C, M., Panda, A., Kushwaha, S. K., Chawade, A., … Whisson, S. C. (2018). Draft genome sequence for the tree pathogen Phytophthora plurivora. Genome Biology and Evolution, 1(August). https://doi.org/10.1093/gbe/evy162

Reynolds, D., Frederic B., Claude W., Aaron B., Joshua B., Francesco C., Argelia L., Chawade A., Khafif, M., Noshita, K., Muelle-Linow, M., Zhou, J., Tardieu, F. (2018). What Is Cost-Efficient Phenotyping? Optimizing Costs for Different Scenarios. Plant Science, July, 1–2. https://doi.org/10.1016/j.plantsci.2018.06.015.

Vetukuri, R. R., Tripathy, S., Malar C, M., Panda, A., Kushwaha, S. K., Chawade, A., Andreasson E., Grenville-Briggs, L. J., Whisson, S. C. (2018). Draft genome sequence for the tree pathogen Phytophthora plurivora. Genome Biology and Evolution, 1(August). https://doi.org/10.1093/gbe/evy162

Ghaffary, S. M. T., Chawade, A., & Singh, P. K. (2018). Practical breeding strategies to improve resistance to Septoria tritici blotch of wheat. Euphytica, 214(7), 122. https://doi.org/10.1007/s10681-018-2205-4

Kumar, M., Brar, A., Yadav, M., Chawade, A., & Pareek, N. (2018). Chitinases — Potential Candidates for Enhanced Plant Resistance towards Fungal Pathogens. Agriculture, 8(88), 1–12. https://doi.org/10.3390/agriculture8070088

Yadav, M., Paritosh, K., Chawade, A., Pareek, N., & Vivekanand, V. (2018). Genetic Engineering of Energy Crops to Reduce Recalcitrance and Enhance Biomass Digestibility. Agriculture, 8(76). https://doi.org/10.3390/agriculture8060076

Kumar, S., Paritosh, K., Pareek, N., Chawade, A., & Vivekanand, V. (2018). De-construction of major Indian cereal crop residues through chemical pretreatment for improved biogas production: An overview. Renewable and Sustainable Energy Reviews, 90, 160–170. https://doi.org/10.1016/j.rser.2018.03.049

Alexandersson, E., Keinänen, M., Chawade, A., & Himanen, K. (2018). Nordic research infrastructures for plant phenotyping The role of plant phenomics and controlled environments in response to climate change. Agriculture and Food Science, 27(1), 7–16. https://doi.org/10.23986/afsci.68870

Eriksson, D., Brinch-Pedersen, H., Chawade, A., Holme, I. B., Hvoslef-Eide, T. A. K., Ritala, A., … Thorstensen, T. (2018). Scandinavian perspectives on plant gene technology: applications, policies and progress. Physiologia Plantarum, 162(2), 219–238. https://doi.org/10.1111/ppl.12661

2017

Chawade, A., Armoniené, R., Odilbekov, F., & Henriksson, T. (2017). Regional variation i resistens mot svartpricksjuka hos höstvetesorter, Nr 70. Rapport från växtodlings- och växtskyddsdagar i Växjö. Meddelande Från Södra Jordbruksvörsöksdistriktet. Växjö: SLU.

Lindstedt, M. M., Borrebaeck, C. A. K., Johansson, H., Albrekt, A.-S., Zeller, K. S., Chawade, A., … FORRERYD, A. A. S. (2017). WO2017162773A1. (Patent)

Selga, C., Chawade, A., Andersson, M., & Ortiz, R. (2017). Phenotyping and genotyping to enable genomic breeding values in potato. In Scientific Smörgåsbord. SEB Gothenburg. (Poster)

Grenville-Briggs, L. J., Kushwaha, S. K., Cleary, M. R., Witzell, J., Savenkov, E. I., Whisson, S. C., … Vetukuri, R. R. (2017). Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech ( Fagus sylvatica ). Genomics Data, 12, 155–156. https://doi.org/10.1016/j.gdata.2017.05.010

Zeller, K., Forreryd, A., Lindberg, T., Gradin, R., Chawade, A., & Lindstedt, M. (2017). The GARD platform for potency assessment of skin sensitizing chemicals. ALTEX. http://doi.org/10.14573/altex.1701101

Kunwar, P., Kushwaha, S., Yadav, M., Pareek, N., Chawade, A., & Vivekanand, V. (2017). Food waste to energy: an overview of sustainable approaches for food waste management and nutrient recycling. Biomed Research International, 2017, 1–19. http://doi.org/10.1155/2017/2370927

Andersson, K. E., Chawade, A., Thuresson, N., Rascon, A., Öste, R., Sterner, O., … Hellstrand, P. (2017). Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport. Molecular Nutrition & Food Research, 61(7), 1600874. https://doi.org/10.1002/mnfr.201600874

2016

Armoniené, R., Koc, A., Caruso, S., Henriksson, T., & Chawade, A. (2016). Predicting yellow rust & Septoria tritici blotch in wheat by hyperspectral phenotyping and machine learning. In 4th IPPN Symposium. Texcocco, Mexico. (Poster)

Zeller, K., Forreryd, A., Lindberg, T., Chawade, A., & Lindstedt, M. (2016). The GARD assay for potency assessment of skin sensitizing chemicals. Estiv 2016, 259, S171. http://doi.org/10.1016/j.toxlet.2016.07.408

Teleman, J., Chawade, A., Sandin, M., Levander, F., & Malmström, J. (2016). Dinosaur: a refined open source peptide MS feature detector. Journal of Proteome Research, acs.jproteome.6b00016. [Abstract]

Chawade, A., Alexandersson, E., Bengtsson, T., Andreasson, E., & Levander, F. (2016). Targeted Proteomics Approach for Precision Plant Breeding. Journal of Proteome Research, 15(2), 638–646. [Abstract]

Lindberg, T., Zeller, K., Forreryd, A., Chawade, A., & Lindstedt, M. (2016). Prediction of skin sensitizing potency of chemicals by the alternative cell based assay GARD. In Society of Toxicology annual meeting (SOT). New Orleans. (Poster)

2015

Spegel, P., Chawade, A., Nielsen, S., Kjellbom, P., & Rützler, M. (2015). Deletion of glycerol channel aquaporin‐9 ( Aqp9 ) impairs long‐term blood glucose control in C57BL/6 leptin receptor–deficient ( db/db ) obese mice. Physiological Reports, 3(9), e12538. [Abstract]

Lindlöf, A., Chawade, A., Sikora, P., & Olsson, O. (2015). Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms. PLOS ONE, 10(5), e0125385. [Abstract]

Sandin, M., Chawade, A., & Levander, F. (2015). Is label-free LC-MS/MS ready for biomarker discovery? PROTEOMICS - Clinical Applications, 9(3–4), 289–294. [Abstract]

Chawade, A., Sandin, M., Teleman, J., Malmström, J., & Levander, F. (2015). Data Processing Has Major Impact on the Outcome of Quantitative Label-Free LC-MS Analysis. Journal of Proteome Research, 14(2), 676–687. [Abstract]

2014

Vivekanand, V., Chawade, A., Larsson, M., Larsson, A., & Olsson, O. (2014). Identification and qualitative characterization of high and low lignin lines from an oat TILLING population. Industrial Crops and Products, 59, 1–8. [Abstract]

Chawade, A., Alexandersson, E., & Levander, F. (2014). Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets. Journal of Proteome Research, 13(6), 3114–3120. [Abstract]

Tejeda, L., Alvarado, J. A., Dębiec, M., Peñarrieta, J. M., Cárdenas, O., Alvarez, M. T., Chawade, A., Nilsson, L., Bergenståhl, B. (2014). Relating genes in the biosynthesis of the polyphenol composition of Andean colored potato collection. Food Science & Nutrition, 2(1), 46–57. [Abstract]

2013

Chawade, A., Lindlöf, A., Olsson, B., & Olsson, O. (2013). Global Expression Profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi. PLoS ONE, 8(12), e81729. [Abstract]

2012

Chawade, A., Lindén, P., Bräutigam, M., Jonsson, R., Jonsson, A., Moritz, T., & Olsson, O. (2012). Development of a Model System to Identify Differences in Spring and Winter Oat. PLoS ONE, 7(1), e29792. JOUR. [Abstract]

Olsson, O., Sikora, P., Olsson, J., Hernandez, O., Sunilkumar, B., & Chawade, A. (2012). Molecular breeding for enhanced food quality in oat. Beijing: 9th International Oat Conference. (Poster)

Olsson, J., Chawade, A., Sikora, P., Fahlberg, P., & Olsson, O. (2012). Towards the development of Fusarium resistant oat. Beijing: 9th International Oat Conference.(Poster)

Chawade, A., Moritz, T., & Olsson, O. (2012). A new model system to develop Swedish winter oat. Beijing: 9th International Oat Conference. (Poster)

2011

Sikora, P., Chawade, A., Larsson, M., Olsson, J., & Olsson, O. (2011). Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding. International Journal of Plant Genomics, 2011, 1–13. [Abstract]

Chawade, A. (2011). Unravelling the complexity of cold acclimation in plants (Thesis). University of Gothenburg. [Abstract]

2010 and older

Chawade, A., Sikora, P., Bräutigam, M., Larsson, M., Vivekanand, V., Nakash, M., … Olsson, O. (2010). Development and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes. BMC Plant Biology, 10(1), 86. JOUR. [Abstract]

Lindlof, A., Brautigam, M., Chawade, A., Olsson, O., & Olsson, B. (2009). In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. Bioinformatics, 25(11), 1345–1348. JOUR. [Abstract]

Lindlöf, A., Bräutigam, M., Chawade, A., Olsson, O., & Olsson, B. (2008). Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets. Bioinformatics and Biology Insights, 2, 215–237. [Abstract]

Brautigam, M., Chawade, A., Jonsson, R., Lindlöf, A., Olsson, B., Sikora, P., & Olsson, O. (2008). Biochemical and Molecular analysis of Swedish winter oat. Minneapolis: 8th International Oat Conference. (Poster)

Chawade, A., Brautigam, M., Sikora, P., & Olsson, O. (2008). Identification of low lignin mutants in an oat TILLING population. Minneapolis: 8th International Oat Conference. (Poster)

Chawade, A., Sikora, P., Brautigam, M., & Olsson, O. (2008). Development and molecular charactarization of a Tilling population for oat. Minneapolis: 8th International Oat Conference. (Poster)

Chawade, A., Bräutigam, M., Lindlöf, A., Olsson, O., & Olsson, B. (2007). Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics, 8(1), 304. JOUR. [Abstract]

Lindlöf, A., Brautigam, M., Chawade, A., Olsson, B., & Olsson, O. (2007). Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets. In S. Hochreiter & R. Wagner (Eds.), Bioinformatics Research and Development – First International Conference, BIRD (pp. 48–65). CONF, Springer-Verlag.

Chawade, A. (2005). Inferring Gene Regulatory Networks in Cold-Acclimated Plants by Combinatorial Analysis of mRNA Expression Levels and promoter regions (MSc Thesis). University of Skövde.

Bräutigam, M., Chawade, A., Gharti-Chhetri, G., Lindlöf, A., Jonsson, A., Jonsson, R., … Olsson, O. (2006). Development of Swedish winter oat with gene technology and molecular breeding. J. Seed Science, 116(1–2), 12–35.

Brautigam, M., Chawade, A., Gharti-Chhetri, G., Zakhrabekova, S., Lindlöf, A., Olsson, B., & Olsson, O. (2005). Development of a Scandinavian winter oat by molecular breeding and transgenic techniques (p. 36). The 5th Workshop in the Nordic Arabidopsis Network Denmark.

Invited Speaker

Invited talk: "Winter wheat pre-breeding with integrated omics". International plant and molecular biology conference, Paris (2018)

Invited talk: ”Regional variation i resistens mot svartpricksjuka hos höstvetesorter”. Meddelande från södra jordbruksförsöksdistriktet, Nr 70. Rapport från växtodlings- och växtsyddsdagarna i Växjö (2017).

Invited talk: "Spektralanalys för gradering av svampsmitta i vete" in the one day seminar "Smarta lösningar med ny sensorteknik och bildanalys - seminarium med fokus på växtskydd" (2017), Alnarp

Invited talk:  "Precision breeding with omics" at the 5th Plant Genomics and gene editing congress (2017), Amsterdam

Invited talk: “Disease resistance breeding using omics” at joint CPSC-PlantLink workshop 2016, Copenhagen, Denmark

Invited talk: “Challenges in denovo transcriptome assembly in polyploids”, PlantLink Server talks 2014, Lund, Sweden

Invited talk: cold tolerance at Nordic Oat conference, 2008, Gothenburg, Sweden


Contact
Associate Senior Lecturer at the Institutionen för växtförädling
Telephone: 040-41 53 28
Postal address:
Växtförädling, Box 101
230 53 ALNARP
Visiting address: Sundsvägen 10, Alnarp