BRIC-National Institute of Plant Genome Research

Dr. Subhra Chakraborty

PhD, FNA, FASc, FNASc, FNAAS
J. C. Bose National Fellow
Ph. D, Jawaharlal Nehru University
Tel: +91-11-26742267, 26735169, 26735186
Fax: +91-11-26741759
Email: subhrac@hotmail.com, schakraborty@nipgr.ac.in, director@nipgr.ac.in

Career

Director, National Institute for Plant Genome Research (2020-2024)

Staff Scientist VII, National Institute for Plant Genome Research (2015-2020)

Staff Scientist VI, National Institute for Plant Genome Research (2011-2015)

Staff Scientist V, National Institute for Plant Genome Research (2007-2011)

Staff Scientist IV, National Institute for Plant Genome Research (2003-2007)

Staff Scientist III, National Institute for Plant Genome Research (2000-2003)

Staff Scientist II, National Institute for Plant Genome Research (1998-2000)

Research Scientist, Jawaharlal Nehru University (1997-1998)

Patents

US Patents

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2015) Polynucleotides derived from chickpea and uses thereof (US Patent No. 9,163,255).

Datta, A., Chakraborty S, Chakraborty N, Meli, V, Ghosh, S. (2015). Polynucleotide Sequence of fruit Softening Associated B-D-N-Acetylhexosaminidase and its uses for enhancing fruit shelf life (US Patent No. 8,987,556)

Datta, A., Chakraborty S, Chakraborty N, Meli, V, Ghosh, S. (2015). Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life (US Patent No. 8,962,918).

Chakraborty N, Chakraborty S, Datta A, Wardhan V and Jahan K. Polynucleotide encoding CaTLP1 protein and uses thereof. (US No.14/399,706). Published by USPTO on 07/05/2015 (US20150128305 A1).

Chakraborty N, Chakraborty S, Jaiswal DK, Mishra P, Subba P and Rathi D. Method of producing stress tolerant plants overexpressing CaSUN1. (US No. 14/588,737). Published by USPTO on 02/07/2015 (US20150184190 A1).

Chakraborty N, Chakraborty S, Verma JK, Gayali S, Dass S and Kumar A. (2015) Method of producing stress tolerant plants overexpressing OsAlba1. (US No. 20,150,247,161). Published by USPTO on 03/09/2015 (US20150247161 A1).

Chakraborty N, Chakraborty S, Datta A and Bhushan D. (2012) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (US patent No. 8,163,977).

Datta A, Raina A and Biswas S. (1998) Method of making seed specific DNA (US Patent No. 5,846,736)

Datta A, Raina A and Biswas S. (1997) Seed storage protein with nutritionally balanced amino acid composition (US Patent No. 5670635).

PCT Patents

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2017) Polynucleotides derived from chickpea and uses thereof for improving immunity to fungal pathogens (CP No. 2,772,654).

Chakraborty, N., Chakraborty, S., Wardhan, V., Rathi, D., Gupta. S. (2017). Method of generating stress tolerant plant over-expressing CaRRP1, reagents and uses thereof (WO2017098530 A1).

Chakraborty S, Chakraborty N, Datta A, Ashraf N, Basu S, Nag P and Singh M (2016) Polynucleotides derived from chickpea and uses thereof (EP No. 2470663).

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2015) Polynucleotides derived from chickpea and uses thereof (APA No. 2010288112).

Datta A, Chakraborty S, Chakraborty N and Meli V (2014) Polynucleotide Sequence of fruit Softening Associated B-D-N-Acetylhexosaminidase and its uses for enhancing fruit shelf life (EP-2315830)

Datta A, Chakraborty S, Chakraborty N, Ghosh S and Meli SV (2015) Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life (EP 2315835).

Chakraborty N, Chakraborty S, Datta A, Wardhan V and Jahan K (2014) Polynucleotide encoding CaTLP1 and uses thereof (WO2013168181 A1).

Chakraborty N, Chakraborty S, Datta A and Bhushan D (2013) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (WO 2007141808 A2).

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2011) Polynucleotides derived from chickpea and uses thereof (WO2011024207A3).

Indian Patents

Chakraborty N, Chakraborty S, Wardhan V, Rathi D, Gupta S (2015) Method of generating stress tolerant plant over-expressing CaRRP1, reagents and uses thereof [IPA No.3983/DEL/2015

Chakraborty N, Chakraborty S, Verma JK, Dass S, Gayali S, Kumar A, Praveen S (2014) A method of producing stress tolerant plants over-expressing OsAlba1 [IPA No. 3759/DEL/2013].

Datta A, Chakraborty N, Chakraborty S, Kamthan M and Kamthan A (2014). Polynucleotide Associated with Ergosterol Biosynthesis and uses thereof [IPA-925/DEL/2014].

Chakraborty N, Chakraborty S, Jaiswal DK, Mishra P, Subba P and Rathi D (2014) A method of producing stress tolerant plants (IPA No. 8/DEL/2014).

Chakraborty N, Chakraborty S, Verma JK, Gayali S, Dass S and Kumar A (2013) A method of producing stress tolerance rice plants (IPA No. 3759/DEL/2013).

Chakraborty N, Chakraborty S, Datta A, Wardhan V and Jahan K (2012) Polynucleotide encoding CaTLP1 and uses thereof (IPA No.1406/DEL/2012)

Datta A, Chakraborty S, Chakraborty N, Kamthan M and Kamthan A (2012) Polynucleotide sequence of an ergosterol biosynthesis enzyme ∆7-sterol-C-5-desaturase and uses thereof (IPA No. 3671/DEL/2012).

Datta A, Chakraborty S, Chakraborty N, Ghosh S and Meli SV (2010) Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life (IPA No.1647/DEL/2008). Published by Indian Patent Office on 16.04.2010.

Datta A, Chakraborty S, Chakraborty N, Ghosh S and Meli SV (2010) Polynucleotide sequence of fruit softening associated β-D-N-acetyhexosaminidase and its uses for enhancing fruit shelf life (IPA No.1648/DEL/2008). Published by Indian Patent Office on 23.04.2010.

Chakraborty S, Datta A, Chakraborty N, Asraf N and Basu S (2009) Functional genomics and stress responsive polynucloetides from chickpea (IPA No.1565/DEL/2009).

Chakraborty N, Chakraborty S, Datta A and Bhushan D (2006) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (IPA No.1371/DEL/2006).

Editorial experience

Academic Editor, Plant Direct.

Editorial Board Member, Crop Design, Elsevier.

Early Career Reviewer, The Journal of Biological Chemistry.

Review editor, Frontiers in plant sciences and pharmaceutical innovations.

Reviewer Board Member, Microorganisms.

Serving as a reviewer in evaluating several research works | Web of Science.

Profile

Research

Our research is focused in three main areas: Nutritional Genomics, Plant Immunity & Stress Genomics, and delayed fruit softening.

Nutritional Genomics

Our aim is to improve the nutritional quality of important food crops since the nutritional health of humans predominantly depends on pant food. As part of protein quality improvement program, we have cloned a seed albumin gene AmA1 from Amaranthus hypochondriacus and developed protein-rich transgenic potato. Currently, our laboratory is developing transgenic cereals using this novel gene for protein quality improvement. Alternatively, for removal of antinutrient element, we focus on oxalate toxicity as it is the major dietary factor involved in kidney related diseases. Towards this end, an oxalate degrading enzyme, oxalate decarboxylase is being used to develop low-oxalate transgenic plants. Also, we are developing enabling technologies for transforming oxalate-rich fruits and vegetables with oxalate decarboxylase.

Stress Genomics

A second area of our interest is Stress Genomics in plants with specific emphasis to fungal pathogenicity. Plants frequently encounter different biotic stresses that adversely affect growth, development and more importantly the overall productivity. Stress signals perceived by plant cells leads to changes in gene expression profiles that dictate how cells overcome these stresses. Oxalic acid is a potent elicitor in fungal pathogenicity in many crop plants. We have developed fungal resistant transgenic tomato plants that express oxalate decarboxylase. Our current interest is to unravel the role of oxalate decarboxylase in fungal tolerance. In addition, we are identifying resistant gene candidates and defense mechanism of plants in response to fungal wilt. Our laboratory is developing a genome wide transcriptome of legume against Fusarium wilt to study stress perception, differential gene expression and thereby changes in metabolic responses. Our aim is to understand the biological and pathophysiological role of differentially expressed gene/s that control fungal pathogens. The ultimate goal is to use few novel genes for developing transgenic crops with improved fungal tolerance.

A third area of our research is to investigate the regulation of fruit softening using tomato as a model system. We are interested in enhancing shelf-life of fruits and vegetables because delay in fruit softening is the key regulatory mechanism to control their spoilage. Experimental approaches include softening related gene mining and developing knock-out transgenic plants for the candidate genes.

The tools used in our laboratory are molecular biology, biochemistry, Microarray, RNA Seq., Proteomic technology, Computational biology and genetic transformation.

Awards and Honors

Fellow, Indian National Science Academy (INSA), Delhi, India

Fellow, Indian Academy of Sciences, Bangalore, India

Fellow, National Academy of Sciences

Fellow, National Academy of Agricultural Sciences

J C Bose National Fellowship, SERB-DST (2020)

Professor (Mrs.) Archana Sharma Memorial Lecture Award, National Academy of Sciences, India (2020)

Sectional President, Biological Sciences, 89th NASI Annual Session (2019)

Platinum Jubilee Lecture Award, 103rd Indian Science Congress (2016)

TATA Innovation Award from The Department of Biotechnology, Govt of India (2014)

An Inspiring Women Engineer/Scientist Award (2014)

NASI-Reliance Industries Platinum Jubilee Award (2010)

Visiting Scientist, Yale University, USA (2008)

DBT Overseas Associateship, Govt. of India, India (2007)

Young Women Bioscientist of Promise, ISCA, India (2004)

National Young Women Bioscientist Award, DBT, India (2002)

Professor Hiralal Chakraborty Award, Indian Science Congress (2002)

Technology Development Award, DBT, Govt. of India (2000)

IRRI Core Research Fellowship, IRRI, Philippines (1995)

Young Scientist Award, IUBMB (1994)

Professor Hiralal Chakraborty Award, National Botanical Society (1990)

Elected Council Member, Human Proteome Organization (HUPO)

Member, Human proteome project-Scientific advisory board (HPP-SAB)

Co-Chair, Food & Nutrition Initiative, under Biology/Disease-driven HPP

Elected Council Member and Country Representative for India in Asia Oceania Agricultural Proteomics Organization (AOAPO)

President & Executive Council Member, Proteomics Society, India (PSI)

Executive Council Member, Society for Molecular Signaling, India

Life Member, Society for Biological Chemists, India

Life Member, Indian Society of Cell Biology

Life Member, Indian Society of Translational Research

Life Member, Indian Science Congress Association

Member, American Chemical Society, USA

Member, Society for Biological Chemists, India

Proteomic Society of India

Selected Publications

Narula K, Elagamey E, Abdellatef M, Sinha A, Ghosh S, Chakraborty N and Chakraborty S (2020) Chitosan-triggered immunity to Fusarium in chickpea is associated with changes in the plant extracellular matrix architecture, stomatal closure and remodelling of the plant metabolome and proteome. Plant J. doi: 10.1111/tpj.14750.

Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N and Chakraborty S (2020) Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea. Proteomics 20: e1900267.

Elagamey E, Narula K, Chakraborty N, Chakraborty S (2020) Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies. Methods Mol Biol. 2057:155-172.

Barua P, Lande NV, Kumar S, Chakraborty S, Chakraborty N (2020) Quantitative phosphoproteomic analysis of legume using TiO2-based enrichment coupled with isobaric labeling. Methods Mol. Biol.2107: 395-406.

Lande NV, Barua P, Gayen D, Kumar S, Varshney S, Sengupta S, Chakraborty S, Chakraborty N (2020) Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses. Plant Physiol. Biochem. 146:337-348.

Lande NV, Barua P, Gayen D, Kumar S, Chakraborty S, Chakraborty N (2020) Proteomic dissection of the chloroplast: Moving beyond photosynthesis. J. Proteomics 212: 103542.

Chakraborty S, Gowrishankar J, Joshi A, Kannan P, Kohli RK, Lakhotia SC, Misra G, Nautiyal CM, Ramasubramanian K, Sathyamurthy N and Singhvi AK (2020) Suggestions for a national framework for publication of and access to literature in science and technology in India. Current Science 118: 1026-1034.

Narula K, Choudhary P, Ghosh S, Elagamey E, Chakraborty N. and Chakraborty S (2019) Comparative nuclear proteomics analysis provides insight into the mechanism of signalling and immune response to blast disease caused by Magnaporthe oryzae in rice. Proteomics 19: 1800188.

Pareek A, Rathi D, Mishra D, Chakraborty S, Chakraborty N (2019) Physiological plasticity to high temperature stress in chickpea: Adaptive responses and variable tolerance. Plant Sci. 289: 110258.

Rathi D, Pareek A, Zhang T, Pang Q, Chen S, Chakraborty S, Chakraborty, N. (2019) Metabolite signatures of grasspea suspension-cultured cells illustrate the complexity of dehydration response. Planta 250: 857-871.

Rathi D, Gayali S, Pareek A, Chakraborty S and Chakraborty N (2019) Transcriptome profiling illustrates expression signatures of dehydration tolerance in developing grasspea seedlings. Planta 250: 839-855.

Gayen D, Barua P, Lande NV, Varshney S, Sengupta S, Chakraborty S and Chakraborty N (2019) Dehydration-responsive alterations in the chloroplast proteome and cell metabolomics profile of rice reveals key stress adaptation responses. Environ. Exp. Bot. 160: 12-24.

Gayen D, Gayali S, Barua P, Lande NV, Varshney S, Sengupta S, Chakraborty S. and Chakraborty N (2019) Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes. J. Proteomics 192: 267-279.

Barua P, Lande NV, Subba P, Gayen D, Pinto S, Prasad TSK, Chakraborty S and Chakraborty N (2019) Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant Cell Environ. 42: 230-244.

Mishra D, Shekhar S, Chakraborty S and Chakraborty N (2018) Carboxylase clamp tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones in Triticaace: an insight into structural and functional diversification. Environ. Exp. Bot. 155: 31-44.

Aggarwal PR, Nag P, Choudhary P, Chakraborty N and Chakraborty S (2018) Genotype-independent Agrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies. Plant Methods14: 55.

Rathi D, Pareek A, Gayali S, Chakraborty S, Chakraborty N (2018) Variety-specific nutrient acquisition and dehydration-induced proteomic landscape of grasspea (Lathyrus sativus L.). J. Proteomics 183:45-57.

Ashraf, N, Basu S, Narula K, Ghosh S, Tayal R, Gangisetty N, Biswas S, Aggarwal P, Chakraborty N. and Chakraborty S (2018) Integrative network analysis of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility. Sci. Rep. 8: 6528.

Parveen S, Pandey A, Jameel N, Chakraborty S and Chakraborty N (2017) Transcriptional regulation of chickpea ferritin CaFer1 influences its role in iron homeostasis and stress response. J. Plant Physiol. 222: 9-16.

Verma JK, Wardhan V, Singh D, Chakraborty S and Chakraborty N (2018) Genome-wide identification of the Alba gene family in plants and stress-responsive expression of the rice Alba genes. Genes9: E183.

Mishra P, Wardhan V, Pandey A, Chakraborty S, Garg G. and Chakraborty N. (2017) Comparative analysis of sequence-structure function relationship of the SUN-domain protein CaSUN1. J. Phylogentics Evol. Biol.5: 189.

Elagamey E, Narula K, Sinha A, Ghosh G, Abdellatef MAE, Chakraborty N and Chakraborty S (2017) Quantitative extracellular matrix proteomics suggests cell wall reprogramming in host-specific immunity during vascular wilt caused by Fusarium oxysporum in chickpea. Proteomics 17: 1600374.

Elagamey E, Sinha A, Narula K, Abdellatef MAE, Chakraborty N and Chakraborty S (2017) Molecular dissection of extracellular matrix proteome reveals discrete mechanism regulating verticillium dahliae triggered vascular wilt disease in potato. Proteomics17: 1600373.

Nag P, Aggarwal PR, Ghosh S, Narula K, Tayal R, Maheshwari N, Chakrabortyand N and Chakraborty S (2017) Interplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans. Cell Death Discov. 3: e17073.

Lande NV, Subba P, Barua P, Gayen D, Keshava PTS, Chakraborty S and Chakraborty, N (2017) Dissecting the chloroplast proteome of chickpea (Cicer arietinum L.) provides new insights into classical and non-classical functions. J. Proteomics165: 11-20.

Barua P, Gayen D, Lande NV, Chakraborty S and Chakraborty N. (2017) Global proteomic profiling and identification of stress-responsive proteins using two-dimensional gel electrophoresis. Methods Mol. Biol.1631: 163-179.

Pandey A, Chakraborty S and Chakraborty N (2017) Nuclear Proteome: Isolation of Intact Nuclei, Extraction of Nuclear Proteins, and 2-DE Analysis.Methods Mol. Biol.1696: 41-55.

Mishra D, Shekhar S, Agrawal L, Chakraborty S and Chakraborty N (2017) Cultivar-specific high temperature stress responses in bread wheat (Triticum aestivum L.) associated with physicochemical traits and defense pathways. Food Chem. 221: 1077-1087.

Parveen S, Gupta DB, Dass S, Kumar A, Pandey A, Chakraborty S and Chakraborty N (2016) Chickpea ferritin CaFer1 participates in oxidative stress response, and promotes growth and development. Sci. Rep. 6: 31218.

Gayali S, Acharya S, Lande NV, Pandey A, Chakraborty S and Chakraborty N (2016) CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors. BMC Plant Biol. 16: 169.

Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N and Chakraborty S (2016) Proteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia. J. Proteomics (doi 10.1016/j.jprot.2016.04.047).

Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N. and Chakraborty S (2016) Proteometabolomic study of compatible interaction in Tomato fruit challenged with Sclerotinia rolfsii illustrates novel protein network during disease progression. Front. Plant Sci (In Press).

Narula K, Ghosh S, Aggarwal PR, Sinha A, Chakraborty N, Chakraborty S. (2016) Comparative proteomics of oxalate downregulated tomatoes points toward cross talk of signal components and metabolic consequences during post-harvest storage. Front. Plant Sci.7: 1147.

Biswas S, Aggarwal PR, Tayal R, Sarkar MP, Chakraborty N and Chakraborty S. (2016) RNA-seq analysis identifies key genes involved in chickpea (Cicer arietinum L.) shoot development. J. Botan. Soc. Bengal70(1): 49-54

Ghosh S, Narula K, Mittal PK, Sarkar MP, Chakraborty N and Chakraborty S. (2016) Proteomic profile reveals the diversity and complexity of leaf proteins in spinach (Beta vulgaris var. all green). J. Prot. Proteomics 7: 121-131.

Elagamey E, Narula K, Sinha A, Aggarwal PR, Ghosh S, Chakraborty N, Chakraborty S^§. (2016) Extracellular matrix proteome and phosphoproteome of potato reveals functionally distinct and diverse canonical and non-canonical proteoforms. Proteomes 4: 20.

Shekhar S, Agrawal L, Mishra D, Buragohain AK, Unnikrishnan M, Chokkappan Mohan C, Chakraborty S^§. and Chakraborty N. (2016) Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato. Sci. Rep. (doi: 10.1038/srep25384).

Kumar V, Chattopadhyay A, Ghosh S, Irfan M, Chakraborty N, Chakraborty S and Datta A (2016) Improving nutritional quality and fungal tolerance in soya bean and grass pea by expressing an oxalate decarboxylase. Plant Biotechnol. J. 14:1394-405.

Narula K, Aggarwal PR, Chakraborty N and Chakraborty S (2016) Plant fungus interaction proteomics: An update. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 2 (pp. 227-250) Switzerland: Springer International Publishing.

Narula K, Sinha A, Haider T, Chakraborty N and Chakraborty S (2016) Seed proteomics: An overview. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 1 (pp. 31-52) Switzerland: Springer International Publishing.

Wardhan V, Pandey A, Chakraborty S, Chakraborty N (2016) Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure. Sci. Rep. 6, 3812.

Barua P, Subba P, Vikram Lande N, Mangalaparthi KK, Keshava Prasad TS, Chakraborty S and Chakraborty N (2016) Gel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire. J. Proteomics [doi:10.1016/j.jprot.2016.04.015].

Shekhar S, Mishra D, Gayali S, Buragohain AK, Chakraborty S and Chakraborty N (2016) Comparison of proteomic and metabolomic profiles of two contrasting ecotypes of sweetpotato (Ipomoea batata L). J. Proteomics (doi: 10.1016/j.jprot.2016.03.028).

Irfan M, Ghosh S, Meli MS, Kumar A, Kumar V, Chakraborty N, Chakraborty S and Datta A. (2016) Fruit ripening regulation of alpha-Mannosidase expression by the MADS box transcription factor RIPENING INHIBITOR and ethylene. Front. Plant Sci. 7: 10.

Kumar V, Irfan M., Ghosh S, Chakraborty N, Chakraborty S and Datta A (2016) Fruit ripening mutants reveal cell metabolism and redox state during ripening. Protoplasma 253: 581-594.

Gupta DB, Rai Y, Gayali S, Chakraborty S and Chakraborty N (2016) Plant organellar proteomics in response to dehydration: turning protein repertoire into insights. Front. Plant Sci. 7: 460.

Rathi D, Gayen D, Gayali S, Chakraborty S and Chakraborty N (2016) Legume proteomics: Progress, prospects and challenges. Proteomics 16: 310-327.

Rathi D, Chakraborty S and Chakraborty N (2015) Proteomics of an orphan legume, grasspea: current status and future strategy. Plant Tissue Cult. & Biotech. 25: 117‐141.

Gupta S, Wardhan V, Kumar A, Rathi D, Pandey A, Chakraborty S and Chakraborty N (2015) Secretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v1-like protein, CaRRP1 that participates in stress response. Sci. Rep. 5: 18427.

Narula K., Pandey A., Gayali S., Chakraborty N., and Chakraborty S (2015) Birth of plant proteomics in India: a new horizon. J. Proteomics (doi: 10.1016/j.jprot.2015.04.020).

Chakraborty S, Salekdeh G.H., Yang P., Woo S.H., Chin C.F., Gehring C., Haynes P.A., Mirzaei M. and Komatsu S. (2015) Proteomics of important food crops in the Asia Oceania region: current status and future perspectives. J. Proteome Res. (doi: 10.1021/acs.jproteome.5b00211).

Shekhar S, Mishra D, Buragohain AK, Chakraborty S and Chakraborty N. (2014) Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.) Food Chem. 173: 957-965.

Irfan M, Ghosh S, Kumar V, Chakraborty N, Chakraborty S and Datta A. (2014) Insights into transcriptional regulation of β-D-N acetylhexosaminidase,an N-glycan-processing enzyme involved in ripening-associated fruit softening. J. Exp. Bot. 65: 5835-5848.

Kumar R, Kumar A, Subba P, Gayali S, Barua P, Chakraborty S and Chakraborty N (2014) Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum L.) and protein-kinase interaction network. J. Proteomics 105: 58-73.

Verma JK, Gayali S, Dass S, Kumar A, Parveen S, Chakraborty S, and Chakraborty N (2014) OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L.), participates in stress adaptation. Phytochemistry 100: 16-25

Jaiswal DK, Mishra P, Subba P, Divya Rathi D, Chakraborty S, and Chakraborty N (2014) Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling. Sci. Rep. 4: 4177 | DOI: 10.1038/srep04177

Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N and Chakraborty S (2013) Comparative proteomics reveals a role for seed storage protein, AmA1 in cellular growth, development and nutrient accumulation. J. Proteome Res. 12: 4904–4930

Chakraborty N, Ghosh R, Ghosh S, Narula K, Tayal R, Datta A, Chakraborty S (2013) Reduction of oxalate levels in tomato fruit and consequent metabolic remodeling following overexpression of a fungal oxalate decarboxylase. Plant Physiol. 162: 364-378.

Ghosh S, Singh UK, Meli VS, Kumar V, Kumar A, Irfan M, Chakraborty N, Chakraborty S, and Datta A (2013) Induction of senescence and identification of differentially expressed genes in tomato in response to monoterpene. PLOS one 8: e76029

Narula K, Datta A, Chakraborty N, and Chakraborty S (2013) Comparative analyses of nuclear proteome: extending its function. Front. Plant Sci. 4: 100.

Subba P, Barua P, Kumar R, Datta A, Soni K, Chakraborty S, and Chakraborty N (2013) Phosphoproteomic Dynamics of Chickpea (Cicer arietinum L.) Reveals Shared and Distinct Components of Dehydration Response. J. Proteome Res. 12: 5025-47

Jaiswal D, Ray D, Choudhary M, Subba P, Kumar A, Verma J, Kumar R, Datta A, Chakraborty S, and Chakraborty N (2013) Comparative proteomics of dehydration response in the rice nucleus: new insights into the molecular basis of genotype specific adaptation. Proteomics. 13: 3478-97

Subba P, Kumar R, Gayali S, Shekhar S, Praveen S, Pandey A, Datta A, Chakraborty S, Chakraborty N (2013) Characterisation of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar. Proteomics 13: 1973–1992

Shekhar S, Agrawal L, Buragohain AK, Datta A, Chakraborty S and Chakraborty N (2013) Genotype independent regeneration and agrobacterium-mediated genetic transformation of sweet potato (Ipomoea batatas L.). Plant Tissue Cult. Biotech. 23: 87-100.

Jaiswal DK, Ray D, Subba P, Mishra P, Gayali S, Datta A, Chakraborty S and Chakraborty N (2012) Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.). Proteome Sci. 10: 59.

Narula K., Elagamy E., Datta A., Chakraborty N., and Chakraborty S (2012) Comparative analyses of extracellular matrix proteome: An under-explored area in plant research. In A. Goyal (ed.) Crop Plants (pp. 145-166), Janeza Tradine, Croatia: InTech.

Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S, and Chakraborty N (2012) Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance. Plant Mol. Biol. 79: 479-493.

Kamathan A, Kamthan M, Azam M, Chakraborty N, Chakraborty S, Datta A (2012) Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality. Sci. Rep. 2: 951.

Kamthan A, Kamthan M, Chakraborty N, Chakraborty S, Datta A (2012) A simple protocol for extraction, derivatization, and analysis of tomato leaf and fruit lipophilic metabolites using GC-MS. Nature Protocols. Protocol Exchange doi:10.1038 /protex. 2012.061

Kamthan M, Mukhopadhyay G, Chakraborty N, Chakraborty S and Datta A (2012) Quantitative proteomics and metabolomics approaches to demonstrate N-acetyl-d-glucosamine inducible amino acid deprivation response as morphological switch in Candida albicans. Fungal Genet. Biol. 49: 369-378.

Gupta S, Wardhan V, Verma S, Gayali S, Rajamani U, Datta A, Chakraborty S and Chakraborty N (2011) Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins. J. Proteome Res.10: 5006-5015.

Bhushan D, Jaiswal DK, Ray D, Basu D, Datta A, Chakraborty S and Chakraborty N (2011) Dehydration-responsive reversible and irreversible changes in the extracellular matrix: comparative proteomics of chickpea genotypes with contrasting tolerance. J. Proteome Res. 10: 2027-2046.

Ghosh S, Meli VS, Kumar A, Thakur A, Chakraborty N, Chakraborty S and Datta A (2011) The N-glycan processing enzymes a-mannosidase and b-D-N-acetylhexosaminidase are involved in ripening-associated softening in the non-climacteric fruits of capsicum. J. Exp. Bot. 62: 571-582.

Chattopadhyay A, Subba P, Pandey A, Bhushan D, Kumar R, Datta A, Chakraborty S and Chakraborty N (2011) Analysis of the grasspea proteome and identification of stress-responsive proteins upon exposure to high salinity, low temperature and abscisic acid treatment. Phytochemistry 72: 1293-1307.

Chakraborty S, Chakraborty N, Agrawal L, Ghosh S, Narula K, Shekhar S, Naik PS, Pande PC, Chakraborti SK and Datta A (2010) Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber. Proc. Natl. Acad. Sci. USA 107: 17533-17538.

Meli VS, Ghosh S, Prabha TN, Chakraborty N, Chakraborty S and Datta A (2010) Enhancement of fruit shelf life by suppressing N-glycan processing enzymes. Proc. Natl. Acad. Sci. USA 107: 2413-2418.

Pandey A, Rajamani U, Verma J, Subba P, Chakraborty N, Datta A, Chakraborty S and Chakraborty N (2010) Identification of Extracellular Matrix Proteins of Rice (Oryza sativa L) Involved in Dehydration-Responsive Network: A Proteomic Approach. J. Proteome Res. 9: 3443-3464.

Choudhary MK, Basu D, Datta A, Chakraborty N and Chakraborty S (2009) Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation and evolutionary perspect. Mol. Cell. Proteomics 8: 1579-1598.

Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mondal MK, Chakraborty N, Datta A and Chakraborty S (2009) Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrates predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 10: 415.

Pandey A, Chakraborty S and Datta A, Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol. Cell. Proteomics 7: 88-107.

Agrawal L, Chakraborty S, Jaiswal DK, Gupta S, Datta A and Chakraborty N (2008) Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum L) J. Proteome Res. 7: 3803-3817.

Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S and Chakraborty N (2007) Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol. Cell. Proteomics 6: 1868-1884.

Pandey A., Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A and Chakraborty N (2006) The nuclear proteome of chickpea (Cicer arietinum L.) reveals predicted and unexpected proteins. J. Proteome Res. 5: 3301-3311.

Bhushan D, Pandey A, Chattopadhyay A, Choudhary MK, Chakraborty S, Datta A and Chakraborty N (2006) Extracellular matrix proteome of chickpea (Cicer arietinum) illustrates pathway abundance, novel protein functions and evolutionary perspect. J. Proteome Res. 5: 1711-1720.

Chakraborty N, Datta A and Chakraborty S (2003) Nutritional genomics: quest for GM crops for better nutrition. Everyman’s Science. 38: 41-43.

Chakraborty S, Chakraborty N, Jain D, Salunke DM, and Datta A (2002) Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine coordinated manganese in substrate recognition. Protein Sci. 11: 2138-2147.

Sarmah B, Chakraborty N, Chakraborty S, and Datta A (2002) Plant pre-Mrna splicing in fission yeast, Schizosaccharomyces pombe. Biochem. Biophy. Res. Commn. 293: 1209-1216.

Chakraborty S, Sarmah B, Chakraborty N and Datta A (2002) Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe. Nuclei Acids. Res. 30: 2940-2949.

Azam M, Kesarwani M, Chakraborty S, Natarajan K and Datta A (2002) Cloning and characterization of 5’-flanking region of oxalate decarboxylase gene from Flammulina velutipes. Biochem J.367: 66-75.

Chakarborty S, Chakarborty N and Datta A (2000) Increased nutritive value of transgenic potato by expressing a nonallergenic seed albumin gene from Amaranthus hypochondriacus. Proc. Natl. Acad. Sci. USA 97: 3724-3729.

Book Chapters

Mishra D, Shekhar S, Singh D, Chakraborty S and Chakraborty N (2018) Heat shock proteins and abiotic stress tolerance in plants. In Regulation of heat shock protein responses. Eds. A. Asea and P. Kaur, Springer, Cham, Switzerland, pp. 41-69.

Pandey A, Chakraborty S and Chakraborty N (2018). Nuclear proteome: isolation of intact nuclei, extraction of nuclear proteins, and 2-de analysis. In Plant Membrane Proteomics. Eds. H. Mock A. Matros and K. Witzel, Humana Press, New York, NY, pp. 41-55.

Narula K, Aggarwal PR, Chakraborty N and Chakraborty S (2016a) Plant fungus interaction proteomics: An update. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 2 (pp. 227-250) Switzerland: Springer International Publishing.

Narula K, Sinha A, Haider T, Chakraborty N and Chakraborty S (2016b) Seed proteomics: An overview. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 1 (pp. 31-52) Switzerland: Springer International Publishing.

Narula K, Elagamy E, Datta A, Chakraborty N and Chakraborty S (2012) Comparative analyses of extracellular matrix proteome: An under-explored area in plant research. In A. Goyal (ed.)Crop Plants (pp. 145-166), Janeza Tradine, Croatia: InTech.

Chakraborty S, Pandey A, Datta A and Chakraborty N (2008) Nucleus. InG.K. Agrawal and R. Rakwa(eds.)Plant Proteomics: Technology, Strategies, and Applications (pp. 327-338)John Wiley & Sons, Inc.

Chakraborty N, Chakraborty S and Datta A (2005) Nutritional genomics: Commitment to society. In P. Tandon, M. Sharma and R. Swarup (eds.) Biodiversity: Status and Prospects (pp.35-42), New Delhi: Narosa Publishing House Pvt. Ltd.

Chakraborty N, Chakraborty S and Datta A (2005) Designer GM potato with increased nutritive value. In JS Singh and VP Sharma (eds.) Glimpses of the work on environment and development in India (pp.269-272), New Delhi: Angkor Publishers (P) Ltd.

Chakraborty N, Chakraborty S, Kesarwani M, Mohammad A and Datta A (1998) Increased nutritive and qualitative value of transgenic plants expressing genes specifying amaranth seed albumin and Collybia oxalate decarboxylase. In K.T. Shao (eds.) Frontiers in Biology: The Challenges of Biodiversity Biotechnology. (pp 125-131), Taipei: Academia Sinica.

Mehta A, Natarajan K, Raina A, Biswas S, Chakraborty N and Datta A (1997) Molecular analysis of genes encoding Amaranthus seed specific protein and Collybia oxalate decarboxylase to develop transgenic plants. Plant Molecular Biology and Biotechnology. In K.K. Tiwari and G.S. Singhal (eds.), (pp 321-326) New Delhi: Narosa Publishing House.

Faculty Member