People

 

                        


Dr. Malali Gowda.









Dr. Malali Gowda obtained M.Sc in the University of Agricultural Sciences Bengaluru and Ph.D from The Maharaja Sayajirao University of Baroda. He has worked at the Michigan State University, North Carolina State University and Ohio State University. Dr. Malali Gowda returned to India in 2010 through the Ramalingaswamy Fellowship program of DBT,GoI. Dr. Gowda as the Head of Genomics, built a state-of-the-art ‘Next-Generation Genomics Facility’ at C-CAMP, Bangalore and has been providing service for genomics applications. More than 1000 genomes (prokaryotes and eukaryotes) involving more than 100 species have been sequenced.

Dr. Gowda is also associated with the University of Agricultural Sciences, Bangalore towards establishing agri-genomics. Dr. Gowda founded a non-profit organisation “Biodiversity Conservation and Research Trust” (BCRT), Anuganalu, Hassan Dist, Karnataka State. BCRT work is considered as a model system to combat climate change and agricultural/ environmental problems.


He has recently founded DNA LIFE Organisation (www.dnalife.org), which bring changes in the ecosystem to conserve life and understand it through high-end technologies.


POSITION

1. Professor, Transdisciplinary University (TDU), Foundation of Revitalization of Local Health Traditions (FRLHT), Bangalore (Jan 2016-Present)

2. Director/Head, Genomics Laboratory/Facility, Center for Cellular and Molecular Platforms, Bangalore (Sept 2010 to Dec 2015).

3. Adjunct Faculty, Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore (May 2014-present)

4. Adjunct Faculty, University of Agricultural Sciences, Bangalore (March 2011 -present).

5. Visiting Scientist at the Laboratory of Dr. Robin Buell, Michigan State University (Jun 2009 - July 2010).

6. Postdoctoral Scientist at the Laboratory of Professor Ralph Dean, North Carolina State University (Sept 2006 – May 2009).

7. Postdoctoral Scientist at the Laboratory of Professor Guo-Liang Wang, The Ohio State University (March 2002 – Aug 2006).


RESEARCH AREA:


Plant - Microbial Interactions

Human leukocyte antigen (HLA)

Genomics and Bioinformatics

Traditional Medicine

Biodiversity Conservation


Selected PUBLICATIONS (*Corresponding)


Mahesh HB, Shirke MD, Singh S, Rajamani A, Manjunath A, Hittalmani S, Wang GL and Malali Gowda*. Indica rice genome assembly, annotation and mining of disease resistance genes. BMC Genomics 2016, 17: 242.

Malali Gowda *, Ambardar A, Dighe N, Ashwini M, Pradeep H, Sundaram S, Ranade S, Jagannathan L*, Krishna S*. Comparative analyses of low, medium and high-resolution HLA typing technologies for human populations. Journal of Clinical  & Cellular Immunology 2016, 7:2.

Kannan Rangiaha Varalaxmi B. A. and Malali Gowda*, UHPLC-MS/SRM method for quantification of neem metabolites from leaf extracts of Meliaceae family plants. Analytical Methods, 2016,8, 2020-2031.

Kuravadi KA, Vijay Y, Rangiah K, Heikham R, Rajamani A, Malarini LR, Sumathiselvaraju M, Shankaralingu C, Siddappa S, Aishwarya R, Sathyanarayana B N and M Gowda*. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree – PeerJ 2015, 3: e1066.

Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, M Gowda* Ramanathan S*. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.  BMC Plant Biology 2015, 15:212.

Gowda M*, Shirke M, Chandarana P, Mahesh HB, Rajamani A and B Chattoo*. Genome analyses of Indian isolates of rice blast fungus, Magnaporthe oryzae Genomics Data 2015; 5: 284–291.

Chen S, Songkumarn P, Venu RC, Gowda M, Bellizzi M, Hu J, Liu W, Ebbole D, Meyers B, Mitchell T, Wang GL. Identification and characterization of in planta-expressed secreted effector proteins from Magnaporthe oryzae that induce cell death in rice. Mol Plant Microbe Interact. 2013; 26:191-202.

Khedkar, S., Prabhakara, S., Loganathan, R.M, S, C., Gowda, M., Arakere, G., and Seshasayee, A.S. Draft genome sequence of Staphylococcus aureus ST672, an emerging disease clone from India. Journal of Bacteriology 2012; 194: 6946-7.

Prabhakara, S., Khedkar, S., Loganathan, R.M., Chandana, S., Gowda, M., Arakere, G., and Seshasayee, A.S. Draft genome sequence 1 of Staphylococcus aureus 118 2 (ST772), a major disease clone from India. Journal of Bacteriology 2012; 194: 3727-3728.

Ramamurthy, A., Kag, B., Hegde, V., Loganathan, M. R., Saiyed, T., Sathyanarayana, B. N. and Gowda, M*. Studies on in vitro regeneration from various explants of a mature neem (Azadirachta indica) tree. Acta Horticulturae 2012; 961:449-456.

Davidson, R.M$., Gowda, M$., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S.H., Jiang, N., and Buell, R.C. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant Journal 2012; 71, 492–502 ($first co-authors).

Davidson, R.M., Hansey, C.N., Gowda, M., Childs, K.L., Lin, H., Vaillancourt B., Sekhon R.S., de Leon, N., Kaeppler, S.M., Jiang, N., Buell, C.R. Utility of RNA-seq for analysis of maize reproductive transcriptomes. The Plant Genome 2011; 4: 191-203. 

Nunes, C.N., Gowda, M., Sailsbery, J., Xue, M., Chen, F., Brown, D., Oh, Y-Y, Mitchell, T., and Dean, A.R. Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics 2011, 12:288.

Gowda, M., Nunes CN, Sailsbery, J., Xhe, M., Chen, F., Nelson, C.A., Brown, D., Meng, S., Mitchell, T., Hagedorn, C.H. and Dean, A.R. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Research 2010; 38: 7558-69.

Gowda, M., Wang, G.L. Robust-LongSAGE (RL-SAGE): an improved LongSAGE method for high-throughput transcriptome analysis. Methods in Molecular Biology 2008; 387: 25-38.

Miguel, E. V., Gowda, M., Wang, G.L. Tag-based approaches for deep transcriptome analysis in plants. Plant Science 2007; 173: 371–380.

Gowda, M*., Li, H., Wang, G*. Robust analysis of 5’-transcript ends (5’-RATE): a high-throughput protocol for characterization of sequence diversity of transcription start sites. Nature Protocols 2007; 2: 1622-32.

Venu, R.C$., Jia, Y$., Gowda, M$., Jia, M.H., Jantasuriyarat, C., Stahlberg, E., Li, H., Rhineheart, A., Boddhireddy, P., Singh, P., Rutger, N., Kudrna, D., Wing, R., Nelson, J.C., Wang, G.L. RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Molecular Genetics & Genomics 2007; 278: 421-31 ($first co-authors).

Gowda, M., Venu, R.C., Li, H., Jantasuriyarat, C., Chen, S., Bellizzi, M., Pampanwar, Kim, H., Dean, R.A., Stahlberg, E., Wing, R., Soderlund, C, Wang, G.L.  Magnaporthe oryzae infection triggers RNA variation and antisense transcript expression in rice. Plant Physiology 2007; 144: 524-33.

Gowda, M., Venu, R.C., Jia, Y., Stahlberg, E., Pampanwar, V., Soderlund, C., Wang, G.L. Use of RL-SAGE analysis to identify novel fungal and plant genes involved in host-pathogen interactions. Methods in Molecular Biology 2007; 354: 131-44.

Gowda, M., Li, H., Alessi. J., Chen, F., Wang, G.L. Robust analysis of 5’-transcript ends (5’-RATE): a novel method for transcriptome profiling and genome annotation. Nucleic Acids Research 2006; 34: e126.

Gowda, M., Venu, R.C., Li, H., Nobuta, K., Babu, M., Wu, H., Kim, H., Stahlberg, E., Wing, R., Couglan, S., Haudenschild, C.D., Dean, R., Meyers, B., Wang, G.L. Deep and comprehensive transcriptome analysis in mycelial and appressorial stages in M. oryzae using MPSS, RL-SAGE, and Oligoarray methods. BMC Genomics 2006; 7: 310.

Gowda, M., Barman, S.R., Chattoo, B.B. Molecular mapping of a novel blast resistance gene Pi38 in rice (Oryza sativa L.) using SSLP and AFLP markers. Plant Breeding 2006; 125: 596–599.

Jantasuriyarat, C., Gowda, M., Haller, K., Hatfield, J., Lu, G., Stahlberg, S., Zhou, B., Li, H., Kim, H.R., Yu, Y.S., Dean, R.A., Wing, R.A., Soderlund, C., Wang, G.L. Large-scale identification of ESTs involved in rice and rice blast (Magnaporthe oryzae) interaction. Plant Physiology 2005; 138: 105-15.

Barman, S.R., Gowda, M., Venu, R.C., Chattoo, B.B. Identification of a major blast resistance gene in the rice cultivar Tetep. Plant Breeding 2004; 123: 300–302.

Gowda, M., Jantasuriyarat, C., Dean, R.A., Wang, G.L. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiology 2004; 134: 890-7.

Gowda, M., Venu, R.C., Roopalakshmi, K., Sreerekha, M.V., Kulkarni, R.S. Advances in rice breeding, genetics and genomics. Molecular Breeding 2003; 11: 337-352.


PATENT: 


In vitro production of metabolites from neem endophytes (Patent pending; CMP-037; http://www.ccamp.res.in/vitro-production-metabolites-neem-endophytes).


TECHNOLOGIES DEVELOPMENT

HLA typing methodologies using NGS technologies.

Rapid deep-sequencing of Infectious disease agents using low amount of DNA or RNA samples using NGS.

In vitro Production of Metabolites from Neem Endophytes (Patent pending; CMP-037; http://www.ccamp.res.in/vitro-production-metabolites-neem-endophytes).

Next-Generation Genomics Technology; www.ccamp.res.in/NGS-Genomics.

CPA-sRNAs (capped and polyadenylated small RNAs; Gowda et al., Nucleic Acids Research 2010).

RL-SAGE (Robust-Long SAGE; Refer: Gowda et al. Plant Physiology 2004; Gowda et al., Plant Physiology 2007).                  

5’ RATE (Rapid Amplification of Transcript Ends; Gowda et al., Nucleic Acids Research 2006; Gowda et al., Nature Protocols 2007).

Reforestation and Medicinal plants restoration (http://www.dnalife.org/DNA_Life_Organisation/Biodiversity.html ).

 

GENOMICS AND FUNCTIONAL GENOMICS DATABASES

Next-Generation Genomics; http://www.ccamp.res.in/NGS-Genomics

Rice genome annotation; http://rice.plantbiology.msu.edu

Rice and Magnaporthe resource; http://www.mgosdb.org

RiceCAP; http://www.uark.edu/ua/ricecap/index.html

Magnaporthe MPSS tags: http://mpss.udel.edu/mg

Biodiversity and environment related work: http://www.dnalife.org/DNA_Life_Organisation/Biodiversity.html

 

Invited Talks AND Conference Presentations


De novo Genome Assembly and Annotation of Indica Rice. International conference on Advances in NGS, May 28-29, 2015, Sheraton Bangalore Hotel at Brigade Gateway, Bangalore

Indica Rice Cultivar Genome Assembly and Annotation. 4th Next Generation Sequencing Asia Congress & 2nd Single Cell Genomics Asia Congress, 7-8 October 2014, MAX Atria at Singapore Expo, Singapore.

Plant genome data and NGS technologies. Workshop on Plant Genome Analysis. June 16-20, 2014, Tamil Nadu Agricultural University, Coimbatore.

Rapid Dissection of Microbiome using NGS Technology. Genomics & Proteomics, June 12-13, 2014, Radisson Blue Plaza, New Delhi.

Pacific Biosciences Asia User Group Meeting, 22–23 May 2014, Grand Corpthorne Waterfront, Singapore.

Genome and Transcriptome Analyses of Indian Isolates of Rice Blast Fungus, Magnaporthe oryzae Plant and Animal Genome Conference, Grand Corpthorne Waterfront, May 19-21, 2014, Singapore.

NGS Accelerating Discovery and Characterization of Meta-Genomes and Meta-Transcriptomes from Environment Soil. National Conference on Productivity and Sustainability: Role of Agriculturally Important Microorganisms. April 10-12, 2014, University of Agricultural Sciences, Bangalore.

Genomics Catalyzing the Clinical Research and Personalized Medicine, 17th ADNAT symposium, Trivandrum, February 23-25, 2014

Novel RNA mechanisms in plant pathogenic fungi, Magnaporthe oryzae. Indo-French Seminar/Workshop on Filamentous fungal pathogens: current trends and future perspectives, January 20-22, 2014, Madurai, TN.

Next generation genomics triggered scientists to dig-deep into biosphere. International Conference on Genomics & Proteomics, September 27-28, 2013, Sheraton Bangalore Hotel at Brigade Gateway, Bangalore.

Non-coding RNA in plants. Advances in non-coding genomics, September 13-14, 2013, Institute of Bioinformatics and Applied Biotechnology, Bangalore.

Next-Generation Genomics at C-CAMP: Accelerating Forest Research in India. National Seminar on Tree Biotechnology, 23-24 September 2013, Institute of Forest Genetics & Tree Breeding, Coimbatore.

Next-Generation Genomics Accelerating Crop Improvement Program, National Conference on "Crop Improvement and Adaptive Strategies to meet challenges of Climate Change", 22-24 February 2013, University of Agricultural Sciences, Bangalore.

Introduction to Next Generation Sequencing (NGS) technology. EBI-C-CAMP Next Generation Genomics Data Analysis Workshop, 13 - 16 January 2013, National Centre for Biological Sciences, Bangalore.

Genomics of Neem tree and its Microbiome, World Neem Conference, 21-24 November 2012, Nagpur.

Next Generation Genomics: Accelerating Biological Research in India. Second International Next Generation Sequencing Data Analysis Workshop. 10 to 13 December 2012, Pune.

Dissecting plant transcriptomes using NGS technology. Symposium-cum-Workshop on High- throughput Data-Driven Biology, 12-14 September 2012, Bangalore.

Complexity of Plant Genomes and Transcriptomes. Next Generation Sequence (NGS) Data Analysis Workshop, Institute of Bioinformatics and Applied Biotechnology, 3-5 September 2011, Bangalore.

Next-Generation Genomics Catalyzing the Biological Research. Dissecting the Complexities of Plant Biotechnology in the Post-Genomic Era. 21st September 2011, Tumkur.

Applications of NGS technology. National Seminar on Genetic Transformation and Transgenic Plants: Concepts, Applications & Concerns, 7-9 September 2010, Vellore Institute of Technology University, Vellore, Tamil Nadu.

Chen S., Gowda, M., Venu, R.C., Songkumarn, P., Bellizzi, M., Ebbole, D., Mitchell, T and G.L. Wang. In-planta expressed secreted proteins from M. oryzae are enriched for extracellular effectors that induce cell death in rice. Plant & Animal Genomes XVII Conference 2009, San Diego.

Nunes, C., Gowda, M., Chen, F., Meng, S., Brown, D., Mitchell, T., Dean, R.A. Massively parallel sequencing of small RNAs from the rice blast fungus, Magnaporthe oryzae. APS Centennial Meeting, July 26-30, 2008, Minneapolis, MN.

Gowda, M., Nunes, C., Meng, S., Chen, F., Rigoutsos, I., brown, D., Mitchell, T., Dean, A.R. Characterization of small RNAs from rice blast fungus, Magnaporthe oryzae. Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, California.

Chen S., Songkumarn, P., Gowda, M., Venu, R.C., Park, C.H., Bellizzi, M., Ebbole, D., and G.L. Wang. Large-scale isolation and functional analysis of putative effectors from m. oryzae using integrated genomics approaches. Plant & Animal Genomes XVI Conference 2008, San Diego.

Gowda, M., Chen, F., Smith, D., Mitchell, T., Dean, A.R. Interrogation of the RNA species in Magnaporthe oryzae. APS/SON Joint Meeting, July 29 - August 1 2007, San Diego, California.

Chen S., Songkumarn, P., Gowda, M., Venu, R.C., Park, C.H., Bellizzi, M., Ebbole, D., and G.L. Wang. Large-scale isolation and functional analysis of putative effectors from m. oryzae using integrated genomics approaches. The 4th International Rice Blast Conference, October 9-14, 2007, Changsha, China.

Mitchell, T., Xu, J-R., Koten, C., Zhu, H., Rho, H., Oh, Y.Y., Gowda, M., and Dean., R.A. Characterization on transcriptional circuitry regulating pathogenicity using a proteomics approach. The 4th International Rice Blast Conference, October 9-14, 2007, Changsha, China.

Gowda, M., Deng, J., Oh, Y.Y., Rho, H-S., Nunes, C., Xu, J-R., Zhu, H., Mitchell, T., Dean, R.A. Protein arrays for transcription factors analysis in Magnaporthe oryzae. The 24th Fungal Genetics Conference, March 20-25, 2007, Asilomar, California.

Gowda, M., Venu, R.C., Li, H., Nobuta, K., Babu, M., Wu, H., Kim, H., Stahlberg, E., Wing, R., Couglan, S., Haudenschild, C., Dean, R., Meyers, B and Wang, G.L. Deep and comprehensive transcriptome analysis of the Magnaporthe oryzae genome using MPSS, RL-SAGE, and oligoarray methods. Plant & Animal Genomes XIII Conference 2006, San Diego.

Gowda, M., Venu, R.C., Li, H., Stahlberg, E., Jantasuriyarat, C., Dave, K., Kim, H., Wing, R and Wang, G.L. Maize (Zea mays) leaf transcriptome analysis using Robust-LongSAGE method. Plant & Animal Genomes XIII Conference 2005, San Diego.

Gowda, M., Venu, R.C., Manikantan, S., Childers, B.S., Hu, X., Pampanwar, V., Jantasuriyarat, C., Yu, Y., Kim, H., Wing, R., Dean, R., Stahlberg, E., Soderlund, C and Wang, G.L. Reprogramming of the rice-Magnaporthe oryzae interactive transcriptome revealed by Robust-LongSAGE. Plant & Animal Genomes XIII Conference 2005, San Diego.

Wang, G.L., Jantasuriyarat, C., Hatfield, J., Gowda, M., Stahlberg, E., Kudrna, D., Yu, Y., Dean, R., Wing, R and Soderlund, C. Deep transcriptional analysis of rice and rice blast interaction using EST and LongSAGE technologies. Plant & Animal Genomes XII Conference 2004, San Diego.

Gowda, M., Hatfield, J., Jantasuriyarat, C., Kudrna, D., Yu, Y., Manikantan, S., Stahlberg, E., Dean, R., Wing, R., Soderlund, C and Wang, G.L. In-depth transcriptome analysis during the rice and Magnaporthe oryzae interaction using LongSAGE technology. Plant & Animal Genomes XII Conference 2004, San Diego.

Jantasuriyarat, C., Hatfield, J., Lu, G., Stahlberg, E., Gowda, M., Zhou, B., Mazur, E., Kudrna, D., Yu, Y., Dean, R., Wing, R., Soderlund, C and Wang, G.L. Large-scale identification of ESTs involved in the interaction between rice and Magnaporthe oryzae. Plant & Animal Genomes XII Conference 2004, San Diego.

Gowda, M., Manikantan, S., Stahlberg, E., Jantasuriyarat, C., Venu, R.C., Kim, H., Yu, Y., Hatfield, J., Dean, R., Wing, R., Soderlund, C and Wang, G.L. Robust-LongSAGE (RL-SAGE) technology for deep transcriptome profiling. Midwest ASPB Sectional Meeting and OSU Plant Molecular Biology and Biotechnology Symposium, March 2004, Columbus.

Gowda, M., Wang, G.L, Doak, J., Manikantan, S and Stahlberg, E. Comparative sequence analysis for SAGE (serial analysis of gene expression) using CBL and PCBL Libraries. Proceedings of the 46th Center for Computational Sciences Conference, May 2004, Knoxville, Tennessee.

Chattoo, B.B., Subramanian, R., Gowda, M., Ahuja, M., Iyer, G., Potnis, A., Patel, V and Rekha, G. Magnaporthe oryzae genome and proteome. Rice Biotechnology Quarterly 1998; 33: RBQ6.


HONORS/ AWARDS/ FELLOWSHIPS


Ramalingaswami Fellowship (2010) of the Department of Biotechnology in recognition of my outstanding research contributions.

Dr. A P J Abdul Kalam (Presidential) Environmental Award (2006): In recognition of the activities of Biodiversity Conservation & Research Trust (BCRT; founded by Malali Gowda), Government of Karnataka has conferred on it the prestigious Dr. A P J Abdul Kalam environmental award for the year 2006-2007.


PROFESSIONAL WORK EXPERIENCE


Centre for Cellular and Molecular Platforms (Sept 2010 to present)

Position: Director/Head, Genomics Laboratory, Centre for Cellular and Molecular Platforms; http://www.ncbi.nlm.nih.gov/biosample/?term=Malali%20Gowda.


Characterization of medicinal plants and associated microbes: India harbour enormous wealth of traditional practices and knowledge on tropical plants and microbes. Traditional knowledge on plants and microbes are gaining interests in the scientific community worldwide. However, there is a lack of basic research in India on these traditional practices associated with plants and microbes, and their products. As a proof of concept, my research program has identified tropical neem tree (perennial) and Tulsi or holy herb (annuals) by applying omic-technologies to dissect scientific basis of traditional practices.

Whole genome assembly Neem tree (A. indica) genome                                      

(NCBI ID: AMWY01000000.1)


Krishna Tulsi (Ocimum tenuiflurum L), a member of Lamiaceae family, is a holy herb and known for its spiritual, religious and medicinal importance in India. We sequenced genome of Krishna Tulsi and transcriptomes of Krishna and Rama Tulsi. We confirmed the presence of eugenol and ursolic acid was confirmed using mass spectrometry from various tulsi subtypes. The availability of the whole genome of Tulsi will accelerate research to identify genes and metabolite pathways involved in special medicinal properties.

Whole genome assembly of Tulsi (O. tenuiflorum) genome                                 

(NCBI ID: JQCZ00000000)


Dissection of rice and Magnaporthe interactions: Through whole genome sequencing, many resistant (R) genes from rice cultivars and avirulence (Avr) genes from rice blast fungus, Magnaporthe isolates have been identified. We are the first to provide high quality rice and Magnaporthe genomes.


Whole genome assembly of indica Rice (O. sativa) genome (H12 cultivar)       

(NCBI ID: AZTA00000000.1)

Whole genome assembly of rice blast fungus, Magnaporthe oryzae                     

(NCBI ID: AXDJ00000000)


Establishment of State-of-the-art Next Generation Genomics Facility at C-CAMP, funded by DBT.

This is the first Genomics facility in an academic set-up in India.

Sequenced over 1000 genomes (including plants, animals and microbes) sequenced in the genomics

More than 100 organizations (National and International) used Genomics Facility Services for Sequencing and Bioinformatics

Trained more than 20 personal on NGS technology including sequencing and data analysis


Contact Email IDs: mg.genomics@gmail.com; malalig@frlht.org; malalig@ncbs.res ; malalig@dnalife.org

Founder