Dr. Sarwar Azam is a distinguished computational biologist, bioinformatician, and specialist in genomics and genetics. He completed his Ph.D. from the Indian Institute of Technology Hyderabad (IITH) (2025) and holds an M.Tech. degree in Computational and Systems Biology from Jawaharlal Nehru University (JNU) (2009). Prior to joining NIAB in November 2013, Dr. Azam gained extensive experience in crop genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), notably contributing significantly to the draft genome sequencing of chickpea and pigeonpea during his tenure as a Visiting Scientist and Special Project Scientist.

At NIAB, Dr. Azam has made seminal and nationally recognized contributions to livestock genomics in India:

• NCBI Reference Genome: He led the successful effort at NIAB to develop a high-quality reference genome for Bos indicus (Zebu cattle). This genome has been officially recognized and assigned by the NCBI as the reference genome for this species.

• Pangenome and Assemblies: Dr. Azam has also developed the pangenome for Indian cattle and generated multiple genome assemblies for different milch cattle breeds, providing crucial resources for genetic diversity studies.

• Genotyping Tools: He was a key member of the team responsible for developing two major national genotyping tools: the IndiGau SNP chip (released by the Union Minister of Science on August 13, 2021) and the Gauchip (LD chip) (dedicated to the nation by the Honorable Prime Minister on October 5, 2024).

Dr. Azam has served as a Principal Investigator and Co-Investigator on key extra-mural projects funded by agencies like DBT. In these roles, he utilizes Genome-Wide Association Studies (GWAS) to identify genetic markers crucial for enhancing traits such as milk yield and increasing resistance to diseases like Paratuberculosis in indigenous breeds. Dr. Azam is also a distinguished developer of easy-to-use bioinformatics tools and pipelines, including the ISMU (Integrated SNP Mining and Utilization) pipeline and PanGA (Pan-Genome Analysis) pipeline.

Selected awards, honors and fellowships:
1. Certificate of Appreciation for the outstanding contribution in the area of Functional Genomics and Bioinformatics as part of Bioclues Innovation, Research and Development (BIRD) award, 2011
2. Exceptional Scientific Article in a High Impact Journal Award, ICRISAT, 2011
3. CSIR – UGC NET examination in Life sciences held in June 2008, December 2008 & June 2009
4. DBT fellowship 2007-2009 for M.Tech. course
5. BCIL Fellowship for BITP from DBT, Govt. of India, 2006

The lab’s recent focus has been on the following scientific work:

1. Genomics for conservation of indigenous cattle breeds and for enhancing milk yield, Phase-I
The Genomics and Computational Biology Laboratory (GCBL) is a cutting-edge research lab dedicated to applying advanced genomic technologies and computational analyses to address critical challenges in animal conservation, livestock improvement, and disease management.

Development of a High Density SNP chip: IndiGau

Figure: Summary of analyses for the development of IndiGau SNPchip

IndiGau

2. Development of a haplotype resolved reference genome assemblies for indigenous cattle (Bos indicus)
Indigenous cattle are known for their resilience to various diseases and abiotic stress, such as drought and heat, have unique traits when compared to their western/exotic counterparts. The aim of this work is to generate a high quality reference genome for indigenous cattle. The reference genome will provide valuable information that can be used to accurately identify genes and variations that are responsible for the unique characteristics of indigenous Cattle. Using the trio-binning approach, in collaboration with USDA-ARS, we assembled two genomes, Sahiwal and Tharparkar, by sequencing the parents (Sahiwal sire and Tharparkar dam) and their daughter using long and short-read sequencing. These genome assemblies will serve as the definitive REFERENCE GENOMES for all future research related to Indigenous cattle. Both genomes have been submitted to the National Centre for Biotechnology Information (NCBI) and dedicated to the nation and global community of cattle researchers.
Figure: Workflow to generate reference grade genome assemblies using trio-binning approach. Statistics of the resultant assemblies are mentioned in the table.

3. Validation of DBT-NIAB SNP chip for breed identification and preliminary genome-wide association studies of milk yield
In this project “Genomics for conservation of indigenous cattle breeds and for enhancing milk yield”, a high density SNPchip (DBT-NIAB-HDchip) was developed that is predicted to truly represent our indigenous breeds. To establish the proof of principle, this chip needs to be validated on our phenotypically purebred herds. In this venture, NIAB will be collaborating with National Dairy Development Board (NDDB); National Dairy Research Institute (NDRI), Karnal; GADVASU, Ludhiana; Lam farm, AP ; etc. NDDB approximately has 1000 animals each of Kankrej and Gir ; and 600 animals of Sahiwal, recorded for milk production. About 400 more Sahiwal, and 500 each of Tharparkar and Ongole will be obtained from the herds available at NDRI, GADVASU, Lam farm etc. Parallelly, genetic potential of indigenous breeds vis – a – vis milk yield will be taken up on a preliminary basis. The genotypes obtained from the chip can be used along with phenotype records available at different centers in different breeds to conduct Genome wide association studies (GWAS) and as well be used for imputation by NDDB.

Figure: A graphical representation of the research activities in the project. The activities highlighted in red will be ones in which I will actively participate and contribute.

4. Developing de novo genome assemblies of milch breeds of cattle i.e. Kankrej, Tharparkar, Red Sindhi, Sahiwal and Gir
The goal of this project is to characterise the genomes of indigenous milch breeds. Thus, a low-cost de-novo assembly using artificial long reads generated using linked-reads technology is proposed in the study. Linked-read libraries will be constructed using the 10X chromium platform, which will be used for NGS data generation. The data will be assembled using the Supernova assembler, which will produce phased, whole genome de-novo assemblies. Genome assemblies of five milch breeds, i.e. Gir, Sahiwal, Kankrej, Tharparkar and Red Sindhi will be constructed. Each draft de novo genome will be further assembled using a reference assembly for comparative analysis and annotation. The ultimate aim of the study is to detect small and large structural variations (SVs) and extract genotypic variations that generally cannot be captured by SNPs, such as large-scale chromosomal rearrangements.

Figure: Workflow to develop de-novo genome assemblies of indigenous cattle breeds.

5. Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
India, with the world’s largest cattle population having more than 50 registered breeds of Bos indicus, stands as a vital reservoir of genetic diversity with a select few designated as dairy breeds. However, the abundant diversity among Indian cattle breeds highlights the inadequacy of relying on the single reference sequence to represent the entire genomic content of desi cattle. We recognize the need to capture the genomic differences within the Bos indicus population as a whole, and specifically within the dairy cattle subset by identifying non-reference sequences and constructing pangenome.

Figure: Identification and characterization of Non-reference Unique Insertions (NUIs) in Bos Indicus.The flowchart illustrates the systematic process for identifying the NUIs. The diagram outlines the sequential steps involved in the selection and refinement of NUIs.

6. Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows
Mycobacterium avium subspecies paratuberculosis (MAP), the cause of Johne’s disease (JD), is endemic in domestic livestock (cows, buffaloes, goats, sheep etc.). JD is chronic, insidious and incurable in nature, results in granulomatous enteritis, leading to diarrhea, progressive weight loss and wasting, emaciation and death. It leads to high morbidity leading to huge economic losses due to reduced productivity, premature culling, increased veterinary costs, increased susceptibility etc. Early detection of infection and removal by culling,segregation and vaccination of infected animals are some of the technologies used to control the disease. However, cows cannot be culled in India for religious reasons.To unravel the host cell factors responsible for imparting resistance/ susceptibility to MAP infection, genome wide profiling of host genes using RNAseq and SNPs analysis will help to identify cows with potentially higher resistance for retention and multiplication for breeding purposes.

Figure: Comprehensive Overview of the Study, presenting objectives and methodologies to delineate the molecular landscape of MAP infection in indigenous cattle

7. Exploring Leptospira genomes for phylogenetic analysis and vaccine candidate
Leptospirosis is an emerging zoonotic and neglected disease across the world, causing huge loss of life and economic hardship. In nature, Leptospira species can be classified as pathogenic, intermediate, or saprophytic. This study proposes to perform comparative genomics on completely sequenced, publicly available Leptospira genomes in order to characterize all of its lineages and their virulence profiles. Differentiating strains of Leptospira species and providing insight into the taxonomic and evolutionary positions of genomes that need to be modified or reclassified are all part of phylogenomic characterisation. The extensive analysis focuses on core genome, pan genome, mobilome associated genes, and the entire virulome annotation. Finally, the study will provide a virulence profile of Leptospira for each species. The study also attempts to group clade-specific genes. Clade-specific and virulent genes can be used as markers in novel Leptospira isolates to define clade and related virulence levels. Wet-lab validation of virulent genes will aid in correctly targeting Leptospira pathogenic pathways and reducing leptospirosis. The project also intends to use reverse vaccinology approaches to find suitable vaccine candidates. The candidates will be chosen based on their immunological characteristics. These candidates will be employed in the development of a Multi-Epitope Vaccine (MEV). MEV design, In Silico characterization, and optimization will be the precursor to wet lab validation. A successful MEV will be a future vaccine and will help in controlling leptospirosis.

Figure: Graphical Abstract of phylogenomic analyses, genomic characterizations and virulence factor profiling of Leptospira.

Top Selected Publications:

27. Azam, S., Sahu, A., Kadivella, M., Khan, A. W., Neupane, M., Tassell, C. P. V., … & Majumdar, S. S. (2025). Genome assemblies of Indian desi cattle reveals hotspots of rearrangements and immune-related genetic diversity. NAR Genomics and Bioinformatics. (Accepted; https://doi.org/10.1093/nargab/lqaf153)

26. Abdullah, M., Kadivella, M., Sharma, R., Baig, M. S., Faisal, S. M., & Azam, S*. (2025). Identification of virulence genes and clade-specific markers through pan-genomic analysis of Leptospira. BMC microbiology, 25(1), 248.

25. Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., … & Majumdar, S. S. (2025). Constructing a draft Indian cattle pangenome using short-read sequencing. Communications Biology, 8(1), 605.

24. Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., … & Majumdar, S. S. (2025). Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus. Journal of Animal Science and Biotechnology, 16(1), 21.

23. Kadivella, M., Varma, V. P., Cp, J., Kavela, S., Azam, S., & Faisal, S. M. (2025). Adjuvant activity of a small molecule TLR4 agonist discovered via structure-based virtual screening. Communications Biology, 8(1), 1382.

22. Panchariya, D. C., Dutta, P., Ananya, Mishra, A., Chawade, A., Nayee, N., Azam, S., … & Kushwaha, S. K. (2024). Genetic marker: a genome mapping tool to decode genetic diversity of livestock animals. Frontiers in Genetics, 15, 1463474.

21. Topno, N. A., Kesarwani, V., Kushwaha, S. K., Azam, S., Kadivella, M., Gandham, R. K., & Majumdar, S. S. (2023). Non-Synonymous Variants in Fat QTL Genes among High-and Low-Milk-Yielding Indigenous Breeds. Animals, 13(5), 884.

20. Azam, S., Parthasarathy, S., Singh, C., Kumar, S., & Siddavattam, D. (2019). Genome organization and adaptive potential of archetypal organophosphate degrading Sphingobium fuliginis ATCC 27551. Genome biology and evolution, 11(9), 2557-2562.

19. Parthasarathy*, S., Azam*, S., Lakshman Sagar, A., Narasimha Rao, et. al. (2017). Genome-guided insights reveal organophosphate-degrading Brevundimonas diminuta as Sphingopyxis wildii and define its versatile metabolic capabilities and environmental adaptations. Genome biology and evolution, 9(1), 77-81.

18. Faisal, S. M., Varma, V. P., Subathra, M., Azam, S., et. al. (2016). Leptospira surface adhesin (Lsa21) induces Toll like receptor 2 and 4 mediated inflammatory responses in macrophages. Scientific Reports, 6.

17. Azam, S., Rao, S. B., Jakka, P., NarasimhaRao, V., Bhargavi, B., Gupta, V. K., & Radhakrishnan, G. (2016). Genetic characterization and comparative genome analysis of Brucella melitensis isolates from India. International Journal of Genomics, 2016.

16. Angela*, HW., Sharma*, M., Thatcher*, LF., Azam*, S., Hane, JK., et al. (2016) Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics, 17:191.

15. Sinha, P., Pazhamala, LT., Singh, VK., Saxena, RK., Krishnamurthy, L., Azam, S., et al. (2015) Identification and validation of selected universal stress protein domain containing drought-responsive genes in pigeonpea (Cajanus cajan L.). Frontiers in plant science, 6:1065.

14. Ali, L., Azam, S., Rubio, J., et al.(2015)Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses. Euphytica, 1-13.

13. Mir, R. R., Kudapa, H., Srikanth, S., Saxena, R. K., Sharma, A., Azam, S., et al. (2014). Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.). Theoretical and Applied Genetics, 127(12), 2663-2678.

12. Jaganathan, D., Thudi, M., Kale, S., Azam, S., et al. (2014). Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea.Molecular Genetics and Genomics, 1-13

11. RK Varshney, RR Mir, S Bhatia, M Thudi, Y Hu, S Azam, et al. (2014) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & integrative genomics 14 (1), 59-73

10. Ruperao, P., Chan, C., Azam, S., et al. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant biotechnology journal, 12(6), 778-786.

9. Kudapa*, H., Azam*, S., Sharpe A.G, et al. (2014) Comprehensive transcriptome assembly of chickpea (Cicer arietinum) using Sanger and Next Generation Sequencing platforms: Development and applications. PLoS One doi: 10.1371/journal.pone.0086039

8. Azam, S. , Rathore, A., Shah, T., et al. (2013) ISMU: Integrated SNP mining and utilization pipeline for accelerated breeding. PLoS One doi: 10.1371/journal.pone.0101754

7. Ali, L., Madrid, E., Varshney, R.K., Azam, S., et al. (2013) Mapping and identification of a Cicer arietinum NSP2 gene involved in nodulation pathway. Theoretical and Applied Genetics doi: 10.1007/s00122-013-2233-3

6. Kim, D., Parupalli, S., Azam, S., Lee, S. and Varshney, R.K. (2013) Comparative sequence analysis of nitrogen fixation-related genes in six legumes. Frontiers in Plant Genomics and Genetics doi: 10.3389/fpls.2013.00300

5. Chen, X., Zhu, W., Azam, S., et al. (2012) Deep sequencing analysis of the transcriptomes of peanut arieal and subterranean young pods identifies potential genes related to early embryo abortion. Plant Biotechnology Journal doi: 10.1111/pbi.12018

4. Gaur, R., Azam, S., Jeena, G., et al. (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research doi:10.1093/dnares/dss018

3. Azam, S., Thakur, V., Pradeep, R., et al.(2012) Coverage based consensus calling (CbCC) of short sequence reads and comparison of CbCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. American journal of Botany 99:186-192

2. Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T.A., Azam, S., et al. (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30:83–89

1. Varshney, R. K., Song, C., Saxena, R. K., Azam, S., Yu, S., et. al.. (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature biotechnology, 31(3), 240-246.

Current Members:

Prajakta surve
Summer Trainee (Dec 2025-July 2026)
B. Tech Bioinformatics and Data science , DY Patil university school of Biotechnology and Bioinformatics, Navi mumbai
Research Interests: Artificial intelligence and machine learning, Next Generation Sequencing analysis, including genomics and transcriptomics analysis

Alumni:

Ms Prerna Gupta
JRF

Ms. Sumaiya Khatun

Ms. Krutideepa Rout

Mr. Ashish Pratim Mahanta

Ms. Rutvi Rajpara

Mr. Lokesh Kumar

Mr. Naveen Kumar Pandey

Ms. Lakshmi S Prasad

1. Role of Investigator: Co-I
Title of the Project: Genomics for conservation of indigenous cattle breeds and for enhancing milk yield, Phase-I
Funding Agency: DBT
Period/Duration: 2017-2020 

2. Role of Investigator: PI
Title of the Project: Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows
Funding Agency: DBT
Period/Duration: 2020-2023

3. Role of Investigator: Co-PI
Title of the Project: Validation of DBT-NIAB SNP chip for breed identification  and preliminary genome-wide association studies of milk yield
Funding Agency: DBT
Period/Duration: 2021-2024 

Genomics and Computational Biology Laboratory, NIAB
National Institute of Animal Biotechnology
Survey No. 37, Opp. Journalist Colony
Extended Q City Road, Near Gowlidoddy
Gachibowli, Hyderabad
Telangana – 500032

Email: sarwar[at]niab[dot]org[dot]in
Tel: +91-(0)40-2312-0134

1. Development of largest cattle HD SNP chip INDIGAU

2. Haplotype resolved Bos indicus Genome assembly
Tharparkar: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_029378745.1
Sahiwal: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_029378735.1

3. Google scholar profile:
https://scholar.google.com/citations?user=Lxi0CHAAAAAJ&hl=en

Positions will be advertised on the NIAB website (www.niab.res.in). Please refer to the website for updates on available positions.