People

Nagarjun Vijay

Assistant Professor (May 2017 onwards): DepartMent of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.

2016-2017: Research Scholar, University of Michigan, USA.

2011-2016: Ph.D. Evolutionary Genomics, Evolutionary Biology Center, Uppsala University, Sweden.

2009-2011: Master of Science in Bioinformatics from Uppsala University, Sweden.

2007-2009: Assistant Systems Engineer, TATA Consultancy Services, Kochi, India.

2003-2007: Bachelor of Engineering in Biotechnology, Visvesvaraya Technological University, Karnataka, India

Buddhabhushan Girish Salve

Ph.D. Student (January 2021- Current)

Thesis title: Ancestral Gene Loss in Extinct and Extant Vertebrates

1. Salve BG£, Kurian  AM$, Vijay N# (2023). Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds. Royal Society Open Science, 10: 230801. PMID: 37621660 PMCID: PMC10445033. DOI= 10.1098/rsos.230801. (@journal) (@biorXiv) (Associated data available here: https://github.com/CEGLAB-Buddhabhushan/WDR93_CFAP46 and have been archived within the Zenodo repository: https://doi.org/10.5281/zenodo.8192181)

2. Salve BG£, Sharma S£, Vijay, N# (2024). Evolutionary diversity of CXCL16 CXCR6: Convergent substitutions and recurrent gene loss in sauropsids. Immunogenetics, 76, 397–415. PMID: 39400711, DOI= 10.1007/s00251-024-01357-5. (@journal) (@biorXiv)  (Associated data are stored in GitHub: https://github.com/CEGLAB-Buddhabhushan/CXCL16-CXCR6.git and have been archived within the Mendeley dataset: https://doi.org/10.17632/swdstcy6tz.1.)

3. Salve BG£, Vijay, N# (2025). Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss. Proc. R. Soc. B 292: 20251339. PMID:40858258. PMCID: PMC12380493. DOI: https://doi.org/10.1098/rspb.2025.1339 (@journal) (@biorXiv). (Associated data are stored in GitHub: https://github.com/CEGLAB-Buddhabhushan/Thylacine_Genome-wide_GENELOSS.git and have been archived at Dryad: https://datadryad.org/dataset/doi:10.5061/dryad.0k6djhbcm)

4. Salve BG£, H Sonal£, Vijay, N# (2025). Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates. (@biorXiv). (Associated data are stored in GitHub:https://github.com/CEGLAB-Buddhabhushan/Missing_genes_in_squamata.git)

Sagar Sharad Shinde

PhD (January 2018- July 2023)

Post-PhD: Vrije Universiteit Brussel, Belgium

Thesis title: Evolution at Different Timescales: Gene, Genome, and Pan-genome

Publications:

1. Shinde SS£, Teekas L£ , Sharma S£ , Vijay N# (2019). Signatures of relaxed selection in the CYP8B1 gene of birds and mammals. Journal of Molecular Evolution 87, 209–220(2019). Also available on biorXiv.

2. Patil A B£, Shinde SS£, Raghavendra S, Satish B.N, Kushalappa C.G#, Vijay N# (2020). The genome sequence of Mesua ferrea and comparative demographic histories of forest trees. Gene, 145214, ISSN 0378-1119 . DOI: https://doi.org/10.1016/j.gene.2020.145214.

3. Sharma S£ , Shinde SS£, Teekas L£ , Vijay N# (2020). Evidence for the loss of plasminogen receptor KT gene in chicken. Immunogenetics, 72(9-10):507-515. PMID: 33247773. doi: 10.1007/s00251-020-01186-2.

4. Shinde SS£, Sharma S£, Teekas L£, Sharma A£, Vijay N# (2021). Recurrent erosion of COA1/MITRAC15 demonstrates gene dispensability in oxidative phosphorylation. Sci Rep 11, 24437 (@biorXiv). Video presentation of the paper: https://www.youtube.com/watch?v=aKNCNyiwvTw

5. Shinde SS£, Sharma A£, Vijay N# (2023). Decoding the Fibromelanosis Locus Complex Chromosomal Rearrangement of Black-Bone Chicken: Genetic differentiation, selective sweeps and protein-coding changes in Kadaknath Chicken. Frontiers in Genetics, 14:1180658. PMID: DOI=10.3389/fgene.2023.1180658. Also available on biorXiv.

6. Sharma A£*, Shinde SS£*, Vijay N# (2023).  Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl. Animal Gene, 30: 200157. DOI:10.1016/j.angen.2023.200157. (@journal) (@biorXiv) (Associated data available here:https://github.com/Ashu2195/Midsize_deletion_in_Gallus_genus and here:https://doi.org/10.17632/k7t62v5frv.1)

Sandhya Sharma

PhD (January 2018- Feb 2024)

Post-PhD: IIT Delhi

Thesis title: Bioinformatics analyses of bird genome

1. Shinde SS£, Teekas L£ , Sharma S£ , Vijay N# (2019). Signatures of relaxed selection in the CYP8B1 gene of birds and mammals. Journal of Molecular Evolution 87, 209–220(2019). Also available on biorxiv.

2. Sharma S£ , Shinde SS£, Teekas L£ , Vijay N# (2020). Evidence for the loss of plasminogen receptor KT gene in chicken. Immunogenetics, 72(9-10):507-515. PMID: 33247773. doi: 10.1007/s00251-020-01186-2 (@journal)

3. Shinde SS£, Sharma S£, Teekas L£, Sharma A£, Vijay N# (2021). Recurrent erosion of COA1/MITRAC15 demonstrates gene dispensability in oxidative phosphorylation. Sci Rep 11, 24437 (@journal)  (@biorxiv). Video presentation of the paper: https://www.youtube.com/watch?v=aKNCNyiwvTw

4. Teekas L£, Sharma S£, Vijay N# (2022). Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes. Genes and Immunity, 23, 218–234. PMID: 36203090. DOI: https://doi.org/10.1038/s41435-022-00186-4.

5. Sharma S£, Teekas L£, Vijay N# (2023). Protein Repeats Show Clade-Specific Volatility in Aves. Molecular Biology, 57 (6): 1199-1211. (@journal) (Associated data available here: https://github.com/Sandhyash/Aves_repeats)

6. Teekas L£, Sharma S£, Vijay N# (2024).  Terminal regions of a protein are a hotspot for low complexity regions and selection. Royal Society Open Biology, 14: 230439. DOI= 10.1098/rsob.230439. (@journal) (@biorXiv) (Associated data available here: https://zenodo.org/records/10245666 and here: https://figshare.com/articles/dataset/Table_S2_rar_from_Terminal_regions_of_a_protein_are_a_hotspot_for_low_complexity_regions_LCRs_and_selection/25943407)

7. Salve BG£, Sharma S£, Vijay, N# (2024). Evolutionary diversity of CXCL16 CXCR6: Convergent substitutions and recurrent gene loss in sauropsids. Immunogenetics, 76, 397–415. PMID: 39400711, DOI= 10.1007/s00251-024-01357-5. (@journal) (@biorXiv)  (Associated data are stored in GitHub: https://github.com/CEGLAB-Buddhabhushan/CXCL16-CXCR6.git and have been archived within the Mendeley dataset: https://doi.org/10.17632/swdstcy6tz.1.)

Ajinkya Patil

PhD (January 2019- March 2024)

Post-PhD: Max Planck Institute for Multidisciplinary Sciences, Germany

Thesis title: Evolutionary Genomics of South and Southeast Asian Biodiversity

1. Patil A B£, Shinde SS£, Raghavendra S, Satish B.N, Kushalappa C.G#, Vijay N# (2020). The genome sequence of Mesua ferrea and comparative demographic histories of forest trees. Gene, 145214, ISSN 0378-1119 . DOI: https://doi.org/10.1016/j.gene.2020.145214. (@journal)

2. Patil, A.B £, Vijay, N# (2021). Repetitive genomic regions and the inference of demographic history. Heredity, 127, pages 151–166 PMID: 34002046. DOI: https://doi.org/10.1038/s41437-021-00443-8. (@journal) (Associated data available here: https://github.com/Ajinkya-IISERB/CoalRep).  Video presentation of the paper: https://www.youtube.com/watch?v=jPwwhGVYgio

3. Sharma A£, Gupta S£, Patil, A B£, Vijay N# (2022). Birth and Death in Terminal Complement Pathway. Molecular Immunology, 149, 174-187. PMID: 35908437. DOI: https://doi.org/10.1016/j.molimm.2022.07.006.

4. Patil A B£, Vajja SS, Raghavendra S, Satish B.N, Kushalappa C.G, Vijay N# (2022). Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus. Frontiers in Plant Science, 13:1029540. PMID: 36578332 DOI: 10.3389/fpls.2022.1029540. 

5. Patil, A B£, Kar D, Datta D, Vijay, N# (2023). Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor-tristis). Physiologia Plantarum, 175 (6):e14119. DOI=https://doi.org/10.1111/ppl.14119. (@journal) (Associated data available here: https://github.com/Ajinkya-IISERB/Parijat and https://doi.org/10.17632/hd84785jkf.1.) (Primary genomic and transcriptomic data generated at IISERB are deposited in the ENA repository (https://www.ebi.ac.uk/ena), with the accession numbers PRJEB56036 and PRJEB56037, respectively.).

6. Patil, A B£, Vijay, N# (2023). Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766). Conservation Genetics, 24 (5). DOI= 10.1007/s10592-023-01580-9. (@journal) (@biorxiv) (Associated data available here: : https://github.com/Ajinkya-IISERB/Pavo/tree/main/Conservation and https://doi.org/10.17632/ddwbwfjtrj.1. )

Lokdeep Teekas 

PhD (January 2018- Oct 2024)

Post-PhD: Queen Mary University London, England

Thesis title: COMPLEXITY OF LOW COMPLEXITY REGIONS (LCRs): FROM EVOLUTION TO DISORDERS

1. Shinde SS£, Teekas L£ , Sharma S£ , Vijay N# (2019). Signatures of relaxed selection in the CYP8B1 gene of birds and mammals. Journal of Molecular Evolution 87, 209–220(2019). Also available on biorxiv.

2. Sharma S£ , Shinde SS£, Teekas L£ , Vijay N# (2020). Evidence for the loss of plasminogen receptor KT gene in chicken. Immunogenetics, 72(9-10):507-515. PMID: 33247773. doi: 10.1007/s00251-020-01186-2.

3. Shinde SS£, Sharma S£, Teekas L£, Sharma A£, Vijay N# (2021). Recurrent erosion of COA1/MITRAC15 demonstrates gene dispensability in oxidative phosphorylation. Sci Rep 11, 24437 (@biorxiv). Video presentation of the paper: https://www.youtube.com/watch?v=aKNCNyiwvTw

4. Teekas L£, Sharma S£, Vijay N# (2022). Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes. Genes and Immunity, 23, 218–234. PMID: 36203090. DOI: https://doi.org/10.1038/s41435-022-00186-4.

5. Sharma S£, Teekas L£, Vijay N# (2023). Protein Repeats Show Clade-Specific Volatility in Aves. Molecular Biology, 57 (6): 1199-1211. (@journal) (Associated data available here: https://github.com/Sandhyash/Aves_repeats)

6. Teekas L£, Sharma S£, Vijay N# (2024).  Terminal regions of a protein are a hotspot for low complexity regions and selection. Royal Society Open Biology, 14: 230439. DOI= 10.1098/rsob.230439. (@journal) (@biorXiv) (Associated data available here: https://zenodo.org/records/10245666 and here: https://figshare.com/articles/dataset/Table_S2_rar_from_Terminal_regions_of_a_protein_are_a_hotspot_for_low_complexity_regions_LCRs_and_selection/25943407)

Ashutosh Sharma

PhD (January 2019- November 2024)

Post-PhD: Purdue University, USA

Thesis title: Insights into the Immunity and Pigmentation of Chicken using Comparative and Population genomics approaches

1. Shinde SS£, Sharma S£, Teekas L£, Sharma A£, Vijay N# (2021). Recurrent erosion of COA1/MITRAC15 demonstrates gene dispensability in oxidative phosphorylation. Sci Rep 11, 24437 (@biorxiv). Video presentation of the paper: https://www.youtube.com/watch?v=aKNCNyiwvTw

2. Sharma A£, Gupta S£, Patil, A B£, Vijay N# (2022). Birth and Death in Terminal Complement Pathway. Molecular Immunology, 149, 174-187. PMID: 35908437. DOI: https://doi.org/10.1016/j.molimm.2022.07.006.

3. Shinde SS£, Sharma A£, Vijay N# (2023). Decoding the Fibromelanosis Locus Complex Chromosomal Rearrangement of Black-Bone Chicken: Genetic differentiation, selective sweeps and protein-coding changes in Kadaknath Chicken. Frontiers in Genetics, 14:1180658. PMID: DOI=10.3389/fgene.2023.1180658. Also available on biorxiv.

4. Sharma A£*, Shinde SS£*, Vijay N# (2023).  Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl. Animal Gene, 30: 200157. DOI:10.1016/j.angen.2023.200157. (@journal) (@biorXiv) (Associated data available here:https://github.com/Ashu2195/Midsize_deletion_in_Gallus_genus and here:https://doi.org/10.17632/k7t62v5frv.1)

5. Sharma A£, Vijay N# (2025). Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities. Journal of Molecular Evolution,,. PMID:39821315. DOI=https://doi.org/10.1007/s00239-025-10233-z. (@journal) (@biorXiv) (Associated data are stored in GitHub: https://github.com/Ashu2195/ID_locus and have been archived within the Mendeley dataset: https://zenodo.org/records/14161977)

6. Sharma A£, Vijay N# (2025).The genomic structure of complex chromosomal rearrangement at the Fm locus in black-bone Silkie chicken. Communications Biology,8(1):53. PMID: 40169711. PMCID: PMC11961755. DOI=https://doi.org/10.1038/s42003-025-07825-2 (@journal) (@biorXiv) (Associated data are stored in GitHub:https://github.com/Ashu2195/Fm_locus and archived on Zenodo at https://doi.org/10.5281/zenodo.14011071).

Bijaya Haobam

Post-doctoral Fellow (November, 2018- Feb 2019)

1. M.Sc (Ag. Microbiology) - Aligarh Muslim University, Uttar Pradesh

2. PhD (Bacterial-Pathogenesis) - Tokyo Medical and Dental University, Tokyo, Japan

3. Research Associate: Indian Institute of Science, Bangalore (2016-2018)

Pritam Kumar Dey

DBT-JRF (November 2018- April 2020)

My project involves the use of the Foldscope as a tool to study tardigrade diversity and behavior.  The results of my project are routinely posted on the microcosmos website with the tag ceglab.

Even before joining this lab, i have been interested in Tardigrades, their biology, species diversity and geographical distribution. My previous work with the Zoological Survey of India is documented here: Dey, P.K. and Mandal,K. 2018. Tardigrada.  In, Faunal  Diversity  of  Indian  Himalaya:  779-783  (Published  by  the  Director, Zool.  Surv.  India,  Kolkata) Tardigrada of Indian Himalaya. Available from: https://www.researchgate.net/publication/324983051_Tardigrada_of_Indian_Himalaya.