Publications

From IISER-B

2023

Teekas L£, Sharma S£, Vijay N# (2023). Terminal regions of a protein are a hotspot for low complexity regions (LCRs) and selection. (@biorXiv)
Teekas L£, Vijay N# (2023). Patterns of low-complexity regions in human genes. (@biorXiv)
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 and here: https://data.mendeley.com/datasets/gfpfs4svg6/1)
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.).
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. )
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. (@journal) (@biorxiv_v2) (@biorxiv_v1) (Primary data generated at IISERB and deposited on ENA under the project# PRJEB51457). This is the first study to perform Whole- Genome sequencing of Kadaknath: an Indian native black-bone chicken breed (Madhya Pradesh). Scripts and data are available at: https://github.com/ceglabsagarshinde/Kadaknath_Project and https://doi.org/10.17632/8f9dn6h76h.1.
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)
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)

2022

Patil AB£, 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. (@journal) (@biorxiv) (Associated data available here: https://github.com/Ajinkya-IISERB/Wild_Jack and here: https://doi.org/10.17632/vc6vwbrzs4.1) (Primary data generated at IISERB and deposited on ENA under the project# PRJEB55580)
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. (@journal) (@ResearchSquare) (Associated data available here: https://github.com/ceglablokdeep/Immune_genes_repeats and here: https://doi.org/10.17632/8zxtjh8fjs.1).
Patil, AB£, Vijay, N# (2022). Genome divergence across the Indo-Burman arc: a tale of two peacocks. bioRxiv. DOI:https://doi.org/10.1101/2022.05.27.493701.
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. (@journal) (@biorxiv)(Associated data available here: https://github.com/Ashu2195/C9) (Primary data generated at IISERB and deposited on ENA under the project# PRJEB51011)

2021

Patil, AB £, 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
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
Ramdas P, Bhardwaj V, Singh A, Vijay N, Chande A# (2021). Coelacanth SERINC2 Inhibits HIV-1 Infectivity and Is Counteracted by Envelope Glycoprotein from Foamy Virus. Journal of Virology, 95, 13. PMID: 33883219. DOI: https://doi.org/10.1128/JVI.00229-21 (@journal)
Patil A B£, Shinde SS£, Raghavendra S, Satish B.N, Kushalappa C.G#, Vijay N# (2021). The genome sequence of Mesua ferrea and comparative demographic histories of forest trees. Gene, 769:145214, ISSN 0378-1119 . DOI: https://doi.org/10.1016/j.gene.2020.145214. (@journal) (Primary data generated at IISERB and deposited on ENA under project# PRJEB36969) (Genome assembly generated as part of this paper is available for download at NCBI: GCA_904814375.1). The annotations are based on multiple rounds of the MAKER annotation pipeline and are not validated using RNA-seq datasets. P.O NO.:P/IND/I/BIO/2018-19/CO-311/179 Dated:- 08-11-2018
Here is the link for the protein fasta file: https://github.com/ceglab/CoalQC/blob/master/Assembly/MF.all.maker.proteins.fasta.gz and the transcript fasta file: https://github.com/ceglab/CoalQC/blob/master/Assembly/MF.all.maker.transcripts.fasta.gz
Jaiswal KS, Gupta A, Shafer ABA, Prasoodanan PKV, Vijay N, Sharma VK# (2021). Genomic Insights Into the Molecular Basis of Sexual Selection in Birds. Frontiers in Ecology and Evolution, 9, 2. DOI=10.3389/fevo.2021.538498 (@journal) (All associated data on the journal website)

2020

Pant D, Narayanan SP, Vijay N#, Shukla S# (2020). Hypoxia-induced changes in intragenic DNA methylation correlates with alternative splicing in breast cancer. Journal of Biosciences, 45:3. (@journal)(Associated data on https://github.com/erpl-iiserb/Hypoxia). Video presentation of the paper: https://www.youtube.com/watch?v=snhilu2aveg
Vijay N# (2020). Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast. PeerJ, 8:e10085. DOI: 10.7717/peerj.10085. (@journal) (All associated data on the journal website)
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) (All associated data on journal website). Video presentation of the paper: https://www.youtube.com/watch?v=KnGTQdwbxIY
Natesh M#, Vinay K L , Ghosh S, Jaypal R, Mukherjee S*, Vijay N*, V V Robin*# (2020) Contrasting trends of population size change for two Eurasian Owlet species -Athene brama and Glaucidium radiatum from South Asia over the late Quaternary. Frontiers in Ecology and Evolution, 8, 469. DOI=10.3389/fevo.2020.608339 (@journal) (Primary data is deposited on ENA under the project# PRJNA665335)
Ramdas P, Bhardwaj V, Singh A, Vijay N, Chande A# (2020). Coevolution of retroviruses with SERINCs following whole-genome duplication divergence (@biorxiv) (Associated data on https://github.com/ceglab/RestrictionFactorsArmsRace)
Patil A B£, Shinde SS£, Raghavendra S, Satish B.N, Kushalappa C.G#, Vijay N# (2020). CoalQC - Quality control while inferring demographic histories from genomic data: Application to forest tree genomes (@biorxiv) (Associated data on https://github.com/ceglab/CoalQC) (Part1: published as The genome sequence of Mesua ferrea and comparative demographic histories of forest trees), (Part2: published as Repetitive genomic regions and the inference of demographic history)

2019

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 . (@journal)(@biorxiv). (Associated data on github/CYP8B1)
Mittal P, Jaiswal KS, Vijay N, Saxena R, Sharma VK#. (2019). Comparative analysis of corrected tiger genome provides clues to their neuronal evolution. Scientific Reports, 9, 18459. (@journal) (@biorxiv) (Associated data on https://github.com/MetabiosysLab/seqbug)

2018

Vijay N#, Chande A. (2018). A hypothetical new role for single-stranded DNA binding proteins in the immune system. Immunobiology, 223, 671-676. (@journal) )(@biorxiv)
Jaiswal KS, Gupta A, Saxena R, Prasoodanan PKV, Sharma AK, Mittal P, Roy A, Shafer ABA, Vijay N, Sharma VK#. (2018) Genome Sequence of Indian Peacock Reveals the Peculiar Case of a Glittering Bird. Frontiers in Genetics, 9, 392. (@journal)(@biorxiv)

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Pre-IISER-B

2019

Knief U, Bossu C, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW#. (2019). Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nature Ecology & Evolution, 3, 570–576. PMID: 30911146 DOI: 10.1038/s41559-019-0847-9

2018

Vijay N*, Park C*, Oh J, Jin S, Kern E, Woo Kim H, Zhang J#, Park JK#. (2018).Population genomic analysis reveals contrasting demographic changes of two closely related dolphin species in the last glacial. Molecular Biology and Evolution, 35, 2026–2033.

2017

Vijay N#, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW#. (2017). Genome‐wide patterns of variation in genetic diversity are shared among populations, species and higher order taxa. Molecular Ecology, 26, 4284–4295.
Dutoit L, Vijay N, Mugal CF, Bossu CM, Burri R, Wolf JBW, Ellegren H#. (2017). Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Proc. R. Soc. B 284-1849

2016

Vijay N#. (2016) Digest: Why are there no ring species? Evolution, 71-2 , 1558-5646
Foote AD*, Vijay N*, Maria Avila-Arcos, Baird R, Durban J, Morin P, Fumagalli M, Gibbs R, Hanson B, Korneliussen T, Martin M, Robertson K, Sousa V, Vieira F, Vinar T, Wade P, Worley K, Excoffier L, Gilbert T, Wolf J#. (2016) Genome-culture coevolution promotes rapid divergence in the killer whale. Nature Communications 7, Article number: 11693
Vijay N*, Bossu C*, Poelstra JW, Weissensteiner M, Suh A, Kryukov P A, Wolf JBW#. (2016) Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nature Communications 7, Article number: 13195

2015

Poelstra JW, Vijay N, Hoeppner MP and Wolf JBW#. (2015) Transcriptomics of colour patterning and colouration shifts in crows. Molecular Ecology, 24, 4617–4628.
Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JRS, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG# (2013) Unsupervised genome-wide recognition of local relationship patterns. BMC Genomics, 14, 347.
Shafer ABA*, Wolf JBW*, Alves PC, Bergström L, Bruford MW, Brännström I, Colling G, Dalen L, Meester LD, Ekblom R, Fawcett KD, Fior S, Hajibabaei M, Hill JA, Hoezel AR, Höglund J, Jensen EL, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popović D, Primmer CR, Reed FA, Roumet M, Salmona J, Schenekar T, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M, Veale A, Vergeer P, Vijay N, Vilà C, Weissensteiner M, Wennerström L, Wheat CW, Zieliński P (2015) Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution, 30, 78–87.
Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, Elk CEV, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics, 47-3, 272-275.

2014

Poelstra JW*, Vijay N*, Bossu C*, Lantz H, Ryll B, Müller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, Wolf JBW# (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344, 1410–1414.

2013

Vijay N*, Poelstra JW*, Künstner A, Wolf JBW# (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22, 620–634.

# Corresponding author

* Shared first author/Equal contribution

£ PhD student from CEG lab

$ BSMS student from CEG lab