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Indian Institute of Science Education and Research Berhampur
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान बरहमपुर
ଭାରତୀୟ ବିଜ୍ଞାନ ଶିକ୍ଷା ଏବଂ ଗବେଷଣା ସଂସ୍ଥାନ ବ୍ରହ୍ମପୁର
An Autonomous Institution under the Ministry of Education, Government of India
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Dr. Arunkumar Krishnan

Biography

Dr. Arunkumar Krishnan is an Assistant Professor in the Department of Biological Sciences at the Indian Institute of Science Education and Research (IISER) Berhampur. He is a computational biologist specializing in comparative and evolutionary genomics, with research interests in prokaryotic defense systems, lineage-specific expansions of gene families, invertebrate genome evolution, and adaptive diversification of protein domains.

Assistant Professor, IISER Berhampur (Since December 2020 Onwards)

Post-Doctoral Fellow, NCBI, NIH (2017-2020), Bethesda, Maryland, US. Dr. L Aravind’s group

Post-Doctoral Fellow, University of Queensland (2016-2017), Australia. Prof. Bernard Degnan’s group

Ph.D in Comparative Genomics (2011-2015), Uppsala University, Sweden. Prof. Helgi Schiöth's group


https://iiserbpr.ac.in/people/profile/akrishnan

Rakesh S, Krishnan A*. Expanding the landscape of BREX diversity: uncovering multi-layered functional frameworks and identification of novel BREX-related defense systems. Nucleic Acids Research. Volume 54, Issue 3, 10 February 2026, gkag035, Weblink

Rakesh S, Behera K, Krishnan A*. Unveiling the structural and functional implications of uncharacterized NSPs and variations in the molecular toolkit across arteriviruses. NAR Genomics and Bioinformatics.  Volume 7, Issue 2, June 2025, lqaf035. Weblink

Nath R, Panda B, Rakesh S, Krishnan A*. Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa. Molecular Biology and Evolution. Volume 42, Issue 3, March 2025, msaf042, Pages 1–25. Weblink 

Rakesh S, Aravind L, Krishnan A*. Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems. Nucleic Acids Research. Volume 52, Issue 3, 9 February 2024, Pages 1005–1026. Weblink (NAR Breakthrough and Cover Page Article) (Featured in Times of India) 

Westbury MV, Le Duc D, Duchêne DA, Krishnan A, Prost S, Rutschmann S, Grau JH, Dalen L, Weyrich A, Norén K, Werdelin L, Dalerum F, Schöneberg T, Hofreiter M*. (2021). Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae. Molecular Biology and Evolution. Volume 38, Issue 9, Pages 3884–3897. Weblink

Krishnan A, Burroughs AM, Iyer LM, Aravind L*. (2020). Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Nucleic Acids Research. Volume 48, Issue 18, Pages 10045–10075. Weblink (Featured Survey and Summary article)

Krishnan A, Burroughs AM, Iyer LM, Aravind L*. (2018). Unexpected evolution of lesion-recognition modules in eukaryotic NER and kinetoplast DNA-dynamics proteins from bacterial mobile elements. iScience. Volume 9, Issue, P192-208. Weblink

Krishnan A, Iyer LM, Holland SJ, Boehm T, Aravind L*. (2018). Diversification of AID-APOBEC-like deaminases in metazoa: identification of novel clades and widespread roles in immunity. PNAS. Vol. 115, no. 14; E3201–E3210. Weblink

Pusapati GV, Kong JH, Patel BB, Krishnan A, Sagner A, Kinnebrew M, Briscoe J, Aravind L, Rohatgi R*. (2018). CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog. Developmental Cell. Jan 8;44(1):113-129.e8. Weblink (Featured Cover page article)

Duc DL, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, Ongyerth M, Bitarello BD, Schiöth HB, Hofreiter M, Stadler PF, Prüfer K,Lambert D, Kelso J, Schöneberg T*. (2015). Kiwi genome provides insights into nocturnal adaptation. Genome Biology. 16:147. Weblink (Covered by 17 news outlets, including The Seattle Times and New Zealand Herald)

Hall MR, Kocot KM, Baughman KW, Fernandez-Valverde SL, Gauthier MEA, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato U, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM, and Degnan BM*. (2017). The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature. 544 (7649): 231-234. Weblink (Covered by 27 news outlets, including The Guardian, BBC, Science Daily, and The Weekend Australian, among many more).

Krishnan A*, Schioth HB. (2015). The role of G protein-coupled receptors in the early evolution of neurotransmission and the nervous system. Journal of Experimental Biology. 218(Pt 4):562-571. Weblink (Special issue on the Evolution of the Nervous System)


Overall Research Theme Of the Lab

Our research group integrates comparative genomics and computational structural biology to investigate fundamental questions across the biological spectrum. We leverage a broad suite of computational approaches to explore diverse biological systems, with a core focus on evolutionary logic and inference.

Guided by the principle that evolutionary thinking offers a powerful lens to decode molecular diversity and innovation, our work builds on the basis that nature—through billions of genetic experiments over evolutionary time—has woven, and continues to weave, a dynamic tapestry of molecular evolution. Comparative and evolutionary genomics provide the means to unravel the dynamic landscape of molecular evolution and reveal the principles—such as divergence, constraint, convergence, and related forces—that drive molecular innovation and functional diversification.

At the molecular scale, we analyze sequence–structure relationships of protein domains and families, track lineage-specific gene expansions, and identify diversification patterns that scale up to organismal adaptation and evolutionary novelty. These approaches allow us to dissect the molecular strategies from prokaryotic defenses against selfish genetic elements to major eukaryotic transitions shaped by gene family expansions and whole-genome duplications. We are also broadly interested in the evolution of protein folds, focusing on how the evolutionary malleability of folds enables proteins to adapt, diversify, and repurpose their functions across diverse biological contexts, and how these functional shifts can be systematically traced and predicted using computational approaches.

Unified by a central interest in the evolution of molecular systems, our research themes apply evolutionary reasoning to understand how proteins and genomes diversify, adapt, and innovate across diverse biological contexts.

The following sections highlight the major research themes currently pursued in our group

      Prokaryotic Defense Systems
      Lineage-Specific Expansions (LSEs) of Gene Families in Metazoans
      Genome Sequencing of Invertebrates to Study the LSEs and Other Adaptive Diversifications
      Comparative Genomics of Lipid-Binding GPCRs: Evolution, Specificity, and Human Variation

      Adaptive Evolution of Diverse Protein Folds and Domains and Their Functional Diversification in Prokaryotes

      For the latest updates, please visit our new lab website "https://www.ceglab-iiserbpr.com/"


  • Comparative and Evolutionary Genomics
  • Rakesh Siuli, rakeshs@iiserbpr.ac.in (Ph.D. student)
  • Biswajit Panda, biswajitp@iiserbpr.ac.in (Ph.D. student)
  • Rohan Nath, rohann20@iiserbpr.ac.in (iPh.D. student)
  • Subhangi Subudhi, subhangis23@iiserbpr.ac.in (PhD Student)
  • Somanath Muduli, 2420101@iiserbpr.ac.in (Ph.D student)
  • Atharv Manojkumar Sambarat 2510104@iiserbpr.ac.in, (PhD Student)
  • Belide saketha ram, belide21@iiserbpr.ac.in, MS Thesis Student 25-26
  • Anik Dey, anikd20@iiserbpr.ac.in , Researcher
  • Ph.D. (Comparative Genomics), 2015, Uppsala University, Sweden
  • MSc (Bioinformatics), 2008, University of Madras
  • Assistant Professor, IISER Berhampur (Since December 2020 onwards)
  • Postdoc, NCBI, NIH (2017-2020). L Aravind’s Group
  • Postdoc, University of Queensland (2016-2017). Bernard Degnan’s group
  • Ramalingaswamy Fellowship Award, 2021
  • DBT SERB-SRG Grant, 2021
  • Postdoctoral Visiting Fellowship Award NIH, 2017
  • Member of the Society for Molecular Biology and Evolution (SMBE)
  • Academic member of the Adhesion GPCR Consortium
  • Manuscripts receiving outstanding recognition such as (i) Featured cover page articles, (ii) Breakthrough articles, (iii) F1000,
  • Manuscripts addressed by numerous News outlets, including The Guardian, BBC, The Seattle Times, Weekend Australian, New Zealand Herald, among others.

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