Krishna Swamy

Assistant Professor
Areas of interest
Evolutionary Systems Biology, Computational Biology, Genetics and Molecular Biology

Dr. Krishna Swamy is an Assistant Professor at the Division of Biological and Life sciences, Ahmedabad University. He has had an exciting multi-disciplinary trajectory during his career. He holds a Masters in Physics from Pune University. He started his research career in biology at Molecular Biophysics Unit, IISc, where he developed algorithms for protein structure and function prediction. He then did his PhD in computational biology at the Institute of Information Science, Academia Sinica, Taiwan in 2012. During his PhD, he developed methods to quantify the influence of cellular factors, such as nucleosomes, on the evolution of transcriptional control sequences. He also studied the confluence between sequence evolution and functional evolution of such non-coding sequences in Yeast, Drosophila, and Primates. He transitioned into an experimental biologist at the Institute of Molecular Biology, Academia Sinica, Taiwan after receiving the prestigious Academia Sinica Distinguished Postdoctoral Fellowship, and worked on deciphering the molecular mechanisms underlying speciation, the evolution of complex traits such as fermentation and stress response and evolution of co-operation.

Krishna is interested in combining theoretical and experimental approaches to uncover the general principles underlying the evolution of novel phenotypes, and how these affect the fitness of the organism across various environments. His lab will approach this problem by performing experimental evolution in microorganisms such as E. coli, S. cerevisiae, and hybrids of S. cerevisiae and other related yeasts in a variety of laboratory environments and mathematical modeling. The goal is to identify the key changes in the genetic program that lead to the organism's adaptation to various stresses, and predict from first principles how such mutations can lead to new phenotypes. Krishna is also interested in developing methods to infer the evolutionary history of the emergence of new phenotypes from genomic and transcriptomic data.

*: Co-first author

#: Corresponding author


  1. Swamy KB#, Zhou N, Experimental evolution: its principles and applications in developing stress-tolerant yeasts. Applied Microbiology and Biotechnology, 103(5), 2067-2077, 10.1007/s00253-019-09616-2


  1. Zhou N, Bottagisi S, Katz M, Schacherer J, Friedrich A, Gojkovic Z, Swamy KB, Knecht W, Compagno C, Piškur J. FEMS yeast research. Yeast–bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri. FEMS Yeast Research, Volume 17, Issue 6,
  2. Zhou N*#, Swamy KB*#, Leu JY, McDonald MJ, Galafassi S, Compango C, Piskur J. PLOS ONE. Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri, Page no.1-19, doi:10.1371/journal.pone.0173318


  1. Lu YJ, Swamy KB, Leu JY. PLOS Genetics. Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast, Page no 1-26,
  2. Majumder P, Chu YJ , Chatterjee B, Swamy,KB, Shen CKJ. Acta Neuropathologica. Co-regulation of mRNA translation by TDP-43 and Fragile X Syndrome protein FMRP, Page no. 1-15, doi:10.1007/s00401-016-1603-8)
  3. Tsai SY, Chang YL, Swamy KB, Chiang RL, Huang DH. Epigenetics & Chromatin. GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes, Page no. 1-20, DOI 10.1186/s13072-016-0082-4


  1. MCDonald MJ, Chou CH, SwamyKB, Huang HD, Leu JY. BMC Evolutionary Biology. The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli. Page no. 1-10 doi: 10.1186/s12862-015-0441-y


  1. Gopinath RK, Yu ST, Swamy KB, Yu JS, Shuyler, SC, Leu, JY. Genome Biology and Evolution. The Hsp90-Dependent Proteome Is Conserved and Enriched for Hub Proteins with High Levels of Protein–Protein Connectivity. Page no. 2851-2865, doi:10.1093/gbe/evu226
  2. Swamy KB, Lin CH, Yen MR, Wang CY, Wang D. BMC Genomics. Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus, Page no;1-12, doi:10.1186/1471-2164-15-521


  1. Chiang S*, Swamy KB*, Hsu TW, Tsai ZTY, Lu, HHS, Wang, D, Tsai HK. Gene. Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast, Page no:237-245,


  1. Swamy KB, Chu WY, Wang CY, Tsai HK, Wang D. BMC Evolutionary Biology. Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast, page no. 1-10, DOI: 10.1186/1471-2148-11-150


  1. Swamy KB, Cho CY, ChiangS, Tsai ZTY, TsaiHK. Nucleic Acids Research. Impact of DNA-binding position variants on yeast gene expression. Page no. 6991-7001, doi:10.1093/nar/gkp743


  1. Mizutani H, Saraboji K, Malathy SSM, Ponnuswamy MN, Kumarevel T, Swamy KB, Simanshu DK, Murthy MR, Kunishima N. Acta CrystallogarD. Systematic study on crystal-contact engineering of diphthine synthase- influence of mutations at crystal-packing regions on X-ray diffraction quality.

Winter 2019: BPS102 Biophysics (With Dr. Ashutosh Kumar and Dr. Neha Jain)


Journal Reviewer:

Nucleic Acids Research

BMC Evolutionary Biology

BMC Genomics

BMC Bioinformatics

Applied Microbiology and Biotechnology

Peer J

Current Science



B18, GICT Building,, Division of Biological & Life Sciences,
Ahmedabad University,
Central Campus,
Navrangpura, Ahmedabad,
Gujarat, India


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