Dr. Nithya Ramakrishnan

Research Focus Keywords:

Computational biology, probabilistic modelling, genomics, mathematical techniques for understanding cancer, immunology, and other biological phenomena

Background

Dr. Nithya Ramakrishnan obtained her Bachelor of Engineering. in Electronics and Communication Engineering from Thiagarajar College of Engineering, Madurai. Subsequently, she completed her PhD in Electrical Engineering from IIT Delhi in the inter-disciplinary area of information theory-based analysis of biological data, with a focus on intron-exon segmentation and cancer detection based on epigenetic information. During her post-doctoral terms at IIT
Bombay and Dalhousie University (Canada), she has worked on modelling epigenetic phenomena and chromatin inheritance using information theory, statistical analyses of multi-omics data and bioinformatic pipelines. Prior to her research career, she worked in the software industry (Sun Microsystems/Oracle) as a lead software developer.

She joined IBAB in Feb 2023.

Education:

• B.E (Electronics and Communication Engineering) – Thiagarajar College of Engineering, Madurai
• PhD – Dept. of Electrical Engineering, IIT Delhi
• Post-doctoral research – Dept of Biosciences and Bioengineering, IIT Bombay
• Post-doctoral research – Dalhousie University, Halifax, Canada.

Professional experiencetion:

• Lead software developer – Cognizant Solutions/Sun Microsystems/Oracle
• Institute Post-doctoral Fellow – Dept of Biosciences and Bioengineering, IIT Bombay
• Post-doctoral Fellow – Dalhousie University, Halifax, Canada

Research interest profile

We apply machine learning, reinforcement learning, and information theoretic techniques to solve problems in biology and understand biological phenomena.

Looking for interested students/researchers to work in some of the above areas – If interested, please reach me at nithya[at]ibab.ac.in, with your CV and a brief write-up on your academic interests.

Collaborators

1. Dr. Tobias Karakach and Dr. Shashi Gujar – Dalhousie University, Canada.
2. Dr. Sanjay Chandrasekharan – Homi Bhabha Center for Science Education, TIFR, Mumbai
3. Dr. Sibi Raj B. Pillai – Professor, Dept of Electrical Engg, IIT Bombay, Mumbai
4. Dr. Tripti Bameta, Scientist, ACTREC, Tata Memorial Hospital, Mumbai

Publications

• Aamir Sahil Chandroth, Nithya Ramakrishnan, Sanjay Chandrasekharan, “The self-organisation of selfishness: Reinforcement Learning shows how selfish behavior can emerge from agent-environment interaction dynamics”, arXiv, 2023
• Ramakrishnan N, Sibi Raj B Pillai, Padinhateeri R, “High fidelity epigenetic inheritance: Information theoretic model predicts k-threshold filling of histone modifications post replication, PLoS Comput Biol. 18(2): e1009861, 2022
• N. Ramakrishnan and R. Bose, “Analysis of healthy and tumor DNA methylation distributions in kidney-renal-clear-cell-carcinoma using Kullback–Leibler and Jensen–Shannon distance measures”, IET Systems Biology, vol. 11, no. 3, pp. 99-104, 2017
• Nithya Ramakrishnan and R. Bose, “Analysis of distribution of DNA methylation in kidney-renal-clear-cell-carcinoma specific genes using entropy”, Genomic Data, vol. 10, pp. 110-116, 2016
• N. Ramakrishnan and R. Bose, “Dipole entropy-based techniques for segmentation of introns and exons in DNA”, Appl. Phys. Lett., vol. 101, no. 8, p. 083701, 2012
• N. Subramanian and R. Bose, “Dipole angular entropy techniques for intron- exon segregation in DNA”, Euro Physics Letters, vol. 98, no. 2, p. 28002, 2012

Conference proceedings

• Nithya Ramakrishnan, Mayuri Rege, Dibyendu Das, Sibiraj B. Pillai and Ranjith P., Computational Analysis of Histone Post-translational Modification Pairs, and their Influence on Genes, EMBO Conference on Histone Chaperones, Crete, Greece, Oct 2019
• Nithya Ramakrishnan and R. Bose, “An Algorithm for the Generation of Random Numbers from DNA Methylation Data”, Presented at the Quantitative Principles in Biology Conference at European Molecular Biological Institute (Heidelberg) pp. 181, 2017
• Nithya Ramakrishnan and R. Bose, “Analysis of DNA Methylation in Tumor Suppressor Genes using Information Theory”, Presented at the Cancer Genomics Conference at European Molecular Biological Institute (Heidelberg) pp. 161, 2015