Publications

@article{Ramaswamy2001,
title = {Genes, brains, and unpredictability: Developments in the sciences and reflections on what it means to be alive},
author = {Ramakrishna Ramaswamy},
url = {https://ramramaswamy.org/papers/R30.pdf},
issn = {00113891},
year = {2001},
date = {2001-01-01},
journal = {Current Science},
volume = {80},
number = {11},
pages = {1381–1386},
abstract = {The most dramatic statement of the reductionist approach in the biological sciences is the ástonishing hypothesis’ of Francis Crick that something as central to our sense of self, namely the human soul, is in effect ‘no more than the behaviour of a vast assembly of nerve cells and their associated molecules’. Recent advances such as the sequencing of entire genomes (the human genome being a well-publicized example) or the elucidation of some of the neuronal mechanisms associated with memory, for instance, appear to support this point of view, that we can eventually possess the recipe for human individuality. This essay contends that the essential limitation of such a programme stems not from the remaining problems of working out the details, but from the fact that living systems are fundamentally complex. Drawing on the ideas of deterministic chaos and complexity theory, it is proposed that while the broad contours of the connection between biological functioning, genetic information and the organization of its nervous system will be accessible, the unique developmental trajectory of any organism – that which constitutes the essence of individuality and confers a notion of being alive – will remain beyond the realm of precise scientific prediction.},
keywords = {Brain, Genes},
pubstate = {published},
tppubtype = {article}
}

@article{Tiwari1997,
title = {Prediction of probable genes by Fourier analysis of genomic sequences},
author = {S Tiwari, S Ramachandran, S Bhattacharya, A Bhattacharya and R Ramaswamy},
url = {https://doi.org/10.1093/bioinformatics/13.3.263},
doi = {10.1093/bioinformatics/13.3.263},
year = {1997},
date = {1997-06-01},
journal = {Bioinformatics},
volume = {13},
number = {3},
pages = {263–270},
abstract = {Motivation: The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA.

Result: The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application.

Availability: A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request},
keywords = {Fourier, Genes, GeneScan},
pubstate = {published},
tppubtype = {article}
}