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Consulta: creatorFacets:"Pabitra Pal Choudhury"
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A novel mathematical tool for generating highly conserved protein domain via different organismal
genomic landscapes
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long
strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above
three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different
chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair
human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA
sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in
nature....
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4850/version/1
DNA Sequence Evolution through Integral Value Transformations
Provedor de dados: 17
Autores: Sk Sarif Hassan; Pabitra Pal Choudhury; Ranita Guha; Shantanav Chakraborty; Arunava Goswami.
In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be
thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as
numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic
one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA
rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in
the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database.
This...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5729/version/1
Protein and DNA evolution: Statistics and combinatorics are the rules of the game
Provedor de dados: 17
Autores: Arunava Goswami; Srimoyee Duttagupta; Chirantan Chakraborty; Amita Pal; Pabitra Pal Choudhury; Sk Sarif Hassan.
Let us assume AVMAYDRYVAIC or MAYDRYVAICCP, most important signature domain of
olfactory
receptor (OR) gene family assembled in evolution following simplest possible laws of statistics which says the addition of V after
A in AVMAYDRYVAIC or addition of A after M are independent events. There are 20 amino acids present in nature so the
probability
of
joint
occurrence
of
such
events
is
1/400.
Therefore
for
making
a
contiguous
string
of
AVMAYDRYVAIC or MAYDRYVAICCP, the probability would be 1 out of 2012. Over millions of
years of evolution this has certainly happened and that is why we see such a signature sequence in OR1D2, OR1D subfamily
member 2 as per "HORDE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4859/version/1
Quadruple context-free L-System mathematical tools as origin of biological evolution
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
It is well known that A, T, G, C annealed together early in evolution and the long stretch of DNA was found which ultimately
resulted into chromosomes of different organisms. But it is unclear till date how exons, introns, conserved protein domains was
formed. Using the DNA sequences of the largest known gene-family present in human genome, i.e., olfactory receptors and
simplest possible quadruple context-free L-Systems, we show that conserved protein domains and intergenic regions which lies at
the heart of the biological evolution started with a sixteen base-pairs stretch of DNA.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4851/version/1
Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava Goswami; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene
expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures,
functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca
mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has
been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value
Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2]. Through this study we have been able to nullify or justify one
given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/1
Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava Goswami; Navonil De Sarkar; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene
expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures,
functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca
mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has
been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value
Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2]. Through this study we have been able to nullify or justify one
given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/2
Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical
Morphology
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; B. S. Dayasagar; Shantanav Chakraborty; Ranita Guha; Arunava Goswami.
Fractals and Mathematical Morphology are immensely used to study many problems in different branches of science and
technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in
Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human,
Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the
quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory
receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can
be exposed through intricate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5674/version/1