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Tapash
Chandra Ghosh
Professor, Bioinformatics
PhD: Kalyani University (1991)
2011
(1)
Sen K, S. Podder and T. C. Ghosh 2011.
On the quest for selective constraints shaping the expressivity of the
genes casting retropseudogenes in human. BMC Genomics (in press).
(2)
Kahali,
B, S. Ahmad and T. C. Ghosh 2011. Selective constraints in
yeast genes with differential expressivity: Codon pair usage and mRNA
stability perspectives. Gene 481, 76-82.
(3)
Bagchi, A and
T.C. Ghosh 2011.
New
Direction to the Solution of Protein Folding Problem.
J
Biomol Struct Dyn.
28, 653-654.
(4)
Podder S,
T.C. Ghosh. 2011. Insights into the Molecular Correlates Modulating
Functional Compensation between Monogenic and Polygenic Disease Gene
Duplicates in Human. Genomics 97, 200-204.
2010
(1)
Podder,
S and T.C. Ghosh. 2010. Exploring the differences in evolutionary
rates between monogenic and polygenic disease genes in human. Mol Biol
Evol. 27:934- 941.
(2)
Basak,S.,
P. Mukhopadhyay, S. K. Gupta, T. C. Ghosh. 2010.
Genomic adaptation of prokaryotic organisms at high temperature.
Bioinformation 4(8): 352-356.
(3)
Mukhopadhyay, P and T. C. Ghosh.
2010. Relationship between gene compactness and base composition in rice and
human genome. J Biomol Struct Dyn.
27:477-488.
(4)
Singh, H, M. Andrabi , B. Kahili , T.C. Ghosh
, A.V. Kochetov and S. Ahmad 2010.
On nucleotide solvent accessibility in RNA structure. Gene 463:
41-48.
(5)
Begum, T and T.C. Ghosh 2010. Understanding the Effect of
Secondary Structures and Aggregation on Human Protein Folding Class
Evolution.
J
Mol Evol.
71: 60-69.
(6)
Bhattacharya, T and T.C. Ghosh. 2010. Protein Connectivity and
Protein Complexity Promotes Human Gene Duplicability in a Mutually Exclusive
Manner. DNA Research 17: 261-270.
(7)
Sur, S., A. Bothra, T.C. Ghosh and A. Sen. 2010. Investigation of the
molecular evolution of nitrogen fixation using nucleotide triplet based
condensed matrix method. International J Integrative Biology 10,
59-65.
(8)
Sen, K., S. Podder and T.C. Ghosh 2010.
Insights into the
genomic features and evolutionary impact of the genes configuring duplicated
pseudogenes in human. FEBS Letters 584: 4015-4018.
(9)
Chakraborty,
S., B. Kahali B and T.C. Ghosh 2010. Protein complex forming ability
is favored over the features of interacting partners in determining the
evolutionary rates of proteins in the yeast protein-protein interaction
networks.
BMC Syst Biol.
2010 Nov 12;4(1):155.
2009
(1)
Podder,
S., P. Mukhopadhyay and T. C. Ghosh. 2009. Multifunctionality
dominantly determines the rate of human housekeeping and tissue specific
interacting protein evolution. Gene 439: 11-16.
(2)
Manna
B., T. Bhattacharya, B. Kahali and T. C. Ghosh 2009
Evolutionary constraints on hub and non-hub proteins in human protein
interaction network: insight from protein connectivity and intrinsic
disorder. Gene 434: 50-55.
(3)
B.
Kahali, S. Ahmad and T. C. Ghosh. 2009. Exploring the evolutionary
rate differences of party hub and date hub proteins in Saccharomyces
cerevisiae protein-protein interaction network 2008. Gene
429: 18-22.
2008
(1)
Mandal, U.K., B. Das,
T.C. Ghosh,
A. Sen and A.K. Bothra. 2008. Nucleotide Triplet Based Molecular Phylogeny
of class-I and class II Aminoacyl t-RNA Synthetase in three Domain of Life
Process: Bacteria, Archaea and Eukarya.
J
Biomol Struct Dynamics
26:
321-328.
(2)
Mukhopadhyay,
P., S. Basak and T. C. Ghosh. 2008. Differential Selective
Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue Specific
Homologous Genes of rice and Arabidopsis. 2008. DNA Research
15: 347-356.
(3)
Kahali, B., S. Basak., and T.C. Ghosh. 2008. Delving deeper into the
unexpected correlation between gene expressivity and codon usage bias of
Escherichia coli genome. J Biomol Struct Dynamics 25:
655-662.
(4)
Patra, S.K.,
A. Patra, F. Rizzi, T. C. Ghosh, S. Bettuzzi.
2008.
Demethylation of
(Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic
pathways of cancer development. Cancer Metastasis Rev. 27:
315-334.
(5)
Bagchi,
A., and T.C. Ghosh. 2008. Structural interaction between DsrE,
DsrF and DsrH in Dsr operon. A. Bagchi and T.C. Ghosh. J Biomol Struct
Dynamics 25: 517-524.
2007
(1)
D’Onofrio, G.,
T.C. Ghosh, and S. Saccone. 2007. Different functional
classes of genes are characterized by different compositional properties.
FEBS Letters 581: 5819-5824.
(2) Basak, S.,
S. Roy, and T.C.
Ghosh.
2007. On the origin of synonymous codon usage divergence between
thermophilic and mesophilic prokaryotes.
FEBS Letters
581:
5825-5830.
(3) Bagchi,
A., and T.C. Ghosh.
2007.Homology modeling and molecular dynamics study of the interactions of
SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions
in Pseudaminobacter salicylatoxidans.
Res. J.Microbiol.
2: 569-576.
(4)
Bagchi, A., and T.C.
Ghosh.
2007. Structural insight into the functionality of the transcriptional
regulator SoxR from Paracoccus pantotrophus in sulfur oxidation operon
Res. J. Microbiol.
2: 735-741.
(5)
Mukhopadhyay,
P., S. Basak, and T. C. Ghosh. 2007. Synonymous codon usage
in different protein secondary structural classes of human genes:
Implication for increased non-randomness of GC3 rich genes
towards protein stability. J Biosciences 32: 947-963.
(6)
Mukhopadhyay,
P., S. Basak, and T. C. Ghosh. 2007. Nature of selective constraints
on synonymous codon usage of rice differs in GC-poor and GC-rich genes.
Gene 400: 71-81.
(7)
Kahali, B.,
S. Basak, and T. C. Ghosh. 2007. Reinvestigating the codon and amino
acid usage of S. cerevisiae genome: A new insight from protein
secondary structure analysis. Biochem. Biophys. Res. Commun. 354:
693-699.
(8)
Sau, K., S.K.
Gupta, S. Sau, S.C. Mandal, and T.C. Ghosh. 2007. Studies on
synonymous codon and amino acid usage biases in the broad-host range
bacteriophage KVP40. J. Microbiol. 45: 58-63.
2006
(1)
Bagchi, A., and T.C. Ghosh. 2006. Structural and functional
characterization of SoxW – a thioredoxin involved in the transport of
reductants during sulfur oxidation by the global sulfur oxidation reaction
cycle. Res. J.Microbiol.1:
392-400.
(2)
Basak, S., and T.C. Ghosh 2006. .Temperature Adaptation of
Synonymous Codon Usage in Different Functional Categories of Genes: A
Comparative Study betweenMethanococcus jannaschii
and Methanococcus
maripaludis Homologous Genes. FEBS Letters 580:
3895-3899.
(3)
Bagchi, A.,
and T.C. Ghosh. 2006. Structural study of two proteins SigE and ORF1
to predict their roles in the biochemical oxidation of sulfur anions via the
global sulfur oxidation operon (sox). Comp. Biol. and Chem.
30: 227-232.
(4)
Joy, F., S.
Basak, S. K. Gupta, P. J. Das, S.K. Ghosh, and T.C. Ghosh. 2006.
Compositional correlations in canine genome reflects similarity with human
genes. J. Biochem. Mol. Biol. 39: 240-246.
(5)
Bagchi, A.,
and T.C. Ghosh. 2006. Structural identification of the interactions
of SoxA and SoxX during the oxidation of sulfur anions via the novel global
sulfur oxidizing (Sox) operon. Res. J.Microbiol.1:
172-182.
(6)
Sau, K.,
S. K. Gupta, S. Sau, S. C. Mandal, and T. C. Ghosh. 2006. Factors
influencing synonymous codon and amino acid usage biases in Mimivirus.
BioSystems 85: 107-113.
(7)
Banerjee,
T., and T.C. Ghosh. 2006. Gene expression
Level Shapes the Amino Acid Usages in Prochlorococcus marinus MED4.
J. Biomol. Struct. Dynamics 23: 547-554.
(8)
Bagchi, A., and T.C. Ghosh. 2006. Structural insight into the
interactions of SoxV, SoxW and SoxS in the process of transport of
reductants during sulfur oxidation by the novel global sulfur oxidation
reaction cycle. Biophys. Chem. 119: 7-13.
2005
(1)
Bagchi, A.,
and T.C. Ghosh. 2005. Structural identification of a novel
thioredoxin SoxS: prediction of the function in the process of transport of
reductants during sulfur oxidation by the novel global sulfur oxidation
reaction cycle. J. Mol. Struct. – Theochem. 758:
113-118.
(2)
Banerjee,
T., S.K. Gupta and T.C. Ghosh. 2005. Compositional transitions
between Oryza sativa and Arabidopsis thaliana genes are linked
to the functional change of encoded proteins. Plant Science
170: 267-273.
(3)
Bagchi, A.,
and T.C. Ghosh. 2005. A structural study towards the understanding of
the interactions of SoxY, SoxZ and SoxB leading to the oxidation of sulfur
anions via the novel global sulfur oxidizing (sox) operon. Biochem.
Biophys. Res. Commun. 335: 609-615.
(4)
Sahu, K., S.
Sau, S. C. Mandal and T.C. Ghosh. 2005. Factors influencing the
synonymous codon and amino acid usage bias in an AT-rich P. aeruginosa phage
PhiKZ. Acta Biochim. Biophys. Sin. 37: 625-633.
(5)
Gupta, S.K.,
T. Banerjee, S. Basak, K. Sahu, S. Sau, and T.C. Ghosh. 2005. Studies
on codon usage in Thermoplasma acidophilum and its possible
implications on the occurrences of lateral gene transfer. J. Basic
Microbiol. 45: 344-354.
(6)
Sahu, K., S.
K. Gupta, S. Sau, and T. C. Ghosh. 2005. Synonymous codon usage bias
in 16 Staphylococcus aureus phages: Implication in phage therapy.
Virus Res. 113: 123-131.
(7)
Sahu, K., S.
K. Gupta, S. Sau, and T. C. Ghosh. 2005. Comparative analysis of the
base composition and codon usages in fourteen mycobacteriophage genomes.
J. Biomol. Struct. & Dynamics 23: 63-72.
(8)
Banerjee,
T., S.K. Gupta, and T.C. Ghosh. 2005. Role of mutational bias
and natural selection on genome-wide nucleotide bias in prokaryotic
organisms. BioSystems 81: 11-18.
(9)
Basak, S., and T. C. Ghosh. 2005.
On the origin of genomic adaptation at high temperature for
prokaryotic organisms. Biochem. Biophys. Res. Commun. 330:
629-632.
(10)
Banerjee,
T., S.K. Gupta, and T.C. Ghosh. 2005. Towards a resolution on the
inherent methodological weakness of the “effective number of codons used by
a gene”. Biochem. Biophys. Res. Commun. 330:
1015-1018.
(11)
D’Onofrio,
G., and T.C. Ghosh. 2005. The compositional transition of vertebrate
genomes: an analysis of the secondary structure of the proteins encoded by
human genes. Gene 345: 27-33.
(12)
Basak, S., S. Mandal, and T. C. Ghosh. 2005.
Correlations between
genomic GC levels and optimal growth temperatures: some comments.
Biochem. Biophys. Res. Commun. 327: 969-970.
2004
(1)
Basak, S.,
T. Banerjee, S.K. Gupta, and T.C. Ghosh. 2004. Investigation on the
Causes of Codon and Amino Acid Usages Variation Between Thermophilic
Aquifex aeolicus and Mesophilic Bacillus subtilis. J.
Biomol. Struct. & Dynamics 22: 205-214.
(2)
Banerjee,
T., S. Basak, S.K. Gupta, and T.C. Ghosh. 2004. Evolutionary Forces
in Shaping the Codon and Amino Acid Usages in Blochmannia floridanus.
J. Biomol. Struct. & Dynamics 22: 13-24.
(3)
Sau, K., S. K. Gupta, T. C. Ghosh, and S. Sau. 2004.
Synonymous codon usage
analysis of mycobacteriophage Bxz1 and its plating bacteria M. smegmatis:
identification of highly and lowly expressed genes of Bxz1 and the possible
function of its tRNA species. J. Biochem. & Mol. Biol. 37:
487-492.
(4)
Subramaniyam, V., S.K. Gupta, and T.C. Ghosh. 2004. Shannon’s
uncertainty principle and gene expression levels. V. Subramaniyam,
Curr Science
86: 1142-1147.
(5)
Gupta, S.K., T.K. Bhattacharyya, and T.C. Ghosh. 2004.
Synonymous codon usage in
Lactococcus lactis:
Mutational Bias Versus Translational Selection.
J. Biomol. Struct. & Dynamics
21: 527-535.
2003
(1)
Gupta, S.K., and T.C. Ghosh. 2003. Reinvestigation on the
causes of genomic GC variation between the orthologous genes
of Mycobacterium tuberculosis and Mycobacterium leprae. Biochem. Biophys.
Res. Commun.
303: 65-68.
2002
(1)
D’Onofrio,
G., T.C. Ghosh and G. Bernardi. 2002. The base composition of
the human genes is correlated with the secondary structures of the encoded
proteins. Gene 300:179-187.
(2)
Gupta, S.K.,
T.K. Bhattacharyya and T.C. Ghosh. 2002. Compositional correlation
and codon usage studies in Buchnera aphidicola. Ind J of
Biochem & Biophys. 39: 35-48.
2001
(1)
Gupta, S.K.
and T.C. Ghosh. 2001. Gene expressivity is the main factor in
dictating the codon usage variation among the genes in Pseudomonas
aeruginosa. Gene 273: 63-70.
(2)
Khetawat,
D., T. C. Ghosh, M.K. Bhattacharya, S.K.Bhattacharya and S.
Chakrabarti. 2001. Molecular characterization of the VP7 gene of Rotavirus
isolated from a clinical sample of Calcutta, India., Virus Res.
74: 53-58.
2000
(1)
Mandal,
D., S. Jana, S. Panda, S. Bhattacharya, T. C. Ghosh, S.K.,
Bhattacharya and S. Chakrabarti. 2000. Distribution of HIV-I
subtypes among female sex workers of Calcutta, India. Ind J Med
Res 112: 165-172.
(2)
Ghosh, T.C.,
S.K. Gupta and S. Majumdar. 2000. Studies on codon usage in Entamoeba
histolytica. Intl J Parasitology 30: 715-722.
(3)
Gupta, S.K.,
S. Majumdar, T.K. Bhattacharya, and T.C. Ghosh. 2000. Studies on the
relationships between the synonymous codon usage and protein secondary
structural units. Biochem Biophys Res Commun. 269:
692-696.
(4)
Gupta, S.K.,
and T.C. Ghosh. 2000. CUCG: A non-redundant codon usage database from
complete genomes. Curr Science 78: 28-29.
1999
(1) Majumdar, S.,
S.K. Gupta, V.S. Sundararajan, and T.C. Ghosh. 1999. Compositional
correlation studies among the three different codon positions in 12
bacterial genomes. Biochem Biophys Res Commun. 266:
66-71.
1997
(1)
Gupta,
S.K., and T.C. Ghosh. 1997. Similarities inferred from the
studies of long range correlations among mitochondrial DNA sequences.
Ind J of Biochem & Biophys. 34: 259-265.
1996
(1) Gupta, S.K.,
and T.C. Ghosh. 1996. Genolyte: a PC-based computer program for
visualisation of genomic DNA sequences. Ind J of Biochem & Biophys.
33: 152-155.
1992
(1)
Pal,
M.K., T.C. Ghosh, J.K.Ghosh, and R.C.Yadav. 1992. Spectroscopic
probe of the distribution of drugs or dyes between different
biopolymers; in biological effects of light by Walter de
Gruyter & co., Berlin, New York printed in Germany, edited by
Michael F. Halick. Albert M. Kligman, , p. 73-79.
1991
(1)
Pal, M.K.,
A. Roy, P.K.Pal, T.C. Ghosh, N. Mandal and R.C. Yadav. 1991.
Induced circular dichroism in conformation studies of polymers in
polymer science; contemporary themes; volume 2, Tata
Mcgraw Hill, edited by sivaram, , p. 1043-1048.
(2)
Pal, M.K.,
and T.C. Ghosh. 1991.Binding of dyes by Teichoic Acid in competition
with other polyanions. Makromol. Chem.191: 67-71.
1990
(1)
Pal, M.K.,
T.C. Ghosh, and J.K. Ghosh. 1990. Studies on conformation and metal ion
binding by Teichoic Acid of Staphylococcus Aureus. Biopolymers
30: 273-277.
(2)
Pal, M.K.,
and T.C. Ghosh. 1990. Induction of Metachromasia and Circular
Dichroism in the dye 1,9 dimethyl methylene blue by S. Aureus wall
teichoic acid. Indian Journal of Biochem. & Biophys. 27:
176-178.
1988
(1) Pal, M.K., and T.C.
Ghosh. 1988. Teichoic Acid: Induction of Metachromasia and Circular
Dichroism in pinacyanol dye. Makromol Chem. Rapid Commun.
9: 97-100.
Contact
tapash@bic.boseinst.ernet.in
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