Dr. Satyabrata Sahoo

RESEARCH ACOMPLISHMENT:

a)Computational Biophysics

Several Statistical and mathematical analysis have been performed on the biological DNA sequences. The study of molecular evolution and different measures of biological sequence similarity and the statistics of sequence comparison have been performed. A number of algorithms have been developed for sequence comparison and finding tRNAs. Nonrandom amino acid sequences in proteins have also been studied in order to understand gene regulation. Compositional complexity such as homopolymers and short period sequence repeats have also been investigated to study the molecular structure and dynamics of these sequences 

b) Condensed matter Physics & Computational nanophysics

A numerical technique namely, Complex Absorbing Potential Method has been developedto study the resonating states of the quantum dots in polar semiconductor,

A theoretical study on the ground and the excited state properties of quantum dots in polar semiconductor is done systematically.

 
c) Computational Atomic Physics

An alternative approach (Complex Absorbing Potential Method) to study the resonating state for the many-electron atomic system has been developed and has been applied to hydrogen, Lithium and Sodium.

Research Project completed:

1. The DNA Sequence Analysis for Gene Identification: A Minor Research project approved by UGC (PSW-060/05-06(ERO) dated 21/3/2006).

                               

1. In Silico Detection of Potential tRNA Genes and tRNA-like Structures in Genomic DNA Sequences: A Minor Research Project approved by UGC (PSW-056/11-12(ERO) dated 20/10.2010).

Ph.D. Thesis guided:

1. Computational Approaches For Gene Expression And Identification Of Highly Expressed   Genes in Diverse Genomes: A Comparative Analysis by Shibsankar Das

:awarded Ph. D. (Sc.) degree at Jadavpur University, INDIA

ON GOING RESEARCH PROJECT:

1. Genome Wide Relative Analysis of Codon Usage Patterns for Studying Expression Profile and Identifying Highly Expressed Genes in Diverse Plant Species: A research Project approved by the Science and Engineering Research Board, DST, Govt. of India under fixed grant scheme MATRICS[File No: MTR/2019/000274]

LIST OF PUBLICATION

[58] Satyabrata Sahoo, Brajadulal Chattopadhyay and Ria Rakshit; Analysis of codon usage pattern in the genome of a novel bacterial strain isolated from Bakreswar Hot spring: Industrial Biotechnology; 2023,19(4),237

[57] Satyabrata Sahoo and Ria Rakshit; The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family:Genomics and Informatics; 2022,20(4),e43

[56] Satyabrata Sahoo; Analysis of codon usage pattern and gene expression in Aspergillus fumigatus;  International Journal of Biosciences; 2021,13(4),181-194 [56] Satyabrata Sahoo; Analysis of codon usage pattern and gene expression in Aspergillus fumigatus;  International Journal of Biosciences; 2021,13(4),181-194

[55] Satyabrata Sahoo; Analysis of Codon Usage Pattern in 2019-nCoV ;  International Journal of Computational Biology and Drug Design; 2021,14(4),273-296

[54] Satyabrata Sahoo; Analysis of Codon Usage Pattern and Predicted Gene Expression in Neurospora Crassa: A Novel in Silico Approach;  International Journal of Life science and Pharma Research; 2021,11(5),35-60

[53] Satyabrata Sahoo; Analysis of Codon Usage and Nucleotide Bias in Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2) Genes ;  International Journal of Biosciences; 2021,19(1),31-45

[52] Satyabrata Sahoo and Ria Rakshit; 2019 Novel Human Coronavirus Sars-Cov-2 And Covid-19: A Brief Review ;  International Journal of Life science and Pharma Research; 2021,11(1),273-283

[51] Uttam Roy Mandal, Shib Sankar Das, Brajadulal Chatcenteradhyay, Satyabrata Sahoo; Identified Hybrid tRNA Structure Genes in Archaeal Genome; Iranian Journal of Biotechnology; 2019, 17(3),1

[50] Satyabrata Sahoo, Shibsankar Das and Ria Rakshit; Codon usage pattern and predicted gene expression in Arabidopsis thaliana ; 2019,Gene X,2,100012

[49] Uttam Roy Mandal, Shib Sankar Das, Brajadulal Chatcenteradhyay, Satyabrata Sahoo Comprehensive Study of Composite tRNA Genes in Archaeal Genome ; Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences; 2018, 4(5),823

 

[48] Uttam Roymandal, Shib Sankar Das, Riya Rakshit and Satyabrata Sahoo;
Suppressive Variants of Selenocysteine Trna in the Complete Genome of Methanopyrus kandleri AV19;2018, J. Pharmacogenomics Pharmacoproteomics , 9(2),179.

[47] Ria rakshit and  Satyabrata Sahoo; In Silico Prediction of Gene expression Based on Codon Usage : A mini Review ;2017, Journal of Investigative Genomics 4(2),63

[46] Shibsankar Das, Brajadulal Chotcenteradhyay, Satyabrata Sahoo; Comparative Analysis of Predicted  Gene Expression among Crenarchaeal Genomes;2017, Genomics & Informatics 1591,38.

[45] Satyabrata Sahoo and Shibsankar Das,Analyzing Gene Expression and Codon Usage Bias in Metallosphaera Sedula; 2014, J. Bioinf. Intell. Control 3, 72-80.

[44]Satyabrata Sahoo and  Shibsankar Das; Analysing gene expression and codon usage bias in diverse genomes using a variety of models;2014, Current Bioinformatics 9(5),102-112.

[43]Smarjit Das, Sanga Mitra, Satyabrata Sahoo and Jayprokas Chakrabarti; Viral/Plasmid captures in Crenarchaea; 2014, Journal of Biomolecular Structure and Dynamics, 32(4),546-554.

[42] Shibsankar Das, Uttam Roymondal, Brajadulal Chotcenteradhyay, Satyabrata Sahoo; Gene expression profile of the cynobacterium synechocystis genome;2012, Gene 497,344.

[41] Sanga Mitra, Smarjit Das,Satyabrata Sahoo, Chandana Sinha and Jayprakash Chakrabarti; Phylogeny derived from homodimeric endonucleage correlates with its pre-RNA substrates;2011, Adv. Biosc. and Biotech. 2,117

[40] Smarjit Das, Sanga Mitra, Satyabrata Sahoo, and Jayprakash Chakrabarti; Novel Hybrid Encodes both Continuous and Split tRNA Genes;2011, J.Bio. Struc. & Dynm. 28,1

[39]Smarjit Das, Ritwik Mukherjee, Satyabrata Sahoo, Rachna Thakkar and Jayprakash Chakrabarti; Structural Clones of UAG Decoding RNA;2009, J.Bio. Struc. & Dynm. 27,1

[38] Satyabrata Sahoo and Y.K.Ho; On the appearance of a Cooper minimum in the photoionization cross sections of the plasma-embedded Li atom; 2010,JQSRT.111,52.

[37] Satyabrata Sahoo and Y.K.Ho;Photoionization of the excited He* atom in Debye plasma; 2009, Research letters in Physics. 832413,1.

[36] Partha Sarathi Das and Satyabrata Sahoo; Bipolaronic excita -tions of interacting electron (hole)gas in one dimensional lattice model; 2009,Physica B,404,4225.

[35] Shibsankar Das, Uttam Roymondal ,  and Satyabrata Sahoo; Analyzing gene expression from relative codon usage bias in Yeast genome : a statistical significance and biological relevance:2009,Gene 443,121.

[34] Uttam Roymondal , Shibskar Das,  and Satyabrata Sahoo; Predicting Gene Expression Level from Relative Codon Usage Bias : An Application to Escherichia Coli  Genome:2009, DNA Research 16,13.

[33]S.Sahoo and Y.C.Lin and Y.K.Ho;2008,Quantum confined hydrogenic impurity in a spherical quantum dot under the influence of parallel electric and magnetic field:Physica E40,3107.

[32]S.Sahoo and Y.K.Ho:2006,Photoionization of Li and Na in Debye plasma environments:Physics of Plasmas 13,1,2006.

[31]I.Mukhopadhyaya,A.Som,S.Sahoo:Word organization
in Coding DNA :a mathematical model:2006,Theory in Biosciences 125,1

[30] J.Chakrabarty, Z. Ghosh, B. Mallick,S. Das, S. Sahoo and H.Singh:2006, tRNA- isoleucine-trypcenterhan composite gene: BBRC 339,37.

[29] J.Chakrabarty,B.Mallick,,S.Sahoo,Z.Ghosh,S.Das; 2005, Identity elements  in Archeal tRNA;DNA Research 12,235

[28]S.Sahoo and Y.K.Ho;2005, Field induced energy shifts and widths of low lying states of Na atom in Parallel Magnetic and Electric Fields. : Chin J. Phys 43,58

[27] S. Das, J. Chakrabarti, Z. Ghosh, S. Sahoo and B. Mallick ; A new measure to study phylogenetic relations in the brown algal order, Ectocarpales : The Codon Impact Parameter ;2005, Journal of Biosciences, 30(5) 101-111.

[26]J.Chakrabarti, S.Sahoo, B.Mallick S. Das and Z. Ghosh: 2005, Algorithm for pattern recognition in nano-sized archaea, Indian J. Phys.(2005), 79(6), 559-562.

[25]S.Sahoo and Y.K.Ho;2004,Anomalous stark effect in the ground state of the confined hydrogen atom in a spherical quantum dot: Phy. Rev. B  69, 165323

[24] A.Som, S.Sahoo and I. Mukhopadhyay and J. Chakrabarti; 2003,Scaling Violations in coding   DNA. ; European Physical Letters 62,271.

[23]A.Som,S.Sahooand J.Chakrabarti;2003,Coding DNA equences: Statistical Distributions; Mathematical Biosciences183,49.

[22]S.Chatcenteradhyay, S.Sahoo, W.A.Kanner and J. Chakrabarti;2003, Pressures in Archeal Protein Coding Genes: A Comparative Study:Comparative and Functional Genomics 4,56.

[21]S.Sahoo and Y.K.Ho;2002, Resonances of Hydrogen and Lithium Atoms in Parallel Magnetic and Electric Fields : Phys.Rev. A 65,15403

[20]S.Sahoo and Y.K.Ho;2000, Determination of Resonance  Energy and Width Using th Method of Complex Absorbing Potential:Chin. J. Phys.  38,127.

[19]S.Sahoo and Y.K.Ho;2000, Complex Absorbing Potential Method to Study the Stark Effect in  Hydrogen and Lithium :J.Phys.B.33,2195.

 

[18]S.Sahoo and Y.K.Ho;2000, Stark Effect on the Low-lying Excited States of the Hydrogen and the Lithium Atoms: J.Phys.B. 33,5151.

[17]S.Chatcenteradhyay,A.Som,S.Sahoo and J.Chakrabarti ;2000,Order and Fluctuation in DNA sequences:Indian J.Phys.74B, 1.

[16] S.Tarafdar, P.Nandy, A.Som, S.Sahooand J.Chakrabarti and N.Nandy;1999, Self-similarity and scaling exponent for DNA walk in two and four dimensions;Indian J.Phys73B(2),337.

[15]S.Sahoo,A.Bandyopadhyay,T.K.Mitra and N.C.Sil; 1999, The ground state energy of the Helium isoelectronic series;Indian J. Phys.73B(1), 25.

[14]A.Bandyopadhyay,S.Sahoo and N.C.Sil;1999, The calculation of the ground state energy of the Positronium negative ion Ps; Indian. J.Phys.
73B(2),337.                                  

[13]S.Sahoo;1999, Formation of the ground and the excited states of the Frohlich bipolaron; Phy. Rev. B60, 10803.

[12]S.Sahoo;1998,Energy levels of the Frohlich polaron in a spherical quantum dot; Phys. Lett. A238,390.

[11]S.Sahoo;1998,The strong coupling polaron in reduced dimensionality;J.Phys.C10,1999.

[10]S.Sahoo;1996,The ground state description of Frohlich polaron in symmetric quantum dot  within the framework of LLP-H approach;Z.Phys.B101,97.

[9]S.Sahoo,1996, On the formation and stability of the Frohlich bipolaron in two and three dimensional system;Nuovo Cimento D18,849.

[8]S.Sahoo, A.Bandyopadhyay, T.K.Mitra and N.C.Sil ; 1996,Helium atom revisited;Indian J.Phys. 70B, 93

[7]S.Sahoo;1995, The regular perturbation theory on the stability of the strong coupling bipolaron;Journal of Phys. C7,4457.

[6]S.Sahoo;1994, A variational calculation on the stability of two centre Frohlich bipolaron; Phys.Lett.A195.

[5]S.Sahoo and T.K.Mitra;1994, On the formation of an optical mode induced single centre bipolaron;Journal of Phys. Soc. of Japan 63,4102. 

[4]S.Sahoo and T.K.Mitra; 1993, Molecular Orbital approach to the Frohlich bipolaron; Phys. Rev. B48,6019.

[3]S.Sahoo and T.K.Mitra;1993, Canonical transformation, perturbation theory and strong coupling Landau-Pekar polaron revisited;Indian J. Phys.67A, 303.

[2]S.Sahoo and T.K.Mitra;1993, Molecular orbital bipolarons and oxide superconductors, Indian J. Phys. 67A, 425.

[1]S.Sahoo and T.K.Mitra;1992,Bipolaron formation in polar solids; Indian J .physics, 66A, 277.

PARTICIPATION IN CONFERENCES, SYMPOSIA, WORKSHOP ETC.

1. Participated in UGC sponsored National Seminar on’Quantum Information: Theory and Computer Science’ organized by Department of mathematics, Jogesh Chandra Choudhury College, Kolkata  in collaboration with Netaji Nagar Day College, Kolkata on 14th -15th February,2012.
2. Participated in ‘An Indo-Singapore Joint Workshop: Role of computational biology in advancing modern medicine’, organized by Centre of Applied mathematics and Computational Science SINP, Kolkata on 2nd-3rd Feb,2012
3. Participated in UGC sponsored National Seminar on’The Physics behind Electronics/Optoelectronics and their applications’ organized by Department of Physics, Sammilani Mahavidyalaya, Kolkata  in collaboration with Cetre for Pedagogical studies in Mathematics, Kolkata on 1st  and 2nd Dec,2011.
4. Participated in UGC sponsored National Seminar on’Cocepts and challenges in Astronomy and Astrophysics’organized by Department of Physics, Sunderban Mahavidyalaya, Kakdwip, South 24 Parganas in collaboration with M.P.Birla Institute of Fundamental Research, Kolkata on 24th 25th Nov,2011 .
5. Participated in the “Fourth Workshop on genetic Epidemiological methods for Discussion on Complex human Traits” held on February 23-28,2009 ,organized by TCG-ISI Centre for Population Genomics, Kolkata, India and Univ. of Pittsburgh,USA.
6. Paper  Presented: Hybrid tRNA gene: A bridge between continuous and split tRNAs,2010, EMBO/EMBL Sympsosium:Non-Coding Genome,p-113, organized by EMBL, Heidelberg, held in, Heidelberg, Germany,13-16 Oct,2010.
7. Paper presented: Annotation of putative pyrolysine tRNAs:Correlation with in-frame usage of amber codon UAG; S.Das, S.Sahoo, R. Mukherjee and J. Chakrabarti,2007, 22nd  International tRNA Workshop, p-75, held in Upsala, Sweden, November 1-6,2007.
8.  Paper presented: Identity determinants for AARS and intron splicing endonucleases; B. Mallik, Z. Ghosh, J. Chakrabarti, S.Das, and S.Sahoo, 2007,International Conference on Chromosomes to Neurons(ICCTN),p37, organized by Dept. of Biophysics, Molecular Biology & Genetics, University of Calcutta and SINP, Kolkata,.held on January 12-14,2007.
9. Paper presented: New Proline-tRNA gene in Methanococcus jannaschii.; Z. Ghosh, B. Mallik,J. Chakrabarti, S.Das, and S.Sahoo, 2007,International Conference on Chromosomes to Neurons(ICCTN),p58, organized by Dept. of Biophysics, Molecular Biology & Genetics, University of Calcutta and SINP, Kolkata,.held on January 12-14,2007.
10. Paper presented: Substrate identities for tRNA-splicing-Endonucleases and AARS in Eukaryotes; B. Mallik, Z. Ghosh,J. Chakrabarti, S.Das, and S.Sahoo, 2006,International Conference on Bioinformatics-2006(InCoB 2006),p232, .held on December 18-20,2006.
11. Paper presented: tRNAs of nonstandard amino acids in Sulfolobus acidocaldarious.; Z. Ghosh, B. Mallik,J. Chakrabarti, S.Das, and S.Sahoo, 2006,International Conference on Bioinformatics-2006(InCoB 2006),p422, .held on December 18-20,2006.
12. Paper presented: tRNA-scape in archaea; Sahoo, S., Mallick, B., Ghosh, Z., Das, S. and Chakrabarti, J. (2005). 21st International tRNA Workshop, p-168, organized by IISc., Bangalore, held on December 2-7,2005.
13. Paper presented: Non-canonical introns in tRNA genes of archaea; J. Chakrabarti , B.Mallick, Z.Ghosh, S.Sahoo, and S. Das, (2004). 2nd RNA Group meeting, Dec 21-22,2004,organized by Biophysics Division ,Saha Institute of Nuclear Physics, Calcutta.
14.  Paper presented: Distribution of Palindromic sSequences in Lambda; Z. Ghosh, S.Sahoo, G. Purokayastha, J. Chakrabarti,(2004), in the symposium on ‘Bioinformatics For Genome Analysis’, organized by Bose Institute, Calcutta during January 29-30,2004.
15.  Participated  in the ‘Workshop on Statistical Computational    Genomics’, organized by Indian Statistical Institute , Calcutta during December 11-20,2001.
16.  Participated in XIIIth  national conference on ‘Atomic and Molecular Physics’ held in Indian Association for the Cultivation of Science, from January 16-20,2001. Contributed paper entitled, ‘ Complex Absorbing Potential Method to find the Resonance in Hydrogen Atom in External Magnetic field.
17.  Participated in the International conference on ‘Few Body Problem in Physics’ held in National Taiwan University, Taipei, Taiwan, from 6-10 March, 2000. Presented Poster entitled, ‘ Complex Absorbing Potential Method to study the Stark effect in Hydrogen and Lithium’.
18.  Participated in national Symposium-cum-workshop on trends in ‘Bioinformatics’ organized by Bose Institute, from March 24-27, 1998. Poster presented entitled’ Scaling exponent in a DNA walk model and implications for coding and non-coding region’.
19.  Participated in national conference on ‘Theoretical physics today’ organized by Indian Association for the Cultivation of Science from April 22-24, 1998. Posters presented entitled, (i) Self-similarity and scaling exponent for DNA walk in two and four dimensions, (ii) The calculation of the ground state energy of the positronium negative ion Ps.
20. Participated in School on Complex Systems, organized by Indian Association for the Cultivation of Science from January 30-February 2, 1995.
21.  Participated in SERC School, Puri, 23rd Jannuary-12th February, 1994.
22.  Participated in the workshop on Electronic Structures of Random Alloys, organized by S.N.Bose National Centre for Basic Sciences from November 20-December 5, 1990.  

Refresher and Orientation Course

w.Participated in UGC sponsored Refresher Course in Physics organized by Academic Staff College, University of Calcutta, from November 06-November 25,2006.
x. Participated in UGC sponsored Refresher Course in Physics organized by Academic Staff College, University of Calcutta, from July 08-July 28,2005.
y. Participated in UGC sponsored Orientation Programme in Physics organized by Academic Staff College, University of Calcutta, from August 30-September 27,2001.

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