Faculty

Faculty Details


Faculty Details

  • Name: Dr. Seema Mishra
  • Mail: smsluohyd.ernet.in
  • Contact:
  • Area Of Research:Our field of research lies in Computational and Systems Biology. We use these futuristic approaches in analyzing big data in cancers and infectious diseases using a variety of tools ranging from machine learning (neural network) to interaction network studies to molecular dynamics. Specifically, our aim is to identify and establish interrelationships between coding (mRNA) and long non-coding (lncRNA) genes playing a key role in pan-cancer development and progression. Their roles in pan-cancer drug resistance and sensitivity are also being analyzed to understand the molecular mechanisms and propose key regulatory paradigms. LncRNA structure-function studies in order to deduce function of unknown lncRNAs are also one of the many aims. We also use molecular dynamics simulations to understand structural basis of drug-protein target interactions in cancer, and putting forward inside views of the domain movements and essential conformational changes. In the case of infectious diseases such as M. tuberculosis infection, we use gene expression and other molecular big data to interrogate molecular mechanisms and identify suitable, novel drug targets. Applying immunoinformatics approaches to kickstart epitope-based vaccine development in SARS-CoV2 has also been one of our frontrunner programs.


Blog: https://seemauoh.wordpress.com/

Study:

B.Sc Botany (Hons.), Delhi University, 1991

M.Sc Biotechnology, Banaras Hindu University, 1993

Ph.D Molecular Biology, National Institute of Immunology, New Delhi, 2000

Certificate course in Bioinformatics and Computational Biology, Indian Institute of Technology-Delhi, 2004

GATE-93 qualified (96.63 percentile)

CSIR-UGC NET 1993 qualified


Work:

Assistant Professor, University of Hyderabad, India since year 2010

Scientist Gr-III, MoHFW Inst (2006-2010)

SRF, AIIMS, New Delhi (2005-2006)

Knowledge Scientist, Wipro-Spectramind Ltd. (2000-2004)


International places visited:

1. Columbia University, New York City, under DBT-CREST award

2. State University at Albany, New York

3. ETH Zurich, Switzerland (Einstein's alma mater)


Teaching:

Basics in Bioinformatics and Computational Biology- I semester M.Sc Biochemistry, 3 credits
Molecular Mechanics, Molecular Dynamics, In-silico Drug Designing- M.Tech Bioinformatics and VIII semester IMSc Systems Biology, 2 credits
Proteomics Elective- III semester M.Sc Biochemistry, 2 credits
Wet Laboratory Practicals in Molecular Biology- II semester M.Sc Biochemistry, Total 6 credits Biochemical Techniques Lab course
Biochemical Techniques-II lab- 3 credits
Biochemical Techniques-IV lab- 1.5 credits
Introduction to Bioinformatics Elective- III semester M.Sc Biochemistry, 2 credits
Comparative Systems Modeling lab-IX semester IMSc Systems Biology, 2 credits
Structure and Function of Biomolecules-IV semester IMSc Systems Biology combined with IMSc students of Physics, Chemical Sciences and Mathematical Sciences- 1.5 credits

Foundation Course in Basics in Bioinformatics and Computational Biology- Foundation Course-II semester IMSc, MSc, MA, 3 credits
M.Sc Biochemistry Projects every year- 8 credits
IMSc Systems Biology project- 18 credits combined in two semesters
Comparative Systems Modelling-IX semester IMSc Systems Biology, Markov Chains and hidden Markov model-4 credits, Synthetic Biology-8 credits
Biostatistics-II Semester M.Sc Biochemistry, 2 credits


Achievements and Awards:

DBT-CREST Award to work at Department of Systems Biology, Columbia University, New York City on the project "Interrogation and analyses for driver genes involved in drug sensitivity/resistance in lung adenocarcinoma"


Awarded Certificate of Merit in English Core in Senior Secondary School Certificate Examination, CBSE in Science in year 1988


Passed GATE-93 in General Sciences with 96.63 percentile score.


Qualified CSIR-UGC NET in year 1993 in Life Sciences. Awarded Fellowship.


Awarded Department of Biotechnology, Govt. of India Scholarship during M.Sc. (Biotechnology) from 1991-1993.


Invited Grants Peer Reviewer:

DST-SERB Extra Mural Research Funding (Individual Centric) research grants almost every year
One DST-SERB IMPacting Research, INnovation and Technology (IMPRINT-2) grant

Invited Journal Peer Reviewer:
Patterns (Cell Press)

Scientific Reports (Springer Nature)
Infection, Genetics and Evolution (Elsevier)
Gut Pathogens (Springer Nature)
Infection, Genetics and Evolution (Elsevier)
RSC Advances Royal Society of Chemistry
BMC Immunology
BMC Genomics (Springer Nature)
Computational Biology and Chemistry (Elsevier)
Molecular Informatics (Wiley Wiley-VCH Verlag GmbH & Co.)
Briefings in Bioinformatics (Oxford University Press)
BMC Bioinformatics (BMC)
Tumor Biology (Springer)

PLoS One (PloS)
Journal of Molecular Graphics and Modeling (Elsevier)
Molecular Biology Reports (Springer)
Journal of Biomolecular Structure and Dynamics (Taylor and Francis Journals)

Journal of Biosciences (Indian Academy of Sciences)
Current Bioinformatics (Bentham Science Publishers)
Journal of Immunological Methods (Elsevier)















No Records Available

Students/Projects Trainees

Name Joined As Mail Contact
Dr. Santosh Kumar Ph.D --- ---
Ms. K. Praveena Ph.D --- ---
Ms. Euphinia Tiberius Ph.D --- ---
Mr. B H Raghunandan Ph.D --- ---

Former Students/Projects Trainees

Name Joined As Working
Dr. A. Saleembhasha Ph.D NIH, USA for Post-doc
Ms. Soumi Mukherjee M.Sc Purdue University for Ph.D
Dr. Sagara N. S. Gurusinghe M.Sc Hebrew University of Jerusalem, Israel, for his Ph.D. Defended successfully in May 2023.
Dr. Rituparna Bhattacharjee M.Sc Ph.D from Otto-von-Guericke-University Magdeburg
Dr. Amita Pal M.Sc Ph.D from UoH
Dr. S. Niranjan M.Sc Ph.D from UoH
Mr. Pankaj Kumar Chauhan IMSc NCBS for his PhD
Dr. Kesaban Ph.D Penn State University, USA for Post-doc
Many other M.Sc students have done their dissertations from our lab. M.Sc
26 Imliyangla Longkumer, Seema Mishra (2022) , Structure–function relationship of long noncoding RNAs: Advances and challenges , Wiley Interdisciplinary Reviews (WIREs) Computational Molecular Science , https://doi.org/10.1002/wcms.1609, Wiley,e1609,, IF - Impact factor 25.113.
25 Santosh Kumar and Seema Mishra (2022) , MALAT1 as master regulator of biomarkers predictive of pan-cancer multi-drug resistance in the context of recalcitrant NRAS signaling pathway identified using systems-oriented approach. , Scientific Reports (Nature Publishing Group), ,12,,7540.
24 Seema Mishra (2022) , Computational Structural and Functional Analyses of ORF10 in Novel Coronavirus SARS-CoV-2 Variants to Understand Evolutionary Dynamics , Evol Bioinform Online, SAGE,18:11769343221108218,,doi: 10.1177/11769343221108218.
23 Mishra S, Kumar S et al. (2021) , Structural exploration with AlphaFold2-generated STAT3a structure reveals selective elements in STAT3a-GRIM-19 interactions involved in negative regulation , Scientific Reports https://doi.org/10.1038/s41598-021-01436-7, Nature Publishing Group,11,23145 ,.
22 Mishra S (2020) , T Cell Epitope-Based Vaccine Design for Pandemic Novel Coronavirus 2019-nCoV , ChemRxiv doi.org/10.26434/chemrxiv.12029523.v1, ,,,.
21 Mishra S (2020) , ORF10: Molecular Insights into the Contagious Nature of Pandemic Novel Coronavirus 2019-nCoV , ChemRxiv, doi.org/10.26434/chemrxiv.12118839.v3, ,,,.
20 Mishra S (2020) , Designing of Cytotoxic and Helper T Cell Epitope Map Provides Insights into the Highly Contagious Nature of the Pandemic Novel Coronavirus SARS-CoV2 , ChemRxiv, doi.org/10.26434/chemrxiv.12253463.v1, ,,,.
19 KS Roy Choudhuri and Seema Mishra (2020) , Structural basis of BMP-2 and BMP-7 interactions with antagonists Gremlin-1 and Noggin in Glioblastoma tumors , Journal of Computational Chemistry, Wiley,41,,2544–2561.
18 Mishra, S (2020) , Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2 , Royal Society Open Science, Royal Society Publishing ,7:201141,,.
17 A. Saleembhasha and Seema Mishra (2019) , Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach. , PeerJ, ,,7:e6388,.
16 KRD Sagara NS Gurusinghe, A Mishra and Seema Mishra (2018) , Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: Molecular dynamics studies. , Scientific Reports, ,,8:5487,.
15 Saleembhasha A, Mishra S. (2017) , Novel molecules lncRNAs, tRFs and circRNAs deciphered from Next Generation Sequencing/RNA Sequencing: computational databases and tools. , Briefings in Functional Genomics, Oxford University Press,1-11,,.
14 Seema Mishra, Seyed E Hasnain (2017) , “Future of Biology: Challenges and Opportunities” , Insights on Global Challenges and Opportunities for the Century Ahead, Edited by: V. Dashavantha Reddy, K. Venkateswara Rao and K. Rama Krishna, Osmania University Centenary Celebrations, ,,ISBN: 978-93-5230-185-0,199-201.
13 Seema Mishra, D.S. Negi and Seyed E. Hasnain (2016) , DNA Fingerprinting: Principles and Applications. , Text Book of Biochemistry, Biotechnology, Allied and Molecular Medicine, Prentice Hall of India ISBN: 978-81-203-5125-7.,,,834-840.
12 Seema Mishra* and Syed Asad Rahman (2016) , Bioinformatics, Genomics, Proteomics and Metabolomics in Biomedical Research. , Text Book of Biochemistry, Biotechnology, Allied and Molecular Medicine, Prentice Hall of India ISBN: 978-81-203-5125-7,,,1549-1558.
11 Khushboo Irshad, Saroj Kant Mohapatra, Chitrangda Srivastava, Harshit Garg, Seema Mishra, Bhawana Dikshit, Chitra Sarkar, Deepak Gupta, Poodipedi Sarat Chandra, Parthaprasad Chattopadhyay, Subrata Sinha, Kunzang Chosdol. (2015) , A Combined Gene Signature of Hypoxia and Notch Pathway in Human Glioblastoma and Its Prognostic Relevance. , PLoS One, ,10(3): e0118201,,.
10 Rituparna Bhattacharjee, Arpita Devi and Seema Mishra (2015) , Molecular docking and molecular dynamics studies reveal structural basis and selectivity of inhibitors EGCG and OSU-03012 towards Glucose Regulated Protein-78 (GRP78) overexpressed in Glioblastoma. , Journal of Molecular Modeling , Springer,21:272,,.
9 Itishri Sahu, Seema Mishra, Rambabu Undi , Ravinder Kandi and Ravi Kumar Gutti (2015) , Wnt canonical and non-canonical pathways: Sequence and Structural difference favors a distinct preference of Wnt3a binding with co-receptor LRP6. , Journal of Biomolecular Structure and Dynamics (DOI: 10.1080/07391102.2014.991352 ), ,33,,2133-44.
8 Itishri Sahu, Seema Mishra, Rambabu Undi , Ravinder Kandi and Ravi Kumar Gutti (2015) , Wnt canonical and non-canonical pathways: Sequence and Structural difference favors a distinct preference of Wnt3a binding with co-receptor LRP6. , Journal of Biomolecular Structure and Dynamics (DOI: 10.1080/07391102.2014.991352 ), ,33,,2133-44.
7 Seema Mishra and Subrata Sinha (2014) , Immunoinformatics, molecular modeling and cancer vaccines. , Methods in Molecular Biology, Humana Press/Springer,1184,,513-521.
6 Seema Mishra (2014) , CSNK1A1 and Gli2 as novel targets identified through an integrative analysis of gene expression data and protein-protein interaction and pathways networks in Glioblastoma tumors: can these two be antagonistic proteins? , Cancer Informatics , ,13,,93-108.
5 Sureshkumar Chalapareddy; Mrinal K Bhattacharyya**; Seema Mishra**; Sunanda Bhattacharyya, **Equal contribution (2014) , Radicicol confers mid schizont arrest by inhibiting mitochondrial replication in Plasmodium falciparum. , Antimicrobial Agents and Chemotherapy, American Society for Microbiology , ,58,,4341-52..
4 Seema Mishra (2013) , Protein Folding: Still an enigma in the time of eHow.com. , Journal of Biomolecular Structure and Dynamics, DOI:10.1080/07391102.2012.748534. , ,31,,976-977.
3 Seema Mishra (2012) , Life? , Journal of Biomolecular Structure and Dynamics , ,29,,633-634.
2 Seema Mishra (2012) , Computational prediction of protein-protein complexes. , BMC Research Notes, ,5,,495.
1 Seema Mishra (2011) , “Chargaff’s Rules” For Protein Folding: Stoichiometric Leitmotif Made Visible. , Journal of Biomolecular Structure and Dynamics , ,28,,649-652.

Bioinformatics and Systems Biology Laboratory