Home Page of Dr. Losiana Nayak

Dr. Losiana Nayak
UGC Post-Doctoral Fellow
Machine Intelligence Unit
Indian Statistical Institute
Kolkata -700108

Research Interests

• Bioinformatics, Computational Biology, Network Biology, Metabolomics, Computational Phylogeny, Signal Transduction Pathways, Omics study of diseases, Neuroinformatics, Health Informatics and Clinical data analysis, and Pathogen Informatics.

Recent Research Activity

Awarded a Post Doctoral Fellowship by University Grants Commission, New Delhi, India for a project titled, "Prediction of system states of Signal Transduction Pathways using Boolean Logic" starting from the year 2013-2014 and valid for 5 years.

PhD (in Biophysics, Molecular Biology and Bioinformatics) for a thesis titled "Computational Methodologies for Modularization of some Biochemical Pathways: Analysis and Annotation" in Calcutta University, Kolkata, India on 3rd June 2013. Research work done at Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India. Download link for thesis

Supervisor: Dr. Rajat K. De, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal, India.

Education

• PhD (Bio-Physics, Molecular Biology and Bioinformatics) – 2008 to 2013 – Department of Bio-Physics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
• Student (DBT Fellowship) – 2004 to 2005 – BTIS, Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India.
• MSc (Bioinformatics) – 2002 to 2004 – Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India.Download link for thesis
• B. Sc (Zoology Hons.) – 1999 to 2002 – Fakir Mohan Autonomous College, Baleswar, Odisha, India.

Work Experience

• May 2014 to till date- UGC Post Doctoral Fellow, Machine Intelligence Unit, Indian Statistical Institute, Kolkata.
• June 2011 to March 2012- Project Linked Personnel, Machine Intelligence Unit, Indian Statistical Institute, Kolkata.
• April 2008 to March 2011- CSIR Senior Research Fellow [Direct], Machine Intelligence Unit, Indian Statistical Institute, Kolkata.
• August 2005 to March 2008- Project linked personnel, Machine Intelligence Unit, Indian Statistical Institute, Kolkata.
• April to August 2005- Bioinformatics studentship, Central Institute of Freshwater Aquaculture, Orissa.
• Feb. and March 2005- Guest faculty, Sri Padmavati Mahila Viswa Vidyalayam, Andhra Pradesh.
• May to October 2004- Trainee for doing M. Sc. (Bioinformatics) dissertation, Indian Statistical Institute, Kolkata.

List of Journal Publications

• L.Nayak and R. K. De,"Precision Oncology with Electronic Medical Records", EMJ Innovations, vol. 2, no. 1,pp. 64-72, 2018.
• L.Nayak, I. Ray and R. K. De,"Precision medicine with electronic medical records: from the patients and for the patients", Annals of Translational Medicine, vol. 4, supp. 1,S61, 2016.
• R. Sen, L. Nayak and R. K. De, "A review on host-pathogen interactions: classification and prediction", European Journal of Clinical Microbiology & Infectious Diseases, pp. 1-19, 2016.
• L. Nayak, N. P. Bhattacharyya, and R. K. De, "Wnt signal transduction pathways: modules, development and evolution", BMC Systems Biology, vol. 10, no. 2, pp. 44, 2016.
• L. Nayak, H. Tunga and R. K. De, "Disease Comorbidity and the Human Wnt Signaling Pathway: A network-wise Study", OMICS: A Journal of Integrative Biology, vol. 7, no. 6, pp. 318-337, 2013. Link to The Human Wnt Diseasome Database
• N. Tomar, L. Nayak and R. K. De, "Comparative analysis of various modularization algorithms and species specific study of VEGF signaling pathways", Journal of Biomedical Science and Engineering, vol. 3, no. 10, pp. 931-942, 2010.
• L. Nayak and R. K. De, "An algorithm for modularization of MAPK and Calcium signalling pathways: Comparative analysis among different species ", Journal of Biomedical Informatics, vol. 40, pp. 726-749, 2007.
• L. Nayak and R. K. De, "Modularized Study of Human Calcium Signaling Pathway", Journal of Biosciences, vol. 32, no. 5, pp. 1009-1017, 2007.

List of Conference Publications

• A. Dasgupta, L. Nayak, R. Das, D. Basu, P. Chandra and R. K. De, "Feature Selection and Fuzzy Rule Mining for Epileptic Patients from Clinical EEG Data", in Proceedings of the 7th International Conference Pattern Recognition and Machine Intelligence (PReMI'17), Kolkata, India, pp. 1-9, 2017.
• L. Nayak, Niati P. Bhattacharyya and R. K. De, "A Module tree of Wnt Signaling Pathways", in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'2015), Washington DC, USA, pp. 43-48, 2015.
• A. Dasgupta, R. Das, L. Nayak, and R. K. De, "Analyzing epileptogenic brain connectivity networks using clinical EEG data", in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'2015), Washington DC, USA, pp. 815-821, 2015.
• L. Nayak and R. K. De, "Finding better partitions and conserved modules in Wnt signaling pathways", in Proceedings of the 2012 International Conference on Bioinformatics and Computational Biology (BIOCOMP'12), Las Vegas, Nevada, USA, pp. 89-95, 2012.
• L. Nayak and R. K. De, "Developmental trend derived from modules of Wnt Signaling Pathways", in Proceedings of the 4th International Conference Pattern Recognition and Machine Intelligence (PReMI'11), Moscow, Russia, pp. 400-405, 2011.
• R. K. De and L. Nayak, "MAPK signaling pathways and their recursive modularization", in Proceedings of the 15th International Conference on Computing (CIC'06), Mexico City, Mexico, 2006, pp. 203-208.

List of Book Chapter Publications

• L. Nayak, A. Datta and R. K. De, "Prediction of System States, Robustness and Stability of the Human Wnt Signal Transduction Pathway using Boolean Logic", in BIOMAT 2015: International Symposium on Mathematical and Computational Biology, pp. 177-191. 2016, World Scientific, ISBN: 978-981-3141-90-2, 2016.
• L. Nayak, N. Tomar and R. K. De, "Computational Phylogeneticity of Biological Pathways: A developmental study of TCA cycle over a set of organisms", in book Recent Trends in Computational Biology and Computational Statistics Applied in Biotechnology and Bioinformatics, chapter 14, pp. 337-369, 2011, New India Publishing AGENCY (NIPA), New Delhi, India.

List of Poster Publications

• R. Sen, L. Nayak and R. K. De, "Classification, Prediction and Analysis of Type VI Secreted Effector Proteins", in HFP2017 Advanced Lecture Course on Molecular Mechanisms of Host-Pathogens Interactions and Virulence in Human Fungal Pathogens, La Colle sur Loup, France, pp. 144, 2017. (Published as abstract)
• R. Sen, L. Nayak and R. K. De, "Signature Pattern Mining of Type VI Effector Proteins", in EMBO Global Exchange Lecture Course on Malaria genomics and public health, Madurai, India, pp. 144, 2017. (Published as extended abstract)
• L. Nayak and R. K. De, "Prediction of System States of Signal Transduction Pathwaus Using Boolean Logic", in Indo-Us Workshop on Biocomputing, Calicut, India, 2011. (published as electronic extended abstract)
• L. Nayak and R. K. De, "Modularization of Signal Transduction Pathways: detecting the trend of development among various species", in Proc. of 3rd Young Researchers Conference on Computational and Omics Biology (AYRCOB'10), National Cheng Kung University, Tainan, Taiwan, pp. 52, 2010. (Published as extended abstract)
• L. Nayak and R. K. De, "From modules to diseasome: Human Wnt signaling pathway", in 4th Workshop of the Seattle-India Joint Research Training Program on Intracellular Pathogens, Goa, India, pp. 40, 2010. (published as abstract)
• R. K. De and L. Nayak, "Understanding Wnt cascades through modularization", in Proc. of HUGO's 13th Human Genome Meeting (HGM'08), Hyderabad, India, 2008. (Published as abstract)
• L. Nayak and R. K. De, "Modularized study of human calcium signaling pathway", in Proc. International Conference on Bioinformatics (INCOB’06), New Delhi, India, 2006. (Published as abstract)

Research Activity

Presented...

• A hands-on session titled "Cytoscape: A tool for gene annotation and much more..." in Workshop on Machine Learning held at The Centre of Excellence in Systems Biology and Bio medical Engineering, University of Calcutta, Kolkata, India during July 11-16, 2016.
• A hands-on session titled "Cytoscape and Gene Ontology for Network Visualization and Gene Annotation" in Summer School on Soft Computing Paradigm and Machine Intelligence Techniques held at Assam Don Bosco University, Guwahati, India in collaboration with Indian Statistical Institute during July 07-10, 2016.
• A hands-on session titled "An Introduction to Cytoscape: Diseasome Construction,"in ISI-NIT SILCHAR Spring School on Computational Biology: Tools and Techniques. March 20-24, 2015. National Institute of Technology, Silchar, Assam, India.
• A talk titled "Modularization of Signal Transduction Pathways: detecting the trend of development among various species" in 3rd Young Researchers Conference on Computational and Omics Biology (AYRCOB'10). March 10-12, 2010. National Cheng Kung University, Tainan, Taiwan.
• A talk titled "Context based literature mining to create pathway specific diseasome" in 4th Workshop of the Seattle-India Joint Research Training Program on Intracellular Pathogens. February 2-7, 2010. International Centre, Goa, India.
• Student talk titled "A graph theoretic Method for comparing TCA cycles of some species" in Computational Insights into Biological Systems, InCoB 2006: Satellite Meeting. December 26-28, 2006. Indian Institute of Science, Bangalore, India.
• Lectures on "Introductions to Biochemistry" and "Introduction to Molecular Biology" in seminar on "Computational Paradigms in Bioinformatics Research". March 31-April 1, 2006. Netaji Subhash Engineering College, Kolkata, India.
• Short talk on "Derivation of Graphs from Metabolic Pathways: Similarity Computation" in national seminar on "Frontier Bioinformatics Tools in Genome & Proteome Analyses." March 14-15, 2005. Orissa University of Agriculture and Technology, Bhubaneswar, Orissa, India.

Attended...

• National Workshop on Introduction to Next Generation Sequencing, November 9-11, 2016, Bioinformatics Infrastructure Facility, Deaprtment of Biochemistry and Biophysics, University of Kalyani, West Bengal, India.
• 2015 IEEE International Conference in Bioinformatics and Biomedicine (BIBM'2015). November 9-12, 2015, Washington DC, USA.
• 15th International Symposium on Mathematical and Computational Biology (BIOMAT 2015). November 1-7, 2015, Indian Institute of Technology, Roorkee, Uttarakhand, India.
• Training/Workshop@SCFBio. July 14-23, 2015, Indian Institute of Technology, Delhi, India.
• SERB School in Neuroscience, 8th Edition (Brain Circuits). December 8-21, 2014, Indian Institute of Science Education and Research, Pune, Maharastra, India.
• Document Freedom Workshop (DFW'12). March 28-29, 2012, Indian Statistical Institute, Kolkata, India.
• Indo-US Workshop on Biocomputing(ISB'11). September 12-13, 2011, National Institute of Technology, Calicut, India and Perdue University Indiana University, Indianapolis, USA.
• Fourth International Conference on Pattern Recognition and Machine Intelligence (PReMI'11). June 27-July 1, 2011, Higher School of Economics, Moscow, Russia.
• Third Young Researchers Conference on Computational and Omics Biology (AYRCOB'10). March 10-12, 2010, National Cheng Kung University, Tainan, Taiwan.
• Fourth Research Training on Intracellular Pathogens. 2-7 February, 2010, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India and Seattle Biomedical Research Institute, Washington, USA (held at International Centre, Goa, India)
• Second Practical Summer Training Course on "Molecular Biology Techniques". May 27-3 June, 2009, School of Biotechnology, Chemical and Biomedical Engineering, VIT University, Vellore, Tamilnadu, India.
• Fourth Workshop on "Genetic Epidemiological Methods for Dissection of Complex Human Traits." February 23-28, 2009, TCG-ISI Centre for Population Genomics (CpG) and University of Pittsburgh, U.S.A. (held at SINP, Kolkata, India)
• National workshop on "Current trends in Evolutionary Biology." February 17-20, 2009. Bioinformatics Infrastructure Facility (BIF), Kalyani University, West Bengal, India
• Second International Conference on "Pattern Recognition and Machine Intelligence (PreMI'07)." December 20-22, 2007, Indian Statistical Institute, Kolkata, India
• Winter School on "Soft Computing Tools, Simulation and Applications." January 10-14, 2006. Indian Statistical Institute, Kolkata, India
• International Workshop on "Algorithms (IWA 2005)." December 15-16, 2005. Indian Statistical Institute, Kolkata, India
• AICTE Approved Short Term Course on " Computational Intelligence and its Applications." May 16-27, 2005. National Institute of Technology, Durgapur, West Bengal, India
• Sixth International Conference on "Information Technology [Bioinformatics Tutorial]." December 22-25, 2003. Orissa information Technology Society, Silicon Institute of Technology, Orissa, India
• National Workshop cum Training on "Bioinformatics Tools for Gene & Protein Analysis." August 9-12, 2003. Sri Krishnadevraya University, Anantapur, Andhra Pradesh, India
• Workshop on "Data Mining Application in Bioinformatics." March 19-21, 2003. Indian Institute of Science, Bangalore, Karnataka, India
• A Continuing Medical Education Programme in Immunology. November 26, 2002. Regional Medical Research Centre (ICMR), Bhubaneswar, Orissa, India

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Contact :

losiananayak[at]gmail[dot]com
updated on 9th May 2018