Mahashweta Basu, Ph. D
Center for Bioinformatics and Computational Biology
3104D, Biomolecular Sciences Building
University of Maryland, College Park,
My interests include application of various machine learning, statistical and computational methods to genomic and genetic variant data to understand the synergy between regulatory mechanisms and genetic component of complex diseases. Additionally, I am also interested in various mathematical modellings, specifically application of Monte-Carlo simulations to study non-equilibrium phase transitions, transport, directed percolation, random walk. EDUCATION
2008- 2014 Ph.D. in Statistical Mechanics and Computational Biology, Saha Institute of Nuclear Physics, India. Thesis Title: ‘MicroRNA co-target networks: structure, universality and evolution’ 2007- 2008 Post. M. Sc. Associateship course, Saha Institute of Nuclear Physics, Kolkata. Project title: Kinetics of Enzyme Reaction
2005- 2007 M. Sc in Physics, University of Calcutta, India. 2002- 2005 B. Sc in Physics, Bethune College, University of Calcutta, India. AWARDS AND HONORS
2014 Gold medal award for distinguished PhD candidate, Awarded on 11th Jan 2014, 64th Foundation Day, Saha Institute of Nuclear Physics. 2008 Topper in General Annual Examination (Chemistry) held in 2003. SKILLS
Programming: Linux/Unix shell, awk, R, Python, C, FORTRAN, Mathematica, Cytoscape, Lapack. Analysis and Modeling: Mathematical Modeling (Monte Carlo simulations), Biostatistics (parametric, non- parametric), Machine Learning (Unsupervised: PCA, hierarchical clustering. Supervised: SVM, random forests, regression).
Bioinformatics Databases: GTEx, David, BioGRID, miRBase, MicroCosm Targets, GeneCodis, GeneDecks, Panther. RESEARCH EXPERIENCE
2009 – 2014, Graduate Researcher, Saha Institute of Nuclear Physics, India.
• Universality of micro-RNA co-target networks for wide class of species.
• Detection of micro-RNA groups which are disease, pathway and tissue specific.
• Exploring differential protein interaction network to identify plausible candidate loss and gain of function in Huntington Disease (mutation of HTT) and Cancer (mutation of TP53).
• Critical behavior of selected 1+1-dimensional models in “Manna class” converges to directed percolation, questioning the existence of an independent Manna class.
• Energy exchange models undergoes a clean percolation (DP) transition in presence of noise and dissipation.
• A novel approach to discontinuous bond percolation transition. ACADEMIC APPOINTMENTS
Dec 2014 – Present, Postdoctoral Research Associate, CBCB, University of Maryland, College Park, USA.
• Deciphering genetic and transcriptomic variation of individuals with complex disease and stratifying them into subgroups of comprehensive phenotype.
• Predict tissue specific gene expression in inaccessible tissues using genotype and expression in other peripheral tissue such as blood.
• Machine learning approach to predict Idiopathic dilated cardiomyopathy driver genes by integrating genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features of the genes.
• Age-associated splicing changes across human tissues and their contributions to age-associated diseases. Apr 2014 - Nov 2014, Research Associate, Saha Institute of Nuclear Physics, India.
• Identify proteins and pathways which are significantly altered in Spinal cord injury of terminal patients. PUBLICATIONS
1. N. U. Nair, A. Das, U. Amit, W. Robinson, S. G. Park, M. Basu, A. Lugo, J. Leor, E. Ruppin, S. Hannenhalli, Putative functional genes in idiopathic dilated cardiomyopathy, Scientific Reports, 8:66 (2018). 2. M. Basu, M. Sharmin, A. Das, N. U. Nair, J. S. Lee, Y. P. Chang, E. Ruppin, S. Hannenhalli, Prediction and subtyping of Hypertension from pan-tissue transcriptomic and genetic analyses, Genetics, 207, 1121 (2017). 3. M. Basu, N. P. Bhattacharyya, P. K. Mohanty, Distribution of microRNA co-targets exhibit universality across a wide class of species, Europhysics Letters, 105, 28007 (2014). 4. M. Basu, N. P. Bhattacharyya, P. K. Mohanty, Universality splitting in distribution of number of miRNA co- targets, Systems and Synthetic Biology 8, 21 (2014). 5. M. B. Sengupta, M. Basu, S. Ishwarari, K. K. Mukhopadhyay, K. Sardar, B. Acharyya, P. K. Mohanty and D. Mukhopadhyay, CSF Proteomics of Secondary Phase Spinal Cord Injury in Human Subjects: Perturbed Molecular Pathways Post Injury, PLOS ONE 9(10), e110885 (2014). 6. M. Basu, Communities of dense weighted networks: MicroRNA co-target network as an example, arXiv: 1401.3587 (2014).
7. M. Basu, N. P. Bhattacharyya, P. K. Mohanty, Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions, PLOS ONE 8(5), e64838 (2013).
8. U. Basu, M. Basu, P. K. Mohanty, Absorbing phase transition in energy exchange models, European Physical Journal B 86, 236 (2013).
9. M. Basu, U. Basu, S. Bandyopadhyay, P. K. Mohanty and H. Hinrichsen, Fixed-Energy Sandpiles Belong Generically to Directed Percolation, Physical Review Letters 109, 015702 (2012). 10. M. Basu, N. P. Bhattacharyya, P. K. Mohanty, Modules of human micro-RNA co-target network, Journal of. Physics: Conference Series 297, 012002 (2011).
11. U. Basu, M. Basu, A. Kundu, P. K. Mohanty, A novel approach to discontinuous bond percolation transition, Europhysics Letters 94, 46002 (2011).
12. M. Basu, P. K. Mohanty, Asymmetric Simple Exclusion Process on a Cayley Tree, Journal of Statistical Mechanics: Theory and Experiment P10014 (2010).
13. M. Basu, P. K. Mohanty, Two-dimensional random walk in a bounded domain, Europhysics Letters 90, 50005 (2010).
14. M. Basu, P. K. Mohanty, Stochastic Modeling of Single Molecule Michaelis Menten Kinetics, arXiv: 0901.2844 (2009).
Manuscript under review and preparation
1. M. Basu, K. Wang, E. Ruppin, S. Hannenhalli, Predictability of tissue-specific gene expression from an individual’s whole blood transcriptome, Manuscript under preparation. 2. K. Wang, M. Basu, S. Hannenhalli, Contribution of interaction of functional SNP and age to age related disease, Manuscript under preparation.
3. K. Wang, D. Wu, H. Zhang, A. Das, M. Basu, J. Malin, K. Cao, S. Hannenhalli, Comprehensive map of age- associated splicing changes across human tissues and their contributions to age-associated diseases, (Under Review) Scientific Reports.
• Biological networks: Complexities and disease, Bollenbach Group, Biological Physics and Systems, IST Austria, July 2014.
• Differential protein interaction networks, Department of Physics, University of Calcutta, India, July 2013. Poster presentations
• Differential protein interaction networks, EMBO Practical Course on Computational biology: From genomes to cells and systems, Turkey, Sep 29 -Oct 4, 2013.
• Mutations alter protein interactions leading to loss and gain of biological functions, Kolkata International School cum conference on systems biology, Bose Institute and Saha Institute of Nuclear Physics, Kolkata, India, 29th Dec 2012 - Jan 3rd, 2013
• Human microRNA co-target network, STATPHYS Kolkata VII, Saha Institute of Nuclear Physics, Kolkata, India, Nov 26 - Nov 30, 2010.
• University in microRNA co-target network, From Physics 2 Life: a workshop and school on biological physics, Weizmann Institute of Science, Israel, May 23 -May 27, 2010.
• Two-dimensional random walk in a bounded domain, ICTS program on Non-Equilibrium Statistical Physics, Indian Institute of Technology, Kanpur, India, Jan 30 -Feb 08, 2010. CONFERENCES ATTENDED
• Summer School on Integrated structural cell biology from molecules to cells and organisms, thinking out of the box held at Les Houches, France, July 7 – August 1 2014.
• EMBO Practical Course on Computational biology: From genomes to cells and systems held at Turkey, Sep 29 -Oct, 4 2013.
• From Physics 2 Life: a workshop and school on biological physics held at Weizmann Institute of Science, Israel, May 23 -May 27, 2010.
• The 2nd IMSc Complex Systems School held at The Institute of Mathematical Sciences, Chennai, India in cooperation with the Santa Fe Institute, Santa Fe, USA, Jan 4 -Jan 29, 2010.
• Quantum Phase Transition and Dynamics: Quenching, Annealing and Quantum Computation, held at Saha Institute of Nuclear Physics, Kolkata, India, Feb 3 -Feb 7, 2009.
• Systems Biology and its use held at Department of Biochemistry and Biophysics, University of Kalyani, India, Nov 18 - Nov 22, 2008.
• Summer School in Biological Physics held at Harish-Chandra Research Institute, Allahabad, India, May 26 - June 7, 2008.
• Recent Trends in Condensed Matter-II held at Saha Institute of Nuclear Physics, Kolkata, India, March 27 - March 29, 2008.
References available upon request.