Computational Cell Biology
Welcome to the Bhaskara lab.
Our team focuses on tackling challenging problems at the interface of Cell Biology, Physics, and, Data Sciences.
We develop and apply theoretical modeling, novel computer simulations, and, data integration methods to understand complex biological systems.
Integrative Modeling
We employ state-of-the-art bioinformatics and AI methods to decode relationships between protein sequence, structure, function & Evolution. We model the 3D organization of proteins, their functional interactions (biological complexes), and post-translational modifications by integrating structural data from various experimental and computational methods.
Biomolecular Simulations
We study biological pathways involving protein-induced membrane mechanics to reveal molecular mechanisms at cellular and organellar membranes (e.g. Autophagy pathways). Within these projects, we aim at capturing the dynamics of biomolecular systems at various temporal and spatial scales in quantitative terms to (i) provide mechanistic understanding & erect testable hypotheses, (ii) guide the design of new experiments, and (iii) provide a theoretical framework for experimental observations and simulations.
Data Integration
We employ data science approaches to integrate disparate datasets effectively. We combine information from large-scale HTP datasets (Proteomic, Genetic, Chemical, and imaging) with bioinformatic predictions and publicly available repositories to mine and learn underlying biological patterns.
Fellowships, Ph.D., and Postdoc positions
Please visit the IBCii Career page for details on current vacancies and open positions.
New Postdoc position to work on Molecular Mechanisms in Selective Autophagy.
We are always looking for motivated and skilled students to join our team and pursue internships, Bachelor's, and Master's thesis projects. Please contact us directly.
Projects for Master's theses, HiWi, and internships: Please contact Dr. Ram Bhaskara for these projects.
Dr. Ramachandra M Bhaskara
Ram Bhaskara received his bachelor's degree in Chemistry and Biochemistry from Osmania University, India. He then joined the Integrated Ph.D. program in Biological Sciences at the Indian Institute of Science, India. During this period, he gained research experience in various labs (from field ecology to molecular biophysics). He then joined Prof. N. Srinivasan's group for his Master's and Ph.D. During this period, he developed novel computational tools and analysis schemes to understand the "Structure, Stability, and Evolution of Multi-domain proteins." Ram was honored with the B. H. Iyer Gold Medal for the best doctoral thesis from the Molecular Biophysics Unit (2014). He then began his post-doctoral stint with Prof. Gerhard Hummer at the Max-Planck Institute of Biophysics, Frankfurt. Ram worked on diverse membrane remodeling processes: curvature induction, budding, fusion, & poration, primarily using physics-based modeling and simulation approaches. He developed and pioneered novel simulation methods to model dynamic processes inaccessible to experiments. Ram moved to the Institute of Biochemistry II, Goethe University, in September 2020 as a team leader for Computational Cell Biology to work on Data integration problems, modeling, and simulations of complex systems. He is interested in understanding biophysical mechanisms shaping the complex cellular architecture at various scales. His research focuses on developing computational tools to analyze and decipher molecular mechanisms.
Alberto Cristiani
Alberto Cristiani studied at the University of Trieste, Italy, and graduated with a degree in Nano-Biotechnology. For his bachelor’s thesis, he worked on identifying inhibitors of Pin1 at the LNCIB laboratory, Italy. He then switched fields to study Computational Biology by joining the Master’s program in Systems Biology at Newcastle University. During this period, he acquired an interdisciplinary skillset and an interest in the quantitative modeling of biological systems. As part of his thesis, he developed a method to automatically detect a set of functional Boolean Networks within the larger gene regulatory networks. After his Master’s degree, he worked briefly as a programmer (AI and Gameplay) at Symmetrical and later as an ETL developer in the Business Intelligence unit of NTT Data, Italy. Alberto then returned to academics and is now a Ph.D. student at the Computational Cell Biology group. He is interested in computational modeling of biological systems using data science approaches and machine learning tools.
Dr. Arghya Dutta
Arghya Dutta completed his B.Sc. in Physics from the University of Calcutta, India in 2007. He then moved to S. N. Bose National Centre for Basic Sciences in Kolkata, India as an integrated Ph.D. student. He did his M.Sc. projects and Ph.D. under the supervision of Prof. Jayanta Bhattacharjee on equilibrium Ginzburg–Landau theories of imbalanced superconductors. In 2014, he joined the Institute of Mathematical Sciences in Chennai, India to do postdoctoral research on the kinetic theory of aggregation and fragmentation. In 2016, he moved to CNRS in Strasbourg, France, and worked on the properties of a nanomotor–polymer complex. During 2018–2021, he worked as a member of “BigMax—a Max Planck network on big-data-driven material science” on the topic of data mining for soft matter systems at the Max Planck Institute for Polymer Research, Mainz, Germany in the theory group of Prof. Dr. Kurt Kremer. He is broadly interested in understanding cellular processes using data-driven methods and phenomenological models.
David Krause
IT System Administrator
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Kateryna Lohachova
Kate Lohachova received her bachelor’s and master’s degrees in Chemistry from V.N. Karazin Kharkiv National University, Ukraine. During this time she worked on the ion-association process in non-liquid systems. In October 2021, she began her doctoral work looking for small-molecule inhibitors of SARS-CoV-2. In May 2022, she joined Goethe University. She is interested in modeling & simulations of membrane proteins.
N. N.
Open position for modeling and simulations of molecular events in selective ER-phagy
Plamen Kondev
Plamen Kondev is currently pursuing his Master's degree in Biochemistry, Goethe University, Frankfurt. He is a part-time intern and is interested in Reticulon proteins.
Sergio Alejandro Poveda Cuevas
Alejandro graduated in biology from the Pedagogical and Technological University of Colombia. He then studied Bioinformatics for his Master's from the University of São Paulo (USP) in 2015. During this period, he worked with Prof. Dr. Fernando Luís Barroso da Silva and studied protein complexes related to cancer. He then pursued his Ph.D. and was co-supervised by Prof. Dr. Barroso (USP) and Dr. Catherine Etchebest (Université Paris Cité). His doctoral thesis includes the study of the NS1 protein of the Zika virus where he evaluated the role of protein oligomerization, binding affinity with membrane, epitope estimates, and glycosylation in infection and virulence. Currently, he is a post-doc in the Computational Cell Biology (CCB) lab, where he is interested in the modeling and simulation of IDRs and their role in membrane remodeling events.
Past Members:
We employ diverse state-of-the-art bioinformatics, physics-based and AI methods to decode relationships between protein sequence, structure, function & Evolution. We model the 3D organization of proteins, their functional interactions (biological complexes), and post-translational modifications by integrating structural data from various experimental and computational methods.
Selected publications
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Herhaus, L., Bhaskara, R.M.†, Lystad, A.H.†, Simonsen, A, Hummer, G., Dikic, I. (2020) TBK1-mediated phosphorylation of LC3C and GABARAPL2 controls autophagosome shedding by ATG4 protease. EMBO Rep. 21: e48317
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Vögele, M., Bhaskara, R.M., Mulvihill, E., van Pee, K., Yildiz, Ö., Kühlbrandt, W., Müller, D.J., Hummer, G. (2019) Membrane perforation by the pore-forming toxin pneumolysin. Proc. Natl. Acad. Sci. USA. 116 (27) 13352-13357.
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Bhaskara, R.M., Grumati, P., Garcia-Padro, J., Kalayil, S., Covarrubais-Pinto., A., Chen, W., Kudrayshev, M., Dikic, I., Hummer, G. (2019) Curvature induction and membrane remodelling by FAM134B reticulon homology domain. Nat. Commun. 10:2370.
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D’Imprima, E., Salzer, R.†, Bhaskara, R.M.†, Sánchez R., Rose, I., Hummer, G., Kühlbrandt, W., Vonck, J., Averhoff, B. (2017) Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 6: e30483.
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Ramachandran, R., Joseph, A.P., Bhaskara, R.M., Srinivasan, N. (2016) Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA Biology 13 (10), 1025-1040
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Craveur, P., Joseph, A.P., Esque, J., Narwani, T.J., Noël, F., Shinada, N., Goguet, M., Leonard, S., Poulain, P., Bertrand, O., Faure, G., Rebehmed, J., Ghozlane, A., Swapna, L.S., Bhaskara, R.M., Barnoud, J., Téletchéa, S., Jallu, V., Cerny, J., Schneider, B., Etchebest, C., Srinivasan, N., Gelly, J.G., de Brevern A.G. (2015) Protein flexibility in the light of structural alphabets. Front Mol. Biosci. 2 (20).
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Bhaskara, R.M., Padhi, A., Srinivasan, N. (2014) Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling. Proteins: Struct., Funct., Bioinf. 82 (7), 1219-1234.
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Bhaskara, R.M., de Brevern, A. G., Srinivasan, N. (2012) Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins. J. Biomol. Struct. Dyn. 31(12), 1467-1480.
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Swapna, L.S., Bhaskara, R.M., Sharma, J., Srinivasan, N. (2012) Roles of residues in the interface of transient protein-protein complexes before complexation. Sci. Rep. 2, 334.
We study biological pathways using various simulation methods. We focus on protein-induced membrane mechanics to reveal molecular mechanisms at cellular and organellar membranes (e.g., Autophagy pathways). Within these projects, we aim at capturing the dynamics of biomolecular systems at various temporal and spatial scales in quantitative terms to (i) provide mechanistic understanding & erect testable hypotheses, (ii) guide the design of new experiments, and (iii) provide a theoretical framework for experimental observations and simulations.
Selected publications
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Reggio A., Bunomo, V., Berkane, R., Bhaskara, R. M., Tellechea, M., Peluso, I., Polischuk, E., Di Lorenzo, G., Crillo, C., Esposito, M., Hussain, A., Huebner, A.K., Settembre, C., Hummer, G., Grumati, P., Stolz, A. (2021) Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy and Collagen quality control EMBO Rep. 22: e52289.
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Ho, N. T., Siggel, M., Camacho, K. V., Bhaskara, R. M., Hicks, J. M., Yao, Y., Zhang, Y., Köfinger, J., Hummer, G., Noy, A. (2021) Membrane fusion and drug delivery with carbon nanotube porins. Proc. Natl. Acad. Sci. USA. 118, e2016974118.
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Siggel, M., Bhaskara, R.M., Moesser, M.K., Dikic, I., Hummer, G. (2021) FAM134B-RHD protein clustering drives spontaneous budding of asymmetric membranes. J. Phys. Chem. Lett. 12 (7), 1926–1931.
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Herhaus, L., Bhaskara, R.M.†, Lystad, A.H.†, Simonsen, A, Hummer, G., Dikic, I. (2020) TBK1-mediated phosphorylation of LC3C and GABARAPL2 controls autophagosome shedding by ATG4 protease. EMBO Rep. 21: e48317
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Siggel, M., Bhaskara, R.M., Hummer, G. (2019) Phospholipid scramblases remodel the shape of asymmetric membranes. J. Phys. Chem. Lett. 10 (20), 6351-6354.
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Vögele, M., Bhaskara, R.M., Mulvihill, E., van Pee, K., Yildiz, Ö., Kühlbrandt, W., Müller, D.J., Hummer, G. (2019) Membrane perforation by the pore-forming toxin pneumolysin. Proc. Natl. Acad. Sci. USA. 116 (27) 13352-13357.
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Bhaskara, R.M., Grumati, P., Garcia-Padro, J., Kalayil, S., Covarrubais-Pinto., A., Chen, W., Kudrayshev, M., Dikic, I., Hummer, G. (2019) Curvature induction and membrane remodeling by FAM134B reticulon homology domain. Nat. Commun. 10:2370.
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Bhaskara, R.M.†, Linker, S.M.†, Vöegele, M., Köfinger, J., Hummer, G. (2017) Carbon nanotubes mediate fusion of lipid vesicles. ACS Nano 11 (2), 1273-1280.
We employ data science approaches to integrate disparate datasets effectively. For example, we combine information from large-scale HTP datasets (Proteomic, Genetic, Chemical & Imaging) with bioinformatic predictions and publically available repositories to quantify data, mine and learn underlying biological patterns and uncover underlying processes.
Selected publications
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Mehrotra, P., Bhaskara, R.M., Gnanavel, M., Rakshambikai, R., Martin, J., Srinivasan, N. (2015) Classification of protein sequences with special references to multi-domain systems. J. Biomol. Struct. Dyn. 33 (sup1), 110
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Gnanavel, M., Mehrotra, P., Rakshambikai, R., Martin, J., Srinivasan, N. Bhaskara, R.M. (2014) CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins. BMC Bioinformatics.15 (343).
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Bhaskara, R.M., Mehrotra, P., Rakshambikai, R., Gnanavel, M., Martin, J., Srinivasan, N. (2014) The relationship between classification of multidomain proteins using an alignment-free approach and their functions: a case study with immunoglobulins. Mol Biosyst. 10 (5), 1082-1093.
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Bhaskara, R.M., and Srinivasan, N. (2011) Stability of domain structures in multi-domain proteins. Sci. Rep. 1, 40.
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Srinivasan, N., Agarwal, G., Bhaskara, R.M., Gadkari, R., Krishnadev, O., Lakshmi, B., Mahajan, S., Mohanty, S., Mudgal, R., Rakshambikai, R., Sandhya, S., Sudha, G., Swapna, L.S., Tyagi, N. (2011) Influence of genomic and other biological data sets in the understanding of protein structures, functions, and interactions. International Journal of Knowledge Discovery in Bioinformatics (IJKDB) 2, 24-44.
Ramachandra M Bhaskara
Email: bhaskara@med.uni-frankfurt.de
Fax: +49 69 798763-42581
Phone: +49 (0) 69 7984-2526
Ramachandra M Bhaskara
Email: bhaskara@med.uni-frankfurt.de
Fax: +49 69 798763-42581
Phone: +49 (0) 69 7984-2526
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