Kumar KYNV
Assistant Professor
Yugandhar.kamma@mahindrauniversity.edu.in
Dr. Kumar completed his PhD in computational biology from IIT Madras, where his research mainly focused on understanding protein-protein binding specificity through computational approaches. He then moved to Cornell University, USA for his postdoctoral studies to work on understanding protein-protein interaction networks using computational as well as experimental mass spectrometry-based proteomics approaches. His work has led to the development of high-impact software tools and methods, contributing to advancements in the field and earning recognition through publications in top-tier scientific journals and a US patent.
Ph.D.
- IIT Madras (Computational Biology): 2011-2016
M.Sc
- University of Madras (Bioinformatics): 2008-2010
2022 - 2024
- Research Associate, Cornell University, USA, (2022 – 2024).
2016 - 2022
- Postdoctoral Associate, Cornell University, USA,(2016 – 2022).
Publications
2023
- Nikam R, Kumar Y. and Gromiha M.M. (2023) Deep learning-based method for predicting and classifying the binding affinity of protein-protein complexes. BBA - Proteins and Proteomics, 1871, 14098.
- Nikam R, Kumar Y. and Gromiha M.M. (2023) DeepBSRPred: deep learning-based binding site residue prediction for proteins. Amino Acids, https://doi.org/10.1007/s00726-022-03228-3.
2021
- Furman CM, Wang TY, Zhao Q, Kumar Y, Yu H. and Alani E. (2021) Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair. Nucleic Acids Research, 49, 9327-9341.
- Joiner A.M.N, Phillips B.P, Kumar Y, Sanford E.J, Smolka M.B, Yu H, Miller E.A. and Fromme J.C. (2021) Structural basis of TRAPPIII-mediated Rab1 activation. The EMBO Journal, 40:e107607.
- Kumar Y#, Zhao Q#, Gupta S#, Xiong D#. and Yu H. (2021) Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics, 21, 2100145 (#Equal Contribution).
- Lanz M.C#, Kumar Y#, Gupta S, Sanford E, Faça V, Vega S, Joiner A, Fromme C, Yu H. and Smolka M.B. (2021) In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome. EMBO Reports, 22, e51121 (#Equal Contribution).
2020
- Kumar Y, Wang Ting-Yi, Wierbowski S.D, Shayhidin E.E. and Yu H. (2020) Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. Nature Methods, 17, 985-988.
- Kumar Y# Wang Ting-Yi.#, Leung A.K.Y., Lanz, M.C., Motorykin, I., Liang, J., Shayhidin, E.E., Smolka, M.B., Zhang, S. and Yu, H. (2020) MaXLinker: proteome-wide cross-link identifications with high specificity and sensitivity. Molecular & Cellular Proteomics, 19, 554-568 (#Equal Contribution).
- Jemimah S#, Kumar Y# and Gromiha MM. (2020) Binding affinity of protein-protein complexes: experimental techniques, databases and computational methods. Book chapter in ‘Protein interactions: Computational methods, analysis and applications’, World Scientific, 87-108 (#Equal Contribution).
2019
- Kumar Y#, Gupta S# and Yu H. (2019) Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: a mini-review. Computational and Structural Biotechnology Journal, 17, 805-811 (#Equal Contribution).
2018
- Nikam R#, Kumar Y# and Gromiha MM. (2018) Discrimination and prediction of protein-protein binding affinity using deep learning approach. International Conference on Intelligent Computing, Springer, 809-815 (#Equal Contribution).
2017
- Kumar Y. and Gromiha MM. (2017) Computational approaches for predicting binding partners, interface residues and binding affinity of protein-protein complexes. Methods in Molecular Biology, 237-253.
- Jemimah S, Kumar Y. and Gromiha MM. (2017) PROXiMATE: a databse of mutant protein-protein complex thermodynamics and kinetics. Bioinformatics, doi: 10.1093/bioinformatics/btx312
- Gromiha MM, Kumar Y. and Jemimah S. (2017) Protein-protein interactions: scoring schemes and binding affinity. Current Opinion in Structural Biology, 44, 31-38.
- Gromiha MM. and Kumar Y. (2017) Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes. Progress in Biophysics and Molecular Biology, 128, 33-38.
- Kulandaisamy A, Lathi V, ViswaPoorani K, Kumar Y. and Gromiha MM. (2017) Important amino acid residues invoved in folding and binding of protein-protein complexes. International Journal of Biological Macromolecules, 94, 438-444.
2016
- Kumar Y. and Gromiha MM. (2016) Analysis of protein-protein interaction networks based on binding affinity. Current protein & Peptide Science, 17, 72-81.
2014
- Kumar Y. and Gromiha MM. (2014) Protein-protein binding affinity prediction from amino acid sequence. Bioinformatics, 30, 3583–3589.
- Kumar Y. and Gromiha MM. (2014) Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches. Proteins, 82, 2088–2096.
Patent(s)
2022
- Large-scale mapping of protein-protein interactions from crosslinking mass spectrometry. 2022, US Patent granted, US11215621B2 (Contribution: Inventor).
Research areas of interest:
- Proteomics
- Systems Biology
- Bioinformatics and computational biology
- Regulatory mechanisms of protein interactions
- Structural Biology
- Protein interaction networks
