Journal of Proteins and Proteomics - Call for Papers: “Deciphering Protein Conversations: A Proteomic Exploration of protein-protein Interactions”
Special Issue in: Journal of Proteins and Proteomics
Guest Editors:
Dr. Amit Kumar Yadav (THSTI)
Dr. Amit Kumar Yadav works at THSTI as Principal Scientist-II. Dr. Yadav obtained his Ph.D. in 2013 in Biotechnology (Computational Biology) from IGIB during which, he developed a novel algorithm, MassWiz, for peptide identification from mass spectrometry data, the first and only algorithm for database searching from India till now. Later, he worked on significance assessment of peptide identifications and integration of multiple search algorithm results to increase sensitivity and specificity by developing Proteome Analyst, an integrated analysis suite leveraging several in-house algorithms which was recognized for its innovative potential by MIT-TR35 award (in March 2013). He joined Translational Health Science and Technology Institute (THSTI, Faridabad) in 2013 with his interest on studying post translational modifications from mass spectrometry data.
He was awarded with Innovative Young Biotechnologist Award (IYBA) 2013 by the Department of Biotechnology (DBT). At THSTI, he works on PTMs, their interactions and crosstalk in driving protein activity, protein-protein interactions (PPIs) and evolution of biological networks in health and disease. He has developed several computational algorithms for quantitative proteomics from iTRAQ and TMT labeling techniques (QuantWiz-IQ), and devised HyperQuant tool, higher order multiplexing algorithm for analysis of complex multiplexed (18 to 72plex) proteomics data, along with tools for large-scale automated identification of PTMs in blind mode (ModST).
He has received several prestigious grants including DBT-IYBA, DBT-Big Data Initiative Grant, SERB-SUPRA grant and DBT-National Network Project. He is an Executive Council Member of Proteomics Society of India. His team at THSTI is working on creating a proteogenomic reference map of human liver by integrating genomics and proteomic data to facilitate studies on non-alcoholic fatty liver disease (NAFLD). His current interest lies in creating India’s first biomolecular knowledge-graph for studying NAFLD progression.
Dr. Trayambak Basak (IIT-Mandi)
Dr. Trayambak Basak has been working as an Assistant Professor at the School of Biosciences and Bioengineering (SBB), IIT-MANDI, Himachal Pradesh since October 2019. He completed his Ph.D on plasma proteomics and metabolomics analyses of coronary artery disease patients, from the CSIR-Institute of Genomics and Integrative Biology, New Delhi in 2015. After completion of his doctoral research, he did Postdoctoral Research on understanding the role of collagen post-translational modifications during fibrosis funded by NIDDK (NIH, USA), at Vanderbilt University Medical Centre, Nashville, TN, USA. During his Ph.D. tenure, state-of-the-art quantitative proteomics methods using iTRAQ technology were standardized and successfully implemented in CSIR-IGIB. He has also been successful in establishing data-independent acquisition (DIA-MS) proteomics workflow, SWATH, and has shown that SWATH has the capability of quantifying low abundant proteins and could be a method of choice for biomarker discovery studies. Currently, his research group is focussing on understanding the extracellular matrix (ECM) remodeling during cardiac fibrosis. Dr. Basak's group has contributed significantly to showcasing the site-specific post-translational modifications of collagen networks during cardiac fibrosis using high-resolution mass spectrometry-based proteomics. The broad aim of the group is to decipher the fibrosis-mediated mechanisms of heart failure and also to identify biomarkers for heart failure. To date, He has published 42 peer-reviewed research articles in international journals with a cumulative citation of 1113 at an ‘h-index’ of 19. He has also published a book chapter on Proteomics from the Royal Society of Chemistry, UK. He is currently the executive council (EC) member of the Proteomics Society of India (PSI) and the International Society for Heart Research-Indian Section (ISHR). His research program is currently funded by the MoE (Ministry of Education), Science and Engineering Research Board (SERB), and the Indian Council of Medical Research (ICMR), Govt. of India.
About the special issue:
Proteins, the versatile workhorses of the cell, perform crucial roles vital for life. They act as enzymes, driving biochemical reactions; offer structural support to cells; engage in cellular signaling; and participate in various cellular functions, from energy production to maintaining homeostatic balance.
However, their true power emerges when they interact with each other. Proteins rarely work in isolation and expand their capabilities by interacting with other proteins. These protein-protein interactions (PPIs) expand their functional repertoire, which can mediate complex functions and regulation of cellular metabolism beyond their normal individual capability.
However, deciphering this complex web of interactions is a huge methodological challenge, for experimental biologists and proteome-informaticians. Understanding how PPIs amplify the capabilities of individual proteins and entire cellular systems is a fascinating puzzle. Unraveling how proteins orchestrate the complex biological systems and unearth the secrets of these interactions is the key to understanding biological functions, which are tightly regulated during development and disease.
JPP encourages scientists and research groups to contribute to the special issue on “Protein-protein interactions”. JPP, an official journal of the Proteomics Society of India (PSI) is convening this call for submission of Original research articles, reviews, commentaries etc. in order to highlight the latest development in this aspect of proteomics research.
Scope of the Special Issue:
We invite the submission of original research articles, reviews, methodologies, and perspectives in the following captivating areas:
Protein Interaction Networks: the hidden patterns, network motifs, and central players in the protein interaction networks.Innovative Experimental Techniques: the latest advances in experimental methods for unveiling the secrets of protein interactions, including but not limited exclusively to mass spectrometry applications.Structural Interactomics: unravelling the structural intricacies of protein complexes, their interfaces, and how form defines function.Function Meets Interaction: investigating the interplay of protein interactions in cellular processes, signalling pathways, and regulatory mechanisms.Interactomics Data Tools: navigating through the vast sea of interactomics data using cutting-edge informatics, bioinformatics, and data analysis techniques.Disease Interactomics: highlighting the roles of protein interactions in the development or progression of diseases, from infectious to metabolic diseases, and applications in drug discovery.Omics Synergy: integrating interactomics data with genomics, proteomics, and other omics for a comprehensive understanding.Emerging Topics: Stay updated with the unfolding stories of single-cell interactomics, spatial proteomics, and multi-modal data integration.
Submission Guidelines:
Submissions should be routed through the journal's online submission portal. All manuscripts will go through a rigorous peer-review process. Don't forget to choose "Special Issue: Deciphering Protein Conversations: A Proteomic Exploration of protein-protein Interactions" when submitting.
Paper Submission deadline: 30th June 2024
Time of Publication: To be published as a special issue in September 2024