DR.AMIT KUMAR YADAV
Ph.D.
PRINCIPAL SCIENTIST-II
- Ph.D. Biotechnology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- M.Sc. Botany, Delhi University
- B.Sc.(Hons.) Botany, Delhi University
Research Interest
My research objective is to understand how the functionality of genetic code is expanded by various post-translational modifications (PTMs) and study the “PTM code” which provides an additional layer of encoding to the heredity information. How do various PTMs and their stoichiometric interplays decide the cell fate and homeostasis? Is this PTM memory conserved and heritable?
My research focus is to understand the patterns of regulatory networks of PTM, their role in modulating protein-protein interactions, cross-talk among different PTMs and their evolution. These studies can help form a framework towards devising predictive models of PTM cross-talk in health and disease with respect to disease development and progression.
By leveraging the power of proteomics, genomics, and computational analysis, we strive to unravel the intricate molecular mechanisms underlying metabolic diseases and pave the way for improved diagnostics, therapies, and personalized medicine approaches.
Other Interests
I am interested in big data in biomedicine, leveraging AI/ML, high throughput data analysis, statistics, data visualization and using computer science methods in biological research and metabolic disorders, social and biological networks.
Awards and Fellowships
- Innovative Young Biotechnologist Award (IYBA) 2013, (Mar 2014)
- Awarded “Innovators Under 35 2013” (TR35) in India by MIT Technology Review, March 2013
- Young Scientist Travel Award from DST (Sep 2011)
- CSIR-JRF, June 2007 (Top 25)
- GATE qualified, Feb 2007
- CSIR-JRF, December 2006
Scientific Memberships
- Elected Executive Council (EC) Member of Proteomics Society, India (PSI), 2023-2025
- Member of Proteomics Society of India (PSI Lifetime member), 2016 onwards
- Associate Member of Human Proteome Organization (HUPO), 2016 onwards
- Member of Human Proteome Organization(HUPO), 2011
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Review Editor for “Frontiers in Bioinformatics and Computational Biology” section for following Journals -
- Frontiers in Genetics
- Frontiers in Plant Science
- Frontiers in Bioengineering and Biotechnology
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Topic Editor for special topic “Post-Translational Modifications - The Dark Matter of Biology in Health and Disease” with following participating journals :
- Frontiers in Genetics
- Frontiers in Physiology
- Frontiers in Applied Mathematics and Statistics
- Frontiers in Neuroscience
Invited Talks
- Proteomics and Proteogenomics: Piecing Together the Molecular Puzzle. 19th Nov 2024. Workshop and Education Day (at BRIC-NCCS), 16th Annual Meeting of Proteomics Society, India titled “Integrated Omics Approaches for Decoding Biological Research.”, November 18-23, 2024, CSIR-NCL, Pune.
- Transforming Precision Medicine with Data-Driven Proteomics and Proteogenomics. 1st Nov 2024. OMICS Series, BioCrats Club, Department of Biosciences and Biomedical Engineering, IIT Indore.
- Advancing precision medicine through clinical proteomics and proteogenomics. 20th Aug 2024. National Symposium and Workshop on Clinical Proteomics” from August 20-23 at ILS, Bhubaneswar.
- False Discovery Rate in proteomics and proteogenomics. 21st Aug 2024. National Symposium and Workshop on Clinical Proteomics” from August 20-23 at ILS, Bhubaneswar.
- Unlocking the Dark Proteome- Illuminating the Path to Disease Understanding through PTMs and Proteoforms.31st Jan 2024. ICMR Workshop on Genomics and Proteomics Data Analysis on January 30-31, 2024. ICMR Headquarters, New Delhi.
- Studying Liver Proteoforms: Bridging Chemistry, Biology, and Computational Sciences.27th Jan 2024. International Conference on Chemical and Biological Sciences (ICCBS) (online), 27th January, 2024 to 29th January, 2024.Atma Ram Sanatan Dharma College, University of Delhi, New Delhi.
- Charting Liver Proteoforms: A Computational Approach Using Mass Spectrometry Data. 21st Nov 2023. 15th Annual meeting of Proteomics Society, India: International Conference on Integrated Proteomics: Application in food, Nutrition & Health. NIPGR, New Delhi, November 20-22, 2023
- Proteomics- a primer. 16th Sep 2023, Pancreas 2023- International joint meeting of the International Association of Pancreatology and Indian Pancreas Club, at New Delhi, from 15th - 17th September 2023.
- Listening to the war cry of the immune system using a novel multiplexing technique.28th Aug 2023, Amity Institute of Biotechnology, Amity University, Mumbai.
- Of proteins, peptides and PTMs: integrating methods for studying diseases. 29th April 2023, One-day symposium on data-driven approaches to understand biological systems, CSIR-IGIB, Delhi, 29th April 2023.
- Quantitative proteomics & PTM analysis. 10th Feb 2023. Workshop on Proteomics and Data Analysis, Translational Health Science and Technology Institute, Faridabad, Haryana, 9-10th Feb 2023.
- Mining tandem mass spectra for identifying peptides, proteins and modifications. PSI meeting education day talk. 2nd Nov 2022, PSI Education Day. 14th Annual Meeting of the Proteomics Society of India and International Conference on Proteins & Proteomics (PSI-ICPP 2022)”, CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, India, 2nd-5th November, 2022.
- Large-scale analysis of protein post-translational modifications (PTMs) from the human proteome and mass spectrometry data.26th Oct 2022 (Online), Virtual Podium Asia Pacific (VPAP) 2022 in Proteomics, Metabolomics and Lipidomics, 25th Oct to 27th Oct 2022.
- From proteins to peptides and back - analysis of tandem mass spectra for inferring peptides, proteins and modifications. 22nd July 2022.Computational Workshop on Genomics, Proteomics and Metagenomics 2022 (CWGPM-2022), CSIR-IGIB, Delhi July 20-23, 2022.
- Studying protein modifications in non-alcoholic fatty liver disease by mining public proteomics data. 21st Oct, 2021 (Online).OMICS-2021 international conference - the 13th Annual Meeting of Proteomics Society of India, Oct-20-23 2021.
- Analyzing your proteomics data - from RAW data to biological interpretation. 20th Oct, 2021 at pre-conference Education Day, OMICS-2021 international conference - the 13th Annual Meeting of Proteomics Society of India, Oct-20-23 2021.
- Disease interrogation using Mass spectrometry.22nd Sep, 2021 (Online) Science Setu, Sri Venkateswara College (SVC), Delhi University.
- Machine learning approaches for analysis of Proteomics data.5th May, 2021 (Online) Faculty Development Program on 'Artificial Intelligence in Health Science' 3rd - 7th May, 2021, School of Biotechnology and Bioinformatics, D. Y. Patil University.
- Large-scale identification of proteins and their modifications through mass spectrometry.17th April, 2021. Online workshop on “Omics Data Analysis”, Department of Biotechnology, JIIT, NOIDA, 16 -17 April, 2021
- The post-translational modification hotspots in human sirtuin interactors- mining and integrating proteomics data resources for studying cardiovascular diseases.13th March, 2021. Virtual conference on “Proteomics in Agriculture and Healthcare”, organized by School of life sciences, University of Hyderabad, in association with Proteomics Society, India (PSI). March 13-14, 2021 celebrating the “Proteomics Day”.
- Proteomics and Mass Spectrometry – from peptides to proteins. 10th Dec, 2020.Webinar: Bioinformatics approaches in Genomics & Proteomics.NITTE University Centre for Science Education and Research, NITTE University, Mangalore.
- Protein post-translational modifications (PTMs) - emergent properties, disease associations and identification from proteomic data. 22nd Nov, 2020.12th Annual Meeting of Proteomics Society, India (PSI 2020)- International Virtual Symposium on “Integrated Omics Approaches in Health and Agriculture”.
- Hitchhiker’s Guide to Integrative Systems Biology. 25th Feb, 2020, Aranyam- Annual Botanical Festival, Acharya Narendra Dev College, University of Delhi, Delhi.
- Multiplexed quantitative proteomics data analysis and visualization- the next frontier is now. 3rd Dec, 2019, 11th Annual Meeting of PSI & International Conference on Proteomics for System Integrated Bio-Omics, One Health and Food Safety. 2-4 Dec 2019, NDRI, Karnal.
- Anatomy of a Database Search in Proteomics. 23rd Sep 2019, ASEAN India 2019 Training Workshop, Sep 2019, CSIR-IGIB, Delhi.
- Interrogating disease mechanisms and biomarkers using mass spectrometry based proteomics.5th Sep, 2019, Medical Biotechnology Course, Miranda House College, University of Delhi, Delhi.
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Higher order multiplexing for quantitative proteomics. 25th May 2019, “Recent Advances
in Bioinformatics” conference, 23rd – 26th May 2019, CSIR-NEIST, Jorhat, Assam. - Field guide to analyze proteomics data - identification & quantitation. 20th Dec, 2018, The RCB-Mass Spectrometry and Proteomics Workshop, Regional Centre for Biotechnology (RCB), Faridabad, Haryana
- Characterizing the cogs in the machinery of life. 4th June, 2018, The Institute of Advanced Study in Science & Technology, Guwahati, Assam.
- Using mass spectrometry to understand disease mechanisms. 21st February, 2018, XXIV QIP on "Recent updates in pharmaceutical chemistry", 19-23 Feb 2018, Delhi Institute of Pharmaceutical Science and Research (DIPSAR), DPSR University, New Delhi.
- Next-generation spatio-temporal proteomics data analysis and visualization. 7th December, 2017, Center for Bioinformatics, Pondicherry University, Puducherry.
- Protein Functional Diversity and Disease Association. 4th March, 2017, National Workshop on "Protein Structure Prediction and Functional Analysis". Banasthali Vidyapith, Banasthali, Rajasthan.
- The Hitchhiker's Guide to Bioinformatics. 7th January, 2017. Banasthali Vidyapith, Banasthali, Rajasthan.
- Proteomics Data Analysis. 12th Dec 2016, PSI 2016 Education Day, National Institute of Plant Genome Research (NIPGR), Delhi.
- The Hitchhiker's Guide to Bioinformatics. 4th October 2016, Molecular Biology Workshop, Sri Guru Tegh Bahadur Khalsa College, University of Delhi, Delhi.
- Quantitative proteomics analysis and visualization. 12th January 2016. Seminar Series, Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT-D), Delhi.
- The Hitchhiker's Guide to Bioinformatics. 3rd November 2015, Medical Biotechnology Course, Miranda House College, University of Delhi, Delhi.
- Quantitative Shotgun Proteomics. 11th October 2015, Instructional Workshop on Proteomics and Proteogenomics: Hands-on Protein Identification and Gene Discovery from Mass Spectrometry Data. Acharya Narendra Dev College, University of Delhi, Delhi.
- Disrupting Proteomics - new tools of the trade. 18th March 2015, Proteomics Day at CSIR-IGIB organized with Proteomics Society of India (PSI), Delhi.
- Identifying Peptides and Proteins from Mass Spectrometry Data: Bioinformatics Session. 10th July 2013, National Training Programme on “Recent Advances in Proteomics for Biomarker Discovery”, NDRI, Karnal.
- Identifying Peptides and Proteins from Mass Spectrometry Data. 12th March 2013, Proteomics Workshop, Genomeet, Delhi 2013.
Workshops/Conferences Conducted
- Shadow a scientist Program in Science Setu , hosted KiroriMal College students in Dec 2018.
- Using mass spectrometry to understand disease mechanisms, 20th Oct 2016,Science Setu Workshop, Manav Rachna University, Faridabad.
- Using mass spectrometry to understand disease mechanisms, 18th Oct 2016,Science Setu Workshop, Maitreyi College, University of Delhi, Delhi.
- Proteome Informatics Workshop - 28-29 May 2016. Acharya Narendra Dev College, University of Delhi, Delhi.
- Organizing Committee: Cardiovascular Research Convergence (CRC-2017) at THSTI, Faridabad
Reviewer
- Bioinformatics (Oxford)
- Frontiers in Genetics (Bioinformatics & Computatonal Biology)
- Journal of Proteome Research
- Current Topics in Medicinal Chemistry
- Frontiers in Oncology
- Frontiers in Physiology (Systems Biology)
- Scientific Reports
- Oncology Letters
- Frontiers in Microbiology (Evolutionary and Genomic Microbiology)
- OMICS: A Journal of Integrative Biology
Research Tools Developed
- UniPEPtor - unique peptide database for species typing in infectious diseases
- TheoLib - tool to generate Theoretical spectral library for any organism.
- Proteome-Explorer - Interactive browsing of shotgun proteomics data for quicker analysis within the browser.
- HyperQuant - analysing large scale hyperplexing (18 plex) data from mass spectrometry proteomics
- ModST (pronounced Modest) - a data-parallel pipeline for automating blind-PTM searches via MODa tool
- MODaPipeline - analysis of post translational modifications (PTMs)
- QuantWizIQ - tool for iTRAQ data analysis
- MassWiz - MS/MS database search engine to identify peptides from shotgun proteomics data.
- FlexiFDR - a rescorer for improving database search results.
- ProteoStats - a code library for statistical FDR estimation and visualization of large scale proteomics database search results.
- ProteinAssembler - an algorithm for protein inference from MS/MS data.
- Proteome Analyst - an integrated meta-analysis software suite for integrating multiple proteomics search algorithm results.
Patents
Ajay Kumar, Shilpa Jamwal, Suruchi Aggarwal, Kanury VS Rao, Amit Kumar Yadav. Method of hyperplexing in mass spectrometry to elucidate temporal dynamics of proteome. (PCT)
Hobbies
My hobbies include playing Cricket, Table Tennis, Chess, Sketching, Painting, Music, Poetry, Reading and Writing.
Publication
You can also visit my scholarly profiles at -
https://orcid.org/0000-0002-9445-81562024
- Shaheen Khan, Suruchi Aggarwal, Pooja Bhatia, Amit Kumar Yadav, Yashwant Kumar, Naga Suresh Veerapu*. Glucose and Glutamine Drive Hepatitis E Virus Replication. Archives of Virology (2024), 169:233. Doi: https://doi.org/10.1007/s00705-024-06160-x
- Amit Kumar Yadav*, Trayambak Basak*. Deciphering protein conversations: a proteomic exploration of protein–protein interactions. Journal of Proteins and Proteomics (2024). Doi: https://doi.org/10.1007/s42485-024-00167-3
- Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A. Neely, Germán L. Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M. Peters-Clarke, Susan B. Egbert, Simion Kreimer, Emma H. Doud, Oliver M. Crook, Amit Kumar Yadav, Muralidharan Vanuopadath, Adrian D. Hegeman, Martín L. Mayta, Anna G. Duboff, Nicholas M. Riley, Robert L. Moritz, Jesse G. Meyer*. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS Measurement Science Au. 2024: 4 (4), 338-417. DOI: 10.1021/acsmeasuresciau.3c00068. (PMID: 39193565)
- Amit Kumar Yadav*, Suruchi Aggarwal. What are Proteome Atlases good for? Current Indian Science 2, 1-5, 2024. DOI: 10.2174/012210299X320402240715065917
- Anurag Raj, Suruchi Aggarwal, Prateek Singh, Amit Kumar Yadav*, Debasis Dash*. PgxSAVy: a tool for comprehensive evaluation of variant peptide quality in proteogenomics–catching the (un) usual suspects.Computational and Structural Biotechnology Journal, 2024. doi: 10.1016/j.csbj.2023.12.033.
2023
- Anurag Raj, Suruchi Aggarwal, Dhirendra Kumar, Amit Kumar Yadav*, Debasis Dash*. Proteogenomics 101: A Primer on Database Search Strategies. Journal of Proteins and Proteomics, (2023), 1-15, https://link.springer.com/article/10.1007/s42485-023-00118-4.
- Sharda Kumari, Bhaswati Bandyopadhyay, Anamika Singh, Suruchi Aggarwal, Amit Kumar Yadav, Naval Kishore Vikram, Prasenjit Guchhait, Arup Banerjee. Extracellular vesicles recovered from plasma of severe dengue patients induce CD4+ T cell suppression through PD-L1/PD-1 interaction. mBio 2023. doi : 10.1128/mbio.01823-23(PMID: 37982662)
- Prabhakar Babele, Amit Kumar Yadav*. Back2Basics: mass-to-charge ratio (m/z) in proteomics. Journal of Proteins and Proteomics, (2023), 1–4. https://doi.org/10.1007/s42485-023-00115-7
- Aleksha Panwar, Rinki Kumar, Renu Goel, Suruchi Aggarwal, Shweta Saraswat, Priyanka Bansal, Zaozianlungliu Gonmei, Gurudyal Toteja, Amit Kumar Yadav, Rakesh Lodha, Nirpendra Singh, Guruprasad Medigeshi*. Severe Dengue in Children associates with Dysregulation of Lipid Homeostasis, Complement Cascade and Retinol Transport. Clinical and Translational Medicine, 2023. doi: 10.1002/ctm2.1271(PMID: 37254651)
- Suruchi Aggarwal, Payal Gupta, Uma Dhawan, Amit Kumar Yadav*. The language of post-translational modifications and deciphering it from proteomics data. Transcription and Translation in Health and Disease (Elsevier) (2023) (doi : 10.1016/B978-0-323-99521-4.00012-X)
- Suruchi Aggarwal, Pallavi Mahajan, Payal Gupta, Alka Yadav, Gagan Dhawan, Uma Dhawan, Amit Kumar Yadav*. The bacterial communication system and its interference as an antivirulence strategy. Bacterial Survival in the hostile environment, (2022). Doi: 10.1016/B978-0-323-91806-0.00010-2.
2022
- Suruchi Aggarwal, Anurag Raj, Dhirendra Kumar, Debasis Dash*, Amit Kumar Yadav*. False Discovery Rate – the Achilles’ heel of Proteogenomics. Briefings in Bioinformatics, (2022), doi: 10.1093/bib/bbac163. (PMID: 35534181).
- Amit Kumar Yadav*, Sanjay Kumar Banerjee, Bhabatosh Das, Kumardeep Chaudhary. Editorial: Systems biology and omics approaches for understanding complex disease biology. Frontiers in Genetics. 2022. doi: 10.3389/fgene.2022.896818. (PMID:35495146)
- Zaigham Abbas Rizvi, Rajdeep Dalal, Srikanth Sadhu, Akshay Binayke, Jyotsna Dandotiya, Yashwant Kumar, Tripti Shrivastava, Sonu Kumar Gupta, Suruchi Aggarwal, Manas Ranjan Tripathy, Deepak Kumar Rathore, Amit Kumar Yadav, Guruprasad R Medigeshi, Amit Kumar Pandey, Sweety Samal, Shailendra Asthana, Amit Awasthi*. Golden Syrian hamster as a model to study cardiovascular complications associated with SARS-CoV-2 infection. eLife 2022; 11: e73522. DOI: 10.7554/eLife.73522. (PMID: 35014610)
- Kiran Bala Sharma, Suruchi Aggarwal, Amit Kumar Yadav, Sudhanshu Vrati*, Manjula Kalia*. Studying Autophagy Using a TMT-based Quantitative Proteomics Approach. Autophagy and Cancer, Methods and Protocols, Methods in Molecular Biology series, 2445:183-203 (SpringerNature), 2022. doi: 10.1007/978-1-0716-2071-7_12. (PMID: 34972993)
2021
- Kiran Bala Sharma, Simran Chhabra, Suruchi Aggarwal, Aarti Tripathi, Arup Banerjee, Amit Kumar Yadav, Sudhanshu Vrati*, Manjula Kalia*. Proteomic landscape of Japanese encephalitis virus-infected fibroblasts. Journal of General Virology, 102(9), 1-17 (2021). Doi: 10.1099/jgv.0.001657. (PMID: 34546869)
- Manish Pandey, Sakshi Bansal, Sudipta Bar, Amit Kumar Yadav, Nicholas S. Sokol, Jason M. Tennessen, Pankaj Kapahi*, Geetanjali Chawla*.miR-125-chinmo pathway regulates dietary restriction dependent enhancement of lifespan in Drosophila. eLife 2021;10:e62621, 1-37, DOI: 10.7554/eLife.62621. (PMID:34100717)
- Suruchi Aggarwal, Priya Tolani, Srishti Gupta, Amit Kumar Yadav*. Posttranslational Modifications in Systems Biology. APCSB: Proteomics and systems biology Volume 127, 93-126, (2021). doi:10.1016/bs.apcsb.2021.03.005. (PMID: 34340775)
- Priya Tolani, Shrishti Gupta, Kirti Yadav, Suruchi Aggarwal, Amit Kumar Yadav*. Big Data, Integrative Omics and Network Biology. APCSB: Proteomics and systems biology Volume 127, 127-160, (2021). doi: 10.1016/bs.apcsb.2021.03.006. (PMID: 34340766)
2020
- Suyasha Roy, Renu Goel, Suruchi Aggarwal, Shailendra Asthana, Amit Kumar Yadav, Amit Awasthi*. Proteome analysis revealed the essential functions of PP2A in the induction of Th9 cells.Scientific Reports, 10, 10992 (2020). doi: 10.1038/s41598-020-67845-2(PMID: 32620893)
- Suruchi Aggarwal, Sanjay K. Banerjee, Narayan C. Talukdar, Amit Kumar Yadav*. Post-translational modification crosstalk and hotspots in sirtuin interactors implicated in cardiovascular diseases. Frontiers in Genetics. 2020, 11:356. doi: 10.3389/fgene.2020.00356 (PMID: 32425973)
- Suruchi Aggarwal, Ajay Kumar, Shilpa Jamwal, Mukul Kumar Midha, Narayan Talukdar, Amit Kumar Yadav*. HyperQuant- a computational pipeline for higher order multiplexed quantitative proteomics. ACS Omega 2020, 5, 19, 10857–10867. doi: 10.1021/acsomega.0c00515. (PMID: 32455206)
2019
- Suruchi Aggarwal, Narayan C. Talukdar, Amit K. Yadav. "Advances in higher order multiplexing techniques in proteomics." Journal of proteome research (2019).
- Ramu Adela, Podduturu Naveen Chander Reddy, Tarini Shankar Ghosh, Suruchi Aggarwal, Amit Kumar Yadav, Bhabatosh Das, Sanjay K. Banerjee*. Serum Protein Signature of Coronary Artery Disease in Type 2 Diabetes Mellitus. Journal of Translational Medicine. 2019, doi: 10.1186/s12967-018-1755-5
- Ramu Adela, Podduturu Naveen Chander Reddy, Tarini Shankar Ghosh, Suruchi Aggarwal, Amit Kumar Yadav, Bhabatosh Das, Sanjay K. Banerjee*. Serum Protein Signature of Coronary Artery Disease in Type 2 Diabetes Mellitus. Journal of Translational Medicine. 2019, doi: 10.1186/s12967-018-1755-5
2018
- Ishita Gupta, Suruchi Aggarwal, Kanika Singh, Amit Yadav, Sameena Khan*. Ubiquitin Proteasome pathway proteins as potential drug targets in parasite Trypanosoma cruzi. Scientific Reports. 2018 May 30;8(1):8399. doi: 10.1038/s41598-018-26532-z
2017
- Suruchi Aggarwal, Manu Kandpal, Shailendra Asthana, Amit Kumar Yadav*. Perturbed Signaling and Role of Posttranslational Modifications in Cancer Drug Resistance. Drug Resistance in Bacteria, Fungi, Malaria, and Cancer (SpringerNature), 2017. doi: 10.1007/978-3-319-48683-3_22
- Manu Kandpal, Suruchi Aggarwal, Shilpa Jamwal, Amit Kumar Yadav*. Emergence of Drug Resistance in Mycobacterium and Other Bacterial Pathogens: The Posttranslational Modification Perspective. Drug Resistance in Bacteria, Fungi, Malaria, and Cancer (SpringerNature), 2017. doi: 10.1007/978-3-319-48683-3_9
- Amit Kumar Yadav*. Commentary: Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells. Frontiers in Physiology, 2017. doi: 10.3389/fphys.2017.00174
- Dhirendra Kumar, Amit Kumar Yadav, Debasis Dash. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data. in Proteome Bioinformatics, Methods in Molecular Biology series, 1549 (SpringerNature), 2017. doi: 10.1007/978-1-4939-6740-7_3
2016
- Ajay Kumar, Shilpa Jamwal, Mukul Kumar Midha, Baseerat Hamza, Suruchi Aggarwal, Amit Kumar Yadav, Kanury V.S. Rao*. Dataset generated using hyperplexing and click chemistry to monitor temporal dynamics of newly synthesized macrophage secretome post infection by mycobacterial strains. Data in Brief, 2016. doi: 10.1016/j.dib.2016.08.055
- Suruchi Aggarwal, Amit Kumar Yadav*. Dissecting the iTRAQ Data Analysis. Statistical Analysis in Proteomics, (Methods in Molecular Biology, Springer), 2016. doi: 10.1007/978-1-4939-3106-4_18
- Suruchi Aggarwal, Amit Kumar Yadav*. False Discovery Rate Estimation in Proteomics. Statistical Analysis in Proteomics, (Methods in Molecular Biology, Springer), 2016. doi: 10.1007/978-1-4939-3106-4_7
- Dhirendra Kumar, Amit Kumar Yadav, Xinying Jia, Jason Mulvenna, Debasis Dash*. Integrated transcriptomic-proteomic analysis using proteogenomic workflow refines rat genome annotation. Molecular & Proteomics, 2016. doi:10.1074/mcp.M114.047126
2014
- Dhirendra Kumar, Anupam Kumar Mondal, Amit Kumar Yadav, Debasis Dash. Discovery of rare protein coding genes in model methylotroph Methylobacterium extorquens AM1. Proteomics, 2014. doi: 10.1002/pmic.201400153
2013
- Rahul D Upadhyay, Amit Kumar Yadav, Shobha Sonawane, Reshma Goankar, Debasis Dash, N.H.Balasinor. Differential proteomic and phosphoproteomic analysis of normal versus failed spermiation condition by LC-MS/MS sequencing. Journal of Analytical & Bioanalytical Techniques, 2013, 4:172. doi: 10.4172/2155-9872.1000172
- Amit Kumar Yadav*, Puneet Kumar Kadimi, Dhirendra Kumar, Debasis Dash*. ProteoStats - a library for estimating false discovery rates in proteomics pipelines. Bioinformatics, 2013. doi: 10.1093/bioinformatics/btt490. (*corresponding author)
- Dhirendra Kumar, Amit Kumar Yadav, Debasis Dash. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline. Molecular & Cellular Proteomics, 2013. doi: 10.1074/mcp.M112.027169
- Anirban Sinha, Amit Kumar Yadav, Samarpana Chakraborty, S.K. Kabra, R. Lodha, Manish Kumar, Ankur Kulshreshtra, Tavpritesh Sethi, Rajesh Pandey, Gaurav Malik, Saurabh Laddha, Arijit Mukhopadhyay, Debasis Dash, Balaram Ghosh, Anurag Agrawal*. Exosome Enclosed MicroRNAs In Exhaled Breath Hold Potential For Biomarker Discovery. Journal of Allergy and Clinical Immunology, 219-222.e7, July 2013. doi: 10.1016/j.jaci.2013.03.035
2012
- Amit Kumar Yadav, Dhirendra Kumar, Debasis Dash*. Learning from decoys to improve the sensitivity and specificity of proteomics database search results. PLoS ONE 7(11): e50651, 2012. doi: 10.1371/journal.pone.0050651
2011
- Dhanashree S Kelkar, Dhirendra Kumar, Praveen Kumar, Lavanya Balakrishnan, Babylakshmi Muthusamy, Amit Kumar Yadav, Priyanka Shrivastava, Arivusudar Marimuthu, Sridhar Anand, Hema Sundaram, Reena Kingsbury, H C Harsha, Bipin Nair, T S Keshava Prasad, Devendra Singh Chauhan, Kiran Katoch, Vishwa Mohan Katoch, Prahlad Kumar, Raghothama Chaerkady, Srinivasan Ramachandran, Debasis Dash, Akhilesh Pandey*. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Molecular & Cellular Proteomics, 10, M111.011627, December 1, 2011. doi: 10.1074/mcp.M111.011627
- Amit Kumar Yadav#, Gourav Bhardwaj#, Trayambak Basak#, Dhirendra Kumar, Shadab Ahmad, Ruby Priyadarshini, Ashish Kumar Singh, Debasis Dash*, Shantanu Sengupta*. A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery. PLoS ONE 6(9): e24442, 2011. doi: 10.1371/journal.pone.0024442 (#equal contribution)
- Amit Kumar Yadav, Dhirendra Kumar, Debasis Dash*. MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. Journal of Proteome Research 10: 5. 2154-2160, 2011. doi: 10.1021/pr200031z
- Suruchi Aggarwal, Payal Gupta, Uma Dhawan, Amit Kumar Yadav*. The language of post-translational modifications and deciphering it from proteomics data. Transcription and Translation in Health and Disease (Elsevier) (2023) (doi : 10.1016/B978-0-323-99521-4.00012-X)
- Suruchi Aggarwal, Pallavi Mahajan, Payal Gupta, Alka Yadav, Gagan Dhawan, Uma Dhawan, Amit Kumar Yadav*. The bacterial communication system and its interference as an antivirulence strategy. Bacterial Survival in the hostile environment, (2022). Doi: 10.1016/B978-0-323-91806-0.00010-2.
- Kiran Bala Sharma, Suruchi Aggarwal, Amit Kumar Yadav, Sudhanshu Vrati*, Manjula Kalia*. Studying Autophagy Using a TMT-based Quantitative Proteomics Approach. Autophagy and Cancer, Methods and Protocols, Methods in Molecular Biology series, 2445:183-203 (SpringerNature), 2022. doi: 10.1007/978-1-0716-2071-7_12. (PMID: 34972993)
- Suruchi Aggarwal, Manu Kandpal, Shailendra Asthana, Amit Kumar Yadav*. Perturbed Signaling and Role of Posttranslational Modifications in Cancer Drug Resistance. Drug Resistance in Bacteria, Fungi, Malaria, and Cancer (SpringerNature), 2017. doi: 10.1007/978-3-319-48683-3_22
- Manu Kandpal, Suruchi Aggarwal, Shilpa Jamwal, Amit Kumar Yadav*. Emergence of Drug Resistance in Mycobacterium and Other Bacterial Pathogens: The Posttranslational Modification Perspective. Drug Resistance in Bacteria, Fungi, Malaria, and Cancer (SpringerNature), 2017. doi: 10.1007/978-3-319-48683-3_9
- Dhirendra Kumar, Amit Kumar Yadav, Debasis Dash. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data. in Proteome Bioinformatics, Methods in Molecular Biology series, 1549 (SpringerNature), 2017. doi: 10.1007/978-1-4939-6740-7_3
- Suruchi Aggarwal, Amit Kumar Yadav*. Dissecting the iTRAQ Data Analysis. Statistical Analysis in Proteomics, (Methods in Molecular Biology, Springer), 2016. doi: 10.1007/978-1-4939-3106-4_18
- Suruchi Aggarwal, Amit Kumar Yadav*. False Discovery Rate Estimation in Proteomics. Statistical Analysis in Proteomics, (Methods in Molecular Biology, Springer), 2016. doi: 10.1007/978-1-4939-3106-4_7
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Inventors - Ajay Kumar, Shilpa Jamwal, Suruchi Aggarwal, Kanury VS Rao, Amit Kumar Yadav. Method of hyperplexing in mass spectrometry to elucidate temporal dynamics of proteome (provisional patent filed)
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Inventors - Ajay Kumar, Shilpa Jamwal, Suruchi Aggarwal, Kanury VS Rao, Amit Kumar Yadav. Method of hyperplexing in mass spectrometry to elucidate temporal dynamics of proteome (PCT filed)
Extramural Projects
- To create a proteogenomic reference map of human liver by integrating genomics and proteomic data to facilitate studies on non-alcoholic fatty liver disease (NAFLD) [part of DBT-National Network Project (NNP) with IGIB (Coordinator), THSTI, NIPGR, ILS and NEHU as members, each with their own project] (as Principal Investigator from THSTI, 2023-2028)
- Assessing Environmental Chemical Risk Factors for Type 2 Diabetes: A 24-Year Follow-up Cohort Study -[BT/PR53821/BMS/85/100/2024 ] (as Co-Investigator, DBT, 2024-2027)
- A Pilot study on the large-scale analysis of chronic pancreatitis through high-throughput mass spectrometry-based proteomics and proteogenomics for biomarker discovery (as Principal-Investigator from THSTI, AIIMS-THSTI collaborative inter-institutional grant, 2023-2025)
- Metabolic associated liver disease (MAFLD) in lean and obese: search for disease and progression biomarkers. (as Co-Investigator, SERB-SUPRA grant, 2022-2025)
- Identification of stage-specific diagnostic and prognostic biomarker(s) of Non-alcoholic fatty liver disease using the multi-omics approach. (as Co-Investigator, AIIMS-THSTI collaborative inter-institutional grant, 2019-2022)
- DBT- BDI Big Data Initiative grant from Department of Biotechnology, titled “Integrating multiple proteomics database search algorithms in a unified framework for time efficient large scale analyses” (as Principal Investigator, Mar 2018-Sep 2021)
- Large-scale proteomics analysis of post-translational modifications and their crosstalks in cardiovascular diseases"- under the IYBA - Innovative Young Biotechnologist Award, 2013 Grant (as Principal Investigator, 2014-2018)
Intramural Project (THSTI):
- Development of an in-silico tool and database for identification of unique peptide(s)/protein(s) among bacterial genomes/proteomes (as Principal Investigator, 2017-2019)
- Integrative data mining for genome based rapid detection of antibiotic resistance in Gram - negative ESKAPE pathogens (as Principal Investigator, 2021-2023)
- Understand the genomic repertoires and proteome of extensively drug resistant Serratia marcescens isolated from rural India (as Co-Investigator, 2022-2024)
- Leveraging Large Language Models for Biomarker and Drug Discovery in MASLD: A Resource-Efficient Approach with Experimental Validation (2024-2026)
As Mentor: (1)
- MK Bhan Young Research Fellowshipto Dr. Suruchi Aggarwal – “Stage-specific molecular signature identification for non-alcoholic fatty-liver disease using integrative analysis of multi-omics data and artificial intelligence” (2023)
- Best Presentation (Runner-up), Virtual Podium Asia Pacific on Proteomics, Metabolomics and Lipidomics, VPAP online (2022)
- Innovative Young Biotechnologist Award (IYBA) 2013
- Awarded “Innovators Under 35 2013” (TR35) in India by MIT Technology Review, March 2013
- Young Scientist Travel Awardfrom DST (Sep 2011)
- CSIR-JRF, June 2007 (Top 25)
- GATE qualified, Feb 2007
- CSIR-JRF, December 2006
Software Copyrights
1. HyperQuant : Diary no. 5027/2016-CO/SW on 26.04.2016. Suruchi Aggarwal, Amit Kumar Yadav.
2. QuantWizIQ : Diary No. 2190/2016-CO/SW on 22.02.2016. Suruchi Aggarwal, Amit Kumar Yadav.
3. MODa Pipeline : Diary no. 2186/2016-CO/SW on 22.02.2016. Manu Kandpal, Suruchi Aggarwal, Amit Kumar Yadav.
4. ModST : Diary no. 13388/2016CO/SW on 22.11.2016. Suruchi Aggarwal, Amit Kumar Yadav.
5. ProteomeExplorer : Diary No. 1539/2017-CO/SW on 27.01.2017. Puneet Kumar Kadimi, Suruchi Aggarwal, Amit Kumar Yadav.
6. TheoLib : Diary No. 2302/2019-CO/SW on 12.02.2019. Pallavi Mahajan, Suruchi Aggarwal, Amit Kumar Yadav.
7. UniPEPtor: Diary No. 2306/2019-CO/SW on 12.01.2019. Amit Kumar Yadav, Pallavi Mahajan, Asmita Bharti.
MR.SANCHIT SINGHANIA
PH.D STUDENT
MS.MANSI RANA
PH.D STUDENT
MS.NIKITA
PROJECT ASSOCIATE-I
MS.USHA M.
PROJECT ASSOCIATE-I
Dr. Ritu Sharaya
Sanchit Singhania
Mansi Rana
Usha M
Nikita Dalal
Priyanshu Sharma
- 01292876490
- AMIT[DOT]YADAV[AT]THSTI[DOT]RES[DOT]IN