People : Scientific : Faculty & Scientists

DR. AMIT KUMAR YADAV, Ph.D. 

Scientist C
+91-129-2876490  (+91-129-2876490)
amit.yadav [at] thsti [dot] res [dot] in
Ph.D. Biotechnology (2012) from from CSIR-Institute of Genomics and Integrative Biology, Delhi, India
M.Sc. Botany (2007) from Delhi University
B.Sc.(Hons.) Botany (2005) from 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.

 

Other Interests

I am interested in big data in biomedicine, 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

  • 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
  • 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

 

Invited Talks

  • 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 Conducted

  • 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.

 

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)

 

Research Tools Developed

  • Proteome-Explorer - Interactive browsing of shotgun proteomics data for quicker analysis within the browser. (Internal link for THSTI users)
  • 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 YadavMethod of hyperplexing in mass spectrometry to elucidate temporal dynamics of proteome.

 

Lab Members

  • Punit Kumar Kadimi - Research Application Developer
  • Suruchi Aggarwal - ICMR-Senior Research Fellow
  • Pallavi Mahajan - Senior Research Fellow
  • Asmita Bharti - Junior Research Fellow

 

Hobbies

My hobbies include playing Cricket, Table Tennis, Chess, Sketching, Painting, Music, Poetry, Reading and Writing.

 

 

 

Goto Google Scholar Profile OR Publications list

 

2017

 

2016

 

2014

 

2013

 

2012

 

2011

  • Inventors - Ajay Kumar, Shilpa Jamwal, Suruchi Aggarwal, Kanury VS Rao, Amit Kumar YadavMethod of hyperplexing in mass spectrometry to elucidate temporal dynamics of proteome (provisional patent filed)

 
  • Large-scale proteomics analysis of post-translational modifications and their crosstalks in cardiovascular diseases"- under the IYBA Innovative Young Biotechnologist Award, 2013 Grant
  • Big Data Inititative (BDI) grant from Department of Biotehcnology, 2017-onwards
  • Intramural grant from THSTI
  • CSIR-JRF Dec 2006
  • CSIR JRF, June 2007
  • GATE qualified, Feb 2007
  • DST Young Scientist Travel Award, 2011
  • MIT TR35, India 2013
  • Innovative Young Bio-technologist Award 2013, from DBT

 

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.     ModSTDiary 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.


MS. SURUCHI AGGARWAL
ICMR SENIOR RESEARCH FELLOW

MS. PALLAVI MAHAJAN
SENIOR RESEARCH FELLOW

MR. PUNEET KUMAR KADIMI
RESEARCH APPLICATION DEVELOPER

MS. ASMITA BHARTI
JUNIOR RESEARCH FELLOW