Hi! My name is Yash.

Computers have always been a source of fascination for me since my childhood, and this fascination has only grown stronger with time. As a result, I pursued a career in Bioinformatics, which combines my interests in both biology and computing. I completed my Masters in Bioinformatics from Jamia Millia Islamia, New Delhi in 2020, which provided me with a comprehensive understanding of the field. Prior to this, I completed my Bachelors in Microbiology from the University of Delhi in 2018, which laid the foundation for my interest in biological sciences.
Currently, I am a PhD Scholar under the supervision of Dr. Md. Imtaiyaz Hassan, focusing on leveraging Artificial Intelligence to tackle complex problems in computational biology. My work involves a diverse array of tasks, ranging from data analysis to the creation of AI models that aid in the discovery and development of new therapeutic agents. In addition to my work in the research lab, I am also actively involved in the scientific community, participating in conferences and workshops related to Bioinformatics. I am passionate about using computational tools and techniques to advance our understanding of the biological world, and I am always eager to collaborate with others who share the same vision. Ultimately, my goal is to make meaningful contributions to the field of Computational Biology and to help drive scientific progress in this exciting and rapidly evolving field.

Publications

Latest to oldest
S. No. Title and Authors Journal Impact Factor
08/2023 Yash Mathur, Alaa Shafie, Bandar Alharbi, Amal Adnan Ashour, Waleed Abu Al-Soud, Hassan H. Alhassan, Salem Hussain Alharethi, and Farah Anjum; Genome-Wide Analysis of Kidney Renal Cell Carcinoma: Exploring Differentially Expressed Genes for Diagnostic and Therapeutic Targets OMICS: A Journal of Integrative Biology (2023) 27(8):393-401; DOI: 10.1089/omi.2023.0056 3.3
06/2023 Afsar Alam, Mohammad Shahzeb Khan, Yash Mathur, Md Nayab Sulaimani, Naqiya Farooqui, Sheikh F. Ahmad, Ahmed Nadeem, Dharmendra Kumar Yadav & Taj Mohammad; Structure-based identification of potential inhibitors of ribosomal protein S6 kinase 1, targeting cancer therapy: a combined docking and molecular dynamics simulations approach Journal of Biomolecular Structure and Dynamics (2023) 26:1-12; DOI: 10.1080/07391102.2023.2228912 3.5
05/2023 Md Imtaiyaz Hassan, Mohd. Umair, Yash Mathur, Taj Mohammad, Afreen Khan, Md Nayab Sulaimani, Afsar Alam & Asimul Islam; Chapter: Molecular Dynamics Simulation to Study Thermal Unfolding in Proteins In book: Protein Folding Dynamics and Stability; DOI: 10.1007/978-981-99-2079-2_12 NA
02/2022 Yash Mathur, Taj Mohammad, Farah Anjum, Alaa Shafie, Abdelbaset Mohamed Elasbali, Vladimir N. Uversky, and Md. Imtaiyaz Hassan; PyPAn: An automated graphical user interface for protein sequence and structure analyses Protein & Peptide Letters (2022) 29(4); DOI: 10.2174/0929866529666220210155421 1.89
10/2021 Taj Mohammad, Arunabh Choudhury, Insan Habib, Purva Asrani,Yash Mathur, Mohd. Umair, Farah Anjum, Alaa Shafie, Dharmendra Kumar Yadav and Md. Imtaiyaz Hassan; Genomic variations in the structural proteins of SARS-CoV-2 and their deleterious impact on pathogenesis: A comparative genomics approach Frontiers in Cellular and Infection Microbiology (2021) 11, 951; DOI: 10.3389/fcimb.2021.765039 5.29
10/2020 Taj Mohammad, Yash Mathur and Md. Imtaiyaz Hassan; InstaDock: A Single-click Graphical User Interface for Molecular Docking-based Virtual High-throughput Screening. Briefings in Bioinformatics (2020) 00, 1-8. (Co-First author); DOI: 10.1093/bib/bbaa279 13.99

Work Experience

PhD Scholar

May 2023 - Current

Working under the supervision of Dr. Md. Imtaiyaz Hassan at the Centre for Interdisciplinary Research in Basic Sciences,
Jamia Millia Islamia, New Delhi, India.

Thesis title: "Employing Generative Deep Learning Models for Strategic Advancements in Drug Development"

My PhD research at Dr. Hassan's lab is centered around the practical application of generative deep learning models to the drug development process. These models are crucial for identifying promising therapeutic targets with greater efficiency. My thesis reflects my hands-on approach to computational biology, aiming to contribute tangible improvements to the way new drugs are developed. My work involves the intricate development and nuanced application of generative AI, which are instrumental in the drug development landscape. The study aims to revolutionize how we approach the creation of new drugs. By pushing the boundaries of current methodologies, I am hoping to contribute to a future where drug development is faster, more accurate, and more accessible.


Project Assistant

August 2020 - April 2023

Working under the supervision of Dr. Md. Imtaiyaz Hassan at the Centre for Interdisciplinary Research in Basic Sciences,
Jamia Millia Islamia, New Delhi, India.

As a researcher, I am proud of the contributions I have made to the field of proteomics and genomics, which have the potential to advance drug discovery and improve public health. One of my significant achievements is the development of an automatic graphical user interface (GUI) protein docking tool using Python. This tool has simplified the process of protein docking, saving researchers time and effort while also enhancing the accuracy of protein binding predictions. Additionally, I have also developed a user-friendly GUI tool aimed at helping beginners in proteomics to access and analyze proteomic data with ease.
Furthermore, I am thrilled to have been part of a highly collaborative study that analyzed the genomic variations of structural proteins of SARS-CoV-2. This research is critical in understanding the virus's evolution and can potentially lead to the development of effective treatments and vaccines. My contribution to this study has given me a deeper understanding of the impact of genomic variations on the virus's structure and function. Overall, I am excited to continue making a positive impact on scientific advancements in the field of proteomics and genomics.

Proficiency

Bioinformatics skills
Common bioinformatics tools such as BLAST, MODELLER, PyMol, PyRx, Discovery Studio, AutoDock, SPDB Viewer, RAxML, Avogadro, and Cytoscape.
Advanced bioinformatics applications such as GROMACS and VMD, Cheminformatics analysis using Marvin and OpenBabel, protein model building and refining using WinCoot.
Programming skills
  • Python Various libraries and architectures including but not limited to: PyQT5, PyTorch, Django & TensorFlow
  • R Essential libraries for data analysis e.g., ggplot2, limma, DESeq2, AnnotationDBI, EdgeR and NOISeq
  • Java BioJava, GUI development & Android Development
  • Kotlin Basic android development and deployment
  • Perl BioPerl, CGI & DBI
  • C++ QT5, OpenGL

Education

Jamia Millia Islamia
2018-2020 Masters of Science (M.Sc.) in Bioinformatics
University of Delhi
2015-2018 Bachelors of Science (B.Sc.) in Microbiology
St. Paul' School
2002-2015 High school subjects included Physics,
Chemistry, Biology and Computer Science

Projects