Publications from DTB, NCI, NIH
Anish Thomas*, Shaun D. Fontaine, Morgan Diolaiti, Parth Desai, Rajesh Kumar, Nobuyuki Takahashi, Linda Sciuto, Samantha Nichols, Alan Ashworth, Gary W. Ashley, Yves Pommier and Daniel V. Santi (2022). PLX038: A long-acting topoisomerase I inhibitor with potent synergy with PARP inhibitors and robust anti-tumor activity in ATM deficient tumors. Molecular cancer therapeutics, MCT-22-0217. https://doi.org/10.1158/1535-7163.MCT-22-0217
Gavriel Fialkoff, Nobuyuki Takahashi, Israa Sharkia, Jenia Gutin, Lorinc Pongor, Arun Rajan, Samantha Nichols, Linda Sciuto, Rasa Vilimas, Chante Graham, Parth Desai, Miriam Maoz, Yakir Rottenberg, Nevo Shoshan, Hovav Nechushtan, Tamar Peretz, Diana Roame, Paula Carter, Rajesh Kumar, Ayala Hubert, Jonathan E Cohen, Deep Upadhyay, Azzam Salah, Mark Temper, Albert Grinshpun, William Douglas Figg, Aviad Zick, Ronen Sadeh, Nir Friedman, Anish Thomas: Subtyping of Small Cell Lung Cancer using plasma cell-free nucleosomes (In Press, Nature Genetics)
Lőrinc Pongor, Christopher Schultz, Lorenzo Rinaldi, Darawalee Wangsa, Christophe Redon, Nobuyuki Takahashi, Gavriel Fialkoff, Parth Desai, Yang Zhang, Sandra Burkett, Nadav Hermoni, Noa Vilk, Jenia Gutin, Gergely Rona, Yongmei Zhao, Samantha Nichols, Rasa Vilimas, Linda Sciuto, Chante Graham, Juan Manuel Caravaca-Guasch, Sevilay Turan, Tsai-Wei Shen, Vinodh Rajapakse, Rajesh Kumar, Deep Upadhyay, Yoo Sun Kim, Suresh Kumar, Nitin Roper, Bao Tran, Stephen Hewitt, David Kleiner, Mirit Aladjem, Nir Friedman, Gordon Hager, Yves Pommier, Thomas Ried, and Anish Thomas: Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity (Cancer discovery, 13(4), 928–949. https://doi.org/10.1158/2159-8290.CD-22-0796)
Parth Anil Desai; Nobuyuki Takahashi; Yingying Cao; Christopher Schultz; Darryl Nousome; Desiree Tillo; Lakshya Chauhan; Mayank tandon; Rajesh kumar Bhardwaj; Delphine Lissa; Vinodh Rajapakse; Suresh kumar; Yang Zhang; Elmeskini Rajaa; Donna Butcher; Linda Scuito; Jingjing Gong; Brett Schroder; Andrew Warner; Samantha Nichols; Jordan Kimberly; Alejandro Schaffer; Mohit kumar Jolly; Stephen Hewitt; Anish Thomas: Distinct immunosuppressive tumor microenvironment modulates small cell lung carcinoma neuroendocrine phenotypic plasticity and heterogeneity (Cancer Res (2023) 83 (7_Supplement): 5828. https://doi.org/10.1158/1538-7445.AM2023-5828)
Melissa Abel, Nobuyuki Takahashi, Cody Peer, Christophe Redon, Samantha Nichols, Rasa Vilimas, Min-Jung Lee, Sunmin Lee, Meenakshi Shelat, Robbie Kattapuram, Linda Sciuto, Danielle Pinkiert, Chante Graham, Donna Butcher, Baktiar Karim, Ajit Sharma, Justin Malin, Rajesh Kumar, Christopher Schultz, Shubhank Goyal, Jaydira Del Rivero, Manan Krishnamurthy, Deep Upadhyay, Brett Schroeder, Tristan Sissung, Manoj Tyagi, Jung Kim, Yves Pommier, Mirit Aladjem, Mark Raffeld, William Figg, Jane Trepel, Liqiang Xi, Parth Desai, and Anish Thomas: Targeting Replication Stress and Chemotherapy Resistance with a Combination of Sacituzumab Govitecan and Berzosertib: A Phase I Clinical Trial (Clinical Cancer Research)
Parth Desai; Nobuyuki Takahashi; Yingying Cao; Desiree Tillo; Samantha Nichols; Allison Hunt; Christopher Schultz; Darryl Nousome; Lakshya Chauhan; Linda Sciuto; Kimberly Jordan; Vinodh Rajapakse; Rajesh Kumar Bhardwaj; Mayank Tandon; Delphine Lissa; Yang Zhang; Suresh Kumar; Lorinc Pongor; Abhay Singh; Brett Schroder; Ajit Sharma; Tiangen Chang; Rasa Vilimas; Danielle Pinkiert; Chante Graham; Donna Butcher; Andrew Warner; Robin Sebastian; Mimi Mahon; Karen Baker; Jennifer Cheng; Ann Berger; Ross Lake; Melissa Abel; Deep Upadhyay; Manan Krishnamurthy; George Chrisafis; Justin Malin; Shubhank Goyal; Devon Atkinson; Govind Nair; Andrea Apolo; Udayan Guha; Baktiar Karim; Rajaa El Meskini; Zoe Weaver Ohler; David Kleiner; Markku Miettinen; G Tom Brown; Stephen Hewitt; Alejandro Schaffer; Mohit Kumar Jolly; Eytan Ruppin; Thomas Conrads; Anish Thomas: Microenvironment Shapes Cell State, Plasticity, and Heterogeneity of Small Cell Lung Cancer (In Press, Cancer Cell)
Publications from Doctoral Research
Thesis Related Publications
Rajesh Kumar, Gandharva Nagpal, Vinod Kumar, Salman Usmani, Piyush Agrawal, & Gajendra P.S. Raghava (2019). HumCFS: a database of fragile sites in human chromosomes. BMC genomics, 19(9), 985. https://doi.org/10.1186/s12864-018-5330-5
Rajesh Kumar, Sumeet Patiyal, Vinod Kumar, Gandharva Nagpal, & Gajendra P.S. Raghava (2019). In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. International journal of molecular sciences, 20(14), 3582. https://doi.org/10.3390/ijms20143582
Rajesh Kumar, Anjali Lathwal, Vinod Kumar, Sumeet Patiyal, Pawan Kumar Raghav, & Gajendra P.S. Raghava (2020). CancerEnD: A database of cancer associated enhancers. Genomics, 112(5), 3696–3702. https://doi.org/10.1016/j.ygeno.2020.04.028
Other Publications
Anjali Lathwal, Rajesh Kumar and Gajendra P.S. Raghava: OvirusTdb: A database of oncolytic viruses for the advancement of therapeutics in cancer. Virology, 2020, https://doi.org/10.1016/j.virol.2020.05.016 (co-first)
Anjali Lathwal, Rajesh Kumar, and Gajendra P.S. Raghava: VLCvirus: Identification of subunit vaccine candidates against lung cancer causing viruses. Elsevier – Computers in Biology and Medicine. (co-first)
Anjali Lathwal, Rajesh Kumar, Chakit Arora, and Gajendra P.S. Raghava: Identification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical data, J Cancer Res Clin Oncol. 2020;10.1007/s00432-020-03318-3. doi:10.1007/s00432-020-03318-3
Vinod Kumar, Piyush Agrawal, Rajesh Kumar, Sherry Bhalla, Salman Sadullah Usmani, Grish C. Varshney, Gajendra P.S. Raghava: Prediction of Cell-Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues. Frontiers in Microbiology 04/2018; 9:725., DOI:10.3389/fmicb.2018.00725. (co-first)
Vinod Kumar, Rajesh Kumar, Piyush Agrawal, Sumeet Patiyal and Gajendra P.S. Raghava: A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure. Front Pharmacol. 2020;11:54. Published 2020 Feb 20. doi:10.3389/fphar.2020.00054
Vinod Kumar, Sumeet Patiyal, Rajesh Kumar, Dilraj Kaur, Anjali Lathwal, and Gajendra P.S. Raghava: B3Pdb: A database of blood brain penetrating peptides. Springer – Brain Structure and Function.
Pawan Kumar Raghav, Rajesh Kumar, Vinod Kumar and Gajendra P.S. Raghava: Docking-based approach for identification of mutations that disrupts binding between Bcl-2 and Bax proteins: Inducing apoptosis in cancer cells. Molecular Genetics & Genomic Medicine.
Salman Sadullah Usmani, Rajesh Kumar, Vinod Kumar, Sandeep Singh, Gajendra P.S. Raghava: AntiTbPdb: a knowledgebase of anti-tubercular peptides. Database 02/2018; 2018:bay025., DOI:10.1093/database/bay025.
Harpreet kaur, Anjali Dhall, Rajesh Kumar and ,Gajendra P.S. Raghava: Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. Front Genet. 2020;10:1306. Published 2020 Jan 10. doi:10.3389/fgene.2019.01306
Piyush Agrawal, Sumeet Patiyal, Rajesh Kumar, Vinod Kumar, Harinder Singh, Pawan Kumar Raghav and Gajendra P.S. Raghava: ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/bay142. PubMed PMID: 30689843; PubMed Central PMCID: PMC6343045.
Sherry Bhalla, Ruchi Verma, Harpreet Kaur, Rajesh Kumar, Salman Sadullah Usmani, Suresh Sharma, Gajendra P.S. Raghava: CancerPDF: A repository of cancer-associated peptidome found in human biofluids. Scientific Reports 12/2017; 7(1)., DOI:10.1038/s41598-017-01633-3.
Piyush Agrawal, Sherry Bhalla, Kumardeep Chaudhary, Rajesh Kumar, Meenu Sharma, Gajendra P.S. Raghava: In Silico Approach for Prediction of Antifungal Peptides. Frontiers in Microbiology 02/2018; 9., DOI:10.3389/fmicb.2018.00323.
Vivek Dhar Dwiwedi, Aditya Arya, Pardeep Yadav, Rajesh Kumar, Vinod Kumar and Gajendra P.S. Raghava: DenvInD: dengue virus inhibitors database for clinical and molecular research. Brief Bioinform. 2020;bbaa098. doi:10.1093/bib/bbaa098
Sumeet Patiyal, Piyush Agrrawal, Vinod Kumar, Anjali Dhall, Rajesh Kumar and Gajendra P.S. Raghava: NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence. Protein Sci. 2020;29(1):201-210. doi:10.1002/pro.3761
Deepika Mathur, Satya Prakash, Priya Anand, Harpreet Kaur, Piyush Agrawal, Ayesha Mehta, Rajesh Kumar, Sandeep Singh, Gajendra P.S. Raghava: PEPlife: A Repository of the Half-life of Peptides. Scientific Reports 11/2016; 6:36617., DOI:10.1038/srep36617.
Akshara Pande, Sumeet Patiyal, Anjali Lathwal, Chakit Arora, Dilraj Kaur, Anjali Dhall, Gaurav Mishra, Harpreet Kaur, Neelam Sharma, Shipra Jain, Salman Sadullah Usmani, Piyush Agrawal, Rajesh Kumar, Vinod Kumar, Gajendra P.S. Raghava: Computing wide range of protein/peptide features from their sequence and structure. Journal of Computational Biology 2022.
Book Chapters
Rajesh Kumar, Anjali Lathwal, Gandharva Nagpal, Vinod Kumar, and Pawan Kumar Raghav: Computational application of chemo informatics tools in biological sciences. Springer – Chemo informatics protocols.
Rajesh Kumar, Shweta Kulshreshta, Anjali Lathwal, and Pawan Kumar Raghav: COVID-19 diagnostic approaches and modern mesenchymal stem cell-based treatment.
Salman Sadullah Usmani, Rajesh Kumar, Sherry Bhalla, Vinod Kumar, Gajendra P.S. Raghava: In silico Tools and Databases for Designing Peptide-Based Vaccine and Drugs. Advances in Protein Chemistry and Structural Biology. Jan 2018.
Review Articles
Harpreet kaur, Rajesh Kumar, Anjali Lathwal, and Gajendra P.S. Raghava: Computational resources on omics data based biomarkers in cancer. Oxford – Briefings in Functional Genomics. (co-first)
Anjali Lathwal, Rajesh Kumar and Gajendra P.S. Raghava: Computer-aided designing of oncolytic viruses for overcoming translational challenges of cancer immunotherapy. Drug Discov Today. 2020;25(7):1198-1205. doi:10.1016/j.drudis.2020.04.008 (co-corresponding)
Conference Article
Pawan Kumar Raghav, Rajesh Bhardwaj and Gajendra P.S. Raghava: Machine learning based identification of stem cell genes involved in stemness: Cell and stem cell research DOI:10.4172/2157-7013-CI-049.
In Press
Piyush Agrawal, Rajesh Kumar, Salman Sadullah Usmani, Anjali Dhall, Sumeet Patiyal, Neelam Sharma, Harpreet Kaur, Vinod Kumar, Dilraj Kaur, Shipra Jain, Akshara Pande, Sherry Bhalla, Gajendra PS Raghava: GPSRdocker: a Docker-based resource for genomics, proteomics and systems biology. (BioRxiv) (co-first)
Anjali Lathwal, Rajesh Kumar, Dilraj kaur, and Gajendra P.S. Raghava: In silico model for predicting IL-2 inducing peptides in human. https://doi.org/10.1101/2021.06.20.449146 (co-first)
Rajesh Kumar, Anjali Lathwal and Gajendra P.S. Raghava: Prognostic biomarker identification for pancreatic adenocarcinoma based on splicing pattern (https://www.biorxiv.org/content/biorxiv/early/2021/06/02/2021.06.02.446780.full.pdf)