Research Publications

Research Interests

1.      Discovery of Disease Biomarker based on multi-omics Profiles/Big data of patients using Artificial Intelligence (Machine learning or Deep learning) Techniques.

2.      Development of novel web-based in silico Tools for predicting the Disease status from patients’ Genomics Profiles.

3.      Designing of new therapeutic strategy to Human Diseases/Public Health implementing Computational Techniques.

4.    Development of Resources/Knowledgebase for Biomarkers/Drug candidates of Human Diseases/Public Health implementing Computational Techniques.

List of Publications

• Latest list of Research publications can be found  at the GOOGLE SCHOLAR

Published Manuscripts

1. Kaur H*, Bhalla S, Kaur D, Raghava GPS. CancerLivER: A Database of Liver Cancer Gene Expression Resources and Biomarkers. Database, 2020. https://doi.org/10.1093/database/baaa012

2. Kaur H*, Dhall A, Kumar R, Raghava GPS. Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma using Large-Scale Transcriptomics Data. Front. Genet. doi: 10.3389/fgene.2019.01306

3. Kaur H*, Bhalla S, Raghava GPS. Classification of Early and Late Stage Liver Hepatocellular Carcinoma Patients from their Genomics and Epigenomics Profiles. PloS One, 14(9), 2019

4. Kaur H*, Kumar R, Lathwal A, Raghava GPS. Computational Resources for Identification of Cancer Biomarkers from Omics Data. Briefings in Functional Genomics

5. S. Bhalla#, H. Kaur#, A. Dhall, GPS Raghava. Prediction and Analysis of Skin Cancer Progression Using Genomics Profiles of Patients. Scientific Reports, 9(1), 1-162018, 2019. #- Equal First Author

6. S. Bhalla#, R. Verma#, H. Kaur#, R. Kumar, S.S. Usmani, S. Sharma, GPS Raghava. CancerPDF: A Repository of Cancer-Associated Peptidome Found in Human Biofluids. Scientific Reports, 9(1), 1-162018, 2017. #Equal First Author

7. Mathur D#, Kaur H#, Raghava GPS. SAPdb: A Database of Short Peptides and the Corresponding Nanostructures Formed by Self-Assembly. Computers in Biology and Medicine. #- Equal First Author

8. Patiyal S#, Kaur D#, Kaur H#, Sharma N#, Dhall A, Sahai S, Agrawal P, Maryam L, Arora C, Raghava GPS. A Web-Based Platform on COVID-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates. Monoclonal Antibodies in Immunodiagnosis and Immunotherapy  #Equal First Author

9. S. Akhter, H. Kaur, P. Agrawal, GPS Raghava. RareLSD: A Manually Curated Database of Lysosomal Enzymes Associated with Rare Diseases. Database, 2019, baz112.

10. S Bhalla, K Chaudhary, R Kumar, M Sehgal, H Kaur, S Sharma, GPS Raghava. Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer (2017). Scientific reports 7, 44997.

11. G Nagpal, SS Usmani, SK Dhanda, H Kaur, S Singh, M Sharma, GPS Raghava. Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Scientific reports 7, 42851, 2017.

12. Mathur D, Prakash S, Anand P, Kaur H, Agrawal P, A Mehta, R Kumar, GPS Raghava. Peplife: A Repository of the Half-life of Peptides. Scientific Reports 2016. (IF: 4.38).

13. Dhall A, Patiyal S, Kaur H, Bhalla S, Arora C, Raghava GPS. Computing Skin Cutaneous Melanoma Outcome from the HLA-alleles and Clinical Characteristics. Front. Genet. | doi: 10.3389/fgene.2020.00221

14. S Bhalla, H Kaur, R Kaur, S Sharma, G Raghava. (2020) Expression based biomarkers and models to classify early and late stage samples of Papillary Thyroid Carcinoma. Plos One.

15. MJ Mason et al. Multiple Myeloma DREAM Challenge Reveals Epigenetic Regulator PHF19 As Marker of Aggressive Disease. Leukemia (2020). https://doi.org/10.1038/s41375-020-0742-z.  (IF: 11.53) Consortium Author.

16. Mi Yang et al. Assessment of the Limits of Predictability of Protein and Phosphorylation Levels in Cancer. Cell Systems (2020) (IF: 8.67)  Consortium Author

17. A Gabor et al., (2021). Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd. Molecular Systems Biology (IF 11.43).  Consortium Author

18. Tarca Adi L et., al (2021). Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. Cell Reports Medicine     Consortium Author

19. Dolaner S, Kaur H$, Brodsky E, Panov J, Mazumder M (2021) Identification of LncRNAs as Therapeutic Targets in Chronic Lymphocytic Leukemia. https://doi.org/10.52214/cusj.v15i1.7787

20. Sapra D, Kaur H, Dhall A, Raghava GPS. ProCanBio: a database of manually curated biomarkers for Prostate Cancer. Journal of Computational Biology 20 (12), 1248-1257

21. Vaja R, Kaur H$, Mazumder M, Brodsky E (2021). In silico Analysis of Transcriptomic Profiling and Affected Biological pathways in Multiple Sclerosis.  Immunogenet Open Access. 7:167. doi: 10.35248/IGOA.22.7.167 $ - Mentor or Co-mentor

22. Dey S, Kaur H$, Brodsky E, Mazumder M (2021) Analysis of Gene Expression Profiles to study Malaria Vaccine Dose Efficacy & Immune Response Modulation. Genomics & Informatics 2022; 20(3): e32. doi: https://doi.org/10.5808/gi.22049. $ - Mentor or Co-mentor

23. Diaz Rosario M, Kaur H, Tasci E, Shankavaram U, Sproull M, Zhuge Y, Camphausen K, Krauze A. The Next Frontier in Health Disparities—A Closer Look at Exploring Sex Differences in Glioma Data and Omics Analysis, from Bench to Bedside and Back. Biomolecules. 2022; 12(9):1203. https://doi.org/10.3390/biom12091203.

24. Tasci E, Zhuge Y, Kaur H, Camphausen K, Krauze AV. Hierarchical Voting-Based Feature Selection and Ensemble Learning Model Scheme for Glioma Grading with Clinical and Molecular Characteristics. International Journal of Molecular Sciences. 2022; 23(22):14155. https://doi.org/10.3390/ijms232214155

25. Pande A, et al.,. Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models. J Comput Biol. 2022 Oct 13. doi: https://doi.org/10.1089/cmb.2022.0241.

26. Sen P, Kaur H$ (2023). In silico transcriptional analysis of asymptomatic and severe COVID-19 patients reveals the susceptibility of severe patients to other comorbidities and non-viral pathological conditions. Human Gene. https://doi.org/10.1016/j.humgen.2022.201135  $ - Corresponding author

27. Deng X, Das S, Kaur H, Wilson E, Camphausen K, Shankavaram U. Glioma-BioDP: database for visualization of molecular profiles to improve prognosis of brain cancer. BMC Med Genomics. 2023 Jul 15;16(1):168. doi: 10.1186/s12920-023-01593-w.

28. Gaines, D., Brodsky, E., Kaur, H. et al. RNA capture pin technology: investigating long-term stability and mRNA purification specificity of oligonucleotide immobilization on gold and streptavidin surfaces. Anal Bioanal Chem (2023). https://doi.org/10.1007/s00216-023-04882-6

29. A Dhall, S Patiyal, H Kaur, GPS Raghava (2023). Risk assessment of cancer patients based on HLA-I alleles, neobinders and expression of cytokines. Computers in Biology and Medicine.  https://doi.org/10.1016/j.compbiomed.2023.107594

30. Basu, S. et al. (2023) Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol 30, 1958–1969 (2023).  https://doi.org/10.1038/s41594-023-01159-5

Published abstract in Journals

1. Kaur H, Das,P, Camphausen K, Shankavaram U (2025).  Streamlining Survival Analysis: An Automated Machine Learning Pipeline for Cancer Patient Survival Predictions: Case Study on Kidney Renal Clear Cell Carcinoma. Cancer Res (2025) 85 (5_Supplement): B040. https://doi.org/10.1158/1538-7445.GENFUNC25-B040

2. Kaur H*, Bhalla S, Garg D, Mehta N, Raghava GPS (2020) Analysis and Prediction of Cholangiocarcinoma from transcriptomics Profiles. Journal of Hepatology 73 (Supplement 1), S16-S17

3. Kaur H*, Lathwal A, Dhall A, Raghava GPS. Integrative multi-omics approach for stratification of tumor recurrence risk groups of Hepatocellular Carcinoma patients. Hepatology 74 (S1), 346A - 347A.

4. Kaur H*, Bhalla S and Raghava GPS. (2018) Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. 17th International Conference on Bioinformatics 2018 (Incob2018), Jawaharlal Nehru University, New Delhi, DDVT-15, Page No.50, 2018

Softwares|Packages

R-package On Bioconductor

1.     CPSM: Cancer patient survival model

Manuscripts (Preprints/Under Review)

1. Kaur H, Das,P, Camphausen K, Shankavaram U (2024). CPSM: R-package of an Automated Machine Learning Pipeline for Predicting the Survival Probability of Single Cancer Patient. bioRxiv 2024.11.14.623597; doi: https://doi.org/10.1101/2024.11.14.623597

2. Kaur H, Lathwal A, Raghava GPS. Integrative multi-omics approach for stratification of tumor recurrence risk groups in Hepatocellular Carcinoma patients.

3. Parekh U, Mazumder M, Kaur H$, Brodsky E. In Silico Analysis and Characterization of Differentially Expressed Genes to Distinguish Glioma Stem Cells from Normal Neural Stem Cells $ (Mentor/Co-mentor).

4. Agrawal P et al. GPSRdocker: A Docker-based resource for genomics, proteomics, and systems biology. BioRxiv, 2019.

5. Diken D, Brodsky E, Kaur H$, Mazumdar M. Radiation Threats to Humans in Space and an Alternative Approach with Probiotics $ (Mentor/Co-mentor).

6. Barua S, Komissarov A, Kaur H$, Brodsky E (2021). Transcriptomic analysis of DNA damage response in zebrafish embryos under simulated microgravity. doi: 10.1101/2021.09.30.462627 $ (Mentor/Co-mentor).

Oral and Poster Presentations in Conferences

1. Kaur H. Analysis and Prediction of Cholangiocarcinoma from Transcriptomics Profiles. The Digital International Liver Congress 2020.

2. Kaur H. Oral presentation as a Workshop Mentor. 197th International Conference on Bioinformatics 2020 (INCOB-2020).

3. Kaur H. 177th International Conference on Bioinformatics 2018 (INCOB-2018), Jawaharlal Nehru University, New Delhi.

4. Kaur H, Camphausen K, Shankavaram U (2023). Identification and Validation of Radiosensitive Prognostic Signature for GBM. RECOMB/ISCB RSGDREAM 2023.

5. Kaur H, Lathawal A, Dhall A, Raghava GPS. Integrative multi-omics approach for stratification of tumor recurrence risk groups in Hepatocellular Carcinoma patients. AASLD - Liver Meeting 2021.

6. Kaur H, Brodsky E, Mazumder M, Mensah B, Ghansah A (2021). Effect of circulating PfAMA1 haplotype variants on merozoite invasion and vaccine development strategies. 8th Annual Louisiana Biomedical Research Network Conference.

7. Dey S, Kaur H$, Mazumder M, Brodsky E (2021). Malaria RTS,S/AS01 Vaccine’s Association with Controlled Inflammation and Increased Protection. Omics Research Symposium 2021.

8. Vaja R, Kaur H$, Mazumder M, Brodsky E (2021). In silico analysis of Transcriptomics Profiling and Biological Pathways in Multiple Sclerosis. Omics Research Symposium 2021.

9. Mehra D, Kaur H$, Brodsky E, Mazumder M (2021). Transcriptomic Analysis of Histological Subtypes in Esophageal Carcinoma. Omics Research Symposium 2021.

10. Singh A, Kaur H$, Brodsky E, Mazumder M (2021). Bioinformatics Analysis of IDH-mutant Glioblastoma. Omics Research Symposium 2021.

11. Sharma K, Kaur H$, Brodsky E, Mazumder M. Transcriptional changes in small cell lung cancer patients with brain metastasis. Omics Research Symposium 2021.

12. Kaur J, Kaur H$, Brodsky E, Mazumder M. Bioinformatics approach to analyze variants in Retinitis Pigmentosa. Omics Research Symposium 2021.

13. Adobor C, Kaur H, Brodsky E, Ghansah A. Mutability studies of sexual-stage specific antigens of Plasmodium falciparum in Africa. Omics Research Symposium 2021.

14. Kaur H. Anti-oxidant and anti-proliferative potential of T. arjuna bark extract. 5th National Conference on Recent Advances in Chemical & Environmental Sciences (RACES-2013).