Computational Genomics & Transcriptomics Laboratory


Publications

*Co-first author; #Corresponding author

2024 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012
Publications from 2024
  1. Kavita Kundal, Neeraj Kumar, Rahul Kumar(2024). Unravelling the Impact of Tumor Location on Patient Survival in Glioblastoma: A Genomics and Radiomics Approach.(preprint). medrxiv doi: https://doi.org/10.1101/2024.10.02.24314823
  2. Jyotika Srivastava, Kavita Kundal, Bhuvnesh Rai, Pragati Saxena, Naresh Tripathy, Ruchi Gupta, Sanjeev Yadav, Rahul Kumar, Soniya Nityanand, Chandra Prakash Chaturvedi (2024). Global microRNA profiling of bone marrow-MSC derived extracellular vesicles identifies miRNAs associated with hematopoietic dysfunction in aplastic anemia. Scientific Reports 14, 19654
  3. Rahul Kumar, Yanfeng Wang, Sandeep Kumar Dhanda (2024). How well does the adaptive feature representation learning approach identify human mRNA N4 - acetylcytidine sites? Molecular Therapy - Nucleic Acids., 35(3).
  4. Claudio Scuoppo, Bowen Cai, Kenneth Ofori, Hanna Scholze, Rahul Kumar, , Katia Basso, Laura Pasqualucci, Riccardo Dalla-Favera(2024). Repurposing NAMPT inhibitors for germinal center B-cell-like diffuse large B-cell lymphoma. Blood Cancer Discovery, 10.1158/2643-3230. BCD-24-0020.
  5. Kavita Kundal, K Venkateswara Rao, Arunabha Majumdar, Neeraj Kumar, Rahul Kumar# (2024). Comprehensive Benchmarking of CNN-Based Tumor Segmentation Methods Using Multimodal MRI Data, Computers in Biology and Medicine, 178, 108799.
  6. Simran Sharma, Kavita Kundal, Ishsirjan Kaur Chandok, Neeraj Kumar, Rahul Kumar(2024). Radiomic based investigation of a potential link between precuneus and fusiform gyrus with Alzheimer's disease. medRxiv doi:https://doi.org/10.1101/2024.05.15.24307.
  7. Bhanu Teja Korra*, Kunjulakshmi R*, Subashani*, Sushree Sangita Kar, Kavita Kundal, Avik Sengupta, Rahul Kumar# (2024). Drug Repurposing. Springer Handbook of Chem and Bioinformatics(Accepted)
  8. Keerthana Vinod Kumar*, Ambuj Kumar*, Kavita Kundal, Avik Sengupta, Kunjulakshmi R, Subashani, Bhanu Teja Korra, Simran Sharma, Vandana Suresh, Mayilaadumveettil Nishana, Rahul Kumar# (2024) AMLdb: A comprehensive multi-omics platform to understand the pathogenesis and discover biomarkers for acute myeloid leukemia. Briefings in Functional Genomics, elae024
  9. Shuvra Roy, Sulochana Bagri, Avik Sengupta, Claudia Regina Then, Rahul Kumar#, Sriram Sridharan, Shantanu Chowdhury (2024). Artificially inserted G-quadruplex DNA secondary structures induce long-distance chromatin activation, eLife, 13:RP96216
  10. Avik Sengupta, Saurabh Kumar Singh, Rahul Kumar#(2024). Support Vector Machine based prediction models for drug repurposing and designing novel drugs for colorectal cancer, ACS Omega, 9(16), 18584-18592
  11. Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar# (2024). AagingBase: A Comprehensive Database of Anti-aging Peptides, Database, 2024, baae016
  12. Ambuj Kumar*, Keerthana Vinod Kumar*, Kavita Kundal, Avik Sengupta, Simran Sharma, Kunjulakshmi R, Rahul Kumar# (2024). MyeloDB: A multi-omics resource for Multiple Myeloma, Functional & Integrative Genomics, 24(1), p.17
  13. Ambuj Kumar*, Keerthana Vinod Kumar*, Kunjulakshmi R*, Kavita Kundal, Avik Sengupta, Rahul Kumar# (2024). Advancement of in silico tools for stem cell research, Computational Biology for Stem Cell Research, (pp. 3-16). Academic Press.
Publications from 2023
  1. Rahul Kumar#, Kumardeep Chaudhary#, Sandeep Kumar Dhanda# (2023) Editorial: Recent Advances in Peptide Informatics: Challenges and Opportunities, Frontiers in Bioinformatics, 3, p.1271932.
  2. Sourbh Rankawat, Kavita Kundal, Shreyayukta Chakraborty, Rahul Kumar, and Sandipan Ray (2023) A Comprehensive Rhythmicity Analysis of Host Proteins and Immune Factors Involved in Malaria Pathogenesis to Decipher the Importance of Host Circadian Clock in Malaria. Frontiers in Immunology. 14:1210299.
  3. Mansi Manchanda, Monica Torres, Farydah Inuossa, Ritu Bansal, Rahul Kumar, Matthew Hunt, Craig E Wheelock, Etty Bachar-Wikstrom, Jakob D. Wikstrom (2023) Metabolic reprogramming and reliance in human skin wound healing. Journal of Investigative Dermatology 143(10):2039-2051.e10.
  4. Viswanathan A*, Kundal K*, Sengupta A, Kumar A, Kumar K V, Holmes A B, Rahul Kumar# (2023) Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome. Briefings in Functional Genomics, 22(1):42-48.
Publications from 2022
  1. Vigneshwaran G, Hasan Q A, Kumar R, Eranki A (2022) Analysis of single-nucleotide polymorphisms in genes associated with triple-negative breast cancer, Frontiers in Genetics, 13, p.1071352.
  2. Shwetha S; Subbamanda Y; Pullaguri N, Sharma A, Sahu C, Kumar R, Bhargava A (2022) Isoform-specific expression of T-type voltage-gated calcium channels and estrogen receptors in breast cancer reveals specific isoforms that may be potential targets. Current Research in Biotechnology , 4:459-467
  3. Bal E., Kumar R., et. al. (2022) Super-Enhancer Hypermutation Alters Oncogene Expression in B-cell Lymphoma.Nature 607, 808–815
  4. Kumar R., Deng Y., Fan JB, Wei L. (2022) Editorial: Early Detection and Diagnosis of Cancer. Frontiers in Genetics 13:875421
Publications from 2021
  1. Riaz N., Sherman E., Pei X., Scho¨ der H., Grkovski M., Paudyal R., Katabi N., Selenica P., Yamaguchi T. N., Ma D., Lee S. K., Shah R., Kumar R. et al (2021). Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial. Journal of National Cancer Institute. 113, 742-751
  2. Varano G., Roberto M. P., Vinas-Castells R., Holmes A. B., Kumar R., Farinha P., Scott D. W., Pasqualucci L., Dominguez-Sola D. (2021). FOXO1 mutations mimic positive selection signals to promote germinal center B cell expansion and lymphomagenesis. 54(8):1807-1824 Immunity.
  3. Fangazio M., Ladewig E., Gomez K., Garcia-Ibanez L., Kumar R., Teruya-Feldstein J. et. al. (2021). Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma. PNAS 118 (22) e2104504118.
  4. Xia B., Yanying H., Selenica P., Mahdi A., Pareja F., Kyker-Snowman K., Chen Y., Kumar R. et. al. (2021).Genetic interactions among Brca1, Brca2, Palb2 and Trp53 in mammary tumor development. npj Breast Cancer, 7, 45.
Publications from 2020
  1. Kumar R.# and Dhanda S. K. (2020) Current Status on Population Genome Catalogues in different Countries. Bioinformation 297-300
  2. Holmes A. B., Corinaldesi C., Shen Q., Kumar R. et. al. (2020) Single-cell analysis identifies subpopulations of germinal-center B-cells informing on lymphoma cell-of-origin and outcome. Journal of Experimental Medicine 217(10):e20200483.
Publications from 2019
  1. Mandelker, D.L.*, Kumar, R.*, Weigelt, B.* et. al. (2019) The Landscape of Somatic Genetic Alterations in Breast Cancers from CHEK2 Germline Mutation Carriers. JNCI Cancer Spectrum 3(2):pkz027
  2. Selenica P.*, Raj N.*, Kumar R.*, et. al. (2019). Solid pseudopapillary neoplasm of the pancreas are dependent on the Wnt pathway. Molecular Oncology. 13:1684-1692
  3. Pareja, F., Lee J. Y., Gularte-Mérida, R., Selenica P., Brown, D.N., Da Cruz Paula, A., Kumar R. et. al. (2019). The genomic landscape of mucinous breast cancer. JNCI: Journal of National Cancer Institute.. 111:737:741.
  4. Dogan S., Ng C. K., Xu B., Kumar R., Wang L., Edelweiss M., et.al. (2019) The Repertoire of Genetic Alterations in Salivary Duct Carcinoma Including a Novel HNRNPH3-ALK Rearrangement. Human Pathology. 88:66-7
  5. Olca Basturk, Britta Weigelt, Volkan Adsay, Jamal K. Benhamida, Gokce Askan, Lu Wang, Maria E. Arcila, Giuseppe Zamboni, Noriyoshi Fukushima, M.D., Rodrigo Gularte-Mérida, Arnaud Da Cruz Paula, Pier Selenica, Rahul Kumar et. al. (2019). Sclerosing Epithelioid Mesenchymal Neoplasm of the pancreas: a proposed new entity. Modern Pathology, 33, 456-467
  6. Anqi Li, Felipe C. Geyer, Pedro Blecua, Ju Youn Lee, Pier Selenica, David N. Brown, Fresia Pareja, Simon S.K. Lee, Rahul Kumar et. al. (2019). Homologous recombination DNA repair defects in PALB2-associated breast cancers. npj Breast Cancer. 5:1-14
  7. Ana Paula Martins Sebastiao, Fresia Pareja, Rahul Kumar, David N. Brown, Catarina Silveira, Edaise M. da Silva, Ju Youn Lee, Angela Del, Nora Katabi, Simion Chiosea, Britta Weigelt, Jorge S. Reis-Filho, Raja R. Seethala. Genomic analysis of recurrences and high-grade forms of polymorphous adenocarcinomas. Histopathology. 75:193-201.
Publications from 2018
  1. Weigelt, B.*, Bi, R.*, Kumar, R.*, et al. (2018) The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers. JNCI: Journal of National Cancer Institute. 110:1030-1034
  2. Pareja, F., Brandes, A.H., Basili, T., Selenica, P., Geyer, F.C., Fan, D., Da Cruz Paula, A., Kumar, R. et al. (2018) Loss-of-function mutations in the pH regulators ATP6AP1 and ATP6AP2 in granular cell tumors. 9:3533. Nature Communications.
  3. Geyer, F.C., Li, A., Papanastasiou, A.D., Smith, A., Selenica, P., Burke, K.A., Edelweiss, M., Wen, H.-C., Piscuoglio, S., Schultheis, A.M., Martelotto L.G., Pareja F., Kumar, R. et al. (2018) Recurrent hotspot mutations in HRAS Q61 and PI3K-AKT pathway genes as drivers of breast adenomyoepitheliomas. 9:1816 Nature Communications.
  4. Bajrami, I., Marlow, R., van de Ven, M., Brough, R., Pemberton, H.N., Frankum, J., Song, F., Rafiq, R., Konde, A., Krastev, D.B., Menon M., Campbell J., Gulati A., Kumar, R. et al. (2018). E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer. Cancer Discovery. 8, 498–515.
  5. Ashley C., Paula A. D. C., Kumar, R. et. al. (2018). Analysis of mutational signatures in primary and metastatic endometrial cancer reveals distinct patterns of DNA repair defects and shifts during tumor progression. Gynecologic Oncology. 152(1):11-19.
  6. Mueller, J.J., Schlappe, B.A., Kumar, R. et al. (2018). Massively parallel sequencing analysis of mucinous ovarian carcinomas: genomic profiling and differential diagnoses. Gynecologic Oncology. 150, 127–135.
  7. Brough, R., Gulati, A., Haider, S., Kumar, R. et. al. (2018). Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer. Oncogene. (IF: 9.86)
  8. Kim, J., Geyer, F.C., Martelotto, L.G., Ng, C.K., Lim, R.S., Selenica, P., Li, A., Pareja, F., Fusco, N., Edelweiss, M., Kumar R. et al. (2018). MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB - NFIB fusion gene. Journal of Pathology. 244, 143–150.
  9. Saraç, Ö.S., Kumar, R., Dhanda, S.K., Balcı, A.T., Bilgen, İ., Romero, R., and Tarca, A.L. (2018). Species translatable blood gene signature as a marker of exposure to smoking: Computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology Challenge. Computational Toxicology 5, 25–30
  10. Belcastro, V., Poussin, C., Xiang, Y., Giordano, M., Tripathi, K.P., Boda, A., Balci, A.T., Bilgen, I., Dhanda, S.K., Duan, Z., Gong X., Kumar R. et al. (2018). The sbv IMPROVER Systems Toxicology computational challenge: Identification of human and species-independent blood response markers as predictors of smoking exposure and cessation status. Computational Toxicology 5, 38–51.
Publications from 2017
  1. Nikkilä, J., Kumar, R. et al. (2017). Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells. British Journal of Cancer 117, 113–123.
  2. Pareja, F., Geyer, F.C., Kumar, R., Selenica, P., Piscuoglio, S., Ng, C.K.Y., Burke, K.A., Edelweiss, M., Murray, M.P., Brogi, E., et al. (2017). Phyllodes tumors with and without fibroadenoma-like areas display distinct genomic features and may evolve through distinct pathways. npj Breast Cancer 3, 40.
Publications from 2016
  1. Kumar, R., and Raghava, G.P.S. (2016). ApoCanD: Database of human apoptotic proteins in the context of cancer. Scientific Reports 6, 20797.
  2. Kumar, R.* et. al. (2016) dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. Scientific Reports 6, 19340.
  3. Gupta, S., Chaudhary, K., Kumar, R., Gautam, A., Nanda, J.S., Dhanda, S.K., Brahmachari, S.K. and Raghava, G.P.S. (2016) Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine. Scientific Reports 6, 23857.
  4. Gupta S, Chaudhary K, Dhanda SK, Kumar R, Kumar S, Sehgal M, et al. (2016). A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer. PLoS ONE 11(11).
  5. Gautam, A., Chaudhary, K., Kumar, R., Gupta, S., Singh, H. and Raghava, G.P.S. (2016) Managing Drug Resistance in Cancer: Role of Cancer Informatics. Methods Mol. Biol., 1395, 299–312. (Book Chapter)
Publications from 2015
  1. Kumar, R.*, Chaudhary, K.*, Singh Chauhan, J.*, Nagpal, G.*, Kumar, R.* et. al. (2015) An in silico platform for predicting, screening and designing of antihypertensive peptides. Scientific Reports 5, 12512.
  2. Singh, H., Kumar, R., Singh, S., Chaudhary, K., Gautam, A. and Raghava, G.P.S. (2015) Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines. BMC Cancer, 16, 77.
  3. Gautam, A., Sharma, M., Vir, P., Chaudhary, K., Kapoor, P., Kumar, R., Nath, S.K. and Raghava, G.P.S. (2015) Identification and characterization of novel protein-derived arginine-rich cell-penetrating peptides. Eur. J. Pharm. Biopharm., 89, 93–106
  4. Boue, S., Fields, B., Hoeng, J., Park, J., Peitsch, M.C., Schlage, W.K., Talikka, M., Binenbaum, I., Bondarenko, V., Bulgakov, O. V, Cherkasova, V., Diaz-Diaz, N., Fedorova, L., Guryanova, S., Guzova, J., Koroleva, G.I., Kozhemyakina, E.,Kumar, R. et al. (2015) Enhancement of COPD biological networks using a web-based collaboration interface. F1000Research, 4, 32.
  5. Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R. and Raghava, G.P.S. (2015) Peptide toxicity prediction. Methods Mol. Biol., 1268, 143–57. (Book Chapter)
  6. Gautam, A., Chaudhary, K., Kumar, R. and Raghava, G.P.S. (2015) Computer-Aided Virtual Screening and Designing of Cell-Penetrating Peptides. Methods Mol. Biol., 1324, 59–69. (Book Chapter)
  7. Kumar, R. et al. In Silico Designing and Screening of Antagonists against Cancer Drug Target XIAP. Current Cancer Drug Targets 15, 836–846.
Publications from 2014
  1. Sharma, A., Kapoor, P., Gautam, A., Chaudhary, K., Kumar, R., Chauhan, J.S., Tyagi, A. and Raghava, G.P.S. (2013) Computational approach for designing tumor homing peptides. Scientific Reports, 3, 1607.
  2. Kumar, R. et al. (2014a). Designing of promiscuous inhibitors against pancreatic cancer cell lines. Scientific Reports 4, 4668.
  3. Ahmad, S., Gupta, S., Kumar, R., Varshney, G.C. and Raghava, G.P.S. (2014) Herceptin resistance database for understanding mechanism of resistance in breast cancer patients. Scientific Reports, 4, 4483.
Publications from 2013
  1. Kumar, R. et. al. (2013b). CancerDR: Cancer Drug Resistance Database. Scientific Reports 3, 1445.
  2. Gautam,A.*, Chaudhary,K.*, Kumar,R.*, et. al. (2013) In silico approaches for designing highly effective cell penetrating peptides. Journal of Translational Medicine, 11, 74
  3. Sharma,A., Kapoor,P., Gautam,A., Chaudhary,K., Kumar,R., Chauhan,J.S., Tyagi,A. and Raghava,G.P.S. (2013) Computational approach for designing tumor homing peptides. Scientific Reports, 3, 1607
  4. Tyagi,A., Kapoor,P., Kumar,R., Chaudhary,K., Gautam,A. and Raghava,G.P.S. (2013) In silico models for designing and discovering novel anticancer peptides. Scientific Reports 3, 2984
  5. Gupta,S., Kapoor,P., Chaudhary,K., Gautam,A., Kumar,R. and Raghava,G.P.S. (2013) In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8, e73957
Publications from 2012
  1. Kapoor,P., Singh,H., Gautam,A., Chaudhary,K., Kumar,R., and Raghava,G.P.S. (2012) TumorHoPe: a database of tumor homing peptides. PLoS One, 7, e35187
  2. Gautam,A., Singh,H., Tyagi,A., Chaudhary,K., Kumar,R., Kapoor,P. and Raghava,G.P.S. (2012) CPPsite: a curated database of cell penetrating peptides. Database (Oxford), 2012, bas015