Department of Computational Biology

Journal Publications

2022

• P. Garg, S. Sacher, Mrinal, Atul, P. Gautam, A. Ray. "CICLOP: A Robust, Faster, and Accurate Computational Framework for Protein Inner Cavity Detection." Bioinformatics.
• S. Sunidhi, S. Sacher, Atul, P. Garg, A. Ray. "Elucidating the Structural Features of ABCA1 in its Heterogeneous Membrane Environment." Frontiers In Molecular Sciences.
• V. Gautam, R. Gupta, D. Gupta, A. Ruhela, A. Mittal, SK. Mohanty, S. Arora, R. Gupta, C. Saini, D. Sengupta, NA. Murugan, G. Ahuja. "deepGraphh: AI-driven web service for graph-based quantitative structure-activity relationship analysis" Briefings in Bioinformatics.
• IC. Mondal, M. Galkin, S. Sharma, NA. Murugan, DA. Yushchenko, K. Girdhar, A. Karmakar, P. Mondal, P. Gaur, S. Ghosh. "Organosulfur/Selenium-Based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging" Chemistry An Asian Journal.
• B. Biswas, S. Dogra, G. Dey, NA. Murugan, P. Mondal, S. Ghosh. "Near-infrared emissive cyanine probes for selective visualization of the physiological and pathophysiological modulation of albumin levels" Journal of Materials chemistry B.
• A. Dhall, S. Jain, N. Sharma, LD. Naorem, D. Kaur, S. Patiyal, GPS Raghava. "In silico tools and databases for designing cancer immunotherapy" Adv Protein Chem Struct Bio.
• N. Sharma, LD. Naorem, S. Jain, GPS Raghava. "ToxinPred2: an improved method for predicting toxicity of proteins" Briefings in Bioinformatics.
• S. Jain, A. Dhall, S. Patiyal, GPS Raghava. "IL13Pred: A method for predicting immunoregulatory cytokine IL-13 inducing peptides" Computers in Biology and Medicine.
• A. Dhall, S. Patiyal, GPS Raghava. "HLAncPred: a method for predicting promiscuous non-classical HLA binding sites" Briefings in Bioinformatics.
• V. Kumar, GPS Raghava. "In Silico Design of Chemically Modified Cell-Penetrating Peptides" Methods in molecular biology.
• S. Patiyal, A. Dhall, GPS Raghava. "A deep learning-based method for the prediction of DNA interacting residues in a protein" Briefings in Bioinformatics.
• S. Patiyal, A. Dhall, GPS Raghava. "Prediction of risk-associated genes and high-risk liver cancer patients from their mutation profile: benchmarking of mutation calling techniques" Biology Methods and Protocols.
• C. Arora, D. Kaur, GPS Raghava. "Universal and cross-cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes" Proteomics and Systems Biology.
• M. Goel, G. Bagler. "Computational gastronomy: A data science approach to food" Journal of Biosciences.
• A. Mittal, SK. Mohanty, V. Gautam, S. Arora, S. Saproo, R. Gupta, R. Sivakumar, P. Garg, A. Aggarwal, P. Raghavachary, NK. Dixit, VP. Singh, A. Mehta, J. Tayal, S. Naidu, D. Sengupta, G. Ahuja. "Artificial intelligence uncovers carcinogenic human metabolites" Natural Chemical Biology.
• P. Gupta, A. Jindal, G. Ahuja, Jayadeva, D. Sengupta. "A new deep learning technique reveals the exclusive functional contributions of individual cancer mutations" Journal of Biological Chemistry.
• M. Sharma, IP. Jha, S. Chawla, N. Pandey, O. Chandra, S. Mishra, V. Kumar. "Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs" Briefings in Bioinformatics.
• R. Awasthi, KK. Guliani, SA. Khan, A. Vashishtha, MS. Gill, A. Bhatt, A. Nagori, A. Gupta, P. Kumaraguru, T. Sethi. "VacSIM: Learning effective strategies for COVID-19 vaccine distribution using reinforcement learning" Intell Based Med.
• YR. Tan, A. Agrawal, MP. Matsoso, R. Katz, SLM. Davis, AS. Winkler, A. Huber, A. Joshi, A. El-Mohandes, B. Mellado, CA. Mubaira, FC. Canlas, G. Asiki, H. Khosa, JV. Lazarus, M. Choisy, M. Recamonde-Mendoza, O. Keiser, P. Okwen, R. English, S. Stinckwich, S. Kiwuwa-Muyingo, T. Kutadza, T. Sethi, T. Mathaha, VK. Nguyen, A. Gill, P. Yap. "A call for citizen science in pandemic preparedness and response: beyond data collection" BMJ Global Health.
• AK. Singh, P. Mehan, D. Sharma, R. Pandey, T. Sethi, P. Kumaraguru. "COVID-19 Mask Usage and Social Distancing in Social Media Images: Large-scale Deep Learning Analysis" JMIR Public Health Surveill.
• S. Nagpal, R. Pal, Ashima, A. Tyagi, S. Tripathi, A. Nagori, S. Ahmad, HP. Mishra, R. Malhotra, R. Kutum, T. Sethi. "Genomic Surveillance of COVID-19 Variants With Language Models and Machine Learning" Frontiers in Genetics.
• R. Pandey, V. Gautam, R. Pal, H. Bandhey, LS. Dhingra, V. Misra, H. Sharma, C. Jain, K. Bhagat, Arushi, L. Patel, M. Agarwal, S. Agrawal, R. Jalan, A. Wadhwa, A. Garg, Y. Agrawal, B. Rana, P. Kumaraguru, T. Sethi. "A machine learning application for raising WASH awareness in the times of COVID-19 pandemic" Scientific Reports.
• R. Awasthi, V. Rakholia, S. Agrawal, LS. Dhingra, A. Nagori, H. Kaur, T. Sethi. "Estimating the impact of health systems factors on antimicrobial resistance in priority pathogens" J Glob Antimicrob Resist.
• S. Alle, A. Kanakan, S. Siddiqui, A. Garg, A. Karthikeyan, P. Mehta, N. Mishra, P. Chattopadhyay, P. Devi, S. Waghdhare, A. Tyagi, B. Tarai, PP. Hazarik, P. Das, S. Budhiraja, V. Nangia, A. Dewan, R. Sethuraman, C. Subramanian, M. Srivastava, A. Chakravarthi, J. Jacob, M. Namagiri, V. Konala, D. Dash, T. Sethi, S. Jha, A. Agrawal, R. Pandey, PK. Vinod, UD. Priyakumar. "COVID-19 Risk Stratification and Mortality Prediction in Hospitalized Indian Patients: Harnessing clinical data for public health benefits" PLOS ONE
• V. Vats, A. Nagori, P. Singh, R. Dutt, H. Bandhey, M. Wason, R. Lodha, T. Sethi. "Early Prediction of Hemodynamic Shock in Pediatric Intensive Care Units With Deep Learning on Thermal Videos" Frontiers in Physiology.
• R. Pal, H. Chopra, R. Awasthi, H. Bandhey, A. Nagori, T. Sethi. "Predicting Emerging Themes in Rapidly Expanding COVID-19 Literature with Unsupervised Word Embeddings and Machine Learning" J Med Internet Res.

2021

• M. Haider, D. Dholakia, A. Panwar, P. Garg, A. Gheware, D. Singh, K. Singhal, S. A. Burse, S Kumari, A. Sharma, A. Ray, G. R. Medigeshi, U. Sharma, B. Prasher, M. Mukerji. "Transcriptome analysis and connectivity mapping of Cissampelos pareira L. provides molecular links of ESR1 modulation to viral inhibition." Scientific Reports.
• K. Gupta, M. Lalit, A. Biswas, C. D. Sanada, C. Greene, K. Hukari, U. Maulik, S. Bandyopadhyay, N. Ramalingam, G. Ahuja, A. Ghosh, D. Sengupta. "Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data." Genome Research.
• S. Ansari, A. Ray, M. F. Ali, S. Bano, M. A. Jairajpuri. "Contrasting conformational dynamics of �-sheet A and helix F with implications in neuroserpin inhibition and aggregation." International Journal of Biological Macromolecules.
• A. Chaudhary, S. Bhalla, S. Patiyal, GPS Raghava, G. Sahni. "FermFooDb: A database of bioactive peptides derived from fermented foods" Heliyon.
• P. Agrawal, D. Bhagat, M. Mahalwal, N. Sharma, GPS Raghava. "AntiCP 2.0: an updated model for predicting anticancer peptides" Briefings in Bioinformatics.
• D Sapra, H Kaur, A Dhall, GPS Raghava. "ProCanBio: A Database of Manually Curated Biomarkers for Prostate Cancer" Journal of Computational Biology.
• V. Kumar, S. Patiyal, R. Kumar, S. Sahai, D. Kaur, A. Lathwal, GPS Raghava. "B3Pdb: an archive of blood-brain barrier-penetrating peptides" Brain Structure and Function.
• D. Kaur, S. Patiyal, C. Arora, R. Singh, G. Lodhi, GPS Raghava. "In-Silico Tool for Predicting,Scanning,and Designing Defensins" Frontiers in Immunology.
• A. Dhall, S. Patiyal, N. Sharma, NL. Devi, GPS Raghava. "Computer-aided prediction of inhibitors against STAT3 for managing COVID-19 associated cytokine storm" Computers in Biology and Medicine.
• N. Sharma, S. Patiyal, A. Dhall, NL. Devi, GPS Raghava. "ChAlPred: A web server for prediction of allergenicity of chemical compounds" Computers in Biology and Medicine.
• D Mathur, H Kaur, A Dhall, N Sharma, GPS Raghava. "SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly" Computers in Biology and Medicine.
• L. Maryam, SS Usmani, GPS Raghava. "Computational resources in the management of antibiotic resistance: Speeding up drug discovery" Drug Discovery Today.
• A. Lathwal, R. Kumar, GPS Raghava. "In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses" Computers in Biology and Medicine.
• D. Kaur, C. Arora, GPS Raghava. "Prognostic Biomarker-Based Identification of Drugs for Managing the Treatment of Endometrial Cancer" Molecular Diagnosis & Therapy.
• A. Dhall,S. Patiyal, N. Sharma, SS. Usmani, GPS Raghava. "Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19" Briefings in Bioinformatics.
• N. Sharma, S. Patiyal, A. Dhall, A. Pande, C. Arora, GPS Raghava. "AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes" Briefings in Bioinformatics.
• V. Kumar, S. Patiyal, A. Dhall, N. Sharma, GPS Raghava. "B3Pred: A Random-Forest-Based Method for Predicting and Designing Blood-Brain Barrier Penetrating Peptides" Pharmaceutics.
• C. Arora, D. Kaur, LD. Naorem, GPS Raghava. "Prognostic biomarkers for predicting papillary thyroid carcinoma patients at high risk using nine genes of apoptotic pathway" PLOS ONE.
• A. Farswan, A. Gupta, K. Sriram, A. Sharma, L. Kumar, R. Gupta. "Does Ethnicity Matter in Multiple Myeloma Risk Prediction in the Era of Genomics and Novel Agents? Evidence From Real-World Data" Frontiers in Oncology.
• K. Gupta, SK. Mohanty, A. Mittal, S. Kalra, S. Kumar, T. Mishra, J. Ahuja, D. Sengupta, G. Ahuja. "The Cellular basis of loss of smell in 2019-nCoV-infected individuals" Briefings in Bioinformatics.
• R. Gupta, A. Mittal, V. Agrawal, S. Gupta, K. Gupta, RR. Jain, P. Garg, SK. Mohanty, R. Sogani, HS. Chhabra, V. Gautam, T. Mishra, D. Sengupta, G. Ahuja. "OdoriFy: A conglomerate of artificial intelligence-driven prediction engines for olfactory decoding" Journal of Biological Chemistry.
• S. Kalra, A. Mittal, M. Bajoria, T. Mishra, S. Maryam, D. Sengupta, G. Ahuja. "Challenges and possible solutions for decoding extranasal olfactory receptors" The FEBS Journal.
• V. Gautam, A. Mittal, S. Kalra, SK. Mohanty, K. Gupta, K. Rani, S. Naidu, T. Mishra, D. Sengupta, G. Ahuja. "EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies" Briefings in Bioinformatics.
• K. Gupta, P. Yadav, S. Maryam, G. Ahuja, D. Sengupta. "Quantification of Age-Related Decline in Transcriptional Homeostasis" Journal of Molecular Biology.
• K. Gupta, K. Balyan, B. Lamba, M. Puri, D. Sengupta, M. Kumar. "Ultrasound placental image texture analysis using artificial intelligence to predict hypertension in pregnancy" The Journal of Maternal-Fetal & Neonatal Medicine.
• RC. Gerkin, K. Ohla, MG. Veldhuizen, PV. Joseph, CE. Kelly, AJ. Bakke, KE. Steele, MC. Farruggia, R. Pellegrino, MY. Pepino, C. Bouysset, GM. Soler, V. Pereda-Loth, M. Dibattista, KW. Cooper, I. Croijmans, A. Di Pizio, MH. Ozdener, AW. Fjaeldstad, C. Lin, MA. Sandell, PB. Singh, VE. Brindha, SB. Olsson, LR. Saraiva, G. Ahuja, MK. Alwashahi, S. Bhutani, A. D'Errico, MA. Fornazieri, J. Golebiowski, L. Dar Hwang, L. Öztürk, E. Roura, S. Spinelli, KL. Whitcroft, F. Faraji, FPS. Fischmeister, T. Heinbockel, JW. Hsieh, C. Huart, I. Konstantinidis, A. Menini, G. Morini, JK. Olofsson, CM. Philpott, D. Pierron, VDC. Shields, VV. Voznessenskaya, J. Albayay, A. Altundag, M. Bensafi, MA. Bock, O. Calcinoni, W. Fredborg, C. Laudamiel, J. Lim, JN. Lundström, A. Macchi, P. Meyer, ST. Moein, E. Santamaría, D. Sengupta, P. Rohlfs Dominguez, H. Yanik, T. Hummel, JE. Hayes, DR. Reed, MY. Niv, SD. Munger, V. Parma; GCCR Group Author. "Recent Smell Loss Is the Best Predictor of COVID-19 Among Individuals With Recent Respiratory Symptoms" Chemical Senses.
• S. Chawla, S. Samydurai, SL. Kong, Z. Wu, Z. Wang, WL. Tam, D. Sengupta, V. Kumar. "UniPath: a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles" Nucleic Acids Research.
• A. Gupta, M. Choudhary, SK. Mohanty, A. Mittal, K. Gupta, A. Arya, S. Kumar, N. Katyayan, NK. Dixit, S. Kalra, M. Goel, M. Sahni, V. Singhal, T. Mishra, D. Sengupta, G. Ahuja. "Machine-OlF-Action: A unified framework for developing and interpreting machine-learning models for chemosensory research" Bioinformatics.
• A. Iyer, K. Gupta, S. Sharma, K. Hari, YF. Lee, N. Ramalingam, YS. Yap, J. West, AA. Bhagat, BV. Subramani, B. Sabuwala, T. Zea Tan, JP. Thiery, MK. Jolly, N. Ramalingam, D. Sengupta. "Erratum: Iyer,A.,et al. Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells. J. Clin. Med. 2020,9,1206" Journal of Clinical Medicine.
• IP. Jha, R. Awasthi, A. Kumar, V. Kumar, T. Sethi. "Learning the Mental Health Impact of COVID-19 in the United States With Explainable Artificial Intelligence: Observational Study" JMIR Mental Health.
• M. Sharma, RK. Verma, S. Kumar, V. Kumar. "Computational challenges in detection of cancer using cell-free DNA methylation" Computational and Structural Biotechnology Journal.
• N. Pandey, O. Chandra, S. Mishra, V. Kumar. "Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain" Frontiers in Genetics.
• G. Arora, J. Joshi, RS. Mandal, N. Shrivastava, R. Virmani, T. Sethi. "Artificial Intelligence in Surveillance,Diagnosis,Drug Discovery and Vaccine Development against COVID-19" Pathogens.
• D. Tamuli, M. Kaur, T. Sethi, A. Singh, M. Faruq, AK. Jaryal, AK. Srivastava, SS. Kumaran, KK. Deepak. "Cortical and Subcortical Brain Area Atrophy in SCA1 and SCA2 Patients in India: The Structural MRI Underpinnings and Correlative Insight Among the Atrophy and Disease Attributes" Neurology India.

2020

• A. Sadat, S. Tiwari, K. Verma, A. Ray, K. Mapa. "GROEL/ES Buffers Entropic Traps in Folding Pathway during Evolution of a Model Substrate." Journal of Molecular Biology.
• P. Singh, R. Chakraborty, R. Marwal, V. S. Radhakrishan, A. K. Bhaskar, H. Vashisht, M. S. Dhar, S. Pradhan, G. Ranjan, M. Imran, A. Raj, U. Sharma, P. Singh, H. Lall, M. Dutta, P. Garg, A. Ray, S. Sengupta et. al. "A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry." Springer Link.
• D. Kaur, C. Arora, G. P. S. Raghava. "A Hybrid Model for Predicting Pattern Recognition Receptors Using Evolutionary Information." Frontiers In Immunology.
• A. Dhall, S. Patiyal, H. Kaur, S. Bhalla, C. Arora, G. P. S. Raghava. "Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics." Frontiers in Genetics.
• V. Kumar, R. Kumar, P. Agrawal, S. Patiyal G. P.S. Raghava. "A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure." Frontiers in Pharmacology.
• P. Agrawal, G. Mishra,G. P. S. Raghava. "SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence." Frontiers in Pharmacology.
• L. Dawman, A. Mukherjee, T. Sethi, A. Agrawal, S. K. Kabra, R. Lodha. "Role of Impulse Oscillometry in Assessing Asthma Control in Children." Indian Pediatrics.
• M. J Mason, G.P.S. Raghava and others. "Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease." Leukemia.
• E. Kurnat-Thoma, T. Sethi, S. Vasudevan et.al. "Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine." Systems Medicine.
• T. M. Liu, E. D. Yildirim, V. Kumar, N. Shyh-Chang et.al. "Ascorbate and Iron Are Required for the Specification and Long-Term Self-Renewal of Human Skeletal Mesenchymal Stromal Cells." Stem Cell Reports.
• G. Kaur, V. Ruhela, L. Rani, A. Gupta, K. Sriram, A. Gogia, A. Sharma, L. Kumar, R. Gupta. "RNA-Seq profiling of deregulated miRs in CLL and their impact on clinical outcome." Blood Cancer Journal.
• A. Mongia, D. Sengupta, A. Majumdar. "deepMc: Deep Matrix Completion for Imputation of Single-Cell RNA-seq Data." Journal of Computational Biology.
• A. Lathwal, R. Kumar, G. P. S. Raghava. "OvirusTdb: A database of oncolytic viruses for the advancement of therapeutics in cancer." Virology.
• V. Dwivedi, A. Arya, P. Yadav, R. Kumar, V. Kumar, G. P. S. Raghava. "DenvInD: dengue virus inhibitors database for clinical and molecular research." Briefings in Bioinformatics.
• R. Kumar, A. Lathwal, V. Kumar, S. Patiyal, P.K. Raghav, G. P. S. Raghava. "CancerEnD: A database of cancer associated enhancers." Genomics.
• S. Bhalla, H. Kaur, R. Kaur, S. Sharma, G. P. S. Raghava. "Expression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma." PLoS ONE
• A. Lathwal, R. Kumar,G. P. S. Raghava. "Computer-aided designing of oncolytic viruses for overcoming translational challenges of cancer immunotherapy." Drug Discovery Today Journal, Elsevier.
• H. Kaur, S. Bhalla, D. Kaur, G. P. S. Raghava. "CancerLivER: a database of liver cancer gene expression resources and biomarkers." Database.
• A. Iyer, K. Gupta, S. Sharma, D. Sengupta et. al. "Integrative Analysis and Machine Learning based Characterization of Single Circulating Tumor Cells ." Journal of Clinical Medicine.
• H. Kaur, A. Dhall, R. Kumar, G. P. S. Raghava. "Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data." Frontiers in Genetics.
• S. Patiyal, D. Kaur, H. Kaur, N. Sharma, A. Dhall, S. Sahai, P. Agrawal, L. Maryam, C. Arora, GPS. Raghava. "A Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic,Drug,and Vaccine Candidates" Monoclonal Antibodies in Immunodiagnosis and Immunotherapy.
• S. Kalra, A. Mittal, K. Gupta, V. Singhal, A. Gupta, T. Mishra, S. Naidu, D. Sengupta, G. Ahuja. "Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis" Communications Biology.
• C. Goswami, S. Chawla, D. Thakral, H. Pant, P. Verma, PS. Malik, Jayadeva, R. Gupta, G. Ahuja, D. Sengupta. "Correction to: Molecular signature comprising 11 platelet-genes enables accurate blood-based diagnosis of NSCLC" BMC Genomics.
• R. Sharma, N. Pandey, A. Mongia, S. Mishra, A. Majumdar, V. Kumar. "FITs: forest of imputation trees for recovering true signals in single-cell open chromatin profiles" NAR Genomics and Bioinformatics.
• A. Lathwal, R. Kumar, C. Arora, GPS Raghava. "Identification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical data" Journal of Cancer Research and clinical Oncology.
• C. Goswami, S. Chawla, D. Thakral, H. Pant, P. Verma, PS. Malik, Jayadeva, R. Gupta, G. Ahuja, D. Sengupta. "Molecular signature comprising 11 platelet-genes enables accurate blood-based diagnosis of NSCLC" BMC Genomics.
• S. Patiyal, P. Agrawal, V. Kumar, A. Dhall, R. Kumar, G. Mishra, GPS Raghava. "NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence" Protein Science.
• SS. Usmani, GPS. Raghava. "Potential Challenges for Coronavirus (SARS-CoV-2) Vaccines Under Trial" Frontiers in Immunology.
• D. Batra, N. Diwan, U. Upadhyay, JS. Kalra, T. Sharma, AK. Sharma, D. Khanna, JS. Marwah, S. Kalathil, N. Singh, R. Tuwani, G. Bagler. "RecipeDB: a resource for exploring recipes" The Journal of Biological Databases and Curation.

2019

• S. Patiyal, P. Agrawal, V. Kumar, A. Dhall, R. Kumar, G. Mishra, G. P.S. Raghava. "NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence." Wiley Online Library.
• S. Akhter, H. Kaur, P. Agrawal, G. P S Raghava. "RareLSD: a manually curated database of lysosomal enzymes associated with rare diseases." Database: The Journal of Biological Databases and Curation.
• A. Lathwal, C. Arora, G. P S Raghava. "Prediction of risk scores for colorectal cancer patients from the concentration of proteins involved in mitochondrial apoptotic pathway." PLoS One.
• P. K. Raghav, R. Kumar, V. Kumar, G. P. S. Raghava. "Docking based approach for identification of mutations that disrupt binding between Bcl-2 and Bax proteins: Inducing apoptosis in cancer cells" Molecular Genetics and Genomic Medicine.
• P. Brown, RELISH Consortium , Y. Zhou. "Large expert-curated database for benchmarking document similarity detection in biomedical literature search." Database.
• D. Sinha, P. Sinha, R. Saha, S. Bandyopadhyay, D. Sengupta. "Improved dropClust R package with integrative analysis support for scRNA-seq data." Bioinformatics.
• Y. Silla, S. Varshney, A. Ray,S. Sengupta et.al. "Hydrolysis of homocysteine thiolactone results in the formation of Protein-Cys-S-S-homocysteinylation." Wiley Online Library.
• S. Acharya, A. Mishra, D. Paul, A. H. Ansari, M. Azhar, M. Kumar, R. Rauthan, N. Sharma, M. Aich, D. Sinha, S. Sharma, S. Jain, A. Ray, D. Chakraborty et.al. "Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing." PNAS.
• V. Kumar, J. J. Peter, A. Sagar, A. Ray, K. Mapa et.al. "Interdomain communication suppressing high intrinsic ATPase activity of Sse1 is essential for its co-disaggregase activity with Ssa1." The FEBS Journal.
• S. Bhalla, H. Kaur, A. Dhall, G. P. S. Raghava. "Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients." Scientific Reports (2019).
• H. Kaur, S. Bhalla, G. P. S. Raghava. "Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles." PLoS ONE (2019).
• S. Kumar, J. Thakur, K. Yadav, M. Mitra, S. Pal, A. Ray, S. Gupta et al. "Cholic Acid-Derived Amphiphile can Combat Gram-Positive Bacteria-mediated Infections via Disintegration of Lipid Clusters." ACS Biomaterials Science & Engineering (2019).
• C. Goswami, S. Poonia, L. Kumar, D. Sengupta. "Staging System to Predict the Risk of Relapse in Multiple Myeloma Patients Undergoing Autologous Stem Cell Transplantation". Frontiers in Oncology, 12 July 2019.
• R. Kumar, S. Patiyal, V. Kumar , G. Nagpal, G.P.S Raghava. "In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma". International Journal of Molecular Sciences 20(14), 3582. (2019).
• S. Ahmad, M. Gromiha, G.P.S. Raghava, C. Schönbach, S. Ranganathan. "APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018.". BMC Genomics. 2019 Apr 18;19(Suppl 9):266.
• D. Kaur, S. Patiyal, N. Sharma, S. S. Usmani, G.P.S Raghava. "PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands". Database, Volume 2019.
• A. Nagori, L. S. Dhingra, A. Bhatnagar, R. Lodha, T. Sethi. "Predicting Hemodynamic Shock from Thermal Images using Machine Learning". Scientific Reports 9, Article number: 91 (2019)
• P. Agrawal, S. Patiyal, R. Kumar, V. Kumar, H. Singh, P. K. Raghav, G. P. S. Raghava. "ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank." Database, Volume 2019.
• A. Mongia, D. Sengupta, A. Majumdar. "McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data." Frontiers in Genetics.
• V. Ravindran, J. C. Nacher, T. Akutsu, M. Ishitsuka, A. Osadcenco, V. Sunitha, G. Bagler, J. Schwartz, D. L. Robertson. "Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems." Scientific Reports 9, Article number: 2066 (2019)
• P. Agrawal, H. Singh, H. K. Srivastava, S. Singh, G. Kishore, G. P. S. Raghava. "Benchmarking of different molecular docking methods for protein-peptide docking." BMC Bioinformatics2019
• S. S. Usmani, P. Agrawal, M. Sehgal, P. K. Patel, G. P S Raghava "ImmunoSPdb: an archive of immunosuppressive peptides." Database, Volume 2019
• P. Agrawal, S. Kumar, A. Singh, G. P. S. Raghava, I. K. Singh. "NeuroPIpred: a tool to predict, design and scan insect neuropeptides." Scientific Reports 9
• R. Kumar, G. Nagpal, V. Kumar, S. S. Usmani, P. Agrawal, G. P. S. Raghava. "HumCFS: a database of fragile sites in human chromosomes." BMC Genomics2019 Database link
• R. Tuwani, S. Wadhwa, G. Bagler. "BitterSweet: Building machine learning models for predicting the bitter and sweet taste of small molecules." Scientific Reports 9, Article number: 7155 (2019).

2018

• P. Agrawal, G. P. S. Raghava. "Prediction of Antimicrobial Potential of a Chemically Modified Peptide from Its Tertiary Structure". Frontiers in Microbiology.
• G. Nagpal, S. S. Usmani, G. P. S. Raghava, "A Web Resource for Designing Subunit Vaccine Against Major Pathogenic Species of Bacteria." Frontiers in Immunology, October 2018. Database link
• S.S. Usmani, S. Bhalla, G.P.S. Raghava. "Prediction of Antitubercular Peptides From Sequence Information Using Ensemble Classifier and Hybrid Features." Front. Pharmacol., 28 August 2018. Database link
• G. Nagpal, G. Chaudhary, P. Agrawal, G. P. S. Raghava. "Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants." Journal of Translational Medicine. 16:181.
• D. Mathur, S. Singh, A. Mehta, P. Agrawal, G. P. S. Raghava. In silico approaches for predicting the half-life of natural and modified peptides in blood. PLoS ONE 13(6): e0196829.
• D. Srivastava, A. Iyer, V. Kumar, D. Sengupta. CellAtlasSearch: A scalable search engine for single cells. Nucleic Acids Research. Volume 46, Issue W1, 2 July 2018, Pages W141-W147.
• P. Agrawal, P. K. Raghav, S. Bhalla, N. Sharma, G.P.S. Raghava. Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction. Current Topics in Medicinal Chemistry. Volume 18, Issue 13, 2018.
• D. Sinha, A. Kumar, H. Kumar, S. Bandyopadhyay, D. Sengupta. DropClust: Efficient clustering of ultra-large scRNA-seq data. Nucleic Acids Research, 46(6):e36.
• V. Kumar, P. Agrawal, R. Kumar,S. Bhalla, S.S. Usmani, G.C. Varshney, G.P.S. Raghava. Prediction of Cell-Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues. Front Microbiol. 9:725. 2018.
• P. Agrawal, S. Bhalla, K. Chaudhary,R. Kumar, M. Sharma, G.P.S. Raghava. In Silico Approach for Prediction of Antifungal Peptides. Front Microbiol. 9:323. 2018
• S.S. Usmani ,R. Kumar, V. Kumar, S. Singh, G.P.S. Raghava. AntiTbPdb: a knowledgebase of anti-tubercular peptides. Database (Oxford). doi:10.1093/database/bay025.
• SS. Usmani, R. Kumar, S. Bhalla, V. Kumar, G.P.S. Raghava. In Silico Tools and Databases for Designing Peptide-Based Vaccine and Drugs. Adv Protein Chem Struct Biol. 112:221-263.
• D. Mathur, A. Mehta, P. Firmal, G. Bedi, C. Sood, A. Gautam, G.P.S. Raghava. TopicalPdb: A database of topically delivered peptides. PLoS One. 13(2):e0190134.
• N. Garg, A. Sethupathy, R. Tuwani, Rakhi NK, S. Dokania, A. Iyer, A. Gupta, S. Agrawal, N. Singh, S. Shukla, K. Kathuria, R. Badhwar, R. Kanji, A. Jain, A. Kaur, R. Nagpal, G. Bagler. FlavorDB: A database of flavor molecules. Nucleic Acids Research, 46, D1, D1210-D1216.Database link
• S. Wadhwa, A. Gupta, S. Dokania, R. Kanji, G. Bagler. A hierarchical anatomical classification schema for prediction of phenotypic side effects. PLoS ONE 13(3): e0193959 (2018).
• A. Jain, G. Bagler. Culinary evolution models for Indian cuisines. Physica A, 503, 170 (2018).
• K. Sriram. Bifurcation analysis of mTOR signalling pathways in cancer cells. IET Systems Biology, (1-9) DOI: 10.1049/iet-syb.2018.0003.

2017

• S. Dawar, V. Goyal, D. Bera. A hybrid framework for mining high-utility itemsets in a sparse transaction database. Applied Intelligence October 2017, Volume 47, Issue 3, pp 809-827.
• H. Li, E. Courtois, D. Sengupta. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nature Genetics 49, 2017 Pages 708-718.
• D. Sinha, D. Sengupta, S. Bandyopadhyay. ParSel: Parallel Selection of Micro RNAs for Survival Classification in Cancers. Molecular Informatics 2017 Jul; 36(7).
• R. Badhwar, G. Bagler. A distance constrained synaptic plasticity model of C. elegans neuronal network. Physica A, 469, 313-322 (2017). 10 pages + Supplementary Data.
• V Ravindran, V. Sunitha, G. Bagler. Identification of critical regulatory genes in cancer signaling network using controllability analysis. Physica A, 474, 134-143 (2017). 10 pages + Supplementary Data.
• S. Shiju, K. Sriram. Hypothesis driven single cell dual oscillator mathematical model of circadian rhythms. PLoS ONE 12(5): e0177197.

2016

• S. Raychaudhuri. In Silico Approach to Find an Optimal Strategy in Selective Targeting of Cancer Cells. Journal of Computer Science & Systems Biology 9:112-118. doi:10.4172/jcsb.1000228.
• S Pathania, G. Bagler, P.S. Ahuja. Differential network analysis reveals evolutionary complexity in secondary metabolism of R. serpentina over C. roseus. Frontiers in Plant Science, 7, 1229 (2016). 17 pages + Supplementary Data.

2015

• S. Raychaudhuri. Kinetic Monte Carlo study of type 1/type 2 choice in apoptosis elucidates selective killing of cancer cells under death ligand induction. Open Journal of Apoptosis 2015 4:22-39.
• K. Newaz, K. Sriram, D. Bera. Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis, PLoS ONE 10(12):e0144389. doi: 10.1371/journal.pone.0144389
• A. Mondal, A. Bhattacherjee. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement. Nucleic Acid Research 2015 Oct 30; 43(19): 9176-9186.
• N. Mustafa, R. Raman, S. Ray: Quasi-Polynomial Time Approximation Scheme for Weighted Geometric Set Cover on Pseudodisks and Halfspaces. SIAM J. Comput. 2015. 44(6): 1650-1669