Publications
Recent Publication
Ujjainiya R, Tyagi A, Sardana V,....., Dash D, Jha S, Sengupta S. High failure rate of ChAdOx1-nCoV19 immunization against asymptomatic infection in healthcare workers during a Delta variant surge. Nature Communications. 2022. 13(1):1726
2022
Gupta, I., Shankrit, S., Narta, K., Ghazi, M., Grover, R., Pandey, R., Kar, H. K., Menon, S. M., Gupta, A., Yenamandra, V. K., Singh, A., Mukerji, M., Mukhopadhyay, A., Rani, R., Gokhale, R. S., Dash, D., & Natarajan, V. T. Whole-Exome Sequencing of Vitiligo Lesions Indicates Lower Burden of Somatic Variations: Implications in Risk for Nonmelanoma Skin Cancers. The Journal of investigative dermatology. 2022. S0022-202X(22)02884-6.
Aggarwal S, Raj A, Kumar D, Dash D, Yadav AK. False discovery rate: the Achilles' heel of proteogenomics. Briefings in bioinformatics. 2022. 23(5):bbac163
Bhaskar AK, Naushin S, Ray A, Singh P, Raj A, Pradhan S, Adlakha K, Siddiqua TJ, Malakar D, Dash D, Sengupta S. A High Throughput Lipidomics Method Using Scheduled Multiple Reaction Monitoring. Biomolecules. 2022. 12(5):709
Ujjainiya R, Tyagi A, Sardana V,....., Dash D, Jha S, Sengupta S. High failure rate of ChAdOx1-nCoV19 immunization against asymptomatic infection in healthcare workers during a Delta variant surge. Nature Communications. 2022. 13(1):1726
Tavakkoli F, Damala M, Koduri MA, Gangadharan A, Rai AK, Dash D, Basu S, Singh V. Transcriptomic Profiling of Human Limbus-Derived Stromal/Mesenchymal Stem Cells-Novel Mechanistic Insights into the Pathways Involved in Corneal Wound Healing. International journal of Molecular Sciences. 2022. 23(15):8226
Singh P, Ujjainiya R, Prakash S, Naushin S, ..., Agrawal A, Sengupta S, Dash D. A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys. Computers in Biology and Medicine. 2022. 146:105419
Abbas T, Chaturvedi G, Prakrithi P, Pathak AK, Kutum R, Dakle P, Narang A, Manchanda V, Patil R, Aggarwal D, Girase B, Srivastava A, Kapoor M, Gupta I, Pandey R, Juvekar S, Dash D, Mukerji M, Prasher B. Whole Exome Sequencing in Healthy Individuals of Extreme Constitution Types Reveals Differential Disease Risk: A Novel Approach towards Predictive Medicine. Journal of personalized medicine. 2022 12(3):489
2021
PS Gidde, SS Prasad, AP Singh, N Bhatheja, S Prakash, P Singh, A Saboo, R Takhar, S Gupta, S Saurav, A Singh, V Sardana, H Mahajan, A Kalyanpur, AS Mandal, V Mahajan, A Agrawal, A Agrawal, VK Venugopal, S Singh, D Dash. Validation of expert system enhanced deep learning algorithm for automated screening for COVID-Pneumonia on chest X-rays. Scientific Reports. 2021 Dec 1;11(1):1-2.
Sahana S, Sivadas A, Mangla M, Jain A...,Dash D, ..., Binukumar BK, Sivasubbu S, Scaria V. Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes. Pharmacogenomics. 2021. 22(10):603-618
MS Dhar, R Marwal, Vs Radhakrishnan, K Ponnusamy, B Jolly, ... , D Dash, ... ,SK Singh, A Agrawal, P Rakshit. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science. 2021 Nov 19;374(6570):995-9.
A Dasgupta, R Chakraborty, B Saha, H SurI, P Singh, A Raj, B Taneja, D Dash, S Sengupta, A Agrawal. Sputum Protein Biomarkers in Airway Diseases: A Pilot Study. International Journal of Chronic Obstructive Pulmonary Disease. 2021;16:2203.
S Naushin, V Sardana, R Ujjainiya, N Bhatheja, ... , A Agrawal, D Dash, S Sengupta Insights from a Pan India sero-epidemiological survey (phenome-India cohort) for SARS-CoV2. Elife. 2021 Apr 20;10:e66537.
A Singh, M Gaur, V Sharma, P Khanna, A Bothra, A BhadurI, AK Mondal, D Dash, Y Singh, R Misra. Comparative genomic analysis of mycobacteriaceae reveals horizontal gene transfer-mediated evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis complex. Msystems. 2021 Jan 19;6(1):e00934-20.
A Jain, RC Bhoyar, K Pandhare, A Mishra, ... , D Dash, ... , B BK, V Scaria, S Sivasubbu. IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. Nucleic acids research. 2021 Jan 8;49(D1):D1225-32.
2020
S Talwar, M Pandey, C Sharma, R Kutum, J Lum, D Carbajo, R Goel, M Poidinger, D Dash, A Singhal, AK Pandey. Role of VapBC12 toxin-antitoxin locus in cholesterol-induced mycobacterial persistence. Msystems. 2020 Dec 15;5(6):e00855-20.
P Singh, R Chakraborty, R Marwal, VS Radhakrishan, AK Bhaskar, H Vashisht, MS Dhar, S Pradhan, G Ranjan, M Imran, A Raj, U Sharma, P Singh, H Lall, M Dutta, P Garg, A Ray, D Dash, S Sivasubbu, H Gogia, P Madan, S Kabra, SK Singh, A Agrawal, P Rakshit, P Kumar, S Sengupta. A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry. Journal of Proteins and Proteomics. 2020 Sep;11(3):159-65.
C Rawat, R Kutum, S Kukal, A Srivastava, U R Dahiya, S Kushwaha, S Sharma, D Dash, L Saso, A K Srivastava, and R Kukreti. Downregulation of peripheral PTGS2/COX-2 in response to valproate treatment in patients with epilepsy. Scientific Reports 2020, 10(1), pp.1-14.
B Mehani, K Narta, D Paul, A Raj, D Kumar, A Sharma, L Kaurani, S Nayak, D Dash, A Suri, C Sarkar, A Mukhopadhyay. Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues. Scientific Reports 2020 Jan 28;10(1):1-2.
2019
AK Mukherjee, S Sharma, S Bagri, R Kutum, P Kumar, A Hussain, P Singh, D Saha, A Kar, D Dash, S Chowdhury. Telomere repeat–binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters. Journal of Biological Chemistry 294 17709-17722 2019
S Ghose, S Ghosh, V S Tanwar, P Tolani, R Kutum, A Sharma, N Bhardwaj, KV Shamsudheen, A Verma, R Jayarajan, D Dash, S Sivasubbu, V Scaria, S Seth, S Sengupta. Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing. Gene 721 144107 2019
I Gupta, A Narang, P Singh, V Manchanda, S Khanna, Indian Genome Variation Consortium, M Mukerji, V T Natarajan, D Dash. VitiVar: A locus specific database of vitiligo associated genes and variations. Gene: X 3 100018 2019
R Konhar, M Debnath, S Vishwakarma, A Bhattacharjee, D Sundar, P Tandon, D Dash, D K Biswal. The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 7 e7756 2019
A Ghosh, A Gangadharan, M Verma, S Das, L Matai, D P Dash, D Dash, K Mapa, K Chakraborty. Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks. Cellular and Molecular Life Sciences 76 (8) 1605-1621 2019
D Menon, K Singh, S M Pinto, A Nandy, N Jaisinghani, R Kutum, D Dash, TSK Prasad, S Gandotra. Quantitative Lipid Droplet Proteomics Reveals Mycobacterium tuberculosis Induced Alterations in Macrophage Response to Infection. ACS infectious diseases 5(4) 559-569 2019
2018
A Nandy, A K Mondal, R Pandey, P Arumugam, S Dawa, N Jaisinghani, V Rao, D Dash, S Gandotra. Adipocyte model of Mycobacterium tuberculosis infection reveals differential availability of iron to bacilli in the lipid-rich caseous environment. Infection and immunity 86(6) e00041-18 2018
N S Chauhan, R Pandey, A K Mondal, S Gupta, M K Verma, S Jain, V Ahmed, R Patil, D Agarwal, B Girase, A Shrivastava, F Mobeen, V Sharma, T P Srivastava, S K Juvekar, B Prasher, M Mukerji, D Dash. Western Indian rural gut microbial diversity in extreme Prakriti endo-phenotypes reveals signature microbes. Frontiers in microbiology 9 118 2018
2017
P Tiwari, R Kutum, T Sethi, A Shrivastava, B Girase, S Aggarwal, R Patil, D Agarwal, P Gautam, A Agrawal, D Dash, S Ghosh, S Juvekar, M Mukerji, B Prasher. Recapitulation of Ayurveda constitution types by machine learning of phenotypic traits. PloS one 12(10) e0185380 2017
A K Mondal, J Kumar, R Pandey, S Gupta, M Kumar, G Bansal, M Mukerji, D Dash, N S Chauhan. Comparative Genomics of Host–Symbiont and Free-Living Oceanobacillus Species. Genome biology and evolution 9(5) 1175-1182 2017
D Kaur, R Kutum, D Dash, S K Brahmachari. Data Intensive Genome Level Analysis for Identifying Novel, Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis. Scientific reports 7 46595 2017
B Prasher, B Varma, A Kumar, B K Khuntia, R Pandey, A Narang, P Tiwari, R Kutum, D Guin, R Kukreti, D Dash, M Mukerji, TRISUTRA Ayurgenomics Consortium. Ayurgenomics for stratified medicine: TRISUTRA consortium initiative across ethnically and geographically diverse Indian populations. Journal of ethnopharmacology 197 274-293 2017
2016
D Kumar, G Bansal, A Narang, T Basak, T Abbas, D Dash* Integrating transcriptome and proteome profiling: strategies and applications. Proteomics 16(19) 2533-44 2016
D Kumar, AK Yadav, X Jia, J Mulvenna, D Dash* Integrated transcriptomic-proteomic analysis using a proteogenomic workflow refines rat genome annotation. Molecular & Cellular Proteomics 15(1) 329-339 2016
D Kumar, AK Mondal, R Kutum, D Dash* Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes. Proteomics 16(2) 226-240 2016
2015
A Anand, P Verma, AK Singh, S Kaushik, R Pandey, C Shi, H Kaur, M Chawla, CK Elechalawar, D Kumar, Yang Y, Bhavesh NS, Banerjee R, Dash D, Singh A, Natarajan VT, Ojha AK, Aldrich CC, Gokhale RS. Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches. Molecular Cell 60(4) 637-650 2015
D Kumar, A Jain, D Dash* Probing the Missing Human Proteome: A Computational Perspective. Journal of Proteome Research 14(12) 4949-4958 2015
A Maji, R Misra, AK Mondal, D Kumar, D Bajaj, A Singhal, G Arora, Bhaduri A, Sajid A, Bhatia S, Singh S, Singh H, Rao V, Dash D, Baby Shalini E, Sarojini Michael J, Chaudhary A, Gokhale RS, Singh Y. Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu of infection at site. Scientific reports 5 15214 2015
DL Brinkman, X Jia, J Potriquet, D Kumar, D Dash, D Kvaskoff, J Mulvenna. Transcriptome and venom proteome of the box jellyfish Chironex fleckeri. BMC genomics 16(1) 1 2015
2014
A Narang, P Jha, D Kumar, R Kutum, AK Mondal, D Dash*, M Mukerji*. Extensive copy number variations in admixed Indian population of African ancestry: Potential involvement in adaptation. Genome biology and evolution 6(12) 3171-3181 2014
RD Roy, M Bhardwaj, V Bhatnagar, K Chakraborty*, D Dash*. How do eubacteria organisms manage aggregation-prone proteome? F1000Research 3 2014
L Kaurani, M Vishal, D Kumar, A Sharma, B Mehani, C Sharma, S Chakraborty, P Jha, J Ray, A Sen, Dash D, Ray K, Mukhopadhyay A. Gene-Rich Large Deletions Are Overrepresented in POAG Patients of Indian and Caucasian Origins Gene-Rich Large Deletions in POAG Patients Investigative ophthalmology & visual science 55(5) 3258-3264 2014
M Faruq, A Narang, R Kumari, R Pandey, A Garg, M Behari, D Dash*, AK Srivastava*, M Mukerji* Novel mutations in typical and atypical genetic loci through exome sequencing in autosomal recessive cerebellar ataxia families. Clinical genetics 86(4) 335-341 2014
D Kumar, AK Mondal, AK Yadav, D Dash* Discovery of rare protein‐coding genes in model methylotroph Methylobacterium extorquens AM1. Proteomics 14(23-24) 2790-2794 2014
RD Roy, D Dash* Selection of relevant features from amino acids enables development of robust classifiers. Amino acids 46(5) 1343-1351 2014
2013
RD Upadhyay, AK Yadav, S Sonawane, R Goankar, D Dash, NH Balasinor. Differential Proteomic and Phospho-proteomic Analysis of Normal versus Failed Spermiation in Adult Rats by Label-Free LC-MS/MS. Journal of Analytical & Bioanalytical Techniques 4 2-11 2013
GP Singh, D Dash* Electrostatic mis-interactions cause overexpression toxicity of proteins in E. coli. PloS one 8(5) e64893 2013
AK Yadav, PK Kadimi, D Kumar, D Dash* ProteoStats - a library for estimating false discovery rates in proteomics pipelines. Bioinformatics 29(21) 2799-2800 2013
A Sinha, AK Yadav, S Chakraborty, SK Kabra, R Lodha, M Kumar, A Kulshreshtha, T Sethi, R Pandey, G Malik, Laddha S, Mukhopadhyay A, Dash D, Ghosh B, Agrawal A Exosome-enclosed microRNAs in exhaled breath hold potential for biomarker discovery in patients with pulmonary diseases. Journal of Allergy and Clinical Immunology 132(1) 219 2013
D Kumar, AK Yadav, PK Kadimi, SH Nagaraj, SM Grimmond, D Dash*. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Molecular & cellular proteomics 12(11) 3388-3397 2013
2012
M Anurag, GP Singh, D Dash* Location of disorder in coiled coil proteins is influenced by its biological role and subcellular localization: a GO-based study on human proteome Molecular BioSystems 8(1) 346-352 2012
AK Yadav, D Kumar, D Dash* Learning from decoys to improve the sensitivity and specificity of proteomics database search results PloS one 7(11) e50651 2012
P Gautam, P Jha, D Kumar, S Tyagi, B Varma, D Dash, A Mukhopadhyay, M Mukerji Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity Human genetics 131(1) 131-143 2012
T Beck, S Gollapudi, S Brunak, N Graf, HU Lemke, D Dash, I Buchan, C Diaz, F Sanz, AJ Brookes Knowledge engineering for health: a new discipline required to bridge the “ICT gap” between research and healthcare Human mutation 33(5) 797-802 2012
R Vashisht, AK Mondal, A Jain, A Shah, P Vishnoi, P Priyadarshini, K Bhattacharyya, H Rohira, GA Bhat, A Passi, …, Dash D, Sharma A, Scaria V, Thomas Z; OSDD Consortium, Chandra N, Brahmachari SK, Bhardwaj A. Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis PLoS One 7(7) e39808 2012
2011
A Narang, P Jha, V Rawat, A Mukhopadhayay, D Dash*, A Basu*, M Mukerji* Recent admixture in an Indian population of African ancestry The American Journal of Human Genetics 89(1) 111-120 2011
D Singla, M Anurag, D Dash, GPS Raghava A web server for predicting inhibitors against bacterial target GlmU protein BMC pharmacology 11(1) 5 2011
AK Yadav, D Kumar, D Dash* MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry Journal of proteome research 10(5) 2154-2160 2011
A Bhardwaj, V Scaria, GPS Raghava, AM Lynn, N Chandra, S Banerjee, MV Raghunandanan, V Pandey, B Taneja, Yadav J, Dash D, Open Source Drug Discovery Consortium, Brahmachari SK Open source drug discovery-A new paradigm of collaborative research in tuberculosis drug development Tuberculosis 91(5) 479-486 2011
AK Yadav, G Bhardwaj, T Basak, D Kumar, S Ahmad, R Priyadarshini, AK Singh, D Dash*, S Sengupta* A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery PLoS One 6(9) e24442 2011
DS Kelkar, D Kumar, P Kumar, L Balakrishnan, B Muthusamy, AK Yadav, …., Dash D, Pandey A Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry Molecular & cellular proteomics 10(12) M111.011627 2011
2010
A Narang, RD Roy, A Chaurasia, A Mukhopadhyay, M Mukerji, D Dash* IGVBrowser–a genomic variation resource from diverse Indian populations Database 2010 baq022 2010
S Aggarwal, S Negi, P Jha, PK Singh, T Stobdan, MAQ Pasha, S Ghosh, A Agrawal, B Prasher, M Mukerji Collaborators:Brahmachari SK, Majumder PP, Mukerji M, Habib S, Dash D, Ray K EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda Proceedings of the National Academy of Sciences 107(44) 18961-18966 2010
2009
AJ Brookes, H Lehvaslaiho, J Muilu, Y Shigemoto, T Oroguchi, T Tomiki, A Mukaiyama, A Konagaya, T Kojima, I Inoue, Kuroda M, Mizushima H, Thorisson GA, Dash D, Rajeevan H, Darlison MW, Woon M, Fredman D, Smith AV, Senger M, Naito K, Sugawara H. The phenotype and genotype experiment object model (PaGE‐OM): a robust data structure for information related to DNA variation Human mutation 30(6) 968-977 2009
M Anurag, D Dash* Unraveling the potential of intrinsically disordered proteins as drug targets: application to Mycobacterium tuberculosis Molecular BioSystems 5(12) 1752-1757 2009
GA Thorisson, O Lancaster, RC Free, RK Hastings, P Sarmah, D Dash, SK Brahmachari, AJ Brookes HGVbaseG2P: a central genetic association database Nucleic acids research 37(suppl1) D797-D802 2009
2008
GP Singh, D Dash* How expression level influences the disorderness of proteins Biochemical and biophysical research communications 371(3) 401-404 2008
Indian Genome Variation Consortium Genetic landscape of the people of India: a canvas for disease gene exploration Journal of genetics 87(1) 03-20 2008
2007
The NMITLI-BioSuite Team BioSuite: a comprehensive bioinformatics software package (A unique industry-academia collaboration) Current Science 92(1) 29-38 2007
GP Singh, D Dash* Intrinsic disorder in yeast transcriptional regulatory network Function and Bioinformatics 68(3) 602-605 2007
GP Singh, M Ganapathi, D Dash* Role of intrinsic disorder in transient interactions of hub proteins Proteins: Structure Function and Bioinformatics 66(4) 761-765 2007
K S Sandhu, D Dash* Dynamic α‐helices: Conformations that do not conform Proteins: Structure Function and Bioinformatics 68(1) 109-122 2007
2006
KS Sandhu, D Dash* Conformational flexibility may explain multiple cellular roles of PEST motifs Proteins: Structure Function and Bioinformatics 63(4) 727-732 2006
GP Singh, M Ganapathi, KS Sandhu, D Dash* Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes Proteins: Structure Function and Bioinformatics 62(2) 309-315 2006
2005
T Prakash, C Ramakrishnan, D Dash, SK Brahmachari Conformational analysis of invariant peptide sequences in bacterial genomes Journal of molecular biology 345 (5) 937-955 2005
Indian Genome Variation Consortium The Indian genome variation database (IGVdb): a project overview Hum Genet 118 01-11 2005
2004
R Sharma, JK Maheshwari, T Prakash, D Dash, SK Brahmachari Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus Bioinformatics 20 (7) 1074-1080 2004
T Prakash, M Khandelwal, D Dasgupta, D Dash*, SK Brahmachari CoPS: comprehensive peptide signature database Bioinformatics 20 (16) 2886-2888 2004
N Pandey, M Ganapathi, K Kumar, D Dasgupta, SKD Sutar, D Dash* Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins Bioinformatics 20 (17) 2904-2910 2004
R Bakshi, T Prakash, D Dash, V Brahmachari In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins Biochemical and biophysical research communications 320 (1) 197-204 2004
2003
T Nandi, D Dash, R Ghai, C B-Rao, K Kannan, SK Brahmachari, C Ramakrishnan, S Ramachandran A novel complexity measure for comparative analysis of protein sequences from complete genomes Journal of Biomolecular Structure and Dynamics 20 (5) 657-667 2003
S Sen, D Dash, S Pasha, SK Brahmachari Role of histidine interruption in mitigating the pathological effects of long polyglutamine stretches in SCA1: A molecular approach Protein science 12 (5) 953-962 2003
2002
C Chauhan, D Dash, D Grover, J Rajamani, M Mukerji Origin and instability of GAA repeats: insights from Alu elements Journal of Biomolecular Structure and Dynamics 20 (2) 253-263 2002
R Kukreti, D Dash, V KE, S Chakravarty, S Kr Das, M De, G Talukder Spectrum of β‐thalassemia mutations and their association with allelic sequence polymorphisms at the β‐globin gene cluster in an eastern Indian population American journal of hematology 70 (4) 269-277 2002
2001
SS Pataskar, D Dash, SK Brahmachari Progressive myoclonus epilepsy [EPM1] repeat d (CCCCGCCCCGCG) n forms folded hairpin structures at physiological pH Journal of Biomolecular Structure and Dynamics 19 (2) 293-305 2001
SS Pataskar, D Dash, SK Brahmachari Intramolecular i-motif structure at acidic pH for progressive myoclonus epilepsy (EPM1) repeat d(CCCCGCCCCGCG) n Journal of Biomolecular Structure and Dynamics 19 (2) 307-313 2001
Q Saleem, D Dash, C Gandhi, A Kishore, V Benegal, T Sherrin, O Mukherjee, S Jain, SK Brahmachari Association of CAG repeat loci on chromosome 22 with schizophrenia and bipolar disorder Molecular psychiatry 6 (6) 694-700 2001
1999
S Ramachandran, D Dash, SK Brahmachari The multitude of'omics' and'omes': Evolution of scientific terms in molecular biology in the new millennium Current science 77 (7) 846-847 1999