List of publications as PI from ILS:

1. Jha A, Ahad A, Mishra GP, Sen K, Sen A, Smita S, Minz AP, Biswas VK, Tripathy A, Senapati S, Gupta B, Acha-Orbea H, Raghav SK. SMRT and NCoR1 fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling. Front Immunol. 2022, September 22.
2. Mohapatra P, Mohanty S, Ansari SA, Shriwas O, Ghosh A, Rath R, Majumdar SKD, Swain RK, Raghav SK, Dash R. CMTM6 attenuates cisplatin-induced cell death in OSCC by regulating AKT/c-Myc-driven ribosome biogenesis. FASEB J. 2022 36: e22566.
3. Parai D, Choudhary HR, Dash GC, Behera S, Mishra N, Pattnaik D, Raghav SK, Mishra SK, Sahoo SK, Swain A, Mohapatra I, Pattnaik M, Moharana A, Jena SR, Praharaj I, Subhadra S, Kanungo S, Bhattacharya D, Pati S. Dynamicity and persistence of severe acute respiratory syndrome coronavirus-2 antibody response after double dose and the third dose with BBV-152 and AZD1222 vaccines: A prospective, longitudinal cohort study. Front Microbiol. 2022 13: 942659.
4. Mishra GP, Jha A, Ahad A, Sen K, Sen A, Podder S, Prusty S, Biswas VK, Gupta B, Raghav SK*. Epigenomics of conventional type-I dendritic cells depicted preferential control of TLR9 versus TLR3 response by NCoR1 through differential IRF3 activation. Cell Mol Life Sci. 2022, 79: 429.
5. Prasad P, Mahapatra S, Mishra R, Murmu KC, Aggarwal S, Sethi M, Mohapatra P, Ghosh A, Yadav R, Dodia H, Ansari SA, De S, Singh D, Suryawanshi A, Dash R, Senapati S, Beuria TK, Chattopadhyay S, Syed GH, Swain R, Raghav SK, Parida A. Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: a potential source of co-infection. Mol Omics. 2022, 18: 490-505.
6. Singh B, Avula K, Chatterjee S, Datey A, Ghosh A, De S, Keshry SS, Ghosh S, Suryawanshi AR, Dash R, Senapati S, Beuria TK, Prasad P, Raghav SK, Swain R, Parida A, Hussain Syed G*, Chattopadhyay S*. Isolation and Characterization of Five Severe Acute Respiratory Syndrome Coronavirus 2 Strains of Different Clades and Lineages Circulating in Eastern India. Front Microbiol. 2022, 13: 856913.
7. Ghosh A, Walia S, Rattan R, Kanampalliwar A, Jha A, Aggarwal S, Fatma S, Das N, Chayani N, Prasad P, Raghav SK*, Parida A. Genomic profiles of vaccine breakthrough SARS-CoV-2 strains from Odisha, India. Int J Infect Dis. 2022, 119: 111-113.
8. Kemp SA, Cheng MTK, Hamilton WL, Kamelian K; Indian SARS-CoV-2 Genomics Consortium (INSACOG), Singh S, Rakshit P, Agrawal A, Illingworth CJR, Gupta RK*. Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. Sci Rep. 2022, 12: 10492.
9. Swain N, Tripathy A, Padhan P, Raghav SK, Gupta B. Toll-like receptor-7 activation in CD8+ T cells modulates inflammatory mediators in patients with rheumatoid arthritis. Rheumatol Int. 2022, 42: 1235-1245.
10. Pathak AK, Mishra GP, Fatihi S, Abbas T, Uppili B, Ghosh A, Banu S, Bhoyar RC, Jain R, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK*, Mukerji M*. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acid Research 2022, 50: 1551-1561.
11. Chatterjee S,  Datey A, Sengupta S, Ghosh A, Jha A, Walia S, Singh S, Suranjika S, Bhattacharya G, Laha E, Keshry SS, Ray A, Pani SS, Suryawanshi A, Dash R, Senapati S, Beuria TK, Syed GH, Prasad P, Raghav S, Devadas S, Swain R, Chattopadhyay S, Parida. Clinical, immunological and genomic characterization of asymptomatic and symptomatic cases with SARS-CoV-2 infection, India. Frontiers in Cellular and Infection Microbiology 2021 (In press).
12. Raghav S, Sen K, Ghosh A, Datta S, Ahad A, Jha A, Chatterjee S, Suranjika S, Sengupta S, Bhattacharya G, Shriwas O, Avula K, Kshatri J, Prasad P, Parida AK. SARS-CoV-2 specific immune-signature in direct contacts of COVID-19 cases protect them from contracting disease: A Retrospective Study. Frontiers in Immunology 2021 (in press).
13. Jha A, Ahad A, Mishra GP, Sen K, Smita S, Minz AP, Biswas VK, Tripathy A, Senapati SB, Gupta B, Orbea HA, Raghav SK. NCoR1 and SMRT fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling. bioRxiv doi: https://doi.org/10.1101/2021.03.11.434976
14. Bhattacharya D, Choudhary HR, Parai D,  Dash GC, Kshatri JS, Mishra N, Choudhary PK, Pattnaik D, Panigrahi K, Behera S, Sahoo NR, Podder S, Mishra A, Raghav SK, Mishra SK, Pradhan SK, Sahoo SK, Pattnaik M, Rout UK, Ranjan R, Mondal N, Kanungo S, Palo SK, Pati S*. Persistence of antibodies against Spike glycoprotein of SARS-CoV-2 in health care workers post double dose of BBV-152 and AZD1222 vaccines. Frontiers in Medicine 2021 (In press).
15. Borah NA, Sradhanjali S, Barik MR, Jha A, Tripathy D, Kaliki S, Rath S, Raghav SK, Patnaik S, Mittal R, Reddy MM. Aurora Kinase B Expression, Its Regulation and Therapeutic Targeting in Human Retinoblastoma. Invest Ophthalmol Vis Sci. 2021 Mar 1;62(3):16. doi: 10.1167/iovs.62.3.16.
16. Maitra A, Raghav S, Dalal A, Ali F, Paynter VM, Paul D, Biswas NK, Ghosh A, Jani K, Chinnaswamy S, Pati S, Sahu A, Mitra D, Bhat MK, Mayor S, Sarin A, The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium, Sauche YS, Seshasayee ASN, Palakodeti D, Bashyam MD, Parida A, Das S. (2020) PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak. BioRxiv08.03.233718. (Equal contribution first author)
17. Tripathy A, Padhan P, Swain N, Raghav SK, Gupta B. Increased Extracellular ATP in Plasma of Rheumatoid Arthritis Patients Activates CD8+T Cells. Arch Med Res. 2021 Feb 1:S0188-4409(21)00001-1.
18. Dash P, Turuk J, Behera SK, Palo SK, Raghav SK, Ghosh A, Sabat J, Rath S, Subhadra S, Rana K, Bhattacharya D, Kanungo S, Kshatri JS, Mishra BK, Dash S, Parida A, Pati S. Sequence analysis of Indian SARS-CoV-2 isolates shows a stronger interaction of mutant receptor-binding domain with ACE2. Int J Infect Dis. 2021 Jan 12;104:491-500. (Co-corresponding author)
19. Mohapatra P, Shriwas O, Mohanty S, Ghosh A, Smita S, Kaushik SR, Arya R, Rath R, Das Majumdar SK, Muduly DK, Raghav SK, Nanda RK, Dash R. CMTM6 drives cisplatin resistance by regulating Wnt signaling through the ENO-1/AKT/GSK3β axis. JCI Insight. 2021 Feb 22;6(4):e143643.
20. Smita S, Ghosh A, Biswas VK, Ahad A, Podder S, Jha A, Sen K, Acha-Orbea H, Raghav SK. Zbtb10 transcription factor is crucial for murine cDC1 activation and cytokine secretion. Eur J Immunol. 2021 Feb 1.
21. Raghav S*, Ghosh A, Turuk J, Kumar S, Jha A, Madhulika S, Priyadarshini M, Biswas VK, Shyamli PS, Singh B, Singh N, Singh D, Datey A, Kiran A, Smita S, Sabat J, Bhattacharya D, Dash R, Senapati S, Beuria TK, Swain R, Chattopadhyay S, Syed GH, Dixit A, Prasad P, Odisha COVID-19 study group, ILS COVID-19 team, Pati S, Parida A*. (2020) SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity. Frontiers in Microbiology. (*Corresponding author)
22. Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. 2021 Feb;54(1):1-12. PMID: 33191792
23. Ahad A, Smita S, Mishra GP, Biswas VK, Sen K, Gupta B, Garcin D, Acha-Orbea H, Raghav SK. NCoR1 fine-tunes type-I IFN response in cDC1 dendritic cells by directly regulating Myd88-IRF7 axis under TLR9. Eur J Immunol. 2020 Dec;50(12):1959-1975
24. Khanna S, Pradhan P, Jaiswal KS, Jain AP, Ghosh A, Tripathy A, Gowda H, Raghav SK, Gupta B. (2020) Altered mitochondrial proteome and functional dynamics in patients with rheumatoid arthritis. Mitochondrion 54:8-14.
25. Das D, Das A, Sahu M, Mishra SS, Khan S, Bejugam PR, Rout PK, Das A, Bano S, Mishra GP, Raghav SK, Dixit A, Panda AC. (2020) Identification and characterization of circular intronic RNAs derived from insulin gene. International Journal of Molecular Sciences 21(12): 4302.
26. Mishra GP, Ghosh A, Jha A, Raghav SK. (2020) BedSect: An integrated web server application to perform intersection, visualization and functional annotation of genomic regions from multiple datasets. Frontiers in Genetics, 11, 3.
27. Ahad A, Stevanin M, Smita S, Mishra GP, Gupta D, Waszak S, Sarkar UA, Basak S, Gupta B, Acha-Orbea H, Raghav SK*. (2019) NCoR1: putting the brakes on the dendritic cell immune tolerance. iScience. 2019; 996-1011
28. Smita S, Ahad A, Ghosh A, Biswas VK, Koga MM, Gupta B, Acha-Orbea H, Raghav SK. Importance of EMT Factor ZEB1 in cDC1 “MutuDC Line” Mediated Induction of Th1 Immune Response. Frontiers in Immunology 2018 Nov 13;9:2604.
29. Jena KK, Kolapalli SP, Mehto S, Nath P, Das B, Sahoo PK, Ahad A, Syed GH, Raghav SK, Senapati S, Chauhan S, Chauhan S. TRIM16 controls assembly and degradation of protein aggregates by modulating the p62-NRF2 axis and autophagy. EMBO J. 2018 Sep 14;37(18).
30. Raghav SK, Gupta B. (2015). Single cell Transcriptomics for autoimmune disorders.  J Mol Genet Med 9: 191.
31. Smita S, Raghav SK. (2017) EMT factor ZEB1 depletion in dendritic cells enhances helminth clearance in mice by increasing Th2 responses. Conference abstract in Canadian Journal of Biotechnology, Volume 1, Special Issue, Page 179.
32. Ahad A, Smita S, Stevanin M, Mishra GP, Waszak SM, Gupta B, Orbea HA, Raghav SK. (2018) NCoR1 is a master regulator of tolerogenic program in dendritic cells. Conference abstract in Canadian Journal of Biotechnology, Volume 1, Special Issue, Page 161.
33. Tripathy A, Khanna S, Padhan P, Smita S, Raghav S, Gupta B. (2017) Direct recognition of LPS drive TLR4 expressing CD8+ T cell activation in patients with rheumatoid arthritis. Sci Rep. 7: 933.
34. Sahu D, Raghav SK, Gautam H, Das HR. (2015) A novel coumarin derivative, 8-methoxy chromen-2-one alleviates collagen induced arthritis by down regulating nitric oxide, NFκB and proinflammatory cytokines. Immunopharmacol. 29, 891-900.
35. Jain S, Suklabaidya S, Das B, Raghav SK, Batra SK, Senapati S. (2015) TLR4 activation by lipopolysaccharide confers survival advantage to growth factor deprived prostate cancer cells. 75:1020-1033.
36. Publications from Postdoc lab during ILS tenure:
    26. Jonathan Aryeh Sobel, Irina Krier, Teemu Andersin, Sunil Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Felix Naef, and the CycliX consortium. (2017) Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biology 15: e2001069.
    27. Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra C. Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil Raghav, and Bart Deplancke. (2017) Dissecting the brown adipogenic regulatory network using integrative genomics. Scientific Reports 7:42130.
    28. Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. (2015) Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell 27: 1039-50.
    29. Gubelmann C, Schwalie PC, Raghav SK, Röder E, Delessa T, Kiehlmann E, Waszak SM, Corsinotti A, Udin G, Holcombe W, Rudofsky G, Trono D, Wolfrum C, Deplancke B. (2014) Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Aug 27:e03346.

     

37. Publication during Postdoc and PhD:
    30. Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. (2014) Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. 30: 165-171.
    31. Kilpinen H, Waszak SM, Gschwind A, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis N, Yurovsky A, Lappalainen Tuuli, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. (2013) Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342: 744-747.
    32. Gubelmann C, Waszak SM, Isakova A, Holcombe W, Hens K, Iagovitina A, Feuz JD, Raghav SK, Simicevic J, Deplancke B (2013). A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Molecular Systems Biology 6; 9:682. PMID:23917988
    33. Hawkins RD*, Larjo A, Tripathi SK, Wagner U, Luu Y, Loneberg T, Raghav SK, Lee LK, Lund R, Lähdesmäki H*, Ren B*, Lahesmaa R* (2013) Global chromatin state analysis reveals lineage-specific enhancers during early cell fate specification of human Th1 and Th2 cells. Immunity 38:1271-1284. PMID:23791644
    34. Simicevic J, Schmid AW, Gilardoni P, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Lisacek F, Deplancke B. (2013) Absolute copy number analysis of transcription factors during cellular differentiation using a multiplex, targeted proteomics approach. Nature Methods 10: 570-576. PMID:23584187
    35. LeMartelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, Hernandez N*, Naef F*, and CycliX consortium including Raghav SK. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during circadian cycles. PLoS Biology 2012 10:e1001442. PMID:23209382
    36. Raghav SK, Waszak MS, Krier I, Gubelmann C, Mikkelsen ST, Deplancke B*. (2012) Integrative genomics identifies SMRT a gatekeeper of early adipogenesis through transcription factors C/EBPβ and KAISO. Molecular Cell 46, 335–350. PMID:22521691
    37. Bernasconi D, Canella D, Gilardi F, LeMartelot GL, Praz V, Migliavacca E, Delorenzi M, Hernandez N*, and CycliX consortium including Raghav SK (2012) A Multiplicity of Factors Contributes to Selective Transcription of a Subset of RNA polymerase III Genes in Mouse Liver. Genome Research 22: 666-680. PMID:22287103
    38. Baitsch L, Baumgaertner P, Devêvre E, Raghav SK, Legat A, Barba L, Wieckowski S, Bouzourene H, Deplancke B, Romero P, Rufer N, Speiser DE*. (2011) Exhaustion of human self/tumor-specific CD8 T-cells in melanoma metastases. Journal of Clinical Investigation, 121: 2350-60. PMID:20620947
    39. Elo LL, Järvenpää H, Tuomela S, Raghav SK, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Orešič M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R*. (2010) IL-4 and STAT6-mediated transcriptional regulation to initiate Th2 program in human T cells. Immunity 6: 852-862. PMID:20620947
    40. Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL*. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics, 18: 618. PMID:20017957
    41. Rautajoki KJ, Kyläniemi MK, Raghav SK, Rao K, Lahesmaa R*. (2008) An insight into molecular mechanisms of human T helper cell differentiation. Annals of Medicine, 40: 322-35. PMID:18484344
    42. Gupta B, Raghav SK, Das HR*. (2008) S-Nitrosylation of mannose binding lectin regulates its functional activities and the formation of autoantibody in rheumatoid arthritis. Nitric oxide: Biology and Chemistry, 18: 266-273. PMID:18348874
    43. Raghav SK, Gupta B, Das HR*. (2007) Inhibition of lipopolysaccharide inducible iNOS and IL-1b expression by active compounds isolated from Ruta graveolens L. through suppression of NF-kB activation in murine macrophages. European Journal of Pharmacology, 560: 69-80. PMID:17292351
    44. Raghav SK, Gupta B, Agrawal C, Chaturvedi VP, Das HR*. (2006) Expression of TNF-a and related signaling molecules in the peripheral blood mononuclear cells of rheumatoid arthritis patients. Mediators of Inflammation, 12682: 1-6. PMID:16951485
    45. Raghav SK, Gupta B, Agrawal C, Saroha A, Das RH, Chaturvedi VP, Das HR*. (2006) Altered expression and glycosylation of plasma proteins in rheumatoid arthritis. Glycoconjugate Journal, 23: 169-175. PMID:16691500
    46. Raghav SK, Gupta B, Agrawal C, Goswami K, Das HR*. (2006) Anti-inflammatory effect of Ruta graveolens L. in murine macrophage cells. Journal of Ethnopharmacology, 104: 234-239. PMID:16207519
    47. Gupta B, Raghav SK, Agrawal C, Das RH, Chaturvedi VP, Das HR*. (2006) Anti-MBL autoantibodies in patients with rheumatoid arthritis: prevalence and clinical significance. Journal of Autoimmunity, 27: 125-133. PMID:16904869
    48. Chaudhury I, Raghav SK, Gautam H, Das HR, Das RH*. (2006) Suppression of inducible nitric oxide synthase by 10-23 DNAzymes in murine macrophages. FEBS Letters, 580: 2046-2052. PMID:16546178
    49. Gupta B, Agrawal C, Raghav SK, Das SK, Das RH, Chaturvedi VP, Das HR*. (2005) Association of mannose-binding lectin gene (MBL2) polymorphisms with rheumatoid arthritis in an Indian cohort of case-control samples. Journal of Human Genetics, 50: 583–591. PMID:16220211
    50. Agrawal C, Raghav SK, Gupta B, Das RH, Chaturvedi VP, Goswami K, Das HR*. (2005) Tumor necrosis factor-alpha microsatellite polymorphism association with rheumatoid arthritis in Indian patients. Archives of Medical Research, 36: 555-559. PMID:16099338
    51. Das HR*, Raghav S, Gupta B and Das RH. (2007) Anti-inflammatory compounds from medicinal plant Ruta graveolens. Acta Horticulture, 756: 389- 398.
    52. Raghav SK, Deplancke B*. (2012) Genome-wide profiling of DNA binding proteins using barcode-based multiplex Solexa sequencing. Methods in Molecular Biology; 786: 247-62. PMID:21938631

    Article in University magazine / Science Horizon magazine

    1. Expanding research horizons abroad, annual magazine of Turku University, 2008.
    2. Genetic variability of SARS-CoV-2 strains and its impact on virus transmission, Atimukta Jha & Sunil K. Raghav, 2021.

    Patents Filed / granted:

    1. Method for the diagnosis of rheumatoid arthritis. Hasi Das, Bhawna Gupta, Sunil Kumar Raghav, Kalyan Goswami, Charu Agrawal and Rakha Hari Das. IPC8 Class: AG01N3353FI, US Patent 7,763,436.
    2. Novel anti-inflammatory compound 3-(1,1-dimethyl-allyl)-6-hydroxy-chromen-2-one isolated from Ruta graveolens L. Hasi Das, Sunil Kumar Raghav, Bhawna Gupta. IPC8 Class: AA61K31352FI, US Patent App. 11/935,985.

    3. Novel diagnostic marker, a diagnostic kit and a method for diagnosis of rheumatoid arthritis. Hasi Das, Bhawna Gupta, Sunil Kumar Raghav, Kalyan Goswami, Charu Agrawal and Rakha Hari Das. US Patent App. 11/281,243.