Publications in peer-reviewed Journals / patents:
List of publications as PI from ILS:
- 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, 05 February.
- 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
- 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. Front Immunol. 2018 Nov 13;9:2604.
- 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).
- Raghav SK, Gupta B. (2015). Single cell Transcriptomics for autoimmune disorders. J Mol Genet Med 9: 191.
- 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.
- 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.
- 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.
- Sahu D, Raghav SK, Gautam H, Das HR. (2015) A novel coumarin derivative, 8-methoxy chromen-2-one alleviates collagen-induced arthritis by downregulating nitric oxide, NFκB and proinflammatory cytokines. Immunopharmacol. 29, 891-900.
- 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. Prostate, 75:1020-1033.
Publications from Postdoc lab during ILS tenure:
- 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.
- 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.
- 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.
- 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.
Publication during Postdoc and Ph.D.:
- 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.
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Das HR*, Raghav S, Gupta B and Das RH. (2007) Anti-inflammatory compounds from medicinal plant Ruta graveolens. Acta Horticulture, 756: 389- 398.
- 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
Expanding research horizons abroad, annual magazine of Turku University, 2008.
Patents
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. |