1. Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F; CycliX consortium. (2017) Direct recognition of LPS drive TLR4 expressing CD8₊T cell activation in patients with rheumatoid arthritis. Tripathy A, Khanna S, Padhan P, Smita S, Raghav S, Gupta B. Sci Rep. 2017, 7: 933.Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol. 15: e2001069.
2. Dissecting the brown adipogenic regulatory network using integrative genomics. (2017) Pradhan RN, Bues JJ, Gardeux V, Schwalie PC, Alpern D, Chen W, Russeil J, Raghav SK, Deplancke B. Sci Rep. 7: 42130.
3. Sengupta S, Naz S, Das I, Ahad A, Padhi A, Naik SK, Ganguli G, Pattanaik KP, Raghav SK, Nandicoori VK, Sonawane A. (2017) Mycobacterium tuberculosisEsxL inhibits MHC-II expression by promoting hypermethylation in class-II transactivator loci in macrophages.  J Biol Chem. 292: 6855-6868.
4. 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. International Immunopharmacology Oct 2.
5. 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: 1039-1050.
6. 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.
7. 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. Bioinformatics. 30:165-171.
8. Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, 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.
9. 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. Mol Syst Biol. 9:682.
10. Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. (2013) Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity. 38:1271-1284.
11. Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B. (2013) Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nat Methods. 10:570-576.
12. Le Martelot 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; CycliX Consortium (including Raghav SK). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol. 2012;10(11):e1001442
13. 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.
14. Bernasconi D, Canella D, Gilardi F, LeMartelot GL, Praz V, Migliavacca E, Delorenzi M, Hernandez N, and CycliX consortium (includes 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.
15. 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 Tcells in melanoma metastases. Journal of Clinical Investigation 121: 2350-2360.
16. 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 (2010) 6: 852-862 (* Equal contribution first author).
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. Agrawal C, Raghav SK, Gupta B, Das RH, Chaturvedi VP, Goswami K, Das HR. (2005) Tumor necrosis factor-alpha microsatellite polymorphism association with rheumatoid. Archives of Medical Research 36: 555-559.

Book Chapters

1. Das HR, Raghav S, Gupta B and Das RH. (2007) Anti-inflammatory compounds from medicinal plant Ruta graveolens. Acta Horticulture, 756: 389- 398.
2. 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.

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.
4. Method to generate tolerogenic dendritic cells capable of enhancing T regulatory cell development : application no-201731006590

Abdul Ahad, SRF

Master in biotechnology in 2012, C.C.S University, Meerut

Qualified CSIR-UGC JRF, DBT-JRF, ICAR-NET, ICAR-SRF

Project: Role of Nuclear receptor co-repressors in dendritic cell function

Shuchi Smita, SRF

Master in biotechnology in 2012 from Banasthali university, Rajasthan

Qualified CSIR-UGC LS

Project: Role of Zinc finger TFs in Dendritic cell activation and maturation

Atimukta Jha, JRF

Master in Microbiology in 2011 from Bangalore University.

Qualified CSIR-UGC LS, GATE

Project: Role of nuclear receptors and their co-regulators in dendritic cells

 Arup Ghosh, JRF

M. Tech. from NIPER Kolkata

Project: Computational modelling of gene regulatory networks underlying dendritic cell function

Gyan Prakash Mishra

M.S. Pharmaco-informaticscs in 2015 from NIPER Kolkata, WB

Project JRF

Work Area : NGS data analysis (ChIP-/RNA-seq) and analysis pipeline development

Open positions:
The laboratory of Immuno-Genomics and Systems Biology at ILS is looking for passionate PhD students and postdocs with a strong interest in the field of immunology and Genomics. Prior exposure to techniques such as cell culture, chromatin immuno-precipitation, bioinformatic analysis using R / analysis of NGS datasets will be an asset.
If interested please write to Dr. Sunil K. Raghav at raghuvanshi2010@yahoo.co.in, sunil.raghav@ils.res.in with a small summary describing your research interests, small research plan that you would like to follow in the lab along with a detailed CV in a single PDF file.