Soumya Raychaudhuri, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation. Genome Medicine. 13: 64. PMID 33879239 DOI: 10.1186/s13073-021-00881-3  0.72
2021 Cook S, Choi W, Lim H, Luo Y, Kim K, Jia X, Raychaudhuri S, Han B. Accurate imputation of human leukocyte antigens with CookHLA. Nature Communications. 12: 1264. PMID 33627654 DOI: 10.1038/s41467-021-21541-5  0.8
2021 Shi H, Gazal S, Kanai M, Koch EM, Schoech AP, Siewert KM, Kim SS, Luo Y, Amariuta T, Huang H, Okada Y, Raychaudhuri S, Sunyaev SR, Price AL. Population-specific causal disease effect sizes in functionally important regions impacted by selection. Nature Communications. 12: 1098. PMID 33597505 DOI: 10.1038/s41467-021-21286-1  0.8
2020 Krebs K, Bovijn J, Zheng N, Lepamets M, Censin JC, Jürgenson T, Särg D, Abner E, Laisk T, Luo Y, Skotte L, Geller F, Feenstra B, Wang W, Auton A, ... ... Raychaudhuri S, et al. Genome-wide Study Identifies Association between HLA-B55:01 and Self-Reported Penicillin Allergy. American Journal of Human Genetics. PMID 32888428 DOI: 10.1016/J.Ajhg.2020.08.008  0.8
2020 Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN- and TNF- drive a + + macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation. Biorxiv : the Preprint Server For Biology. PMID 32793902 DOI: 10.1101/2020.08.05.238360  0.72
2020 Choi W, Luo Y, Raychaudhuri S, Han B. HATK: HLA Analysis Toolkit. Bioinformatics (Oxford, England). PMID 32735319 DOI: 10.1093/Bioinformatics/Btaa684  0.8
2020 Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. The New England Journal of Medicine. 383: 218-228. PMID 32668112 DOI: 10.1056/Nejmoa2004114  0.72
2020 Asgari S, Luo Y, Akbari A, Belbin GM, Li X, Harris DN, Selig M, Bartell E, Calderon R, Slowikowski K, Contreras C, Yataco R, Galea JT, Jimenez J, Coit JM, ... ... Raychaudhuri S, et al. A positively selected FBN1 missense variant reduces height in Peruvian individuals. Nature. PMID 32499652 DOI: 10.1038/S41586-020-2302-0  0.8
2020 Wei K, Korsunsky I, Marshall JL, Gao A, Watts GFM, Major T, Croft AP, Watts J, Blazar PE, Lange JK, Thornhill TS, Filer A, Raza K, Donlin LT, ... ... Raychaudhuri S, et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature. PMID 32499639 DOI: 10.1038/S41586-020-2222-Z  0.72
2020 Gutierrez-Arcelus M, Baglaenko Y, Arora J, Hannes S, Luo Y, Amariuta T, Teslovich N, Rao DA, Ermann J, Jonsson AH, Navarrete C, Rich SS, Taylor KD, Rotter JI, ... ... Raychaudhuri S, et al. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nature Genetics. PMID 32066938 DOI: 10.1038/S41588-020-0579-4  0.8
2019 Amariuta T, Luo Y, Knevel R, Okada Y, Raychaudhuri S. Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis. Immunological Reviews. PMID 31782165 DOI: 10.1111/Imr.12827  0.8
2019 Luo Y, Suliman S, Asgari S, Amariuta T, Baglaenko Y, Martínez-Bonet M, Ishigaki K, Gutierrez-Arcelus M, Calderon R, Lecca L, León SR, Jimenez J, Yataco R, Contreras C, Galea JT, ... ... Raychaudhuri S, et al. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nature Communications. 10: 3765. PMID 31434886 DOI: 10.1038/S41467-019-11664-1  0.8
2019 Nathan A, Baglaenko Y, Fonseka CY, Beynor JI, Raychaudhuri S. Multimodal single-cell approaches shed light on T cell heterogeneity. Current Opinion in Immunology. 61: 17-25. PMID 31430664 DOI: 10.1016/J.Coi.2019.07.002  0.72
2019 Pouget JG, Han B, Wu Y, Mignot E, Ollila HM, Barker J, Spain S, Dand N, Trembath R, Martin J, Mayes MD, Bossini-Castillo L, López-Isac E, Jin Y, ... ... Raychaudhuri S, et al. Cross-disorder analysis of schizophrenia and 19 immune-mediated diseases identifies shared genetic risk. Human Molecular Genetics. PMID 31211845 DOI: 10.1093/Hmg/Ddz145  0.8
2019 Croft AP, Campos J, Jansen K, Turner JD, Marshall J, Attar M, Savary L, Wehmeyer C, Naylor AJ, Kemble S, Begum J, Dürholz K, Perlman H, Barone F, McGettrick HM, ... ... Raychaudhuri S, et al. Distinct fibroblast subsets drive inflammation and damage in arthritis. Nature. PMID 31142839 DOI: 10.1038/S41586-019-1263-7  0.72
2019 Kuo D, Ding J, Cohn IS, Zhang F, Wei K, Rao DA, Rozo C, Sokhi UK, Shanaj S, Oliver DJ, Echeverria AP, DiCarlo EF, Brenner MB, Bykerk VP, Goodman SM, ... Raychaudhuri S, et al. HBEGF macrophages in rheumatoid arthritis induce fibroblast invasiveness. Science Translational Medicine. 11. PMID 31068444 DOI: 10.1126/Scitranslmed.Aau8587  0.72
2019 Amariuta T, Luo Y, Gazal S, Davenport EE, van de Geijn B, Ishigaki K, Westra HJ, Teslovich N, Okada Y, Yamamoto K, Price AL, Raychaudhuri S. IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors. American Journal of Human Genetics. PMID 31006511 DOI: 10.1016/J.Ajhg.2019.03.012  0.8
2019 Radley G, Mulhearn B, Donlin L, Anolik JH, Brenner M, Raychaudhuri S, Hyrich K, Morgan A, Wilson G, Isaacs J, Hussell T, Barton A, Viatte S. Sat0062 Stratified Medicine For Rheumatoid Arthritis: Predicting Response To Biologic Therapy Using Immune Cell Signatures Annals of the Rheumatic Diseases. DOI: 10.1136/Annrheumdis-2019-Eular.2371  0.4
2018 Davenport EE, Amariuta T, Gutierrez-Arcelus M, Slowikowski K, Westra HJ, Luo Y, Shen C, Rao DA, Zhang Y, Pearson S, von Schack D, Beebe JS, Bing N, John S, Vincent MS, ... ... Raychaudhuri S, et al. Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial. Genome Biology. 19: 168. PMID 30340504 DOI: 10.1186/S13059-018-1560-8  0.8
2018 Westra HJ, Martínez-Bonet M, Onengut-Gumuscu S, Lee A, Luo Y, Teslovich N, Worthington J, Martin J, Huizinga T, Klareskog L, Rantapaa-Dahlqvist S, Chen WM, Quinlan A, Todd JA, Eyre S, ... ... Raychaudhuri S, et al. Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes. Nature Genetics. PMID 30224649 DOI: 10.1038/S41588-018-0216-7  0.8
2018 Rao DA, Bocharnikov AV, Fonseka CY, Keegan J, Diamond B, Anolik JH, Nigrovic PA, Raychaudhuri S, Lederer JA, Brenner MB. AI-19 T peripheral helper cells are expanded in the circulation of active SLE patients and correlate with CD21low B cells Lupus Science & Medicine. 5. DOI: 10.1136/Lupus-2018-Lsm.19  0.56
2017 Fonseka CY, Rao DA, Raychaudhuri S. Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis. Current Opinion in Immunology. 49: 27-36. PMID 28888129 DOI: 10.1016/J.Coi.2017.08.005  0.56
2017 Aung T, Ozaki M, Lee MC, Schlötzer-Schrehardt U, Thorleifsson G, Mizoguchi T, Igo RP, Haripriya A, Williams SE, Astakhov YS, Orr AC, Burdon KP, Nakano S, Mori K, Abu-Amero K, ... ... Raychaudhuri S, et al. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. Nature Genetics. PMID 28553957 DOI: 10.1038/Ng.3875  0.36
2016 Hinks A, Bowes J, Cobb J, Ainsworth HC, Marion MC, Comeau ME, Sudman M, Han B, Becker ML, Bohnsack JF, de Bakker PI, Haas JP, Hazen M, Lovell DJ, ... ... Raychaudhuri S, et al. Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases. Annals of the Rheumatic Diseases. PMID 27998952 DOI: 10.1136/Annrheumdis-2016-210025  0.8
2016 Li Z, Xia Y, Feng LN, Chen JR, Li HM, Cui J, Cai QQ, Sim KS, Nairismägi ML, Laurensia Y, Meah WY, Liu WS, Guo YM, Chen LZ, Feng QS, ... ... Raychaudhuri S, et al. Genetic risk of extranodal natural killer T-cell lymphoma: a genome-wide association study. The Lancet. Oncology. PMID 27470079 DOI: 10.1016/S1470-2045(16)30148-6  0.72
2016 Prins BP, Abbasi A, Wong A, Vaez A, Nolte I, Franceschini N, Stuart PE, Guterriez Achury J, Mistry V, Bradfield JP, Valdes AM, Bras J, Shatunov A, ... ... Raychaudhuri S, et al. Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study. Plos Medicine. 13: e1001976. PMID 27327646 DOI: 10.1371/Journal.Pmed.1001976  0.4
2016 Han B, Pouget JG, Slowikowski K, Stahl E, Lee CH, Diogo D, Hu X, Park YR, Kim E, Gregersen PK, Dahlqvist SR, Worthington J, Martin J, Eyre S, Klareskog L, ... ... Raychaudhuri S, et al. A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases. Nature Genetics. PMID 27182969 DOI: 10.1038/Ng.3572  0.4
2016 Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, et al. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nature Genetics. PMID 26974007 DOI: 10.1038/Ng.3528  0.4
2016 Han B, Duong D, Sul JH, de Bakker PI, Eskin E, Raychaudhuri S. A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping. Human Molecular Genetics. PMID 26908615 DOI: 10.1093/Hmg/Ddw049  0.8
2016 Gutierrez-Arcelus M, Rich SS, Raychaudhuri S. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nature Reviews. Genetics. 17: 160-74. PMID 26907721 DOI: 10.1038/Nrg.2015.33  0.36
2015 Gutierrez-Achury J, Zorro MM, Ricaño-Ponce I, Zhernakova DV, Diogo D, Raychaudhuri S, Franke L, Trynka G, Wijmenga C, Zhernakova A. Functional implications of disease-specific variants in loci jointly associated to coeliac disease and rheumatoid arthritis. Human Molecular Genetics. PMID 26546613 DOI: 10.1093/Hmg/Ddv455  0.72
2015 Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K, Ripke S, Day FR, ... ... Raychaudhuri S, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature Genetics. PMID 26414678 DOI: 10.1038/Ng.3404  0.72
2015 Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Huizinga TW, Abecasis G, Becker J, Boeckxstaens GE, Chen WM, Franke A, Gladman DD, ... ... Raychaudhuri S, et al. Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases. Nature Genetics. PMID 26258845 DOI: 10.1038/Ng.3379  0.4
2015 Hu X, Deutsch AJ, Lenz TL, Onengut-Gumuscu S, Han B, Chen WM, Howson JM, Todd JA, de Bakker PI, Rich SS, Raychaudhuri S. Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk. Nature Genetics. 47: 898-905. PMID 26168013 DOI: 10.1038/Ng.3353  0.4
2015 Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B, Raychaudhuri S. Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci. American Journal of Human Genetics. 97: 139-52. PMID 26140449 DOI: 10.1016/J.Ajhg.2015.05.016  0.4
2015 Ghoshal N, Talapatra S, Talukder P, Sengupta M, Ray SK, Chakraborty A, Raychaudhuri SS. Cross-adaptation to cadmium stress in Plantago ovata by pre-exposure to low dose of gamma rays: Effects on metallothionein and metal content. International Journal of Radiation Biology. 1-13. PMID 25968556 DOI: 10.3109/09553002.2015.1047984  0.56
2015 Hayes JE, Trynka G, Vijai J, Offit K, Raychaudhuri S, Klein RJ. Overlap of lymphoma risk SNPs with regulatory regions in GM12878. Plos One. DOI: 10.1371/Journal.Pone.0139360.G002  0.72
2015 Viatte S, Plant D, Han B, Fu B, Yarwood A, Thomson W, Symmons DPM, Worthington J, Young A, Hyrich KL, Morgan AW, Wilson AG, Isaacs JD, Raychaudhuri S, Barton A. O49. Personalized Genetic Medicine: Amino Acid Positions 11, 71 and 74 in HLA-DRB1 Predict Disease Severity, Mortality and Treatment Response in Rheumatoid Arthritis—Multi-Centre Prospective Cohort Studies Rheumatology. 54. DOI: 10.1093/Rheumatology/Kev087.001  0.8
2014 Frisell T, Hellgren K, Alfredsson L, Raychaudhuri S, Klareskog L, Askling J. Familial aggregation of arthritis-related diseases in seropositive and seronegative rheumatoid arthritis: a register-based case-control study in Sweden. Annals of the Rheumatic Diseases. PMID 25498119 DOI: 10.1136/Annrheumdis-2014-206133  0.4
2014 Okada Y, Kim K, Han B, Pillai NE, Ong RT, Saw WY, Luo M, Jiang L, Yin J, Bang SY, Lee HS, Brown MA, Bae SC, Xu H, Teo YY, ... ... Raychaudhuri S, et al. Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Human Molecular Genetics. 23: 6916-26. PMID 25070946 DOI: 10.1093/Hmg/Ddu387  0.8
2014 Talapatra S, Ghoshal N, Raychaudhuri SS. Molecular characterization, modeling and expression analysis of a somatic embryogenesis receptor kinase (SERK) gene in Momordica charantia L. during somatic embryogenesis Plant Cell, Tissue and Organ Culture. 116: 271-283. DOI: 10.1007/s11240-013-0401-4  0.56
2013 Ghoshal N, Talapatra S, Moulick A, Chakraborty A, Raychaudhuri SS. Alterations in transcriptome and proteome on metallothioneins following oxidative stress induced by sublethal doses of cadmium and gamma rays in Plantago ovata. International Journal of Radiation Biology. 89: 571-82. PMID 23461270 DOI: 10.3109/09553002.2013.782109  0.56
2013 Sengupta M, Chakraborty A, Raychaudhuri SS. Ionizing radiation induced changes in phenotype, photosynthetic pigments and free polyamine levels in Vigna radiata (L.) Wilczek. Applied Radiation and Isotopes : Including Data, Instrumentation and Methods For Use in Agriculture, Industry and Medicine. 75: 44-9. PMID 23454839 DOI: 10.1016/j.apradiso.2013.01.036  0.56
2013 Yarwood A, Lunt M, Han B, Raychaudhuri S, Bowes J, Barton A, Eyre S, Raci. THU0010 A Weighted Genetic Risk Score Using 46 Loci to Predict Rheumatoid Arthritis Risk Annals of the Rheumatic Diseases. 72. DOI: 10.1136/Annrheumdis-2013-Eular.538  0.8
2013 Bandyopadhyay S, Raychaudhuri SS. Development and comparison of RAPD, SCAR and AFLP markers for distinguishing some medicinally important species of the genus Phyllanthus Plant Biosystems. 147: 12-20. DOI: 10.1080/11263504.2011.635714  0.56
2012 Banerjee A, Bandyopadhyay S, Raychaudhuri SS. In vitro regeneration of hypericum perforatum L. using thidiazuron and analysis of genetic stability of regenerants Indian Journal of Biotechnology. 11: 92-98.  0.56
2011 Saha P, Bandyopadhyay S, Raychaudhuri SS. Formulation of nutrient medium for in vitro somatic embryo induction in plantago ovata forsk Biological Trace Element Research. 140: 225-243. PMID 20405339 DOI: 10.1007/s12011-010-8684-3  0.56
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