A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus

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33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)

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MicroRNA-30e-5p has an Integrated Role in the Regulation of the Innate Immune Response during Virus Infection and Systemic Lupus Erythematosus

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SLE Plasma Profiling Identifies Unique Signatures of Lupus Nephritis and Discoid Lupus

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Innate-like Gene Expression of Lung-Resident Memory CD8+ T Cells during Experimental Human Influenza: A Clinical Study

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Global gene expression changes in type 1 diabetes: Insights into autoimmune response in the target organ and in the periphery

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The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health

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RNA-Stabilized Whole Blood Samples but Not Peripheral Blood Mononuclear Cells Can Be Stored for Prolonged Time Periods Prior to Transcriptome Analysis

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Coordination between innate immune cells, type I IFNs and IRF5 drives SLE pathogenesis

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A Modular Cytokine Analysis Method Reveals Novel Associations With Clinical Phenotypes and Identifies Sets of Co-signaling Cytokines Across Influenza Natural Infection Cohorts and Healthy Controls

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Emerging technologies for systems vaccinology — multi-omics integration and single-cell (epi)genomic profiling

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Human systems immunology: Hypothesis-based modeling and unbiased data-driven approaches

Arazi, A., Pendergraft, W. F., Ribeiro, R. M., Perelson, A. S., & Hacohen, N. (2013) · Seminars in Immunology · doi:10.1016/j.smim.2012.11.003 · Cited by 38

Genetic and Genomic Markers of Anti-TNF Treatment Response in Rheumatoid Arthritis

Oliver, J., Plant, D., Webster, A. P., & Barton, A. C. (2015) · Biomarkers in Medicine · doi:10.2217/bmm.15.18 · Cited by 34

Blockade of GM-CSF pathway induced sustained suppression of myeloid and T cell activities in rheumatoid arthritis

Guo, X., Higgs, B., Bay-Jensen, A., Wu, Y.-L., Karsdal, M., Kuziora, M., Godwood, A., Close, D., Ryan, P. C., Roskos, L., et al. (2018) · Rheumatology · doi:10.1093/rheumatology/kex383 · Cited by 37

A Neutrophil-Driven Inflammatory Signature Characterizes the Blood Transcriptome Fingerprint of Psoriasis

Rawat, A., Rinchai, D., Toufiq, M., Marr, A. K., Kino, T., Garand, M., Tatari-Calderone, Z., Kabeer, B. S. A., Krishnamoorthy, N., Bedognetti, D., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.587946 · Cited by 35

Zetomipzomib (KZR-616) attenuates lupus in mice via modulation of innate and adaptive immune responses

Muchamuel, T., Fan, R., Anderl, J. L., Bomba, D., Johnson, H. W. B., Lowe, E., Tuch, B. B., McMinn, D. L., Millare, B., & Kirk, C. J. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1043680 · Cited by 34

A Network Modeling Approach to Analysis of the Th2 Memory Responses Underlying Human Atopic Disease

Bosco, A., McKenna, K., Firth, M. J., Sly, P. D., & Holt, P. G. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0804125 · Cited by 33

Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge

Rojas-Peña, M. L., Vallejo, A. F., Herrera, S. V., Gibson, G. C., & Arévalo‐Herrera, M. (2015) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0003978 · Cited by 32

Major pathogenic steps in human lupus can be effectively suppressed by nucleosomal histone peptide epitope-induced regulatory immunity

Zhang, L., Bertucci, A. M., Ramsey‐Goldman, R., Harsha-Strong, E. R., Burt, R. K., & Datta, S. K. (2013) · Clinical Immunology · doi:10.1016/j.clim.2013.08.008 · Cited by 33

Biomarkers that differentiate false positive urinalyses from true urinary tract infection

Shaikh, N., Martin, J. M., Hoberman, A., Skae, M., Milkovich, L., McElheny, C. L., Hickey, R. W., Gabriel, L., Kearney, D. H., Majd, M., et al. (2019) · Pediatric Nephrology · doi:10.1007/s00467-019-04403-7 · Cited by 32

Innate immune signatures to a partially-efficacious HIV vaccine predict correlates of HIV-1 infection risk

Andersen‐Nissen, E., Fiore-Gartland, A. J., Ballweber-Fleming, L., Carpp, L. N., Naidoo, A., Harper, M. S., Voillet, V., Grunenberg, N. A., Laher, F., Innes, C., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009363 · Cited by 32

An Interferon-Related Signature in the Transcriptional Core Response of Human Macrophages to Mycobacterium tuberculosis Infection

Wu, K., Dong, D., Fang, H., Levillain, F., Jin, W., Mei, J., Gicquel, B., Du, Y., Wang, K., Gao, Q., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038367 · Cited by 30

Genome-Wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination

Haralambieva, I. H., Oberg, A. L., Ovsyannikova, I. G., Kennedy, R. B., Grill, D. E., Middha, S., Bot, B. M., Wang, V. W., Smith, D. I., Jacobson, R. M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062149 · Cited by 30

Detecting specific infections in children through host responses

Mejías, A., Suárez, N. M., & Ramilo, O. (2014) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000000065 · Cited by 30

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Chen, X. X., Wang, Y., Cappuccio, A., Cheng, W.-S., Ruf-Zamojski, F. M., Nair, V. D., Miller, C. M., Rubenstein, A. B., Nudelman, G., Tadych, A., et al. (2023) · Nature Computational Science · doi:10.1038/s43588-023-00476-5 · Cited by 31

Systems biology applied to vaccine and immunotherapy development

Buonaguro, L., Wang, E., Tornesello, M. L., Buonaguro, L., & Marincola, F. M. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-146 · Cited by 31

Herpes simplex virus oncolytic vaccine therapy in melanoma

Sivendran, S., Pan, M., Kaufman, H. L., & Saenger, Y. M. (2010) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.2010.495383 · Cited by 30

Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period

Rothen, J., Murie, C., Carnes, J., Anupama, A., Abdulla, S., Chemba, M., Mpina, M., Tanner, M., Sim, B. K. L., Hoffman, S. L., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0199392 · Cited by 30

Host and Bacterial Markers that Differ in Children with Cystitis and Pyelonephritis

Shaikh, N., Martin, J. M., Hoberman, A., Skae, M., Milkovich, L., Nowalk, A. J., McElheny, C. L., Hickey, R. W., Kearney, D. H., Majd, M., et al. (2019) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2019.01.012 · Cited by 30

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

McLoughlin, K. E., Correia, C. N., Browne, J. A., Magee, D. A., Nalpas, N., Rue-Albrecht, K., Whelan, A. O., Villarreal‐Ramos, B., Vordermeier, H. M., Gormley, E. P., et al. (2021) · Frontiers in Veterinary Science · doi:10.3389/fvets.2021.662002 · Cited by 31

Co-infection withMycobacterium tuberculosisand human immunodeficiency virus: an overview and motivation for systems approaches

Deffur, A., Mulder, N., & Wilkinson, R. J. (2013) · Pathogens and Disease · doi:10.1111/2049-632x.12060 · Cited by 31

Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection

Hou, J., Brouwer, W. P., Kreefft, K., Gama, L., Price, S. L., Janssen, H. L. A., French, P. J., Vanwolleghem, T., & Boonstra, A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0179920 · Cited by 31

Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function

Martínek, J., Lin, J., Kim, K. I., Wang, V. G., Wu, T.-C., Chiorazzi, M., Boruchov, H., Gulati, A., Seeniraj, S., Sun, L., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100621 · Cited by 29

Transcriptional changes induced by candidate malaria vaccines and correlation with protection against malaria in a human challenge model

Dunachie, S. J., Berthoud, T. K., Hill, A. V. S., & Fletcher, H. A. (2015) · Vaccine · doi:10.1016/j.vaccine.2015.07.087 · Cited by 28

Th17-related mammary immunity, but not a high systemic Th1 immune response is associated with protection against E. coli mastitis

Cebron, N., Maman, S., Walachowski, S., Gausserès, B., Cunha, P., Rainard, P., & Foucras, G. (2020) · npj Vaccines · doi:10.1038/s41541-020-00258-4 · Cited by 31

Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study

Shui, I. M., Liu, X. Q., Zhao, Q., Kim, S. T., Sun, Y. M., Yearley, J. H., Choudhury, T., Webber, A. L., Krepler, C., Cristescu, R., et al. (2022) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2022-004879 · Cited by 29

Reducing cell intrinsic immunity to mRNA vaccine alters adaptive immune responses in mice

Wang, Z., Jacobus, E. J., Stirling, D. C., Krumm, S. A., Flight, K. E., Cunliffe, R. F., Mottl, J., Singh, C., Mosscrop, L. G., Santiago, L. A., et al. (2023) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2023.102045 · Cited by 30

Interferon and B-cell Signatures Inform Precision Medicine in Lupus Nephritis

Parodis, I., Lindblom, J., Dominguez, D. T., Beretta, L., Borghi, M. O., Castillo, J., Carnero‐Montoro, E., Enman, Y., Mohan, C., Alarcón-Riquelme, M. E., et al. (2024) · Kidney International Reports · doi:10.1016/j.ekir.2024.03.014 · Cited by 27

A prospective cohort for the investigation of alteration in temporal transcriptional and microbiome trajectories preceding preterm birth: a study protocol

Brummaier, T., Kabeer, B. S. A., Lindow, S. W., Konje, J. C., Pukrittayaamee, S., Utzinger, J., Toufiq, M., Antoniou, A., Marr, A. K., Suriyakan, S., et al. (2019) · BMJ Open · doi:10.1136/bmjopen-2018-023417 · Cited by 26

Transcription of proteinase 3 and related myelopoiesis genes in peripheral blood mononuclear cells of patients with active Wegener's granulomatosis

Cheadle, C., Berger, A. E., Andrade, F., James, R., Johnson, K., Watkins, T., Park, J. K., Chen, Y., Ehrlich, E., Mullins, M., et al. (2010) · Arthritis & Rheumatism · doi:10.1002/art.27398 · Cited by 27

Pharmacological Management of Childhood-Onset Systemic Lupus Erythematosus

Thorbinson, C., Oni, L., Smith, E. M. D., Midgley, A., & Beresford, M. W. (2016) · Pediatric Drugs · doi:10.1007/s40272-016-0170-8 · Cited by 27

Gene Expression Profiling To Predict and Assess the Consequences of Therapy-Induced Virus Eradication in Chronic Hepatitis C Virus Infection

Hou, J., van Oord, G. W., Groothuismink, Z. M. A., Claassen, M. A. A., Kreefft, K., Zaaraoui‐Boutahar, F., van IJcken, W. F. J., Osterhaus, A. D. M. E., Janssen, H. L. A., Andeweg, A. C., et al. (2014) · Journal of Virology · doi:10.1128/jvi.00775-14 · Cited by 26

Using Blood Informative Transcripts in Geographical Genomics: Impact of Lifestyle on Gene Expression in Fijians

Nath, A. P., Arafat, D., & Gibson, G. C. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00243 · Cited by 26

A genomic approach to biomarker discovery in human autoimmune diseases

Pascual, V. (2010) · Journal of Translational Medicine · doi:10.1186/1479-5876-8-s1-i2

An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity

Bettacchioli, É., Chiche, L., Chaussabel, D., Cornec, D., Jourde‐Chiche, N., & Rinchai, D. (2024) · Database · doi:10.1093/database/baae045 · Cited by 1

A Transcriptome Fingerprinting Assay for Clinical Immune MonitoringPreprint

Altman, M. C., Baldwin, N. E., Whalen, E., Al‐Shaikhly, T., Presnell, S., Khaenam, P., Gersuk, V. H., Chiche, L., Jourde‐Chiche, N., Phillips, J. T., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/587295 · Cited by 5

Development of a Fixed Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Immunological StatesPreprint

Altman, M. C., Rinchai, D., Baldwin, N. E., Toufiq, M., Whalen, E., Garand, M., Kabeer, B. S. A., Alfaki, M., Presnell, S., Khaenam, P., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-58602/v1

Combining DNA-microarray data in systemic lupus erythematosus

Verweij, C. L., & Vosslamber, S. (2011) · Genome Medicine · doi:10.1186/gm246 · Cited by 2