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

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) · Science · doi:10.1126/science.286.5439.531 · Cited by 11,516 · see citing works

Graph theory

Harary, F. (1969) · Cited by 10,764 · see citing works

PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., et al. (2000) · Nature · doi:10.1038/35000501 · Cited by 9,925 · see citing works

Applied Longitudinal Analysis

Fitzmaurice, G. M., Laird, N. M., & Ware, J. H. (2011) · Wiley Series in Probability and Statistics · doi:10.1002/9781119513469 · Cited by 4,639 · see citing works

Derivation of the sledai. A disease activity index for lupus patients

Bombardier, C., Gladman, D. D., Urowitz, M. B., Caron, D., Chang, C. H., Austin, A., Bell, A., Bloch, D. A., Corey, P. N., Decker, J. L., et al. (1992) · Arthritis & Rheumatism · doi:10.1002/art.1780350606 · Cited by 4,570 · see citing works

Linear Mixed Models for Longitudinal Data

Verbeke, G. (1997) · Lecture Notes in Statistics · doi:10.1007/978-1-4612-2294-1_3 · Cited by 3,506 · see citing works

Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus

Baechler, E. C., Batliwalla, F., Karypis, G., Gaffney, P. M., Ortmann, W. A., Espe, K. J., Shark, K. B., Grande, W. J., Hughes, K. M. H., Kapur, V., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0337679100 · Cited by 2,246 · see citing works

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

MAQC Consortium, Shi, L., Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., Collins, P. J., de Longueville, F., et al. (2006) · Nature Biotechnology · doi:10.1038/nbt1239 · Cited by 2,126 · see citing works

Molecular classification of cutaneous malignant melanoma by gene expression profiling

Bittner, M. L., Meltzer, P. S., Chen, Y., Jiang, Y. Y., Seftor, E. A., Hendrix, M. J. C., Radmacher, M. D., Simon, R., Zohar Yakhini, B., Ben‐Dor, A., et al. (2000) · Nature · doi:10.1038/35020115 · Cited by 1,989 · see citing works

Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood

Bennett, L. B., Palucka, K., Arce, E., Cantrell, V., Borvák, J., Banchereau, J., & Pascual, V. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20021553 · Cited by 1,962 · see citing works

A network-based analysis of systemic inflammation in humans

Program, I. A. H. R. T. I. L. S. C. R., Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., et al. (2005) · Nature · doi:10.1038/nature03985 · Cited by 1,429 · see citing works

Applied longitudinal analysis

(2004) · Choice Reviews Online · doi:10.5860/choice.42-2265 · Cited by 1,385 · see citing works

Prediction of cancer outcome with microarrays: a multiple random validation strategy

Michiels, S., Koscielny, S., & Hill, C. (2005) · The Lancet · doi:10.1016/s0140-6736(05)17866-0 · Cited by 1,029 · see citing works

Multiple-laboratory comparison of microarray platforms

Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., et al. (2005) · Nature Methods · doi:10.1038/nmeth756 · Cited by 862 · see citing works

Linear mixed models for longitudinal data

(2000) · Springer Series in Statistics · doi:10.1007/b98969 · Cited by 818 · see citing works

Reliability and validity of six systems for the clinical assessment of disease activity in systemic lupus erythematosus

Liang, M. H., Socher, S. A., Larson, M. G., & Schur, P. H. (1989) · Arthritis & Rheumatism · doi:10.1002/anr.1780320909 · Cited by 787 · see citing works

Derivation of the sledai

Schned, E. S., Glickstein, S. L., & Doyle, M. T. A. (1993) · Arthritis & Rheumatism · doi:10.1002/art.1780360623 · Cited by 726 · see citing works

A module map showing conditional activity of expression modules in cancer

Segal, E., Friedman, N., Koller, D., & Regev, A. (2004) · Nature Genetics · doi:10.1038/ng1434 · Cited by 685 · see citing works

The BILAG index: a reliable and valid instrument for measuring clinical disease activity in systemic lupus erythematosus

Hay, E. M., Bacon, P. A., Gordon, C., Isenberg, D. A., Maddison, P. J., Snaith, M. L., Symmons, D. P. M., Viner, N. J., & Zoma, A. A. (1993) · QJM · doi:10.1093/oxfordjournals.qjmed.a068841 · Cited by 571 · see citing works

Gene expression patterns in blood leukocytes discriminate patients with acute infections

Ramilo, O., Allman, W., Chung, W. K., Mejías, A., Ardura, M. I., Glaser, C., Wittkowski, K. M., Piqueras, B., Banchereau, J., Palucka, K., et al. (2006) · Blood · doi:10.1182/blood-2006-02-002477 · Cited by 474 · see citing works

Standardizing global gene expression analysis between laboratories and across platforms

Weis, B. K. (2005) · Nature Methods · doi:10.1038/nmeth754 · Cited by 465 · see citing works

Independence and reproducibility across microarray platforms

Larkin, J. E., Frank, B. C., Gavras, H. P., Sultana, R., & Quackenbush, J. F. (2005) · Nature Methods · doi:10.1038/nmeth757 · Cited by 420 · see citing works

Coordinate overexpression of interferon‐α–induced genes in systemic lupus erythematosus

Kirou, K. A., Lee, C. L. L., George, S., Louca, K., Papagiannis, I. G., Peterson, M. G. E., Ly, N. P., Woodward, R. N., Fry, K. E., Lau, A., et al. (2004) · Arthritis & Rheumatism · doi:10.1002/art.20798 · Cited by 418 · see citing works

From signatures to models: understanding cancer using microarrays

Segal, E., Friedman, N., Kaminski, N., Regev, A., & Koller, D. (2005) · Nature Genetics · doi:10.1038/ng1561 · Cited by 380 · see citing works

Microarray Analysis of Interferon-regulated Genes in SLE

Crow, M. K., Kirou, K. A., & Wohlgemuth, J. G. (2003) · Autoimmunity · doi:10.1080/08916930310001625952 · Cited by 287 · see citing works

Classification and definition of major flares in SLE clinical trials

Petri, M., Buyon, J., & Kim, M. (1999) · Lupus · doi:10.1191/096120399680411281 · Cited by 282 · see citing works

Microarrays and molecular research: noise discovery?

Ioannidis, J. P. A. (2005) · The Lancet · doi:10.1016/s0140-6736(05)17878-7 · Cited by 271 · see citing works

Opiate-like effects of sugar on gene expression in reward areas of the rat brain

Spangler, R., Wittkowski, K. M., Goddard, N. L., Avena, N. M., Hoebel, B. G., & LEIBOWITZ, S. F. (2004) · Molecular Brain Research · doi:10.1016/j.molbrainres.2004.02.013 · Cited by 255 · see citing works

Molecular Classification of Crohn's Disease and Ulcerative Colitis Patients Using Transcriptional Profiles in Peripheral Blood Mononuclear Cells

Burczynski, M. E., Peterson, R. L., Twine, N. C., Zuberek, K., Brodeur, B. J., Casciotti, L., Maganti, V., Reddy, P., Strahs, A. L., Immermann, F., et al. (2006) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2006.050079 · Cited by 249 · see citing works

Application of genome-wide expression analysis to human health and disease

Cobb, J. P., Mindrinos, M. N., Miller‐Graziano, C. L., Calvano, S. E., Baker, H. V., Xiao, W., Laudański, K., Brownstein, B. H., Elson, C. M., Hayden, D. L., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409768102 · Cited by 234 · see citing works

Addendum: Standardizing global gene expression analysis between laboratories and across platforms

Bammler, T. K., Beyer, R. P., Bhattacharya, S., Boorman, G. A., Boyles, A. L., Bradford, B. U., Bumgarner, R. E., Bushel, P. R., Chaturvedi, K., Choi, D., et al. (2005) · Nature Methods · doi:10.1038/nmeth0605-477a · Cited by 230 · see citing works

Blood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockade

Allantaz, F., Chaussabel, D., Stichweh, D., Bennett, L. B., Allman, W., Mejías, A., Ardura, M. I., Chung, W. K., Smith, E. J., Wise, C. A., et al. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20070070 · Cited by 228 · see citing works

Gene Expression in Peripheral Blood Mononuclear Cells from Children with Diabetes

Kaizer, E., Glaser, C., Chaussabel, D., Banchereau, J., Pascual, V., & White, P. C. (2007) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2007-0979 · Cited by 219 · see citing works

Are data from different gene expression microarray platforms comparable?

Järvinen, A., Hautaniemi, S., Edgren, H., Auvinen, P., Saarela, J., Kallioniemi, O., & Monni, O. M. (2004) · Genomics · doi:10.1016/j.ygeno.2004.01.004 · Cited by 188 · see citing works

Mining for regulatory programs in the cancer transcriptome

Rhodes, D. R., Sundaram, S. K., Mahavisno, V., Barrette, T. R., Ghosh, D., & Chinnaiyan, A. M. (2005) · Nature Genetics · doi:10.1038/ng1578 · Cited by 166 · see citing works

Disease activity in systemic lupus erythematosus: report of the Consensus Study Group of the European Workshop for Rheumatology Research. III. Development of a computerised clinical chart and its application to the comparison of different indices of disease activity. The European Consensus Study Group for Disease Activity in SLE.

Bencivelli, W., Vitali, C., Isenberg, D. A., Smolen, J. S., Snaith, M. L., Sciuto, M. E., & Bombardieri, S. (1992) · PubMed · Cited by 154 · see citing works

Mining microarray expression data by literature profiling

Chaussabel, D., & Sher, A. (2002) · Genome biology · doi:10.1186/gb-2002-3-10-research0055 · Cited by 137 · see citing works

Immunotherapy: Bewitched, Bothered, and Bewildered No More

Steinman, R. M., & Mellman, I. (2004) · Science · doi:10.1126/science.1099688 · Cited by 135 · see citing works

Reliability and validity of systemic lupus activity measure-revised (SLAM-R) for measuring clinical disease activity in systemic lupus erythematosus

Bae, S.-C., Koh, H.-K., Chang, D.-K., Kim, M.-H., Park, J. K., & Kim, S. Y. (2001) · Lupus · doi:10.1191/096120301678646146 · Cited by 121 · see citing works

Transcriptional Profiles in Peripheral Blood Mononuclear Cells Prognostic of Clinical Outcomes in Patients with Advanced Renal Cell Carcinoma

Burczynski, M. E., Twine, N. C., Dukart, G., Marshall, B., Hidalgo, M. M., Stadler, W. M., Logan, T. F., Dutcher, J. P., Hudes, G. R., Trepicchio, W. L., et al. (2005) · Clinical Cancer Research · doi:10.1158/1078-0432.1181.11.3 · Cited by 118 · see citing works

Combining several ordinal measures in clinical studies

Wittkowski, K. M., Lee, E., Nussbaum, R., Chamian, F. N., & Krueger, J. G. (2004) · Statistics in Medicine · doi:10.1002/sim.1778 · Cited by 93 · see citing works

Microarrays and molecular research: noise discovery?

Ioannidis, J. P. A. (2005) · The Lancet · doi:10.1016/s0140-6736(05)70249-x · Cited by 84 · see citing works

Gene expression microarrays: glimpses of the immunological genome

Hyatt, G., Melamed, R., Park, R., Seguritan, R., Laplace, C., Poirot, L., Zucchelli, S., Obst, R., Matos, M., Venanzi, E. S., et al. (2006) · Nature Immunology · doi:10.1038/ni0706-686 · Cited by 76 · see citing works

Cross platform microarray analysis for robust identification of differentially expressed genes

Bosotti, R., Locatelli, G., Healy, S., Scacheri, E., Sartori, L., Mercurio, C., Calogero, R., & Isacchi, A. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s1-s5 · Cited by 71 · see citing works

An array of problems

Frantz, S. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1746 · Cited by 71 · see citing works

A Plaidoyer for ‘Systems Immunology’

Benoist, C. O., Germain, R. N., & Mathis, D. J. (2006) · Immunological Reviews · doi:10.1111/j.0105-2896.2006.00374.x · Cited by 54 · see citing works

Analysis of Significance Patterns Identifies Ubiquitous and Disease‐Specific Gene‐Expression Signatures in Patient Peripheral Blood Leukocytes

Chaussabel, D., Allman, W., Mejías, A., Chung, W. K., Bennett, L. B., Ramilo, O., Pascual, V., Palucka, K., & Banchereau, J. (2005) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1358.017 · Cited by 48 · see citing works

Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes

Thach, D., Agan, B. K., Olsen, C., Diao, J., Lin, B., Gómez, J. L., Jesse, M., Jenkins, M., Rowley, R. K., Hanson, E., et al. (2005) · Genes and Immunity · doi:10.1038/sj.gene.6364244 · Cited by 25 · see citing works

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

Berry, M. P. R., Graham, C. M., McNab, F. W., Xu, Z., Bloch, S. A. A., Oni, T., Wilkinson, K. A., Banchereau, R., Skinner, J., Wilkinson, R. J., et al. (2010) · Nature · doi:10.1038/nature09247 · Cited by 1,898 · see citing works

Netting Neutrophils Are Major Inducers of Type I IFN Production in Pediatric Systemic Lupus Erythematosus

García-Romo, G. S., Caielli, S., Vega, B., Connolly, J., Allantaz, F., Xu, Z., Punaro, M., Baisch, J. M., Guiducci, C., Coffman, R. L., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3001201 · Cited by 1,387 · see citing works

The Immune Response in Tuberculosis

O’Garra, A., Redford, P. S., McNab, F. W., Bloom, C. I., Wilkinson, R. J., & Berry, M. P. R. (2013) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032712-095939 · Cited by 1,351 · see citing works

Rare and common variants: twenty arguments

Gibson, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3118 · Cited by 1,278 · see citing works

The HLA genomic loci map: expression, interaction, diversity and disease

Shiina, T., Hosomichi, K., Inoko, H., & Kulski, J. K. (2009) · Journal of Human Genetics · doi:10.1038/jhg.2008.5 · Cited by 788 · see citing works

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

Li, S., Rouphael, N., Duraisingham, S., Romero‐Steiner, S., Presnell, S., Davis, C. W., Schmidt, D. S., Johnson, S. E., Milton, A., Rajam, G., et al. (2013) · Nature Immunology · doi:10.1038/ni.2789 · Cited by 772 · see citing works

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

Banchereau, R., Hong, S., Cantarel, B. L., Baldwin, N. E., Baisch, J. M., Edens, M., Cepika, A., Acs, P., Turner, J., Anguiano, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.008 · Cited by 735 · see citing works

Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosusPreprint

Javierre, B. M., Fernández, A. F., Richter, J., Al‐Shahrour, F., Martín-Subero, J. I., Rodríguez‐Ubreva, J., Berdasco, M., Fraga, M. F., OʼHanlon, T. P., Rider, L. G., et al. (2009) · Genome Research · doi:10.1101/gr.100289.109 · Cited by 669 · see citing works

Sexual-dimorphism in human immune system aging

Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Nehar-Belaid, D., Eroglu, A., Mellert, D. J., Kuchel, G. A., Banchereau, J., & Ucar, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14396-9 · Cited by 584 · see citing works

Type I Interferon in the Pathogenesis of Lupus

Crow, M. K. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1002795 · Cited by 565 · see citing works

Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease

Roy, E. R., Wang, B., Wan, Y.-W., Chiu, G., Cole, A., Yin, Z., Propson, N. E., Xu, Y., Jankowsky, J. L., Liu, Z., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci133737 · Cited by 563 · see citing works

A multicentre, randomised, double-blind, placebo-controlled trial with the interleukin-1 receptor antagonist anakinra in patients with systemic-onset juvenile idiopathic arthritis (ANAJIS trial)

Quartier, P., Allantaz, F., Cimaz, R., Pillet, P., Messiaen, C., Bardin, C., Bossuyt, X., Boutten, A., Bienvenu, J., Duquesne, A., et al. (2010) · Annals of the Rheumatic Diseases · doi:10.1136/ard.2010.134254 · Cited by 553 · see citing works

Network Analysis Reveals Centrally Connected Genes and Pathways Involved in CD8+ T Cell Exhaustion versus Memory

Doering, T. A., Crawford, A., Angelosanto, J., Paley, M., Ziegler, C. G. K., & Wherry, E. J. (2012) · Immunity · doi:10.1016/j.immuni.2012.08.021 · Cited by 542 · see citing works

Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency

Boisson, B., Laplantine, E., Prando, C., Giliani, S. C., Israelsson, E., Xu, Z., Abhyankar, A., Israël, L., Trevejo-Nuñez, G., Bogunovic, D., et al. (2012) · Nature Immunology · doi:10.1038/ni.2457 · Cited by 470 · see citing works

Mapping systemic lupus erythematosus heterogeneity at the single-cell level

Nehar-Belaid, D., Hong, S., Marcheş, R., Guo, C., Bolisetty, M. T., Baisch, J. M., Walters, L., Punaro, M., Rossi, R. J., Chung, C., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0743-0 · Cited by 433 · see citing works

Taming lupus-a new understanding of pathogenesis is leading to clinical advances

Liu, Z., & Davidson, A. (2012) · Nature Medicine · doi:10.1038/nm.2752 · Cited by 433 · see citing works

Modular Transcriptional Repertoire Analyses of Adults With Systemic Lupus Erythematosus Reveal Distinct Type I and Type II Interferon Signatures

Chiche, L., Jourde‐Chiche, N., Whalen, E., Presnell, S., Gersuk, V. H., Dang, K. K., Anguiano, E., Quinn, C., Burtey, S., Berland, Y., et al. (2014) · Arthritis & Rheumatology · doi:10.1002/art.38628 · Cited by 416 · see citing works

Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection

Piters, W. A. A. D. S., Heinonen, S., Hasrat, R., Bunsow, E., Smith, B., Suárez-Arrabal, M. C., Chaussabel, D., Cohen, D. M., Sanders, E. A. M., Ramilo, O., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201602-0220oc · Cited by 423 · see citing works

Assessment of Variability in the SOMAscan Assay

Candia, J., Cheung, F., Kotliarov, Y., Fantoni, G., Sellers, B. A., Griesman, T., Huang, J., Stuccio, S., Zingone, A., Ryan, B. M., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-14755-5 · Cited by 399 · see citing works

Systems Vaccinology

Pulendran, B., Li, S., & Nakaya, H. I. (2010) · Immunity · doi:10.1016/j.immuni.2010.10.006 · Cited by 384 · see citing works

A Systems Analysis Identifies a Feedforward Inflammatory Circuit Leading to Lethal Influenza Infection

Brandes, M., Klauschen, F., Kuchen, S., & Germain, R. N. (2013) · Cell · doi:10.1016/j.cell.2013.06.013 · Cited by 379 · see citing works

TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus

Guiducci, C., Gong, M., Xu, Z., Gill, M. A., Chaussabel, D., Meeker, T., Chan, J. H., Wright, T. B., Punaro, M., Bolland, S. M., et al. (2010) · Nature · doi:10.1038/nature09102 · Cited by 380 · see citing works

A Prescription for Human Immunology

Davis, M. M. (2008) · Immunity · doi:10.1016/j.immuni.2008.12.003 · Cited by 346 · see citing works

Prediction and Pathogenesis in Type 1 Diabetes

Ziegler, A.-G., & Nepom, G. T. (2010) · Immunity · doi:10.1016/j.immuni.2010.03.018 · Cited by 346 · see citing works

Common patterns and disease-related signatures in tuberculosis and sarcoidosis

Maertzdorf, J., Weiner, J. M., Mollenkopf, H., T. Accelerating Medicines Partnership in RA SLE Network, Bauer, T. T., Prasse, A., Müller–Quernheim, J., Kaufmann, S. H. E., Bellinger, O., Diel, R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121072109 · Cited by 320 · see citing works

A Type I Interferon Transcriptional Signature Precedes Autoimmunity in Children Genetically at Risk for Type 1 Diabetes

Ferreira, R. C., Guo, H., Coulson, R., Smyth, D. J., Pękalski, M. Ł., Burren, O. S., Cutler, A. J., Doecke, J. D., Flint, S. M., McKinney, E. F., et al. (2014) · Diabetes · doi:10.2337/db13-1777 · Cited by 313 · see citing works

Whole Blood Gene Expression Profiles to Assess Pathogenesis and Disease Severity in Infants with Respiratory Syncytial Virus Infection

Mejias, A., Dimo, B., Suarez, N. M., Garcia, C., Suarez-Arrabal, M. C., Jartti, T., Blankenship, D., Jordan-Villegas, A., Ardura, M. I., Xu, Z., et al. (2013) · PLoS Medicine · doi:10.1371/journal.pmed.1001549 · Cited by 313 · see citing works

A comprehensive evaluation of module detection methods for gene expression data

Saelens, W., Cannoodt, R., & Saeys, Y. (2018) · Nature Communications · doi:10.1038/s41467-018-03424-4 · Cited by 312 · see citing works

Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology

Pulendran, B. (2009) · Nature reviews. Immunology · doi:10.1038/nri2629 · Cited by 306 · see citing works

Immunomodulatory Activity of Nivolumab in Metastatic Renal Cell Carcinoma

Choueiri, T. K., Fishman, M. N., Escudier, B., McDermott, D. F., Drake, C. G., Kluger, H., Stadler, W. M., Perez-Gracia, J. L., McNeel, D. G., Curti, B., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2839 · Cited by 295 · see citing works

Systems Scale Interactive Exploration Reveals Quantitative and Qualitative Differences in Response to Influenza and Pneumococcal Vaccines

Obermoser, G., Presnell, S., Domico, K., Xu, H., Wang, Y., Anguiano, E., Thompson-Snipes, L., Ranganathan, R., Zeitner, B., Bjork, A., et al. (2013) · Immunity · doi:10.1016/j.immuni.2012.12.008 · Cited by 279 · see citing works

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

Godec, J., Tan, Y. Q., Liberzon, A., Tamayo, P., Bhattacharya, S., Butte, A. J., Mesirov, J. P., & Haining, W. N. (2016) · Immunity · doi:10.1016/j.immuni.2015.12.006 · Cited by 289 · see citing works

The Importance of Dendritic Cells in Maintaining Immune Tolerance

Audiger, C., Rahman, M. J., Yun, T. J., Tarbell, K. V., & Lesage, S. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1601629 · Cited by 276 · see citing works

Systems immunology: just getting started

Davis, M. M., Tato, C. M., & Furman, D. (2017) · Nature Immunology · doi:10.1038/ni.3768 · Cited by 273 · see citing works

Activation of Mammalian Target of Rapamycin Controls the Loss of TCRζ in Lupus T Cells through HRES-1/Rab4-Regulated Lysosomal Degradation

Fernández, D., Caza, T. N., Bonilla, E., Li, Q., Banerjee, S. K., Middleton, F. A., Phillips, P. E., Crow, M. K., Oess, S., Müller‐Esterl, W., et al. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0803600 · Cited by 259 · see citing works

Assessing the human immune system through blood transcriptomics

Chaussabel, D., Pascual, V., & Banchereau, J. (2010) · BMC Biology · doi:10.1186/1741-7007-8-84 · Cited by 252 · see citing works

Impaired interferon signaling is a common immune defect in human cancer

Critchley-Thorne, R. J., Simons, D. L., Yan, N., Miyahira, A. K., Dirbas, F. M., Johnson, D. L., Swetter, S. M., Carlson, R. W., Fisher, G. A., Koong, A. C., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901329106 · Cited by 249 · see citing works

Distinct Phases of Blood Gene Expression Pattern Through Tuberculosis Treatment Reflect Modulation of the Humoral Immune Response

Cliff, J. M., Lee, J., Constantinou, N., Cho, J.-E., Clark, T. G., Ronacher, K., King, E. C., Lukey, P. T., Duncan, K., van Helden, P. D., et al. (2012) · The Journal of Infectious Diseases · doi:10.1093/infdis/jis499 · Cited by 239 · see citing works

Rheumatoid Arthritis Synovial Fluid Neutrophils Drive Inflammation Through Production of Chemokines, Reactive Oxygen Species, and Neutrophil Extracellular Traps

Wright, H. L., Lyon, M., Chapman, E. A., Moots, R. J., & Edwards, S. W. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2020.584116 · Cited by 235 · see citing works

Unravelling the mechanisms of durable control of HIV-1

Walker, B. D., & Yu, X. G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3478 · Cited by 234 · see citing works

Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE

Caielli, S., Cardenas, J., de Jesus, A. A., Baisch, J., Walters, L., Blanck, J. P., Balasubramanian, P., Stagnar, C., Ohouo, M., Hong, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.021 · Cited by 228 · see citing works

Systemic sclerosis and lupus: Points in an interferon‐mediated continuum

Assassi, S., Mayes, M. D., Arnett, F. C., Gourh, P., Agarwal, S. K., McNearney, T. A., Chaussabel, D., Oommen, N., Fischbach, M., Shah, K. R., et al. (2010) · Arthritis & Rheumatism · doi:10.1002/art.27224 · Cited by 215 · see citing works

Democratizing systems immunology with modular transcriptional repertoire analyses

Chaussabel, D., & Baldwin, N. E. (2014) · Nature reviews. Immunology · doi:10.1038/nri3642 · Cited by 207 · see citing works

Systems vaccinology: Probing humanity’s diverse immune systems with vaccines

Pulendran, B. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400476111 · Cited by 208 · see citing works

Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger

Mahajan, P., Kuppermann, N., Mejías, A., Suárez, N. M., Chaussabel, D., Casper, T. C., Smith, B., Alpern, E. R., Anders, J., Atabaki, S. M., et al. (2016) · JAMA · doi:10.1001/jama.2016.9207 · Cited by 207 · see citing works

Sustained efficacy and seroconversion with the Toll-like receptor 7 agonist GS-9620 in the Woodchuck model of chronic hepatitis B

Menne, S., Tumas, D. B., Liu, K. H., Thampi, L. M., Aldeghaither, D. S., Baldwin, B. H., Bellezza, C. A., Côté, P. J., Zheng, J., Halcomb, R. L., et al. (2015) · Journal of Hepatology · doi:10.1016/j.jhep.2014.12.026 · Cited by 209 · see citing works

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis

Linsley, P. S., Speake, C., Whalen, E., & Chaussabel, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109760 · Cited by 210 · see citing works

Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis

Sranujit, R. P., Buddhisa, S., Berry, M. P. R., Blankenship, D., Bancroft, G. J., Banchereau, J., Lertmemongkolchai, G., & Chaussabel, D. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r127 · Cited by 208 · see citing works

Type I interferon system activation and association with disease manifestations in systemic sclerosis

Eloranta, M., Franck‐Larsson, K., Lövgren, T., Kalamajski, S., Rönnblom, A., Rubin, K., Alm, G. V., & Rönnblom, L. (2010) · Annals of the Rheumatic Diseases · doi:10.1136/ard.2009.121400 · Cited by 203 · see citing works

The chromatin accessibility signature of human immune aging stems from CD8+ T cells

Ucar, D., Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Uyar, A., Wu, T.-C., George, J., Stitzel, M. L., Palucka, A. K., et al. (2017) · Journal of Experimental Medicine · doi:10.1084/jem.20170416 · Cited by 200 · see citing works

Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases

Barturen, G., Babaei, S., Català‐Moll, F., Martínez‐Bueno, M., Makowska, Z., Martorell‐Marugán, J., Carmona‐Sáez, P., Dominguez, D. T., Carnero‐Montoro, E., Teruel, M., et al. (2020) · Arthritis & Rheumatology · doi:10.1002/art.41610 · Cited by 198 · see citing works

Plasticity and Virus Specificity of the Airway Epithelial Cell Immune Response during Respiratory Virus Infection

Ioannidis, I., McNally, B. A., Willette, M., Peeples, M. E., Chaussabel, D., Durbin, J. E., Ramilo, O., Mejías, A., & Flaño, E. (2012) · Journal of Virology · doi:10.1128/jvi.06757-11 · Cited by 192 · see citing works

Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

Kotliarov, Y., Sparks, R., Martins, A. J., Mulè, M. P., Lu, Y. C., Goswami, M., Kardava, L., Banchereau, R., Pascual, V., Biancotto, A., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0769-8 · Cited by 193 · see citing works

Innate Immune Activity Is Detected Prior to Seroconversion in Children With HLA-Conferred Type 1 Diabetes Susceptibility

Kallionpää, H., Elo, L. L., Laajala, E., Mykkänen, J., Ricaño-Ponce, I., Vaarma, M., Laajala, T. D., Hyöty, H., Ilonen, J., Veijola, R., et al. (2014) · Diabetes · doi:10.2337/db13-1775 · Cited by 187 · see citing works

Human asthma phenotypes: from the clinic, to cytokines, and back again

Bhakta, N. R., & Woodruff, P. G. (2011) · Immunological Reviews · doi:10.1111/j.1600-065x.2011.01032.x · Cited by 186 · see citing works

The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps

Apel, F., Andreeva, L., Knackstedt, S. L., Streeck, R., Frese, C. K., Goosmann, C., Hopfner, K., & Zychlinsky, A. (2021) · Science Signaling · doi:10.1126/scisignal.aax7942 · Cited by 180 · see citing works

Clinical, Molecular, and Genetic Characteristics of PAPA Syndrome: A Review

Smith, E. J., Allantaz, F., Bennett, L. B., Zhang, D., Gao, X., Wood, G., Kastner, D. L., Punaro, M., Aksentijevich, I. A., Pascual, V., et al. (2010) · Current Genomics · doi:10.2174/138920210793175921 · Cited by 177 · see citing works

Gene expression profiling of whole blood in ipilimumab-treated patients for identification of potential biomarkers of immune-related gastrointestinal adverse events

Shahabi, V., Berman, D., Chasalow, S. D., Wang, L., Tsuchihashi, Z., Hu, B., Panting, L., Jure‐Kunkel, M., & Ji, R. (2013) · Journal of Translational Medicine · doi:10.1186/1479-5876-11-75 · Cited by 182 · see citing works

Exposure-Dependent Control of Malaria-Induced Inflammation in Children

Portugal, S., Moebius, J., Skinner, J., Doumbo, S., Doumtabé, D., Koné, Y., Dia, S., Kanakabandi, K., Sturdevant, D. E., Virtaneva, K. I., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004079 · Cited by 169 · see citing works

Effects of Systemically Administered Hydrocortisone on the Human Immunome

Olnes, M. J., Kotliarov, Y., Biancotto, A., Cheung, F., Chen, J., Shi, R., Zhou, H., Wang, E., Tsang, J. S., Nussenblatt, R. B., et al. (2016) · Scientific Reports · doi:10.1038/srep23002 · Cited by 168 · see citing works

Merck Ad5/HIV induces broad innate immune activation that predicts CD8 + T-cell responses but is attenuated by preexisting Ad5 immunity

Zak, D. E., Andersen‐Nissen, E., Peterson, E. R., Sato, A., Hamilton, M. K., Borgerding, J. A., Krishnamurty, A. T., Chang, J. T., Adams, D. J., Hensley, T. R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208972109 · Cited by 162 · see citing works

Type I IFN system in the development and manifestations of SLE

Elkon, K. B., & WIEDEMAN, A. E. (2012) · Current Opinion in Rheumatology · doi:10.1097/bor.0b013e3283562c3e · Cited by 163 · see citing works

Sarcoidosis Blood Transcriptome Reflects Lung Inflammation and Overlaps with Tuberculosis

Koth, L. L., Solberg, O. D., Peng, J. C., Bhakta, N. R., Nguyen, C. P., & Woodruff, P. G. (2011) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201106-1143oc · Cited by 161 · see citing works

The human immune response to tuberculosis and its treatment: a view from the blood

Cliff, J. M., Kaufmann, S. H. E., McShane, H., van Helden, P. D., & O’Garra, A. (2015) · Immunological Reviews · doi:10.1111/imr.12269 · Cited by 158 · see citing works

Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza

Dunning, J. W., Blankley, S., Hoang, L. T., Cox, M. J., Graham, C. M., James, P. L., Bloom, C. I., Chaussabel, D., Banchereau, J., Brett, S. J., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0111-5 · Cited by 156 · see citing works

A third generation vaccine for human visceral leishmaniasis and post kala azar dermal leishmaniasis: First-in-human trial of ChAd63-KH

Osman, M., Mistry, A., Keding, A., Gabe, R., Cook, L., Forrester, S. J., Wiggins, R. C., Marco, S. D., Colloca, S., Siani, L., et al. (2017) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0005527 · Cited by 158 · see citing works

Complement pathway amplifies caspase-11–dependent cell death and endotoxin-induced sepsis severity

Napier, B. A., Brubaker, S. W., Sweeney, T. E., Monette, P., Rothmeier, G. H., Gertsvolf, N. A., Puschnik, A., Carette, J. E., Khatri, P., & Monack, D. M. (2016) · Journal of Experimental Medicine · doi:10.1084/jem.20160027 · Cited by 149 · see citing works

Superiority of Transcriptional Profiling Over Procalcitonin for Distinguishing Bacterial From Viral Lower Respiratory Tract Infections in Hospitalized Adults

Suárez, N. M., Bunsow, E., Falsey, A. R., Walsh, E. E., Mejías, A., & Ramilo, O. (2015) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiv047 · Cited by 152 · see citing works

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Tarn, J. R., Howard-Tripp, N., Lendrem, D. W., Xavier Mariette, A., Saraux, A., Devauchelle‐Pensec, V., Séror, R., Skelton, A. J., James, K., McMeekin, P. J., et al. (2019) · The Lancet Rheumatology · doi:10.1016/s2665-9913(19)30042-6 · Cited by 151 · see citing works

Clinical and transcriptional response to the long‐acting interleukin‐1 blocker canakinumab in Blau syndrome–related uveitis

Simonini, G., Xu, Z., Caputo, R., de Libero, C., Pagnini, I., Pascual, V., & Cimaz, R. (2012) · Arthritis & Rheumatism · doi:10.1002/art.37776 · Cited by 148 · see citing works

A Genomic Approach to Human Autoimmune Diseases

Pascual, V., Chaussabel, D., & Banchereau, J. (2010) · Annual Review of Immunology · doi:10.1146/annurev-immunol-030409-101221 · Cited by 146 · see citing works

The pathogenesis of systemic lupus erythematosus: Harnessing big data to understand the molecular basis of lupus

Catalina, M. D., Owen, K. A., Labonte, A. C., Grammer, A. C., & Lipsky, P. E. (2019) · Journal of Autoimmunity · doi:10.1016/j.jaut.2019.102359 · Cited by 145 · see citing works

Unifying immunology with informatics and multiscale biology

Kidd, B. A., Peters, L. A., Schadt, E. E., & Dudley, J. T. (2014) · Nature Immunology · doi:10.1038/ni.2787 · Cited by 142 · see citing works

Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis

Plumlee, C. R., Duffy, F. J., Gern, B. H., Delahaye, J. L., Cohen, S. B., Stoltzfus, C. R., Rustad, T. R., Hansen, S. G., Axthelm, M. K., Picker, L. J., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.10.003 · Cited by 135 · see citing works

Unraveling the Genetics of Autoimmunity

Zenewicz, L. A., Abraham, C., Flavell, R. A., & Cho, J. H. (2010) · Cell · doi:10.1016/j.cell.2010.03.003 · Cited by 136 · see citing works

Flt3 ligand augments immune responses to anti-DEC-205-NY-ESO-1 vaccine through expansion of dendritic cell subsets

Bhardwaj, N., Friedlander, P. A., Pavlick, A. C., Ernstoff, M. S., Gastman, B., Hanks, B. A., Curti, B. D., Albertini, M. R., Luke, J. J., Blazquez, A. B., et al. (2020) · Nature Cancer · doi:10.1038/s43018-020-00143-y · Cited by 134 · see citing works

Type I Interferon and Systemic Lupus Erythematosus

Elkon, K. B., & Stone, V. V. (2011) · Journal of Interferon & Cytokine Research · doi:10.1089/jir.2011.0045 · Cited by 131 · see citing works

Genetics of SLE: evidence from mouse models

Morel, L. M. (2010) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2010.63 · Cited by 129 · see citing works

Systems vaccinology: Enabling rational vaccine design with systems biological approaches

Hagan, T., Nakaya, H. I., Subramaniam, S., & Pulendran, B. (2015) · Vaccine · doi:10.1016/j.vaccine.2015.03.072 · Cited by 127 · see citing works

Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells

Sen, P., Kemppainen, E., & Orešič, M. (2018) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2017.00096 · Cited by 124 · see citing works

Signatures of inflammation and impending multiple organ dysfunction in the hyperacute phase of trauma: A prospective cohort study

Cabrera, C., Manson, J., Shepherd, J. M., Torrance, H. D. T., Watson, D., Longhi, M. P., Hoti, M., Patel, M. B., O’Dwyer, M. J., Nourshargh, S., et al. (2017) · PLoS Medicine · doi:10.1371/journal.pmed.1002352 · Cited by 123 · see citing works

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

Żyła, J., Marczyk, M., Domaszewska, T., Kaufmann, S. H. E., Polańska, J., & Weiner, J. M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz447 · Cited by 118 · see citing works

Protecting the kidney in systemic lupus erythematosus: from diagnosis to therapy

Maria, N. I., & Davidson, A. (2020) · Nature Reviews Rheumatology · doi:10.1038/s41584-020-0401-9 · Cited by 121 · see citing works

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease

Taroni, J., Grayson, P. C., Hu, Q., Eddy, S. F., Kretzler, M., Merkel, P. A., & Greene, C. S. (2019) · Cell Systems · doi:10.1016/j.cels.2019.04.003 · Cited by 120 · see citing works

Stratification of Systemic Lupus Erythematosus Patients Into Three Groups of Disease Activity Progression According to Longitudinal Gene Expression

Dominguez, D. T., Martorell‐Marugán, J., GOLDMAN, D. W., Petri, M., Carmona‐Sáez, P., & Alarcón-Riquelme, M. E. (2018) · Arthritis & Rheumatology · doi:10.1002/art.40653 · Cited by 117 · see citing works

Immunodeficiency and autoimmunity: lessons from systemic lupus erythematosus

Grammatikos, A. P., & Tsokos, G. C. (2011) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2011.10.005 · Cited by 114 · see citing works

OUP accepted manuscript

de Hair, M. J. H., Jacobs, J. W. G., Schoneveld, J. L. M., & van Laar, J. M. (2017) · Lara D. Veeken · doi:10.1093/rheumatology/kex349 · Cited by 115 · see citing works

Assessment of immune status using blood transcriptomics and potential implications for global health

Chaussabel, D. (2015) · Seminars in Immunology · doi:10.1016/j.smim.2015.03.002 · Cited by 111 · see citing works

Systems Biology Approaches Reveal a Specific Interferon-Inducible Signature in HTLV-1 Associated Myelopathy

Tattermusch, S., Skinner, J. A., Chaussabel, D., Banchereau, J., Berry, M. P. R., McNab, F. W., O’Garra, A., Taylor, G. P., & Bangham, C. R. M. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002480 · Cited by 109 · see citing works

Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis

Heinonen, S., Jartti, T. T., García, C., Oliva, S., Smitherman, C., Anguiano, E., Piters, W. A. A. D. S., Vuorinen, T., Ruuskanen, O., Dimo, B., et al. (2015) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201504-0749oc · Cited by 109 · see citing works

Type I interferon and lupus

Rönnblom, L., Alm, G. V., & Eloranta, M. (2009) · Current Opinion in Rheumatology · doi:10.1097/bor.0b013e32832e089e · Cited by 108 · see citing works

Repeated administration of dapirolizumab pegol in a randomised phase I study is well tolerated and accompanied by improvements in several composite measures of systemic lupus erythematosus disease activity and changes in whole blood transcriptomic profiles

Chamberlain, C., Colman, P., Ranger, A. M., Burkly, L. C., Johnston, G. I., Otoul, C., Stach, C. M., Zamacona, M. K., Dörner, T., Urowitz, M. B., et al. (2017) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2017-211388 · Cited by 107 · see citing works

Systems vaccinology: learning to compute the behavior of vaccine induced immunity

Nakaya, H. I., Li, S., & Pulendran, B. (2011) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.163 · Cited by 106 · see citing works

Host Immune Transcriptional Profiles Reflect the Variability in Clinical Disease Manifestations in Patients with Staphylococcus aureus Infections

Banchereau, R., Jordán-Villegas, A., Ardura, M. I., Mejías, A., Baldwin, N. E., Xu, H., Saye, E. J., Rosselló-Urgell, J., Nguyen, P., Blankenship, D., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034390 · Cited by 106 · see citing works

Oral Neutrophil Transcriptome Changes Result in a Pro-Survival Phenotype in Periodontal Diseases

Lakschevitz, F. S., Aboodi, G. M., & Glogauer, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068983 · Cited by 106 · see citing works

Re‐evaluation of hepatitis B virus clinical phases by systems biology identifies unappreciated roles for the innate immune response and B cells

Vanwolleghem, T., Hou, J., van Oord, G., Andeweg, A. C., Osterhaus, A. D. M. E., Pas, S. D., Janssen, H. L. A., & Boonstra, A. (2015) · Hepatology · doi:10.1002/hep.27805 · Cited by 110 · see citing works

Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria

Tran, T. M., Jones, M. B., Ongoïba, A., Bijker, E. M., Schats, R., Venepally, P., Skinner, J., Doumbo, S., Quinten, E., Visser, L. G., et al. (2016) · Scientific Reports · doi:10.1038/srep31291 · Cited by 105 · see citing works

The Transcriptional Signature of Active Tuberculosis Reflects Symptom Status in Extra-Pulmonary and Pulmonary Tuberculosis

Blankley, S., Graham, C. M., Turner, J., Berry, M. P. R., Bloom, C. I., Xu, Z., Pascual, V., Banchereau, J., Chaussabel, D., Breen, R. A. M., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162220 · Cited by 105 · see citing works

Evidence for additive and interaction effects of host genotype and infection in malaria

Idaghdour, Y., Quinlan, J., Goulet, J.-P., Berghout, J., Gbeha, E., Bruat, V., de Malliard, T., Grenier, J., Gomez, S., Gros, P., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204945109 · Cited by 104 · see citing works

Transcriptomic analysis of the woodchuck model of chronic hepatitis B

Fletcher, S. P., Chin, D. J., Ji, Y., Iniguez, L. A., Taillon, B. E., Swinney, D. C., Ravindran, P., Cheng, D. T., Bitter, H., Lopatin, U. A., et al. (2012) · Hepatology · doi:10.1002/hep.25730 · Cited by 100 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works