Xavier, Ramnik J.

Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine

Bel, S., Pendse, M., Wang, Y., Li, Y., Ruhn, K. A., Hassell, B., Leal, T., Winter, S. E., Xavier, R. J., & Hooper, L. V. (2017) · Science

Autophagy in Disease and TherapyCellular transport and secretion

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Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2

Early, J. O., Menon, D., Wyse, C. A., Cervantes-Silva, M. P., Zaslona, Z., Carroll, R. G., Palsson-McDermott, E. M., Angiari, S., Ryan, D. G., Corcoran, S. E., et al. (2018) · Proceedings of the National Academy of Sciences

Circadian rhythm and melatoninGenomics, phytochemicals, and oxidative stress

Cited by 389

Receptor interacting protein kinase 2–mediated mitophagy regulates inflammasome activation during virus infection

Lupfer, C., Thomas, P. G., Anand, P. K., Vogel, P., Milasta, S., Martinez, J., Huang, G., Green, M., Kundu, M., Chi, H., et al. (2013) · Nature Immunology

Inflammasome and immune disordersAutophagy in Disease and Therapy

Cited by 384

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense

Lassen, K. G., Kuballa, P., Conway, K. L., Patel, K. K., Becker, C. E., Peloquin, J. M., Villablanca, E. J., Norman, J. M., Liu, T.-C., Heath, R. J., et al. (2014) · Proceedings of the National Academy of Sciences

Autophagy in Disease and TherapyInflammatory Bowel Disease

Cited by 373

Inflammatory Bowel Disease as a Model for Translating the Microbiome

Huttenhower, C., Kostic, A. D., & Xavier, R. J. (2014) · Immunity

Gut microbiota and healthInflammatory Bowel Disease

Cited by 332

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

Li, Y., Oosting, M., Smeekens, S. P., Jaeger, M., Aguirre-Gamboa, R., Le, K. T. T., Deelen, P., Ricaño-Ponce, I., Schoffelen, T., Jansen, A. F. M., et al. (2016) · Cell

Genetic Associations and EpidemiologyImmune Response and Inflammation

Cited by 324

IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans

de Luca, A., Smeekens, S. P., Casagrande, A., Iannitti, R., Conway, K. L., Gresnigt, M. S., Begun, J., Plantinga, T. S., Joosten, L. A. B., van der Meer, J. W. M., et al. (2014) · Proceedings of the National Academy of Sciences

Neutrophil, Myeloperoxidase and Oxidative MechanismsImmunodeficiency and Autoimmune Disorders

Cited by 313

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Vatanen, T., Kostic, A. D., d’Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A.-M., et al. (2016) · Cell

Gut microbiota and healthImmune Response and Inflammation

Cited by 298

Mobile genes in the human microbiome are structured from global to individual scales

Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature

Gut microbiota and healthBacteriophages and microbial interactions

Cited by 288

An integrative view of microbiome-host interactions in inflammatory bowel diseases

Wlodarska, M., Kostic, A. D., & Xavier, R. J. (2015) · Cell Host & Microbe

Gut microbiota and healthInflammatory Bowel Disease

Cited by 287

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

Xu, H., Ding, J., Porter, C. B. M., Wallrapp, A., Tabaka, M., Ma, S., Fu, S., Guo, X., Riesenfeld, S. J., Su, C., et al. (2019) · Immunity

IL-33, ST2, and ILC PathwaysMast cells and histamine

Cited by 273

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

Jagadeesh, K. A., Dey, K. K., Montoro, D. T., Mohan, R., Gazal, S., Engreitz, J. M., Xavier, R. J., Price, A. L., & Regev, A. (2022) · Nature Genetics

Genetic Associations and EpidemiologySingle-cell and spatial transcriptomics

Cited by 239

The LRR and RING Domain Protein LRSAM1 Is an E3 Ligase Crucial for Ubiquitin-Dependent Autophagy of Intracellular Salmonella Typhimurium

Huett, A., Heath, R. J., Begun, J., Sassi, S. O., Baxt, L. A., Vyas, J. M., Goldberg, M. B., & Xavier, R. J. (2012) · Cell Host & Microbe

Autophagy in Disease and TherapyUbiquitin and proteasome pathways

Cited by 239

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans

Smeekens, S. P., Ng, A., Kumar, V., Johnson, M. D., Plantinga, T. S., van Diemen, C., Arts, P., Verwiel, E. T. P., Gresnigt, M. S., Fransen, K., et al. (2013) · Nature Communications

Antifungal resistance and susceptibilityinterferon and immune responses

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A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Dorrestein, P., Gentry, E., Collins, S., Panitchpakdi, M., Belda-Ferre, P., Stewart, A., Wang, M., Jarmusch, A., Avila-Pacheco, J., Plichta, D., et al. (2021) · Nature

Metabolomics and Mass Spectrometry StudiesGut microbiota and health

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Host genetic variation and its microbiome interactions within the Human Microbiome Project

Kolde, R., Franzosa, E. A., Rahnavard, G., Hall, A. B., Vlamakis, H., Stevens, C., Daly, M. J., Xavier, R. J., & Huttenhower, C. (2018) · Genome Medicine

Gut microbiota and healthGenetic Associations and Epidemiology

Cited by 182

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study

Kurilshikov, A., van den Munckhof, I. C. L., Chen, L., Bonder, M. J., Schraa, K., Rutten, J. H. W., Riksen, N. P., de Graaf, J., Oosting, M., Sanna, S., et al. (2019) · Circulation Research

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 178

Host genetic regulation of human gut microbial structural variation

Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature

Gut microbiota and healthGenetic Associations and Epidemiology

Cited by 174

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Ma, S., Shungin, D., Mallick, H., Schirmer, M., Nguyen, L. H., Kolde, R., Franzosa, E., Vlamakis, H., Xavier, R., & Huttenhower, C. (2022) · Genome biology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 164

The human gut microbiota in people with amyotrophic lateral sclerosis

Nicholson, K., Bjornevik, K., Abu-Ali, G., Chan, J., Cortese, M., Dedi, B., Jeon, M., Xavier, R., Huttenhower, C., Ascherio, A., et al. (2021) · Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 123

Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution

Watson, B. R., Paul, B., Rahman, R. U., Amir-Zilberstein, L., Segerstolpe, Å., Epstein, E. T., Murphy, S., Geistlinger, L., Lee, T., Shih, A., et al. (2025) · Nature Communications

Single-cell and spatial transcriptomicsLiver physiology and pathology

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RNF166 determines recruitment of adaptor proteins during antibacterial autophagy

Heath, R. J., Goel, G., Baxt, L. A., Rush, J. S., Mohanan, V., Paulus, G. L. C., Jani, V., Lassen, K. G., & Xavier, R. J. (2016) · Cell Reports

Autophagy in Disease and TherapyUbiquitin and proteasome pathways

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Genome-wide siRNA screen for mediators of NF-κB activation

Gewurz, B. E., Towfic, F., Mar, J. C., Shinners, N. P., Takasaki, K., Zhao, B., Cahir-McFarland, E. D., Quackenbush, J., Xavier, R. J., & Kieff, E. (2012) · Proceedings of the National Academy of Sciences

NF-κB Signaling PathwaysSignaling Pathways in Disease

Cited by 108

Identification of trypsin-degrading commensals in the large intestine

Li, Y., Watanabe, E., Kawashima, Y., Plichta, D. R., Wang, Z., Ujike, M., Ang, Q. Y., Wu, R., Furuichi, M., Takeshita, K., et al. (2022) · Nature

Gut microbiota and healthEscherichia coli research studies

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