Xavier, Ramnik J.

Identification of commensals and molecular components mediating trypsin degradation in the large intestine

Honda, K., Atarashi, K., Sasajima, S., Wang, Z., Nishiyama, K., Matsunaga, T., Zhang, X., Olle, B., Norman, J., Suda, W., et al. (2022) · Nature

Gut microbiota and healthEscherichia coli research studies

Cited by 106

Dectin-1–Dependent LC3 Recruitment to Phagosomes Enhances Fungicidal Activity in Macrophages

Tam, J. M., Mansour, M. K., Khan, N. S., Seward, M., Puranam, S., Tanne, A., Sokolovska, A., Becker, C. E., Acharya, M., Baird, M. A., et al. (2014) · The Journal of Infectious Diseases

Autophagy in Disease and TherapyAntifungal resistance and susceptibility

Cited by 101

Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA

Kobayashi-Kirschvink, K. J., Comiter, C. S., Gaddam, S., Joren, T., Grody, E. I., Ounadjela, J. R., Zhang, K., Ge, B., Kang, J. W., Xavier, R. J., et al. (2024) · Nature Biotechnology

Spectroscopy Techniques in Biomedical and Chemical ResearchSingle-cell and spatial transcriptomics

Cited by 93

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

Stražar, M., Temba, G. S., Vlamakis, H., Kullaya, V. I., Lyamuya, F., Mmbaga, B. T., Joosten, L. A. B., van der Ven, A. J. A. M., Netea, M. G., de Mast, Q., et al. (2021) · Nature Communications

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 91

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

Rivas, M. A., Avila, B. E., Koskela, J., Huang, H., Stevens, C., Pirinen, M., Haritunians, T., Neale, B. M., Kurki, M., Ganna, A., et al. (2018) · PLoS Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 87

Annotating metabolite mass spectra with domain-inspired chemical formula transformers

Goldman, S., Wohlwend, J., Stražar, M., Haroush, G., Xavier, R. J., & Coley, C. W. (2023) · Nature Machine Intelligence

Metabolomics and Mass Spectrometry StudiesMass Spectrometry Techniques and Applications

Cited by 87

An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread

Tan, J. M. J., Mellouk, N., Osborne, S. E., Ammendolia, D. A., Dyer, D. N., Li, R., Brunen, D., van Rijn, J. M., Huang, J., Czuczman, M. A., et al. (2018) · Nature Microbiology

Autophagy in Disease and TherapyCellular transport and secretion

Cited by 76

Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn’s disease

Kong, L., Lloyd-Price, J., Vatanen, T., Seksik, P., Beaugerie, L., Simon, T., Vlamakis, H., Sokol, H., & Xavier, R. J. (2020) · Gastroenterology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 69

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Fiskin, E., Lareau, C. A., Ludwig, L. S., Eraslan, G., Liu, F., Ring, A. M., Xavier, R. J., & Regev, A. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 68

Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease

Hu, S., Uniken Venema, W. T., Westra, H.-J., Vich Vila, A., Barbieri, R., Voskuil, M. D., Blokzijl, T., Jansen, B. H., Li, Y., Daly, M. J., et al. (2021) · Nature Communications

Inflammatory Bowel DiseaseGenetic Associations and Epidemiology

Cited by 59

TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41

Carey, K. L., Paulus, G. L. C., Wang, L., Balce, D. R., Luo, J. W., Bergman, P., Ferder, I. C., Kong, L., Renaud, N., Singh, S., et al. (2020) · Cell Reports

Autophagy in Disease and TherapyCalcium signaling and nucleotide metabolism

Cited by 55

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

Kumbhari, A., Cheng, T. N. H., Ananthakrishnan, A. N., Kochar, B., Burke, K. E., Shannon, K., Lau, H., Xavier, R. J., & Smillie, C. S. (2024) · Cell Host & Microbe

Gut microbiota and healthInflammatory Bowel Disease

Cited by 54

Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling

Pawlak, M., DeTomaso, D., Schnell, A., Meyer zu Horste, G., Lee, Y., Nyman, J., Dionne, D., Regan, B. M. L., Singh, V., Delorey, T., et al. (2022) · Immunity

Psoriasis: Treatment and PathogenesisT-cell and B-cell Immunology

Cited by 49

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

Kang, J. B., Shen, A. Z., Gurajala, S., Nathan, A., Rumker, L., Aguiar, V. R. C., Valencia, C., Lagattuta, K. A., Zhang, F., Jonsson, A. H., et al. (2023) · Nature Genetics

Genetic Associations and EpidemiologySingle-cell and spatial transcriptomics

Cited by 49

Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes

Ogasawara, D., Konrad, D. B., Tan, Z. Y., Carey, K. L., Luo, J., Won, S. J., Li, H., Carter, T. R., DeMeester, K. E., Njomen, E., et al. (2024) · Cell Chemical Biology

Click Chemistry and ApplicationsChemical Synthesis and Analysis

Cited by 31

Protein language models uncover carbohydrate-active enzyme function in metagenomics

Thurimella, K., Mohamed, A. M. T., Li, C., Vatanen, T., Graham, D. B., Owens, R. M., La Rosa, S. L., Plichta, D. R., Bacallado, S., & Xavier, R. J. (2025) · BMC Bioinformatics

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 9

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics

Thurimella, K., Mohamed, A. M. T., Graham, D. B., Owens, R. M., La Rosa, S. L., Plichta, D. R., Bacallado, S., & Xavier, R. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 7