Biography

Jose is a second-year Postdoctoral Fellow in the Shalek lab where he is interested in utilizing single-cell genomics to understand the organizing principles of mucosal barrier tissues in health and how to re-balance them in disease. Jose’s research specifically looks at the human gastrointestinal tract and respiratory airways in inflammatory and allergic states, respectively.

Jose grew up in the Boston area, circling the perimeter with high school in Framingham, MA, college at Tufts University, and graduate studies in the Harvard Immunology program. During his undergraduate, Jose worked in human immunology labs at Biogen Idec, University College London, and Children’s Hospital Boston where he focused on monogenic immune deficiencies. For his PhD work, Jose trained with Uli von Andrian studying how the nervous system and the immune system function together as the principal sensory interfaces between the internal and external environment. Due to his problem of reading too much, realizing that this only covered two broad classes of cells, and wanting to return to the human system, he decided to take the plunge into the field of single cell genomics to be able to work on all cell types all the time. Jose is a recently retired amateur bike racer and a perpetually amateur chef.

Publications

Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • bioRxiv,
  • 2020
  • Immunology
  • Genomics
  • Biology
  • Sam Allon
  • José Ordovas-Montañes
  • Alex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
  • Biology
  • Infectious Disease
  • Genomics
  • Cell Atlas
  • Immunology
  • Travis Hughes
  • Marc Wadsworth II
  • Conner Kummerlowe
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Alex K. Shalek
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
  • Hughes et al.,
  • Immunity,
  • 2020
  • Biology
  • R&D
  • Cell Atlas
  • Chemistry
  • Technology
  • Genomics
  • Immunology
  • Travis Hughes
  • Marc Wadsworth II
  • José Ordovas-Montañes
  • Alex K. Shalek
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
  • Mitsialis et al.,
  • Gastroenterology,
  • 2020
  • Biology
  • Genomics
  • Immunology
  • José Ordovas-Montañes
  • Marko Vukovic
  • Alex K. Shalek
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
  • Tkachev et al.,
  • bioRxiv,
  • 2020
  • Biology
  • Immunology
  • Genomics
  • Jim Kaminski
  • José Ordovas-Montañes
  • Alex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
  • Mead et al.,
  • bioRxiv,
  • 2020
  • R&D
  • Technology
  • Medicine
  • Biology
  • Genomics
  • Ben Mead
  • Marko Vukovic
  • José Ordovas-Montañes
  • Alex K. Shalek
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
  • Sungnak et al.,
  • Nature Medicine,
  • 2020
  • Immunology
  • Infectious Disease
  • Biology
  • Genomics
  • José Ordovas-Montañes
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  • Ziegler et al.,
  • Cell,
  • 2020
  • Statistics
  • Infectious Disease
  • Immunology
  • Cell Atlas
  • Genomics
  • Biology
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Constantine Tzouanas
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Ben Mead
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
  • Muus et al.,
  • bioRxiv,
  • Statistics
  • Computational Methods
  • Cell Atlas
  • Biology
  • Infectious Disease
  • Immunology
  • Genomics
  • Sam Allon
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Marc Wadsworth II
  • Carly Ziegler
  • Alex K. Shalek
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
  • Cao et al.,
  • bioRxiv,
  • 2020
  • Genomics
  • Microbiology
  • Immunology
  • Infectious Disease
  • Biology
  • José Ordovas-Montañes
  • Alex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
  • Infectious Disease
  • Genomics
  • Statistics
  • Immunology
  • Biology
  • Computational Methods
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Vincent Miao
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
  • Ziegler et al.,
  • SSRN,
  • Infectious Disease
  • Genomics
  • Cell Atlas
  • Computational Methods
  • Immunology
  • Medicine
  • Biology
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Constantine Tzouanas
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Distribution and storage of inflammatory memory in barrier tissues
  • Ordovas-Montanes et al.,
  • Nature Reviews Immunology,
  • 2020
  • Biology
  • Immunology
  • Genomics
  • Infectious Disease
  • José Ordovas-Montañes
  • Alex K. Shalek
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
  • Huang et al.,
  • bioRxiv,
  • 2019
  • Computational Methods
  • Genomics
  • Cell Atlas
  • Biology
  • Immunology
  • Carly Ziegler
  • Marko Vukovic
  • José Ordovas-Montañes
  • Alex K. Shalek
Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
  • Smillie et al.,
  • Cell,
  • 2019
  • Biology
  • Genomics
  • Cell Atlas
  • Immunology
  • José Ordovas-Montañes
  • Alex K. Shalek
Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
  • Hughes T.K. et al.,
  • bioRxiv,
  • 2019
  • Technology
  • R&D
  • Immunology
  • Genomics
  • Biology
  • Travis Hughes
  • Marc Wadsworth II
  • José Ordovas-Montañes
  • Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
  • Infectious Disease
  • Genomics
  • Biology
  • Immunology
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
  • Pepe-Mooney et al.,
  • Cell Stem Cell,
  • 2019
  • Biology
  • Medicine
  • Cell Atlas
  • José Ordovas-Montañes
  • Alex K. Shalek
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
  • Biton et al.,
  • Cell,
  • 2018
  • Immunology
  • Medicine
  • Genomics
  • José Ordovas-Montañes
  • Alex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
  • Smillie et al.,
  • BioRxiv,
  • 2018
  • Computational Methods
  • Biology
  • Medicine
  • Immunology
  • Cell Atlas
  • José Ordovas-Montañes
  • Alex K. Shalek
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes et al.,
  • Nature,
  • 2018
  • Immunology
  • Cell Atlas
  • Medicine
  • Biology
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marko Vukovic
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
  • Mead B.E.* et al.,
  • BMC Biology,
  • 2018
  • Ben Mead
  • José Ordovas-Montañes
  • Travis Hughes
  • Marc Wadsworth II
  • Alex K. Shalek
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
  • Martin-Gayo et al.,
  • Genome Biology,
  • 2018
  • Immunology
  • Computational Methods
  • Infectious Disease
  • Medicine
  • Genomics
  • Kellie Kolb
  • José Ordovas-Montañes
  • Alex K. Shalek
Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
  • Jose Ordovas-Montanes et al.,
  • BioRxiv,
  • 2017
  • Medicine
  • Immunology
  • Cell Atlas
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek
Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
  • Nandin I.S. et al.,
  • Journal of Experimental Medicine,
  • 2017
  • Immunology
  • Microbiology
  • Medicine
  • Genomics
  • Infectious Disease
  • Sam Kazer
  • José Ordovas-Montañes
  • Alex K. Shalek