Abstract: A method of treating an injury in an organ or tissue includes administering to a subject in need thereof an agent that modulates expression and/or activity of one or more genes involved in the regeneration and functional compensation of the tissue or organ in response to the injury.

Abstract: The present invention generally relates to a combination of molecular barcoding and emulsion-based microfluidics to isolate, lyse, barcode, and prepare nucleic acids from individual cells in a high-throughput manner.

Abstract: Described in certain example embodiments herein are systems, methods, and uses thereof for high-throughput in vitro evaluating multiple test compounds in parallel for biological or pharmacological functions. In certain embodiments, the system allows the selection of a subset of test compounds from a group of test compounds to form an optimized pool, and methods are provided to use such optimized pool of test compounds to identify and validate therapeutic agents for treating diseases and driving guided differentiation of stem cells into desired types of cells. The systems described herein can provide, for example, a cost-effective and high-quality high-throughput approach for drug screening.

Abstract: In certain example embodiments, the invention provides a method of generating an ex vivo cell-based system comprising dissociating an original tissue sample obtained from a subject into a single cell population; determining an in vivo phenotype of the tissue sample by conducting single-cell RNA analysis on a first portion of the single cells; establishing an ex vivo cell-based system from a second portion of the single cells; and culturing the ex vivo cell-based system in a medium or conditions selected to maintain the in vivo phenotype. In some embodiments, the original tissue sample is a tumor tissue sample, such as a pancreatic ductal adenocarcinoma (PDAC) tumor sample.

Abstract: The subject matter disclosed herein is generally directed to modulation of genes and pathways that drive differentiation of LGR5+ stem cells. The methods and compositions can be used to treat diseases associated with aberrant epithelial barrier function.

Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions between cells. The present invention provides tools and methods for modulating cell phenotypes and compositions, combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Abstract: A method of modulating immune response to an infection in a subject, the method comprising contacting CD4+ T cells, monocytes, cytotoxic lymphocytes (CTLs), natural killer (NK) cells, and/or proliferating T cells in the subject with one or more modulating agents, wherein the one or more modulating agents modulate genes in one or more of pathways and cell populations.

Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Abstract: This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences T cell balance, for example, Th17 cell differentiation, maintenance and/or function, as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences T cell balance in a variety of therapeutic and/or diagnostic indications. This invention also relates generally to identifying and exploiting target genes and/or target gene products that modulate, control or otherwise influence T cell balance in a variety of therapeutic and/or diagnostic indications.

Abstract: Methods and compositions for treating or preventing a disease by modulating a microenvironment of a cell or cell mass in a subject, the method comprising administrating an effective amount of one or more modulating agents that modulate mast cells, plasma cells, Th1-Th17 cells, and/or CD8+ T cells in the subject.

Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The gene signatures can be detected in samples obtained from the extracellular fluid of a subject suffering from cancer. The novel gene signatures can be used to predict and monitor responses to immunotherapy in cancer and can be targeted therapeutically. The immunotherapy can be immune checkpoint inhibition therapy.

Abstract: The present invention provides for a human cell atlas of the colon from healthy and diseased subjects. The atlas was obtained by single sequencing of about 117,000 cells. The present invention discloses novel markers for cell types. Moreover, genes associated with disease are identified in the colon and colon specific cell types. The invention provides for diagnostic assays based on gene markers and cell composition, as well as target cell types that express genes associated with disease. Finally, disclosed are novel cell types and methods of quantitating, detecting and isolating the cell types.

Abstract: Provided herein are compositions and methods for therapeutic and/or prophylactic treatment of an intracellular bacterial infection in a subject in need thereof, comprising one or more modulating agents, wherein the one or more modulating agents increase expression of IFN?, IL-2, TNF, and/or IL-17 in systemic and/or lung T cells. In some embodiments, the increase of expression of IFN?, IL-2, TNF, and/or IL-17 occurs in lung T cells. The lung T cells can be lung resident T cells or systemic T cells that are recruited to the lung. In some embodiments, the T cells are CD4+ and/or CD8+ T cells. In some embodiments, the intracellular bacterial infection is a Mycobacterium tuberculosis (MTB) infection.

Abstract: Gene expression signatures and pathways associated with tuberculosis are identified. The invention provides for diagnostic assays based on gene markers and cell composition, as well as therapeutic targets for modulating tuberculosis infection. In addition, tuberculosis copy number contained in cells and methods of detecting high and low copy number are disclosed.

Abstract: Described in exemplary embodiments herein are methods, compositions, and kits for diagnosing, prognosing, monitoring, treating and/or preventing a hemopoietic malignancy and/or relapse thereof in a subject. In some embodiments, the methods can include determining an average cellular mass of cells in a sample from the subject and/or detecting one or more molecular signatures in one or more of the cells. In some embodiments, treatment includes administering one or more BCR-ABL tyrosine kinase inhibitors or a pharmaceutical formulation thereof, one or more pre-BCR signaling pathway inhibitors or a pharmaceutical formulation thereof, one or more p38 MAPK inhibitors or a pharmaceutical formulation thereof or any combination thereof.

Abstract: The present invention discloses novel methods, uses thereof, and compositions for modulating immune responses and homeostasis in a lymph node (LN). Moreover, structural and molecular characteristics of LN-innervating sensory neurons are provided. The present invention also discloses the target cells for LN-innervating sensory neurons in LN and molecular profiles of these target cells. These molecular characteristics provide therapeutic targets for modulating immune response and immune homeostasis in LN in an animal or a human.

Abstract: The present invention discloses novel markers for cell types found in breastmilk. Moreover, genes associated with various stages of lactation are identified and in vitro alveolar-like organoid models derived from breastmilk cells are disclosed. Methods of screening modulating agents with the alveolar-like organoid model are also provided. Therapeutic targets for controlling differentiation, proliferation, maintenance and/or function of the cell types disclosed herein, as well as novel cell types and methods of quantitating, detecting and isolating the cell types are disclosed.

Abstract: Embodiments disclosed herein provide a pan-tissue cell atlas of healthy and diseased subjects obtained by single cell sequencing. The present invention discloses novel markers for cell types. Moreover, genes associated with disease, including HIV infection and tuberculosis are identified. The invention provides for diagnostic assays based on gene markers and cell composition, as well as therapeutic targets for controlling immune regulations and cell-cell communication of the cell types disclosed herein. In addition, novel cell types and methods of quantitating, detecting and isolating the cell types are disclosed.

Abstract: The present invention relates to functionalized solid supports and methods of making functionalized solid supports. Methods for preparing a population of high quality functionalized solid supports for use in various nucleic acid analysis methods are provided. The invention also provides methods for validation and quality control of the functionalization steps.

Abstract: This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences dendritic cell (DC) response(s), for example, dendritic cell maturation, dendritic cell antiviral response(s) and/or dendritic cell inflammatory response(s), as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences dendritic cell response(s) in a variety of therapeutic and/or diagnostic indications.