A5006360401- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- Single-cell and spatial transcriptomics
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- Cancer Immunotherapy and Biomarkers
- RNA Interference and Gene Delivery
- Cancer-related molecular mechanisms research
- Radiomics and Machine Learning in Medical Imaging
- Advanced biosensing and bioanalysis techniques
- Ferroptosis and cancer prognosis
- RNA modifications and cancer
- CAR-T cell therapy research
- Gut microbiota and health
- Parasites and Host Interactions
- Nematode management and characterization studies
- Diabetes and associated disorders
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
- RNA Research and Splicing
- Monoclonal and Polyclonal Antibodies Research
- Molecular Biology Techniques and Applications
- Immune Response and Inflammation
- Extracellular vesicles in disease
University of Chicago
2015-2025
Toyota Technological Institute at Chicago
2015-2024
University of Massachusetts Chan Medical School
2024
University of Illinois Chicago
2024
Chan Zuckerberg Initiative (United States)
2024
Chan Zuckerberg Biohub Chicago
2024
Tempus Labs (United States)
2018-2022
University of Karachi
2017-2021
University of Malakand
2021
Pakistan Agricultural Research Council
2017-2020
Dietary intervention with extensively hydrolyzed casein formula supplemented Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants cow's milk allergy (CMA). We examined whether this effect is attributable, at least part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and CMA (n=19) before after treatment EHCF (n=12) without (n=7) supplementation LGG were compared by 16S rRNA-based operational taxonomic unit clustering...
Interferon regulatory factor 4 (IRF4) and IRF8 regulate B, T, macrophage, dendritic cell differentiation. They are recruited to cis-regulatory Ets-IRF composite elements by PU.1 or Spi-B. How these IRFs target genes in most T cells is enigmatic given the absence of specific Ets partners. Chromatin immunoprecipitation sequencing helper 17 (T(H)17) reveals that IRF4 targets sequences enriched for activating protein 1 (AP-1)-IRF (AICEs) co-bound BATF, an AP-1 required T(H)17, BATF bind...
High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data, but their coverage is still low and the PPI data also very noisy. Computational prediction PPIs can be used to discover new identify errors in data.We present novel deep learning framework, DPPI, model predict from sequence information alone. Our efficiently applies deep, Siamese-like convolutional neural network combined with random projection augmentation PPIs, leveraging...
We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations microsatellite instability in solid tumors hematologic malignancies. This targeted oncology utilizes tumor-normal matched samples for highly accurate alteration calling whole transcriptome RNA unbiased identification of gene fusion events. The was with combination clinical specimens cell lines, recorded sensitivity 99.1% single nucleotide variants, 98.1% indels, 99.9%...
Coordinated repression of gene expression by evolutionarily conserved microRNA (miRNA) clusters and paralogs ensures that miRNAs efficiently exert their biological impact. Combining both loss- gain-of-function genetic approaches, we show the miR-23∼27∼24 regulate multiple aspects T cell biology, particularly helper (Th) 2 immunity. Low this miRNA family confers proper effector function at physiological pathological settings. Further studies in cells with exaggerated regulation individual...
The B-cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-sequencing (RNA-seq) have enabled high throughput profiling of transcript expression single cells, the unique task assembling full-length heavy light chain sequences from cell RNA-seq (scRNA-seq) has been largely unstudied.We developed a new software tool, BASIC, which allows investigators use scRNA-seq for BCR at single-cell resolution. To demonstrate...
Patient-derived tumor organoids (TOs) are emerging as high-fidelity models to study cancer biology and develop novel precision medicine therapeutics. However, utilizing TOs for systems-biology-based approaches has been limited by a lack of scalable reproducible methods profile these models. We describe robust pan-cancer TO platform with chemically defined media optimized on cultures acquired from over 1,000 patients. Crucially, we demonstrate genetic transcriptomic concordance this approach...
Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic coevolution that can isolate matched pairs interacting muteins from complex libraries. This large dataset coevolved complexes drove systems-level analysis molecular recognition between Z domain–affibody spanning wide range structures, affinities, cross-reactivities, and orthogonalities, captured broad spectrum...
Large-scale cancer genomics projects are profiling hundreds of tumors at multiple molecular layers, including copy number, mRNA and miRNA expression, but the mechanistic relationships between these layers often excluded from computational models.We developed a supervised learning framework for integrating profiles with regulatory sequence information to reveal programs in cancer, miRNA-mediated regulation.We applied our approach 320 glioblastoma identified key miRNAs transcription factors as...
Dendritic cells (DCs) promote either tolerogenic or immunogenic T cell responses, the latter upon sensing microbes. Using an in vitro system, we analyzed transcriptional determinants that enable mature DCs to direct these opposing outcomes. In absence of microbial products, transcription factor interferon regulatory 4 (IRF4) promotes (Treg) generation by enhancing expression genes required for antigen presentation along with those tolerance. IRF4-deficient were impaired Treg vivo. When...
Reciprocal interactions between B and follicular T helper (Tfh) cells orchestrate the germinal center (GC) reaction, a hallmark of humoral immunity. Abnormal GC responses could lead to production pathogenic autoantibodies development autoimmunity. Here we show that miR-146a controls by targeting multiple CD40 signaling pathway components in cells; contrast, loss does not alter responses. However, specific deletion both its paralog, miR-146b, increases Tfh cell numbers enhanced reactions....
Environmental influences (infections and diet) strongly affect a host's microbiota. However, host genetics may influence commensal communities, as suggested by the greater similarity between microbiomes of identical twins compared to non-identical twins. Variability human genomes complicates understanding polymorphic mechanisms regulating communities. Whereas animal studies allow genetic modifications, they are sensitive known "cage" or "legacy" effects. Here, we analyze ex-germ-free mice...