A5004840481- Renal and related cancers
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Computational Drug Discovery Methods
- RNA modifications and cancer
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Neurogenesis and neuroplasticity mechanisms
- Plant Molecular Biology Research
- Plant-Microbe Interactions and Immunity
- Neuroinflammation and Neurodegeneration Mechanisms
- Retinal Development and Disorders
- Genomics and Rare Diseases
- Neuroscience and Neuropharmacology Research
- Tissue Engineering and Regenerative Medicine
- Cell Image Analysis Techniques
- Cancer Genomics and Diagnostics
- Genetic Syndromes and Imprinting
- Animal Genetics and Reproduction
- Genetic and Kidney Cyst Diseases
- Plant Parasitism and Resistance
- Pancreatic function and diabetes
- Genetics, Bioinformatics, and Biomedical Research
University of Alabama at Birmingham
2016-2025
In all organisms, major biological processes are controlled by complex protein-protein interactions networks (interactomes), yet their structural complexity presents analytical challenges. Here, we integrate a compendium of over 4300 phenotypes with Arabidopsis interactome (AI-1
Cytokinin is a phytohormone that well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response less defined manner. Arabidopsis (Arabidopsis thaliana) Response Factor 6 (CRF6) cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays key role inhibition of dark-induced senescence. CRF6 expression induced by oxidative stress, here we show novel function relation identify...
Alzheimer's disease is the most common cause of dementia and characterized by amyloid-β plaques, tau neurofibrillary tangles, neuronal loss. Although loss a primary hallmark disease, it known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis health through neuron-glia glial crosstalk. Many signaling pathways have been proposed to be dysregulated in including WNT, TGFβ, p53, mTOR, NFkB, Pi3k/Akt signaling. Here, we predict altered cell-cell...
The SET binding protein 1 ( SETBP1 ) gene encodes a transcription factor (TF) involved in various cellular processes. Variants can result three different diseases determined by the introduction (germline vs. somatic) and location of variant. Germline variants cause ultra-rare pediatric Schinzel Giedion Syndrome (SGS) haploinsufficiency disorder -HD), characterized severe multisystemic abnormalities with neurodegeneration or less brain phenotype accompanied hypotonia strabismus, respectively....
Abstract Schinzel Giedion Syndrome (SGS) is an ultra‐rare autosomal dominant Mendelian disease presenting with abnormalities spanning multiple organ systems. The most notable phenotypes involve severe developmental delay, progressive brain atrophy, and drug‐resistant seizures. SGS caused by spontaneous variants in SETBP1 , which encodes for the epigenetic hub transcription factor (TF). causing classical cluster at degron, disrupting protein degradation resulting toxic accumulation, while...
One layer of the innate immune system allows plants to recognize pathogen-associated molecular patterns (PAMPS), activating a defense response known as PAMP-triggered immunity (PTI). Maintaining an active response, however, comes at cost plant growth and development; accordingly, optimization balance between development is critical fitness. The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor family consists well-characterized transcriptional regulators...
Abstract Plants use surface receptors to perceive information about many aspects of their local environment. These physically interact form both steady state and signalling competent complexes. The events downstream receptor activation impact plant developmental immune responses. Here, we present a comprehensive study the physical interactions between extracellular domains leucine-rich repeat kinases (LRR-RKs) in Arabidopsis. Using sensitized assay, tested reciprocal among 200 225...
With an increasing amount of biological data available publicly, there is a need for guide on how to successfully download and use this data. The 10 simple rules using public are: (1) purposefully in your research; (2) evaluate case; (3) check reuse requirements embargoes; (4) be aware ethics reuse; (5) plan storage compute requirements; (6) know what you are downloading; (7) programmatically verify integrity; (8) properly cite data; (9) make reprocessed models Findable, Accessible,...
Given the high attrition rate of de novo drug discovery and limited efficacy single-agent therapies in cancer treatment, combination therapy prediction through silico repurposing has risen as a time- cost-effective alternative for identifying novel potentially efficacious cancer. The purpose this review is to provide an introduction computational methods summarize recent studies that implement each these methods. A systematic search PubMed database was performed, focusing on published within...
Abstract Background Autosomal dominant polycystic kidney disease (ADPKD) is one of the most prevalent monogenic human diseases. It mostly caused by pathogenic variants in PKD1 or PKD2 genes that encode interacting transmembrane proteins polycystin-1 (PC1) and polycystin-2 (PC2). Among many processes described ADPKD, those associated with cAMP signaling, inflammation, metabolic reprogramming appear to regulate manifestations. Tolvaptan, a vasopressin receptor-2 antagonist regulates pathway,...
As cancer remains resistant to several modes of treatment, novel therapeutics are still under active investigation overcome treatment inefficacy in cancer. Given the high attrition rate de novo drug discovery, screening, and repurposing have offered time- cost-effective alternative strategies for identification potentially effective therapeutics. In contrast large-scale screens, computational approaches leverage increasing amounts biomedical data predict candidate therapeutic agents prior...
Abstract Schinzel Giedion Syndrome (SGS) is an ultra-rare autosomal dominant Mendelian disease presenting with abnormalities spanning multiple organ systems. The most notable phenotypes involve severe developmental delay, progressive brain atrophy, and drug-resistant seizures. SGS caused by spontaneous variants in SETBP1 , which encodes for the epigenetic hub transcription factor (TF). causing classical cluster at degron, disrupting protein degradation resulting toxic accumulation, while...
Abstract Background The SET binding protein 1 ( SETBP1 ) gene encodes a transcription factor (TF) involved in various cellular processes. Distinct variants have been linked to three different diseases. Germline cause the ultra-rare pediatric Schinzel Giedion Syndrome (SGS) and haploinsufficiency disorder -HD), characterized by severe multisystemic abnormalities with neurodegeneration or less brain phenotype accompanied hypotonia strabismus, respectively. Somatic are associated hematological...
Abstract Background Alzheimer’s disease is the most common cause of dementia and characterized by amyloid-β plaques, tau neurofibrillary tangles, neuronal loss. Although loss a primary hallmark disease, it known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis health through neuron-glia glial crosstalk. Many signaling pathways have been proposed to be dysregulated in including WNT, TGFβ, p53, mTOR, NFkB, Pi3k/Akt signaling. Here, we predict...
Abstract Schinzel-Giedion Syndrome (SGS) is an ultra-rare Mendelian disorder caused by gain-of-function mutations in the SETBP1 gene. While previous studies determined multiple roles for how and associated pathways may cause disease manifestation, they have not assessed whether cell-type-specific alternative splicing (AS) plays a role SGS. We used STARsolo to quantify gene splice junction (SJ) expression 51,465 nuclei previously generated from cerebral cortex of atypical Setbp1 S858R SGS...
Summary Drug repurposing is promising because approving a drug for new indication requires fewer resources than drug. Signature reversion detects perturbations most inversely related to the disease-associated gene signature identify drugs that may reverse signature. We assessed performance and biological relevance of three approaches constructing signatures (i.e, limma, DESeq2, MultiPLIER) prioritized resulting candidates four low-survival human cancers. Our results were enriched had been...
As cancer remains resistant to several modes of treatment, novel therapeutics are still under active investigation overcome treatment inefficacy in cancer. Given the high attrition rate de novo drug discovery, screening, and repurposing have offered time- cost-effective alternative strategies for identification potentially effective therapeutics. In contrast large-scale screens, computational approaches leverage increasing amounts biomedical data predict candidate therapeutic agents prior...
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or AS. Therefore, measuring accurately efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read approaches, third-generation platforms facilitate high-throughput...
Drug repurposing is promising because approving a drug for new indication requires fewer resources than drug. Signature reversion detects perturbations most inversely related to the disease-associated gene signature identify drugs that may reverse signature. We assessed performance and biological relevance of three approaches constructing signatures (i.e., limma, DESeq2, MultiPLIER) prioritized resulting candidates four low-survival human cancers. Our results were enriched had been used in...
Abstract Alzheimer’s disease (AD) is the most common form of dementia and characterized by progressive memory loss cognitive decline, affecting behavior, speech, motor abilities. The neuropathology AD includes formation extracellular amyloid-β plaque intracellular neurofibrillary tangles phosphorylated tau, along with neuronal loss. While an hallmark, cell-cell communication between non-neuronal cell populations maintains health brain homeostasis. To study changes in cellcell during...
Abstract Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or AS. Therefore, measuring accurately efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read approaches, third-generation platforms facilitate...