A5041484612- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Bayesian Modeling and Causal Inference
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Genetic Associations and Epidemiology
- Receptor Mechanisms and Signaling
- Gene expression and cancer classification
- Metabolomics and Mass Spectrometry Studies
- Pharmacogenetics and Drug Metabolism
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Cancer-related Molecular Pathways
- Protein Structure and Dynamics
- Cancer Genomics and Diagnostics
- Radiomics and Machine Learning in Medical Imaging
- Genetics, Bioinformatics, and Biomedical Research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Cell Image Analysis Techniques
- Fault Detection and Control Systems
- Neural Networks and Applications
City of Hope
2016-2025
Beckman Research Institute
2007-2025
City Of Hope National Medical Center
2003-2025
Van Andel Institute
2015
University of Houston
2013
The University of Texas Health Science Center at Houston
1996-2012
PharmacoGenetics (China)
2010
The University of Texas at Austin
2003-2009
Emory University
2008
Mayo Clinic
2008
We conducted a genome-wide association study to identify novel genes influencing diastolic blood pressure (BP) response hydrochlorothiazide, commonly prescribed thiazide diuretic preferred for the treatment of high BP. Affymetrix GeneChip Human Mapping 100K Arrays were used measure single nucleotide polymorphisms across 22 autosomes in 194 non-Hispanic black subjects and 195 white with essential hypertension selected from opposite tertiles race- sex-specific distributions age-adjusted BP...
Synthesis of proteins is based on the genetic code - a nearly universal assignment codons to amino acids (aas). A major challenge understanding origins this archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine dilemma in light 1) fundamental veto "foresight evolution", 2) modular structures tRNAs and aminoacyl-tRNA synthetases, 3) updated library aa-binding sites RNA aptamers successfully selected vitro for eight acids. The arginine, isoleucine tyrosine contain both their...
Pax proteins are a family of transcription factors with highly conserved paired domain; many members also contain paired-type homeodomain and/or an octapeptide. Nine mammalian genes known and classified into four subgroups: Pax-1/9 , Pax-2/5/8 Pax-3/7 Pax-4/6 . Most these involved in nervous system development. In particular, Pax-6 is key regulator that controls eye development vertebrates Drosophila Although the subgroup seems to be more closely related than or its evolutionary origin...
The wealth of single nucleotide polymorphism (SNP) data within candidate genes and anticipated across the genome poses enormous analytical problems for studies genotype-to-phenotype relationships, modern mining methods may be particularly well suited to meet swelling challenges. In this paper, we introduce method Belief (Bayesian) networks domain analyses provide an example application.A network is a graphical model probabilistic nature that represents joint multivariate probability...
Genetic variability within the SLCO1B1 and ABCB1 transporter genes has been associated with modification of statin effectiveness in cholesterol management.We conducted a case-control study using population-based registry pharmacy records linked to hospital discharge records. Within hypercholesterolemic cohort, we included 668 myocardial infarction cases 1217 controls.We tested 24 tagging SNPs found two (rs3789244, p = 0.01; rs1922242, 0.01) interact treatment. In addition, nonsignificant...
Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled (same individual at different time points) would overcome problem often limited by the relatively numbers available paired samples and statistics being used. To these limitations, we have developed a new vector-based approach, termed...
Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic epigenetic cellular pathway metabolomic). It especially relevant in the context modern (ongoing prospective) studies generate heterogeneous high-throughput omics datasets. However, there are both theoretical practical obstacles seamless application BN...
Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical data sets. Concurrently, our ability perform long-time scale molecular dynamics (MD) simulations on proteins and other materials increased exponentially. However, analysis MD simulation trajectories not data-driven but rather dependent user's prior knowledge...
Abstract Prior studies have shown that approximately 40% of estrogen receptor positive (ER+) breast cancer (BC) patients harbor immune signaling defects in their blood at diagnosis, and the presence these predicts overall survival. Therefore, it is interest to quantitatively characterize measure errors systems patients. Here we propose a novel approach combining communication theory signal processing concepts model ligand discrimination cells peripheral blood. We use specificity molecular...
Identifying target-specific drugs remains a challenge in pharmacology, especially for highly homologous proteins such as dopamine receptors D2R and D3R. Differences cryptic druggable sites arise from the distinct conformational ensembles underlying their dynamic behavior. While Molecular Dynamics (MD) simulations has emerged powerful tool dissecting protein dynamics, sheer volume of MD data requires scalable unbiased analysis strategies to pinpoint residue communities regulating state...
Bayesian Network (BN) modeling is a prominent methodology in computational systems biology. However, the incommensurability of datasets frequently encountered life science domains gives rise to contextual dependence and numerical irregularities behavior model selection criteria (such as MDL, Minimum Description Length) used BN reconstruction. This renders features, first foremost dependency strengths, incomparable difficult interpret. In this study, we derive evaluate principle that...
The JAK-STAT signaling pathway is fundamental for immune system regulation. It involves phosphorylation of several types STAT proteins in response to binding cytokines cell receptors. Traditionally, the studies focus on measuring levels phosphorylated STATs (pSTATs) following individual cytokine application. We developed an experimental approach, based multiparametric flow cytometry, simultaneously measure five pSTATs after 15 minutes treatment with high doses and their paired combinations....
The "chicken-or-egg" dilemma dictates that archaic tRNAs be aminoacylated by ribozymic aminoacyl-tRNA synthetases, rAARSs, with protein synthetases (pAARSs) emerging later and, strikingly in two versions. However, the distribution of these versions among codons also suggests their involvement development genetic code. Here we propose a solution to this controversy, which relies on primordial complementarity hypothesis strand-symmetric RNA world both complementary replicas many genes could...
The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided two classes (I and II) that recognize tRNAs from the minor major groove sides of acceptor stem, respectively. We have reported recently that: (1) ribozymic precursors synthetases seem to used same sterically mirror modes tRNA recognition, (2) having these might helped in preventing erroneous aminoacylation ancestral with complementary anticodons, yet (3) risk confusion for presumably...
Cancer immunotherapy, specifically immune checkpoint blockade, has been found to be effective in the treatment of metastatic cancers. However, only a subset patients achieve clinical responses. Elucidating pretreatment biomarkers predictive sustained response is major research priority. Another priority evaluating changes system before and after responders vs. nonresponders. Our group studying networks as an accurate reflection global state. Flow cytometry (FACS, fluorescence-activated cell...