A5071172253- Statistical Methods and Inference
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Genetic Associations and Epidemiology
- Statistical Methods in Clinical Trials
- Cancer, Lipids, and Metabolism
- Cancer-related molecular mechanisms research
- Computational Drug Discovery Methods
- Cancer Genomics and Diagnostics
- Statistical Methods and Bayesian Inference
- Genetic Mapping and Diversity in Plants and Animals
- Sepsis Diagnosis and Treatment
- Machine Learning in Healthcare
- Neurobiology and Insect Physiology Research
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Plant and animal studies
- Insect and Arachnid Ecology and Behavior
- Advanced Causal Inference Techniques
- Gene Regulatory Network Analysis
- Insect and Pesticide Research
- Animal Behavior and Reproduction
- Optimal Experimental Design Methods
- Biomedical Text Mining and Ontologies
- Advanced Statistical Methods and Models
University of Illinois Urbana-Champaign
2015-2024
Georgia Institute of Technology
2023
Fujian Provincial Cancer Hospital
2023
Fujian Medical University
2023
Urbana University
2023
Center for Genomic Science
2010-2022
International University of the Caribbean
2022
Xiangya Hospital Central South University
2022
Central South University
2022
University of Pennsylvania
2014-2018
It is often of interest to understand how the structure a genetic network differs between two conditions. In this paper, each condition-specific modeled using precision matrix multivariate normal random vector, and method proposed directly estimate difference matrices. contrast other approaches, such as separate or joint estimation individual matrices, direct does not require those matrices be sparse, thus can allow networks contain hub nodes. Under assumption that true differential...
Salivary duct carcinomas (SDC) are a rare and aggressive subtype of salivary gland cancers for which cytotoxic chemotherapy has limited efficacy. We investigated whether genotyping analysis could detect novel tumor-specific mutations that would help direct SDC patient treatment using targeted agents.We genotyped 27 archival specimens from patients followed at Massachusetts General Hospital Eye Ear Infirmary (Boston, MA) between 2000 2011. These included the tumors 8 who were tested...
Abstract During development, neural progenitors are temporally patterned to sequentially generate a variety of types. In Drosophila called neuroblasts, temporal patterning is regulated by cascades Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. addition, many fundamental questions remain concerning the TTF cascade initiation, progression, termination. this work, we use single-cell RNA sequencing medulla...
The growth of antimicrobial resistance (AMR) highlights an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe infections profoundly alter host metabolism, prior studies have largely ignored microbial metabolism in this context. Here, we describe iterative, comparative metabolomics pipeline uncover metabolic features the complex setting a and apply it investigate gram-negative bloodstream infection (BSI) patients. We find...
Abstract Autoimmune diseases (AIDs) are polygenic affecting 7–10% of the population in Western Hemisphere with few effective therapies. Here, we quantify heritability paediatric AIDs (pAIDs), including JIA, SLE, CEL, T1D, UC, CD, PS, SPA and CVID, attributable to common genomic variations (SNP -h 2 ). SNP- h estimates most significant for T1D (0.863±s.e. 0.07) JIA (0.727±s.e. 0.037), more modest UC (0.386±s.e. 0.04) CD (0.454±0.025), largely consistent generally greater than that previously...
Sepsis is a leading cause of death and the most expensive condition to treat in U.S. hospitals. Despite targeted efforts automate earlier detection sepsis, current techniques rely exclusively on using either standard clinical data or novel biomarker measurements. In this study, we apply machine learning assess predictive power combining multiple measurements from single blood sample with electronic medical record (EMR) for identification patients early peak phase sepsis large community...
Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief interactions can shape the future landscape. However, molecular mechanisms contributing are unclear. Here, we show that genome dynamically responds with multiple waves of transcription associated distinct functions brain male threespined sticklebacks, a species famous for its repertoire evolution. Some biological (e.g., hormone activity) peaked soon after territorial challenge then...
Significance Sociobiological theory proposed that similarities between human and animal societies reflect similar evolutionary origins. We used comparative genomics to test this controversial idea by determining whether superficial behavioral humans honey bees shared molecular mechanisms. found unique significant enrichment for autism spectrum disorder-related genes in the neurogenomic signatures of a high-level integration center insect brain unresponsive two different salient social...
Agonistic encounters are powerful effectors of future behavior, and the ability to learn from this type social challenge is an essential adaptive trait. We recently identified a conserved transcriptional program defining response across animal species, highly enriched in transcription factor (TF), energy metabolism, developmental signaling genes. To understand trajectory uncover most important regulatory influences controlling response, we integrated gene expression data with chromatin...
Abstract Cross-validation (CV) is a technique to assess the generalizability of model unseen data. This relies on assumptions that may not be satisfied when studying genomics datasets. For example, random CV (RCV) assumes randomly selected set samples, test set, well represents assumption doesn’t hold true where samples are obtained from different experimental conditions, and goal learn regulatory relationships among genes generalize beyond observed conditions. In this study, we investigated...
Significance Honey bee colony defense is an emergent trait composed of individual aggressive responses. Here, we investigated the relationship between genotype, allele frequency, and aggression in bees. Our findings show that colony-level response strongly correlates with frequency a way can be used to identify causative genomic regions. Importantly, were able validate key associated region as also being under selection. As very similar correlations are observed both soldier forager bees,...
Mediation analysis is difficult when the number of potential mediators larger than sample size. In this paper we propose new inference procedures for indirect effect in presence high-dimensional linear mediation models. We develop methods both incomplete mediation, where a direct may exist, and complete known to be absent. prove consistency asymptotic normality our estimators. Under equivalent total effect, further that approach gives more powerful test compared directly testing effect....
Abstract Motivation : The successful translation of genomic signatures into clinical settings relies on good discrimination between patient subgroups. Many sophisticated algorithms have been proposed in the statistics and machine learning literature, but practice simpler are often used. However, few simple formally described or systematically investigated. Results We give a precise definition popular method we refer to as más-o-menos, which calculates prognostic scores for by summing...
Social challenges like territorial intrusions evoke behavioral responses in widely diverging species. Recent work has showed that evolutionary "toolkits"-genes and modules with lineage-specific variations but deep conservation of function-participate the response to social challenge. Here, we develop a multispecies computational-experimental approach characterize such toolkit at systems level. Brain transcriptomic challenge was probed via RNA-seq profiling three diverged species-honey bees,...
We propose new nonparametric empirical Bayes methods for high-dimensional classification. Our classifiers are designed to approximate the classifier in a hypothesized hierarchical model, where prior distributions model parameters estimated nonparametrically from training data. As is common with Bayes, proposed effective settings even when underlying fact nonrandom. use maximum likelihood estimates of distributions, following elegant approach studied by Kiefer & Wolfowitz 1950s. However, our...
<h3>Objectives</h3> To determine the incidence of postchemoradiotherapy (post-CRT) neck dissection (ND) complications; to ascertain whether timing (<12 vs ≥12 weeks) from CRT ND or other factors are associated with increased and influences disease control survival. <h3>Design</h3> Ten-year retrospective analysis. <h3>Setting</h3> Tertiary care center. <h3>Patients</h3> One hundred five patients head cancer undergoing after CRT. <h3>Main Outcome Measures</h3> Complications survival...