Bryan R. Helm
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View article: Insulin-like growth factor 2 as a driving force for exponential expansion and differentiation of the neonatal thymus
Insulin-like growth factor 2 as a driving force for exponential expansion and differentiation of the neonatal thymus Open
Like all organs, the thymus grows in size and function rapidly during development, but this growth comes to a halt after birth. However, the molecular mechanisms behind such a transition in the thymus remain obscure. Using single-cell RNA …
View article: Coordinated changes in thymic stromal and hematopoietic cells that define the perinatal to juvenile transition
Coordinated changes in thymic stromal and hematopoietic cells that define the perinatal to juvenile transition Open
SUMMARY T cells in the perinatal thymus have distinct phenotypes and functions that may be instructed by age-specific features of the microenvironment. We evaluated molecular and cellular profiles of thymic stromal cells, including thymic …
View article: Benchmarking Spatial Co-Localization Methods for Single-Cell Multiplex Imaging Data with Applications to High-Grade Serous Ovarian and Triple Negative Breast Cancer
Benchmarking Spatial Co-Localization Methods for Single-Cell Multiplex Imaging Data with Applications to High-Grade Serous Ovarian and Triple Negative Breast Cancer Open
Single-cell multiplex imaging (scMI) measures cell locations and phenotypes within a tissue and can be used to understand the tumor microenvironment. In scMI studies, it is often of interest to quantify spatial co-localization of immune ce…
View article: Body and Wing Allometries Reveal Flight-Fecundity Tradeoff in Response to Larval Provisioning in <i>Osmia lignaria</i> (Hymenoptera: Megachilidae)
Body and Wing Allometries Reveal Flight-Fecundity Tradeoff in Response to Larval Provisioning in <i>Osmia lignaria</i> (Hymenoptera: Megachilidae) Open
Variation in body size has important implications for physical performance and fitness. For insects, adult size and morphology are determined by larval growth and metamorphosis. Female blue orchard bees, Osmia lignaria, (Say) provision a f…
View article: A Retrospective Comparison of In Silico Pharmaceutical Recommendations with Tumor Board Recommendations in Pediatric Oncology
A Retrospective Comparison of In Silico Pharmaceutical Recommendations with Tumor Board Recommendations in Pediatric Oncology Open
Background and Hypothesis: The objective of this study was to analyze available whole genome sequencing from an adolescent male patient diagnosed with osteosarcoma (OS) in 2014. OS is a primary bone malignancy that most commonly affects th…
View article: Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations Open
Background Recent advances in kernel-based Deep Learning models have introduced a new era in medical research. Originally designed for pattern recognition and image processing, Deep Learning models are now applied to survival prognosis of …
View article: Gene Co-Expression Networks Restructured Gene Fusion in Rhabdomyosarcoma Cancers
Gene Co-Expression Networks Restructured Gene Fusion in Rhabdomyosarcoma Cancers Open
Rhabdomyosarcoma is subclassified by the presence or absence of a recurrent chromosome translocation that fuses the FOXO1 and PAX3 or PAX7 genes. The fusion protein (FOXO1-PAX3/7) retains both binding domains and becomes a novel and potent…
View article: BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes Open
To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments. We present BERMUDA (Batch Eff…
View article: Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer
Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer Open
Tumors are heterogeneous tissues with different types of cells such as cancer cells, fibroblasts, and lymphocytes. Although the morphological features of tumors are critical for cancer diagnosis and prognosis, the underlying molecular even…
View article: BERMUDA: A novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
BERMUDA: A novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes Open
To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for cell lineation and identifying bona fide transcriptional signals, it is necessary to combine data from multiple experiments. We present BERMUDA (Batch-Ef…
View article: SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer
SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer Open
Improved cancer prognosis is a central goal for precision health medicine. Though many models can predict differential survival from data, there is a strong need for sophisticated algorithms that can aggregate and filter relevant predictor…
View article: Integration of Mouse and Human Single-cell RNA Sequencing Infers Spatial Cell-type Composition in Human Brains
Integration of Mouse and Human Single-cell RNA Sequencing Infers Spatial Cell-type Composition in Human Brains Open
Technical advances have enabled the identification of high-resolution cell types within tissues based on single-cell transcriptomics. However, such analyses are restricted in human brain tissue due to the limited number of brain donors. In…
View article: BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes Open
To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments. We present BERMUDA (Batch Eff…
View article: Micro-computed tomography of pupal metamorphosis in the solitary bee Megachile rotundata
Micro-computed tomography of pupal metamorphosis in the solitary bee Megachile rotundata Open
Insect metamorphosis involves a complex change in form and function. In this study, we examined the development of the solitary bee, Megachile rotundata, using micro-computed tomography (μCT) and volume analysis. We describe volumetric cha…
View article: Phenotypic integration in an extended phenotype: among‐individual variation in nest‐building traits of the alfalfa leafcutting bee (<i>Megachile rotundata</i>)
Phenotypic integration in an extended phenotype: among‐individual variation in nest‐building traits of the alfalfa leafcutting bee (<i>Megachile rotundata</i>) Open
Structures such as nests and burrows are an essential component of many organisms’ life‐cycle and require a complex sequence of behaviours. Because behaviours can vary consistently among individuals and be correlated with one another, we h…
View article: Metamorphosis is induced by food absence rather than a critical weight in the solitary bee,<i>Osmia lignaria</i>
Metamorphosis is induced by food absence rather than a critical weight in the solitary bee,<i>Osmia lignaria</i> Open
Significance In this study, we characterize the developmental mechanisms shaping body size in the solitary bee pollinator, Osmia lignaria . This study manipulates larval development in a solitary bee to understand how developmental mechani…
View article: The geometric framework for nutrition reveals interactions between protein and carbohydrate during larval growth in honey bees
The geometric framework for nutrition reveals interactions between protein and carbohydrate during larval growth in honey bees Open
In holometabolous insects, larval nutrition affects adult body size, a life history trait with a profound influence on performance and fitness. Individual nutritional components of larval diets are often complex and may interact with one a…