Analysis of tumor associated macrophages’ heterogeneity in colorectal cancer patients using single-cell RNA-seq data

Colorectal cancer (CRC) is one of the deadliest malignancies worldwide. Though immune checkpoint inhibition has proven effective for a number of other tumors, it offers benefits in only a small group of CRC. In general, heterogenous cell groups in the tumor microenvironment (TME) are considered as the major barrier for unveiling the causes of low immune response. Therefore, deconvolution of cellular components in highly heterogeneous microenvironments is crucial for understanding those mechanisms. Single cell sequencing technology revolutionized TME research enabling profiling cells in high resolution.  We have analyzed scRNA-seq data from 23 CRC patients with pre-treatment primary tumors using Seurat…

Scientific illustrations as a source of biological pathway information

The idea of cross-referencing distinct areas of knowledge to glean new insights is not new, but not much work has been done with automatic analysis of different expressions of the same knowledge source, such as a given scientific text and illustrations that accompany it. The NLM grant “Image-guided Biocuration of Disease Pathways From Scientific Literature” attempts to do just that, using state-of-the-art NLP and graph technologies to extract published knowledge and convert it into both machine- and human-readable formats. With thousands of scientific papers being published every month, such a system can significantly improve visibility of new research and speed…

Synteny and compositional domains in honey bee genomes

Analysis of synteny, the conservation of gene order between homologs along chromosome segments, is a standard investigative strategy done in many comparative genomic studies to understand genomic conservation and evolution. It allows us to study the evolutionary history between genomes. Conservation of synteny can reflect highly important regions in the genome or critical functional relationships between orthologous genes. Our recent study of genome compositional features of Hymenopteran provided insights into genomic compositional features of Apis and other insects with different levels of eusociality. To further understand the biological meaning of different GC regions within the honey bee genomes, we analyzed…

A Case-Control based Genomic Analysis of Chronic Obstructive Pulmonary Disease

Chronic Obstructive Pulmonary Disease (COPD) is a respiratory illness that affects millions of people all over the world. It is a major cause of chronic morbidity and mortality and a serious global public health problem. COPD is the fourth leading cause of death worldwide. Although the environmental causes of COPD which predominantly include cigarette smoking are well-documented, to this date the genetic underpinnings of COPD remain largely unknown. Furthermore, in the current landscape of a respiratory pandemic, COPD patients are at a much higher risk for developing other respiratory illnesses and co-morbidities. In this study we use genomic data from…

Large Scale Study of the Long-Term Effects of COVID-19 Infection Using Aggregated EHR Data

COVID-19 is known to have complex multi-system effects but the lasting effects of infection remain poorly understood. With the number of confirmed infections globally surpassing 200 million it is more important than ever to understand the potential long-term implications of COVID-19 infection on patient health. We have created a pipeline to analyze data from over 1.4 billion medical encounters recorded in the Cerner Real World Data EHR database. We apply this pipeline to analyze the effect of COVID-19 infection on the rate of subsequent new dementia diagnoses 30+ days after the infection period in patients hospitalized with pneumonia with no…

FASTAptameR 2.0: A Web Server for Combinatorial Selections Analysis

Combinatorial selection strategies are powerful tools that allow researchers to simulate selective pressures over time on randomized sequence libraries. This is important for lead discovery and optimization and for understanding selection dynamics. Given the evolutionary nature of these experiments, high-fitness sequences will enrich, whereas low-fitness sequences will deplete. These experiments can generate large magnitudes of data, thus driving a need for high-throughput sequence (HTS) analyses that can utilize sequence-specific evolutionary trajectories. Recently, the selections field has benefitted from several software for HTS analysis. However, these software have a high entrance barrier for many users because they are only accessible through…

Detection of changes in allelic frequencies due to selection on complex traits in the genomes of pigs from four genetic lines using generation proxy selection mapping

Most economically relevant traits in pig breeding programs are controlled by numerous causal variants spread across the genome and undergo selection pressure to improve the genetic merit of commercial pigs.  As a result, small changes in allele frequency over relatively short time scales are induced at these loci.  Identification of genomic loci that exhibit directional changes in allele frequency due to artificial selection identifies areas of the genome that can aid in genetic improvement of populations of pigs.  Thus, the objective of this research was to use Generation Proxy Selection Mapping (GPSM) of the dependent variable birth date to detect…

CANCER PRIORITY BY RACE

Cancer is one of the most common and deadly diseases and its incidence is increasing. There are over one hundred types of cancer and they have a varied impact on society and the individuals affected. Racial disparities play a role in the outcome of many diseases. How does race impact the types of cancer that should be prioritized? How does incidence rate, death rate, and stage at diagnosis vary by race/ethnicity? Could cancer rates be improved by considering race/ethnicity? Please contact Robert Sanders (sandersrl@missouri.edu) for Zoom information.

De-novo SuperTranscriptome assembly from the nodal root growth zone of maize inbred line FR697

Certain cultivars of maize show increased resistance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaption, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de-novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated…