A5061979946- Evolution and Genetic Dynamics
- Plant and animal studies
- Insect and Arachnid Ecology and Behavior
- Insect behavior and control techniques
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Insect-Plant Interactions and Control
- Insect and Pesticide Research
- Chromosomal and Genetic Variations
- RNA regulation and disease
- Genetic diversity and population structure
- Water Quality Monitoring Technologies
- Data Mining Algorithms and Applications
- Protein Degradation and Inhibitors
- Peptidase Inhibition and Analysis
- Cancer-related gene regulation
- Blood groups and transfusion
- Amphibian and Reptile Biology
- Molecular Biology Techniques and Applications
- Viral Infectious Diseases and Gene Expression in Insects
- Prostate Cancer Treatment and Research
- Evolutionary Game Theory and Cooperation
- Plant Virus Research Studies
- Multiple Myeloma Research and Treatments
- melanin and skin pigmentation
University of Chicago
2012-2025
Tempus Labs (United States)
2020-2023
University of Illinois Urbana-Champaign
2011-2015
Institute of Human Genetics
2012
Howard Hughes Medical Institute
2012
Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With rapid decrease in sequencing costs, we argue that time revive it.
For bees, many roads lead to social harmony Eusociality, where workers sacrifice their reproductive rights support the colony, has evolved repeatedly and represents most form of evolution in insects. Kapheim et al. looked across genomes 10 bee species with varying degrees sociality determine underlying genomic contributions. No one path led eusociality, but similarities were seen features such as increases gene regulation methylation. It also seems that selection pressures relaxed after...
To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data 10 Western chimpanzees, Pan troglodytes verus. Compared human map, broad-scale tend be conserved, but with exceptions, particularly regions chromosomal rearrangements and around site ancestral fusion chromosome 2. At fine scales, chimpanzee is dominated by hotspots, which show no overlap those humans even though are similarly elevated CpG...
Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living small colonies with overt conflict over reproduction to which contain hundreds of thousands highly specialized sterile workers produced by one or a few queens. Although the evolution eusociality been intensively studied, genetic changes involved relatively unknown. We examined patterns molecular across three...
The ABO histo-blood group, the critical determinant of transfusion incompatibility, was first genetic polymorphism discovered in humans. Remarkably, antigens are also polymorphic many other primates, with same two amino acid changes responsible for A and B specificity all species sequenced to date. Whether this recurrence is result an ancient maintained across or due numerous, more recent instances convergent evolution has been debated decades, a current consensus support evolution. We show...
Abstract Background Multiple myeloma (MM) is characterized by abnormal plasma cell proliferation in the bone marrow, leading to symptoms like osteolytic lesions, anemia, hypercalcemia, and elevated serum creatinine. RNA-sequencing-based prognostic indicators for MM have shown promise stratifying risk assessing first-line treatment options. This study uses machine learning techniques leverages RNA-sequencing, clinical, biochemical data from Myeloma Research Foundation (MMRF) CoMMpass cohort...
Selection against maladaptive hybridization can drive the evolution of reproductive isolation in a process called reinforcement. While importance reinforcement has been historically debated, many examples now exist. Despite these examples, we typically lack detailed understanding mechanisms limiting spread reinforced phenotypes throughout species' range. Here address this issue fruit fly Drosophila yakuba, species that hybridizes with its sister D. santomea and is undergoing well-defined...
Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high-quality genome assembly from this taxon, limiting population conservation genetic studies. One critically blue-eyed black Eulemur flavifrons. This fixed for blue irises, a convergent trait that evolved at least four times was subject positive selection...
ABSTRACT Phylogenetic tests of adaptive evolution, which infer positive selection from an excess nonsynonymous changes, assume that nucleotide substitutions occur singly and independently. But recent research has shown multiple errors at adjacent sites often in single events during DNA replication. These multinucleotide mutations (MNMs) are overwhelmingly likely to be nonsynonymous. We therefore evaluated whether phylogenetic such as the widely used branch-site test, might misinterpret...
RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying fusion events. Although RNA-seq detect germline variants, the complexities of variable transcript abundance, target capture amplification introduce challenging sources error. Here, we extend DeepVariant, a deep-learning-based variant caller, learn account for unique challenges presented by data. Our DeepVariant model produces highly accurate...
Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared the general population. However, little is known about underlying heterogeneity within veteran population its impact on patient management treatment. Using targeted tumor sequencing data from National Affairs health system, we conducted retrospective cohort study 45 patients advanced cancer in Precision Oncology Data Commons (VPODC), most of whom were metastatic...
Abstract Cancer researchers are increasingly conducting multi-omic research and performing integrative analyses on combinations of genomic, proteomic, transcriptomic, imaging, single cell other data modalities. However, it is quite challenging for a researcher to effectively access, aggregate analyze metadata from different sources in scalable reproducible manner, as the individual datasets may be disconnected each other, have separate authentication authorization requirements. We developed...
Over the past few years, a growing number of data platforms have emerged, including commons, repositories, and databases containing biomedical, environmental, social determinants health other relevant to improving outcomes. With platforms, interoperating multiple form meshes, fabrics types ecosystems reduces silos, expands use, increases potential for new discoveries. In this paper, we introduce ten principles, which call pillars, meshes. The goals principles are 1) make it easier, faster,...
ABSTRACT When the ranges of two hybridizing species overlap, individuals may ‘waste’ gametes on inviable or infertile hybrids. In these cases, selection against maladaptive hybridization can lead to evolution enhanced reproductive isolation in a process called reinforcement. On slopes African island São Tomé, Drosophila yakuba and its endemic sister D. santomea have well-defined hybrid zone. females from within this zone show increased postmating-prezygotic towards males when compared with...
e15664 Background: Homologous recombination deficiency (HRD) is the primary biomarker for sensitivity to PARP inhibitors, but identifying genetic and transcriptomic characteristics that fully capture all HRD patients has remained difficult. For example, DNA-based approaches are limited with pathogenic mutations loss of heterozygosity (LOH) events, can fail properly classify variants unknown significance. To more dynamic cellular processes arise immediately upon induction through silencing or...
Abstract RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci, and identifying fusion events. Although RNA-seq detect germline variants, the complexities of variable transcript abundance, target capture, amplification introduce challenging sources error. Here, we extend DeepVariant, a deep-learning based variant caller, learn account for unique challenges presented by data. Our DeepVariant model produces highly...