A5042478590- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Fungal and yeast genetics research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Viral Infectious Diseases and Gene Expression in Insects
- Evolutionary Algorithms and Applications
- Fermentation and Sensory Analysis
- Adipose Tissue and Metabolism
- Horticultural and Viticultural Research
- Peroxisome Proliferator-Activated Receptors
- Bacterial Genetics and Biotechnology
- Effects of Environmental Stressors on Livestock
- Fuel Cells and Related Materials
- Microtubule and mitosis dynamics
- Cell Image Analysis Techniques
- Genomics and Chromatin Dynamics
- Advanced Memory and Neural Computing
- Pluripotent Stem Cells Research
- Bayesian Methods and Mixture Models
- Cellular transport and secretion
- Wheat and Barley Genetics and Pathology
- Genomics and Phylogenetic Studies
Ginkgo BioWorks (United States)
2021-2022
Harvard University
2017-2021
University of Wisconsin–Madison
2015-2020
Boston University
2020
Kansas State University
2010
Aneuploidy is highly detrimental during development yet common in cancers and pathogenic fungi – what gives rise to differences aneuploidy tolerance remains unclear. We previously showed that wild isolates of Saccharomyces cerevisiae tolerate chromosome amplification while laboratory strains used as a model for aneuploid syndromes do not. Here, we mapped the genetic basis Ssd1, an RNA-binding translational regulator functional aneuploids but defective strain W303. Loss SSD1 recapitulates...
Peroxisomal biogenesis disorders (PBDs) are genetic of peroxisome and metabolism that characterized by profound developmental neurological phenotypes. The most severe class PBDs—Zellweger spectrum disorder (ZSD)—is caused mutations in peroxin genes result both non‐functional peroxisomes mitochondrial dysfunction. It is unclear, however, how defective contribute to impairment. In order understand the molecular basis this inter‐organellar relationship, we investigated fate peroxisomal mRNAs...
How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two of Saccharomyces cerevisiae in some cases environment but show relatively little gene flow. We profiled stress sensitivity a group vineyard isolates oak-soil strains found several niche-related phenotypes distinguish populations. performed bulk-segregant mapping on distinguishing traits: The...
Summary A comprehensive understanding of the genetic basis phenotypic adaptation in nature requires identification functional allelic variation underlying adaptive phenotypes. The manner which organisms respond to temperature extremes is an many species. In current study, we investigate role molecular senescence marker protein-30 ( Smp-30 ) on natural cold tolerance Drosophila melanogaster . encodes a product that thought be involved regulation Ca 2+ ion homeostasis and has been shown...
Abstract Motivation Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments cover all possible combinations perturbations is infeasible. In this paper, we present the host model (HRM), a machine learning approach that maps single transcriptional combination Results The HRM combines high-throughput sequencing with infer links between experimental context, prior knowledge cell regulatory networks,...
Abstract We describe an experimental campaign that replicated the performance assessment of logic gates engineered into cells Saccharomyces cerevisiae by Gander et al. Our used a novel high-throughput experimentation framework developed under Defense Advanced Research Projects Agency’s Synergistic Discovery and Design program: remote robotic lab at Strateos executed parameterized protocol. Using this protocol execution, we generated two orders magnitude more flow cytometry data than original...
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between collapse, forming hybrid niche with features of both environments. We previously reported that distinctions vineyards oak soil present an ecological barrier restricts lineages Saccharomyces cerevisiae. Vineyard isolates are tolerant stresses associated grapes while North American strains particularly freeze-thaw cycles....
For cluster analysis, high-dimensional data are associated with instability, decreased classification accuracy and high-computational burden. The latter challenge can be eliminated as a serious concern. applications where dimension reduction techniques not implemented, we propose temporary transformation which accelerates computations no loss of information. algorithm applied for any statistical procedure depending only on Euclidean distances implemented sequentially to enable analyses that...
Abstract A challenge in the design and construction of synthetic genetic circuits is that they will operate within biological systems have noisy changing parameter regimes are largely unmeasurable. The outcome these do not specifications or a narrow operational envelope which can function. This behavior often observed as lack reproducibility function from day to lab lab. Moreover, this range operating conditions does promote reproducible circuit deployments where environmental for chassis...
Abstract Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments cover all possible combinations perturbations is infeasible. In this paper, we present the host model (HRM), a machine learning approach that takes cell single as input predicts whole transcriptional combination inducers. We find HRM able qualitatively predict directionality dysregulation inducers with an accuracy >90% using data...
Abstract We describe an experimental campaign that replicated the performance assessment of logic gates engineered into cells S. cerevisiae by Gander, et al . Our used a novel high throughput experimentation framework developed under DARPA’s Synergistic Discovery and Design (SD2) program: remote robotic lab at Strateos executed parameterized protocol. Using this protocol execution, we generated two orders magnitude more flow cytometry data than original experiments. discuss our results,...
Abstract Peroxisomal Biogenesis Disorders (PBDs) are a class of inherited metabolic disorders with profound neurological and other phenotypes. The most severe PBDs caused by mutations in peroxin genes, which result nonfunctional peroxisomes typically through impaired protein import. In order to better understand the molecular causes Zellweger Spectrum Disease (ZSD) -the -, we investigated fate peroxisomal mRNAs proteins ZSD model systems. We found that loss import has no effect on mRNA...