A5084611442- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Groundwater flow and contamination studies
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Pluripotent Stem Cells Research
- Biomedical Ethics and Regulation
- CRISPR and Genetic Engineering
- Environmental Education and Sustainability
- American Constitutional Law and Politics
- Ethics and Legal Issues in Pediatric Healthcare
- Ethics in medical practice
- Genetics, Bioinformatics, and Biomedical Research
- Bacteriophages and microbial interactions
- Genetics, Aging, and Longevity in Model Organisms
- Building Energy and Comfort Optimization
- Gene expression and cancer classification
- Digestive system and related health
- Epigenetics and DNA Methylation
- CO2 Sequestration and Geologic Interactions
- Microbial Community Ecology and Physiology
- Atmospheric and Environmental Gas Dynamics
Colorado State University
2021-2023
University of the Arts London
2017
Sheffield Children's Hospital
2016
Novartis (Switzerland)
2015
Future Science Group (United Kingdom)
2015
National University of Singapore
2014
University of California, Berkeley
2012
Columbia University
2010
Houghton University
2010
Pennsylvania State University
2003-2009
This article describes a set of alignments 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The can be viewed on Human Browser (March 2006 assembly) at http://genome.ucsc.edu , downloaded in bulk anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way or analyzed with Galaxy server http://g2.bx.psu.edu . illustrates power this resource for exploring and mammalian evolution, using three examples. First, we present several vignettes involving...
The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including contributions distal versus proximal cis -regulatory modules, co-occupancy with other factors, effects histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes...
Techniques of comparative genomics are being used to identify candidate functional DNA sequences, and objective evaluations needed assess their effectiveness. Different analytical methods score distinctive features whole-genome alignments among human, mouse, rat predict regions. We evaluated three these for ability the positions known regulatory regions in well-studied HBB gene complex. Two methods, multispecies conserved sequences phastCons, quantify levels conservation estimate a...
The histone methyltransferase Enhancer of Zeste Homolog 2 (EZH2) is frequently dysregulated in cancers, and gain-of-function (GOF) EZH2 mutations have been identified non-Hodgkin lymphomas. Small-molecule inhibitors against demonstrated anti-tumor activity EZH2-mutated lymphomas entered clinical trials. Here, we developed models acquired resistance to inhibitor EI1 with lymphoma cells. Resistance was generated by secondary both wild-type (WT) GOF Y641N alleles. These mutants retained the...
Abstract Natural source zone depletion ( NSZD ) has emerged as a practical alternative for restoration of light non‐aqueous phase liquid (LNAPL) sites that are in the later stages their remediation lifecycle. Due to significant research, conceptual model evolved dramatically recent years, and methanogenesis is now accepted dominant attenuation process (e.g., Lundegard Johnson ; Ng et al. ). Most methane generated within pore space adjacent LNAPL (Ng from where it migrates through unsaturated...
Genomic sequence signals—such as base composition, presence of particular motifs, or evolutionary constraint—have been used effectively to identify functional elements. However, approaches based only on specific signals known correlate with function can be quite limiting. When training data are available, application computational learning algorithms multispecies alignments has the potential capture broader and more informative patterns that better characterize a class effective exploitation...
Abstract Background Establishing genomic resources for closely related species will provide comparative insights that are crucial understanding diversity and variability at multiple levels of biological organization. We developed ESTs Mexican axolotl ( Ambystoma mexicanum ) Eastern tiger salamander A. tigrinum ), with deep diverse research histories. Results Approximately 40,000 quality cDNA sequences were isolated these from various tissues, including regenerating limb tail. These an...
Identification of functional genomic regions using interspecies comparison will be most effective when the full span relationships between function and evolutionary constraint are utilized. We find that sets putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide histories, ranging from stringent shown deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity histories can captured, at least in part, suite available...
Summary Antigen‐specific multifunctional T cells that secrete interferon‐ γ , interleukin‐2 and tumour necrosis factor‐ α simultaneously after activation are important for the control of many infections. It is unclear if these CD8 + at an early or late stage differentiation whether telomere erosion restricts their replicative capacity. We developed a multi‐parameter flow cytometric method investigating relationship between (CD45RA CD27 surface phenotype), function (cytokine production)...
Bunyaviruses ( Negarnaviricota : Bunyavirales ) are a large and diverse group of viruses that include important human, veterinary, plant pathogens. The rapid characterization known new emerging pathogens depends on the availability comprehensive reference sequence databases can be used to match unknowns, infer evolutionary relationships pathogenic potential, make response decisions in an evidence-based manner. In this study, we determined coding-complete genome sequences 99 bunyaviruses...
With a sample of nearly 900 voluntary associations, we give detailed account what membership benefits are provided by interest groups, and place these results in the context typology groups. Using multivariate analysis inducements, show that pursuit collective goods groups is not always mere "by-product" made possible provision selective material incentives, as Olson (1965) contended. Three things help overcome dilemma: (1) members representing institutions more likely than autonomous...
Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis -regulatory modules (CRMs) accurately from such remains an elusive goal. We predict CRMs for mammalian genes expressed in red blood cells by combining two properties gleaned aligned, noncoding sequences: a positive regulatory potential (RP) score, which detects similarity patterns distinctive regions, and conservation binding site motif the essential erythroid transcription factor GATA-1....
Abstract There are several key data gaps in our understanding of Natural Source Zone Depletion (NSZD) processes at sites impacted by light nonaqueous phase liquid (LNAPL), and quantifying NSZD rates can be challenging due to the inherent differences measurement methods. In this study, four different methods (oxygen influx measured Gradient Method, long‐term carbon dioxide efflux with Carbon Traps, instantaneous Dynamic Closed Chambers (DCC LI‐COR), heat flux from biodegradation Thermal...
Aneuploidy, the incorrect number of whole chromosomes, is a common feature tumors that contributes to their initiation and evolution. Preventing aneuploidy requires properly functioning kinetochores, which are large protein complexes assembled on centromeric DNA link mitotic chromosomes dynamic spindle microtubules facilitate chromosome segregation. The kinetochore leverages at least two mechanisms prevent aneuploidy: error correction assembly checkpoint (SAC). BubR1, factor involved in both...
This paper presents an approach to statically retrofit legacy servers with mechanisms for authorization policy enforcement. The is based upon the observation that security-sensitive operations performed by a server are characterized idiomatic resource manipulations, called fingerprints. Candidate fingerprints automatically mined clustering manipulations using concept analysis. These then used identify server. Case studies three real-world show can be few hours of manual effort and modest...
Abstract Low complexity domains (LCDs) in proteins are regions predominantly composed of a small subset the possible amino acids. LCDs involved variety normal and pathological processes across all life. Existing methods define using information-theoretical thresholds, sequence alignment with repetitive regions, or statistical overrepresentation acids relative to whole-proteome frequencies. While these have proven valuable, they indirectly quantifying acid composition, which is fundamental...
DNA sequence motifs and epigenetic modifications contribute to specific binding by a transcription factor, but the extent which each feature determines occupancy in vivo is poorly understood. We addressed this question erythroid cells identifying segments occupied GATA1 measuring level of trimethylation histone H3 lysine 27 (H3K27me3) monomethylation 4 (H3K4me1) along 66 Mb region mouse chromosome 7. While 91% GATA1-occupied contain consensus binding-site motif WGATAR, only approximately...
Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process subject to strong selective constraint. While some studies show that highly constrained noncoding regions act enhance transcription, other DNA segments with biochemical signatures regulatory regions, such as occupancy by a transcription factor, seemingly unconstrained across mammalian evolution. To test possible...
In cold aisle containment (CAC) the supply of air is separated within contained volume. The hot exhaust leaves IT and increases room’s temperature before returning to cooling unit. On other hand, (HAC) generates a cooler environment in data center room as whole by segregating containment. Hot routed back unit return drop ceiling or chimney. Each system has different characteristics airflow paths. For instance, leakage introduces effects for CACs HACs since aisles are switched. This article...
Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, potential normalization and assay platform stability advantages over gene expression Here, we present a computational framework developing AS diagnostic biomarkers. Leveraging large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection whole-blood...