David DeCaprio
A5070541983- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Fungal and yeast genetics research
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- AI in cancer detection
- Insect symbiosis and bacterial influences
- Animal Genetics and Reproduction
- Computational Drug Discovery Methods
- Mosquito-borne diseases and control
- COVID-19 epidemiological studies
- Genetics, Bioinformatics, and Biomedical Research
- Chronic Disease Management Strategies
- Mycotoxins in Agriculture and Food
- Plant Disease Resistance and Genetics
- Genetic diversity and population structure
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Genetic Mapping and Diversity in Plants and Animals
- Health Systems, Economic Evaluations, Quality of Life
- Artificial Intelligence in Healthcare and Education
- COVID-19 and healthcare impacts
- Insect Resistance and Genetics
GNS Healthcare (United States)
2011-2012
Broad Institute
2004-2010
Massachusetts Institute of Technology
2007-2008
Stanford University
2008
Harvard University
2008
European Bioinformatics Institute
2007
Wellcome Trust
2007
Virginia Tech
2007
Johns Hopkins University
2007
Technical University of Munich
2007
Ustilago maydis is an important fungal pathogen of maize, causing corn smut. It well adapted to its host and proliferates in living plant tissue without inducing a defence response. The genome sequence U. has now been determined, the first for biotrophic parasite. Several gene clusters that encode secreted proteins unknown function were identified: genome-wide expression analysis shows clustered genes are upregulated during disease. Mutations these frequently affect virulence, ranging from...
We present a draft sequence of the genome Aedes aegypti, primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times size malaria Anopheles gambiae. Nearly 50% Ae. aegypti consists transposable elements. These contribute to factor 4 6 increase in average gene length sizes intergenic regions relative An. gambiae Drosophila melanogaster. Nonetheless, chromosomal synteny generally maintained among all three insects, although conservation...
We sequenced and annotated the genome of filamentous fungus Fusarium graminearum , a major pathogen cultivated cereals. Very few repetitive sequences were detected, process repeat-induced point mutation, in which duplicated are subject to extensive may partially account for reduced repeat content apparent low number paralogous (ancestrally duplicated) genes. A second strain F. contained more than 10,000 single-nucleotide polymorphisms, frequently located near telomeres within other discrete...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence proteogenomic map for piscine mycoplasma Mycoplasma mobile , noted its robust gliding motility. For first time, proteomic data are used in primary annotation new genome, providing validation expression many predicted proteins. Several novel features were discovered including long...
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, reliance on an inefficient vaccine absence biomarkers clinical status. promise genomics era TB is substantial, but hindered lack a central repository that collects integrates genomic experimental data about this organism in way can be readily accessed analyzed. Tuberculosis Database (TBDB) integrated database providing access to resources, relevant discovery...
Abstract Deep learning, which describes a class of machine learning algorithms, has recently showed impressive results across variety domains. Biology and medicine are data rich, but the complex often ill-understood. Problems this nature may be particularly well-suited to deep techniques. We examine applications biomedical problems—patient classification, fundamental biological processes, treatment patients—and discuss whether will transform these tasks or if sphere poses unique challenges....
We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike best standalone predictors, which are generalized hidden Markov models (GHMMs) and trained by maximum likelihood, Conrad is discriminatively to maximize annotation accuracy. In addition, unlike pipelines, rely heuristic ad hoc decision rules combine predictors with additional information such as ESTs protein homology, encodes all sources of features treats equally in...
We report the discovery and validation of a set single nucleotide polymorphisms (SNPs) between reference Neurospora crassa strain Oak Ridge Mauriceville (FGSC 2555), sufficient density to allow fine mapping most loci. Sequencing cDNAs alignment completed genomic sequence identified 19,087 putative SNPs. Of these, subset was validated by cleaved amplified polymorphic (CAPS), simple robust PCR-based assay that reliably distinguishes SNP alleles. Experimental confirmation resulted in...
Tumor necrosis factor α (TNF-α) is a key regulator of inflammation and rheumatoid arthritis (RA). TNF-α blocker therapies can be very effective for substantial number patients, but fail to work in one third patients who show no or minimal response. It therefore necessary discover new molecular intervention points involved treatment patients. We describe data analysis strategy predicting gene expression measures that are critical using combination comprehensive genotyping, whole blood...
Abstract Summary: Combo is a comparative genome browser that provides dynamic view of whole alignments along with their associated annotations. two different visualization perspectives. The perpendicular (dot plot) dot plot synchronized display annotations each axis. parallel displays horizontally, through panel displaying local as trapezoids. Users can zoom to any resolution, from chromosomes individual bases. They select, highlight and detailed information specific an organism agnostic...
Abstract Algorithms play an increasingly prevalent role in healthcare, and are used to target interventions, reward performance, distribute resources, including funding. Yet it is widely recognized that many algorithms today may inadvertently encode perpetuate biases contribute health inequities. Artificial intelligence algorithms, addition being assessed for accuracy, must be evaluated with respect whether they could impact disparities outcomes. This paper presents details results of...
People with diabetes and poor glycemic control (HbA1c ≥9%) have a greater likelihood of complications, increased healthcare utilization, higher total cost care (TCOC). Novel approaches to identify patients at high risk for worsening can improve outcomes contain costs within ACNs. We used XGBoost Decision Trees build validate model predicting increase ≥1.5% over 12 months) using Medicare ACN administrative claims electronic health record data. Eligible members had ≥18 mos. continuous...