Derek Aguiar
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Explore the profile of Derek Aguiar including associated specialties, affiliations and a list of published articles.
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14
Citations
177
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Recent Articles
1.
Hosseini M, Palmer A, Manka W, Grady P, Patchigolla V, Bi J, et al.
Bioinformatics
. 2023 Jun;
39(39 Suppl 1):i242-i251.
PMID: 37387144
Motivation: Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated...
2.
Alpay B, Gosink M, Aguiar D
Drug Discov Today
. 2022 Sep;
27(11):103364.
PMID: 36115633
There are many machine learning models that use molecular fingerprints of drugs to predict side effects. Characterizing their skill is necessary for understanding their usefulness in pharmaceutical development. Here, we...
3.
Li C, Qu L, Matz A, Murphy P, Liu Y, Manichaikul A, et al.
Circulation
. 2021 Dec;
145(3):206-218.
PMID: 34913723
Background: Whereas several interventions can effectively lower lipid levels in people at risk for atherosclerotic cardiovascular disease (ASCVD), cardiovascular event risks remain, suggesting an unmet medical need to identify factors...
4.
Alpay B, Demetci P, Istrail S, Aguiar D
Bioinformatics
. 2020 Jul;
36(Suppl_1):i194-i202.
PMID: 32657373
Motivation: Genome-wide association studies (GWAS) have discovered thousands of significant genetic effects on disease phenotypes. By considering gene expression as the intermediary between genotype and disease phenotype, expression quantitative trait...
5.
Aguiar D, Cheng L, Dumitrascu B, Mordelet F, Pai A, Engelhardt B
Nat Commun
. 2018 Apr;
9(1):1681.
PMID: 29703885
Most human protein-coding genes can be transcribed into multiple distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity, and dysregulation of isoform expression plays an important role in disease...
6.
McDowell I, Nikapitiya C, Aguiar D, Lane C, Istrail S, Gomez-Chiarri M
PLoS One
. 2014 Aug;
9(8):e105097.
PMID: 25122115
The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused...
7.
Aguiar D, Wong W, Istrail S
Pac Symp Biocomput
. 2013 Dec;
:3-14.
PMID: 24297529
The growing availability of inexpensive high-throughput sequence data is enabling researchers to sequence tumor populations within a single individual at high coverage. But, cancer genome sequence evolution and mutational phenomena...
8.
Aguiar D, Istrail S
Bioinformatics
. 2013 Jul;
29(13):i352-60.
PMID: 23813004
Motivation: Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the...
9.
Tulin S, Aguiar D, Istrail S, Smith J
Evodevo
. 2013 Jun;
4:16.
PMID: 23731568
Background: The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript complexity. We sought to define a pipeline...
10.
Aguiar D, Istrail S
J Comput Biol
. 2012 Jun;
19(6):577-90.
PMID: 22697235
Genome assembly methods produce haplotype phase ambiguous assemblies due to limitations in current sequencing technologies. Determining the haplotype phase of an individual is computationally challenging and experimentally expensive. However, haplotype...