Jack W Roddy
Overview
Explore the profile of Jack W Roddy including associated specialties, affiliations and a list of published articles.
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Articles
5
Citations
8
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Recent Articles
1.
Olson D, Colligan T, Demekas D, Roddy J, Youens-Clark K, Wheeler T
bioRxiv
. 2025 Feb;
PMID: 39896534
Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be...
2.
Geller-McGrath D, Konwar K, Edgcomb V, Pachiadaki M, Roddy J, Wheeler T, et al.
Elife
. 2024 May;
13.
PMID: 38696239
The reconstruction of complete microbial metabolic pathways using 'omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or...
3.
Copeland C, Roddy J, Schmidt A, Secor P, Wheeler T
NAR Genom Bioinform
. 2024 Apr;
6(2):lqae030.
PMID: 38584872
Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some...
4.
Roddy J, Rich D, Wheeler T
bioRxiv
. 2024 Feb;
PMID: 38352323
Background: The extreme diversity of newly sequenced organisms and considerable scale of modern sequence databases lead to a tension between competing needs for sensitivity and speed in sequence annotation, with...
5.
Copeland C, Roddy J, Schmidt A, Secor P, Wheeler T
bioRxiv
. 2023 Oct;
PMID: 37905003
Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some...
6.
Roddy J, Lesica G, Wheeler T
NAR Genom Bioinform
. 2022 Oct;
4(4):lqac077.
PMID: 36212708
We present SODA, a lightweight and open-source visualization library for biological sequence annotations that enables straightforward development of flexible, dynamic and interactive web graphics. SODA is implemented in TypeScript and...