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Ryan M. Wyllie

dblp:319/1610 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2022
0000-0001-9959-2197ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › synthetic biology
oligonucleotide design
0.612022
A reinforcement learning framework for pooled oligonucleotide design · Bioinform. 2022
Bioinformatics and computational biology › synthetic biology › oligonucleotide design
barcode design
0.212022
A reinforcement learning framework for pooled oligonucleotide design · Bioinform. 2022

Methods — techniques the papers use, named apart from their topics

reinforcement learning · 0.6
YearPublicationVenuePosition
2022 A reinforcement learning framework for pooled oligonucleotide design
abstract
MOTIVATION: The goal of oligonucleotide (oligo) design is to select oligos that optimize a set of design criteria. Oligo design problems are combinatorial in nature and require computationally intensive models to evaluate design criteria. Even relatively small problems can be intractable for brute-force approaches that test every possible combination of oligos, so heuristic approaches must be used to find near-optimal solutions. RESULTS: We present a general reinforcement learning (RL) framework, called OligoRL, to solve oligo design problems with complex constraints. OligoRL allows 'black-box' design criteria and can be adapted to solve many oligo design problems. We highlight the flexibility of OligoRL by building tools to solve three distinct design problems: (i) finding pools of random DNA barcodes that lack restriction enzyme recognition sequences (CutFreeRL); (ii) compressing large, non-degenerate oligo pools into smaller degenerate ones (OligoCompressor) and (iii) finding Not-So-Random hexamer primer pools that avoid rRNA and other unwanted transcripts during RNA-seq library preparation (NSR-RL). OligoRL demonstrates how RL offers a general solution for complex oligo design problems. AVAILABILITY AND IMPLEMENTATION: OligoRL and all simulation codes are available as a Julia package at http://jensenlab.net/tools and archived at https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bmdavid2/OligoRL. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Benjamin M. David, Ryan M. Wyllie, Ramdane Harouaka, Paul A. Jensen
Bioinform.2