Tim Dunn
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View article: Development of a Rapid, Culture-Free, Universal Microbial Identification System Using Internal Transcribed Spacer Targeting Primers
Development of a Rapid, Culture-Free, Universal Microbial Identification System Using Internal Transcribed Spacer Targeting Primers Open
The indiscriminate administration of broad-spectrum antibiotics is a primary contributor to the increasing prevalence of antibiotic resistance. Unfortunately, culture, the gold standard for bacterial identification is a time intensive proc…
View article: Jointly benchmarking small and structural variant calls with vcfdist
Jointly benchmarking small and structural variant calls with vcfdist Open
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. Firs…
View article: Jointly benchmarking small and structural variant calls with vcfdist
Jointly benchmarking small and structural variant calls with vcfdist Open
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. Firs…
View article: Phased HG002-GRCh38 small and structural variant calls
Phased HG002-GRCh38 small and structural variant calls Open
This repository holds the input data for the manuscript "Jointly benchmarking small and structural variant calls with vcfdist". This data was previously generated by others at several consortia, including GIAB, T2T, HPRC, and NIST.
View article: Phased HG002-GRCh38 small and structural variant calls
Phased HG002-GRCh38 small and structural variant calls Open
This repository holds the input data for the manuscript "Jointly benchmarking small and structural variant calls with vcfdist". This data was previously generated by others at several consortia, including GIAB, T2T, HPRC, and NIST.
View article: vcfdist: accurately benchmarking phased small variant calls in human genomes
vcfdist: accurately benchmarking phased small variant calls in human genomes Open
View article: GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis
GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis Open
This artifact contains the code and instructions for paper: "GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis" in International Symposium on Computer Architecture (ISCA), 2023.
View article: GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis
GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis Open
This artifact contains the code and instructions for paper: "GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis" in International Symposium on Computer Architecture (ISCA), 2023.
View article: GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis
GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis Open
This artifact contains the code and instructions for paper: "GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis" in International Symposium on Computer Architecture (ISCA), 2023.
View article: nPoRe: n-polymer realigner for improved pileup-based variant calling
nPoRe: n-polymer realigner for improved pileup-based variant calling Open
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, IND…
View article: vcfdist: Accurately benchmarking phased small variant calls in human genomes
vcfdist: Accurately benchmarking phased small variant calls in human genomes Open
Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representa…
View article: A cloud-based pipeline for analysis of FHIR and long-read data
A cloud-based pipeline for analysis of FHIR and long-read data Open
Motivation As genome sequencing becomes cheaper and more accurate, it is becoming increasingly viable to merge this data with electronic health information to inform clinical decisions. Results In this work, we demonstrate a full pipeline …
View article: <i>n</i>PoRe:<i>n</i>-Polymer Realigner for improved pileup variant calling
<i>n</i>PoRe:<i>n</i>-Polymer Realigner for improved pileup variant calling Open
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now regularly exceeds …
View article: SquiggleFilter: An Accelerator for Portable Virus Detection
SquiggleFilter: An Accelerator for Portable Virus Detection Open
The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RN…
View article: SquiggleFilter: An Accelerator for Portable Virus Detection
SquiggleFilter: An Accelerator for Portable Virus Detection Open
The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RN…
View article: SquiggleFilter: An Accelerator for Portable Virus Detection.
SquiggleFilter: An Accelerator for Portable Virus Detection. Open
The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RN…
View article: JNCC seabird distribution and abundance data (all trips) from ESAS database
JNCC seabird distribution and abundance data (all trips) from ESAS database Open
Original provider: European Seabirds at Sea Dataset credits: Joint Nature Conservation Committee (United Kingdom) Nederlands Instituut voor Onderzoek der Zee (the Netherlands) Ornis Consult (Denmark) National Institute for Coastal and Mari…
View article: Cue Awareness in Avoiding Effortful Control (in press)
Cue Awareness in Avoiding Effortful Control (in press) Open
Based on a cue-based metacognitive account, cognitive effort is the result of an inferential evaluation made over explicitly available cues. Following from this account, we present here a pre-registered experiment that tested the specific …
View article: Distributed Metacognition: Deficits in Metacognitive Accuracy when Retrieving Information from the Internet
Distributed Metacognition: Deficits in Metacognitive Accuracy when Retrieving Information from the Internet Open