John Harer
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View article: The parasite intraerythrocytic cycle and human circadian cycle are coupled during malaria infection
The parasite intraerythrocytic cycle and human circadian cycle are coupled during malaria infection Open
During infections with the malaria parasites Plasmodium vivax , patients exhibit rhythmic fevers every 48 h. These fever cycles correspond with the time the parasites take to traverse the intraerythrocytic cycle (IEC). In other Plasmodium …
View article: The Parasite Intraerythrocytic Cycle and Human Circadian Cycle are Coupled During Malaria Infection
The Parasite Intraerythrocytic Cycle and Human Circadian Cycle are Coupled During Malaria Infection Open
Summary During infections with malaria parasites P. vivax , patients exhibit rhythmic fevers every 48 hours. These fever cycles correspond with the time parasites take to traverse the Intraerythrocytic Cycle (IEC) and may be guided by a pa…
View article: Assessment of Simulated Surveillance Testing and Quarantine in a SARS-CoV-2–Vaccinated Population of Students on a University Campus
Assessment of Simulated Surveillance Testing and Quarantine in a SARS-CoV-2–Vaccinated Population of Students on a University Campus Open
IMPORTANCE: The importance of surveillance testing and quarantine on university campuses to limit SARS-CoV-2 transmission needs to be reevaluated in the context of a complex and rapidly changing environment that includes vaccines, variants…
View article: Time-varying Reeb graphs for continuous space–time data
Time-varying Reeb graphs for continuous space–time data Open
The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimension…
View article: Benefits of Surveillance Testing and Quarantine in a SARS-CoV-2 Vaccinated Population of Students on a University Campus
Benefits of Surveillance Testing and Quarantine in a SARS-CoV-2 Vaccinated Population of Students on a University Campus Open
Surveillance testing and quarantine have been effective measures for limiting SARS-CoV-2 transmission on university campuses. However, the importance of these measures needs to be re-evaluated in the context of a complex and rapidly changi…
View article: Persistent obstruction theory for a model category of measures with applications to data merging
Persistent obstruction theory for a model category of measures with applications to data merging Open
Collections of measures on compact metric spaces form a model category (“data complexes”), whose morphisms are marginalization integrals. The fibrant objects in this category represent collections of measures in which there is a measure on…
View article: Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus — Duke University, Durham, North Carolina, August 2–October 11, 2020
Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus — Duke University, Durham, North Carolina, August 2–October 11, 2020 Open
On university campuses and in similar congregate environments, surveillance testing of asymptomatic persons is a critical strategy (1,2) for preventing transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). …
View article: An intrinsic oscillator drives the blood stage cycle of the malaria parasite <i>Plasmodium falciparum</i>
An intrinsic oscillator drives the blood stage cycle of the malaria parasite <i>Plasmodium falciparum</i> Open
Plasmodium 's inner clock Malarial fevers are notably regular, occurring when parasitized red blood cells rupture synchronously to release replicated parasites. It has long been speculated that the Plasmodium parasites that cause malaria m…
View article: Guidelines for Genome-Scale Analysis of Biological Rhythms
Guidelines for Genome-Scale Analysis of Biological Rhythms Open
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the d…
View article: Persistent Obstruction Theory for a Model Category of Measures with\n Applications to Data Merging
Persistent Obstruction Theory for a Model Category of Measures with\n Applications to Data Merging Open
Collections of measures on compact metric spaces form a model category ("data\ncomplexes"), whose morphisms are marginalization integrals. The fibrant objects\nin this category represent collections of measures in which there is a measure\…
View article: Multi-Scale Geometric Summaries for Similarity-Based Sensor Fusion
Multi-Scale Geometric Summaries for Similarity-Based Sensor Fusion Open
In this work, we address fusion of heterogeneous sensor data using wavelet-based summaries of fused self-similarity information from each sensor. The technique we develop is quite general, does not require domain specific knowledge or phys…
View article: Geometric cross-modal comparison of heterogeneous sensor data
Geometric cross-modal comparison of heterogeneous sensor data Open
In this work, we address the problem of cross-modal comparison of aerial data streams. A variety of simulated automobile trajectories are sensed using two different modalities: full-motion video, and radio-frequency (RF) signals received b…
View article: Guidelines for Genome-Scale Analysis of Biological Rhythms
Guidelines for Genome-Scale Analysis of Biological Rhythms Open
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the d…
View article: Supervised Learning of Labeled Pointcloud Differences via Cover-Tree Entropy Reduction
Supervised Learning of Labeled Pointcloud Differences via Cover-Tree Entropy Reduction Open
We introduce a new algorithm, called CDER, for supervised machine learning that merges the multi-scale geometric properties of Cover Trees with the information-theoretic properties of entropy. CDER applies to a training set of labeled poin…
View article: Supervised Learning of Labeled Pointcloud Differences via Cover-Tree\n Entropy Reduction
Supervised Learning of Labeled Pointcloud Differences via Cover-Tree\n Entropy Reduction Open
We introduce a new algorithm, called CDER, for supervised machine learning\nthat merges the multi-scale geometric properties of Cover Trees with the\ninformation-theoretic properties of entropy. CDER applies to a training set of\nlabeled p…
View article: Topological and statistical behavior classifiers for tracking applications
Topological and statistical behavior classifiers for tracking applications Open
We introduce the first unified theory for target tracking using Multiple Hypothesis Tracking, Topological Data Analysis, and machine learning. Our string of innovations are 1) robust topological features are used to encode behavioral infor…
View article: Local Edge Machine (Lem)
Local Edge Machine (Lem) Open
Local Edge Machine (LEM) Beginning with time-series gene expression data, the Local Edge Machine (LEM) seeks to find functional network models capable of exhibiting the dynamic behavior of the data. It combines nonlinear kinetic equations,…
View article: Scaffoldings and Spines: Organizing High-Dimensional Data Using Cover Trees, Local Principal Component Analysis, and Persistent Homology
Scaffoldings and Spines: Organizing High-Dimensional Data Using Cover Trees, Local Principal Component Analysis, and Persistent Homology Open
We propose a flexible and multi-scale method for organizing, visualizing, and understanding datasets sampled from or near stratified spaces. The first part of the algorithm produces a cover tree using adaptive thresholds based on a combina…
View article: Additional file 7 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 7 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Saccharomyces cerevisiae gene expression dynamics used in this study. The wild-type gene expression data of 28 genes over approximately two cell cycles were obtained from previous work [2]. Expression values from each profile were s…
View article: Additional file 3 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 3 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Evidence for regulatory interactions in yeast cell-cycle networks 1â 5. Each row corresponds to a regulatory interaction (edge), where an upstream regulator acts on a target gene. p values from four high-throughput chromatin immunop…
View article: Additional file 2 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 2 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Biological prior information about gene function used for LEM inference on yeast cell-cycle networks 1â 5. LEM can incorporate biological priors to remove any impossible edges (e.g., a TF known to be an activator cannot repress a gi…
View article: Additional file 16 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 16 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Compilation of literature that supports the designation of circadian core nodes. The first column gives the names of the genes that were considered to be circadian core genes in our analysis. The second column provides any alternati…
View article: Additional file 8 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 8 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Compilation of literature that supports regulatory interactions in yeast cell-cycle networks 1â 5. Numbers in the first column match literature citations from Additional files 2 and 3. Each number corresponds to a different study th…
View article: Additional file 17 of The Local Edge Machine: inference of dynamic models of gene regulation
Additional file 17 of The Local Edge Machine: inference of dynamic models of gene regulation Open
Table: Ranking of candidate circadian regulators. We used LEM to discover new potential regulators of circadian core nodes (see Additional file 16) by first selecting the top periodic gene sets from 12 mouse organs (see Additional file 1: …
View article: Geometric Models for Musical Audio Data
Geometric Models for Musical Audio Data Open
We study the geometry of sliding window embeddings of audio features that summarize perceptual information about audio, including its pitch and timbre. These embeddings can be viewed as point clouds in high dimensions, and we add structure…