Complete mitochondrial genome of the introduced Indian walking stick (Lonchodidae, Insecta) from California.

We present the complete mitochondrial genome of from Salinas, CA. The mitochondrial genome of is circular, AT rich (78.1%), and 16,671 bp in length.

Complete chloroplast genome of the marine red alga (Rhodochortonaceae, Rhodophyta) from San Juan Island, Washington.

We present the complete chloroplast genome sequence of from San Juan Island, Washington. The chloroplast genome of is 192,037 bp in length, contains 244 genes, and is similar in content to is genetically distinct from from the North Atlantic Ocean.

LimoRhyde2: Genomic analysis of biological rhythms based on effect sizes.

Genome-scale data have revealed daily rhythms in various species and tissues. However, current methods to assess rhythmicity largely restrict their focus to quantifying statistical significance, which may not reflect biological relevance. To address this limitation, we developed a method called LimoRhyde2 (the successor to our method LimoRhyde), which focuses instead on rhythm-related effect sizes and their uncertainty.

New branched Porolithon species (Corallinales, Rhodophyta) from the Great Barrier Reef, Coral Sea, and Lord Howe Island.

Porolithon is one of the most ecologically important genera of tropical and subtropical crustose (non-geniculate) coralline algae growing abundantly along the shallow margins of coral reefs and functioning to cement reef frameworks. Thalli of branched, fruticose Porolithon specimens from the Indo-Pacific Ocean traditionally have been called P. gardineri, while massive, columnar forms have been called P.

The phenotype-genotype reference map: Improving biobank data science through replication.

Population-scale biobanks linked to electronic health record data provide vast opportunities to extend our knowledge of human genetics and discover new phenotype-genotype associations. Given their dense phenotype data, biobanks can also facilitate replication studies on a phenome-wide scale. Here, we introduce the phenotype-genotype reference map (PGRM), a set of 5,879 genetic associations from 523 GWAS publications that can be used for high-throughput replication experiments.

Taxonomic contributions to Hapalidiales (Corallinophycidae, Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations.

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp.

Complete Chloroplast Genome of an Endophytic sp. (Ostreobiaceae) from the U.S. Virgin Islands.

We present the complete chloroplast genome sequence of an endophytic sp. isolated from a 19th-century coralline red algal specimen from St. Croix, U.

Complete Chloroplast Genome Sequence of the Western Poison Oak, Toxicodendron diversilobum (Anacardiaceae), from California.

Here, we present the complete chloroplast genome sequence of Toxicodendron diversilobum, western poison oak, from Pacific Grove, California. The genome is 159,543 bp in length, contains 133 genes, and has a high level of gene synteny to other species of .

LimoRhyde2: genomic analysis of biological rhythms based on effect sizes.

Genome-scale data have revealed daily rhythms in various species and tissues. However, current methods to assess rhythmicity largely restrict their focus to quantifying statistical significance, which may not reflect biological relevance. To address this limitation, we developed a method called LimoRhyde2 (the successor to our method LimoRhyde), which focuses instead on rhythm-related effect sizes and their uncertainty.

Sex Inclusion in Transcriptome Studies of Daily Rhythms.

Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms.

The seeker R package: simplified fetching and processing of transcriptome data.

Transcriptome data have become invaluable for interrogating biological systems. Preparing a transcriptome dataset for analysis, particularly an RNA-seq dataset, entails multiple steps and software programs, each with its own command-line interface (CLI). Although these CLIs are powerful, they often require shell scripting for automation and parallelization, which can have a high learning curve, especially when the details of the CLIs vary from one tool to another.

Resolving some of the earliest names for Corallina species (Corallinales, Rhodophyta) in the North Pacific by sequencing type specimens and describing the cryptic C. hakodatensis sp. nov. and C. parva sp. nov.

Partial rbcL sequences from type specimens of three of the earliest described Corallina species showed that C. arbuscula (type locality: Unalaska Island, Alaska, USA) and C. pilulifera (type locality: Okhotsk Sea, Russia) are synonymous, with C.

The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants.

Summary: Electronic health record (EHR) data linked to DNA biobanks are a valuable resource for understanding the phenotypic effects of human genetic variation. We previously developed the phenotype risk score (PheRS) as an approach to quantify the extent to which a patient's clinical features resemble a given Mendelian disease. Using PheRS, we have uncovered novel associations between Mendelian disease-like phenotypes and rare genetic variants, and identified patients who may have undiagnosed Mendelian disease.

Comparative Analysis of the Chloroplast Genomes of and the Presumptive Parents and (Fagaceae) from California.

Here, we present the complete chloroplast genomes of , , and from California. The genomes are 161,119 to 161,130 bp and encode 132 genes. and are identical in sequence but differ from by three indels and eight SNPs.

Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies.

Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to more accurately predict gene expressions. PUMICE helps define and prioritize regions that harbor cis-regulatory variants, which outperforms competing methods.

Complete Chloroplast Genome of Topotype Material of the Coast Live Oak Née var. (Fagaceae) from California.

Here, we present the chloroplast genome sequence of Quercus agrifolia Née, the California live oak, an ecologically important oak species along the coast of California. The genome is 161,283 bp in length, encodes 132 genes, and has a high level of gene synteny to other Fagaceae.

Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS.

Motivation: Logistic regression models are used in genomic studies to analyze the genetic data linked to electronic health records (EHRs), and do not take full usage of the time-to-event information available in EHRs. Previous work has shown that Cox regression, which can account for left truncation and right censoring in EHRs, increased the power to detect genotype-phenotype associations compared to logistic regression. We extend this to evaluate the relative performance of Cox regression and various logistic regression models in the presence of positive errors in event time (delayed event time), relating to recorded event time accuracy.

The complete chloroplast genome of the threatened Napa False Indigo var. Jeps. 1925 (Fabaceae) from Northern California, USA.

var. Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California.

Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic-like changes in the mammalian circadian clock.

Circadian clocks play key roles in how organisms respond to and even anticipate seasonal change in day length, or photoperiod. In mammals, photoperiod is encoded by the central circadian pacemaker in the brain, the suprachiasmatic nucleus (SCN). The subpopulation of SCN neurons that secrete the neuropeptide VIP mediates the transmission of light information within the SCN neural network, suggesting a role for these neurons in circadian plasticity in response to light information that has yet to be directly tested.

Boundary work as a buffer against burnout: Evidence from healthcare workers during the COVID-19 pandemic.

Burnout represents a significant problem for many modern-day workers, but perhaps none more acutely than those in healthcare. Imbued with the chronic stressors that often accompany high-risk, interpersonal work, the healthcare industry is rife with stories of burnout, and the addition of a pandemic has intensified the challenges of an already demanding work environment. With an aim toward understanding the root causes of pandemic-exacerbated burnout, we document the experiences of 93 healthcare workers during the COVID-19 pandemic and, in doing so, explore an important link between burnout and work-nonwork boundaries.

The complete mitochondrial genome of the strawberry aphid Cockerell, 1901 (Hemiptera: Aphididae) from California, USA.

The aphid Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome.

The Role of Electronic Health Records in Advancing Genomic Medicine.

Recent advances in genomic technology and widespread adoption of electronic health records (EHRs) have accelerated the development of genomic medicine, bringing promising research findings from genome science into clinical practice. Genomic and phenomic data, accrued across large populations through biobanks linked to EHRs, have enabled the study of genetic variation at a phenome-wide scale. Through new quantitative techniques, pleiotropy can be explored with phenome-wide association studies, the occurrence of common complex diseases can be predicted using the cumulative influence of many genetic variants (polygenic risk scores), and undiagnosed Mendelian syndromes can be identified using EHR-based phenotypic signatures (phenotype risk scores).

Automated quality control and cell identification of droplet-based single-cell data using dropkick.

A major challenge for droplet-based single-cell sequencing technologies is distinguishing true cells from uninformative barcodes in data sets with disparate library sizes confounded by high technical noise (i.e., batch-specific ambient RNA).

pmparser and PMDB: resources for large-scale, open studies of the biomedical literature.

PubMed is an invaluable resource for the biomedical community. Although PubMed is freely available, the existing API is not designed for large-scale analyses and the XML structure of the underlying data is inconvenient for complex queries. We developed an R package called pmparser to convert the data in PubMed to a relational database.

DNA sequencing of type material and newly collected specimens reveals two heterotypic synonyms for Harveylithon munitum (Metagoniolithoideae, Corallinales, Rhodophyta) and three new species.

Nongeniculate coralline algae are difficult to identify based solely on morpho-anatomy. To address the systematics of several taxonomically challenging taxa, we analyzed DNA sequences of a short portion (118-296 base pairs) of the 3' end of the rbcL gene from three type specimens. The analyses revealed that Harveylithon munitum (basionym: Lithophyllum munitum), described in 1906 from Cave Cays, Exuma Chain, Bahamas, is conspecific with both Goniolithon accretum and Goniolithon affine, described in 1906 from Sand Key, Florida and in 1907 from Culebra Island, Puerto Rico, respectively.