bioRxiv Science⌕ Search

Biology subjects

Levy, D.

Publications and source records attributed to Levy, D..

At least 19 recordsLinked to original sources

Predicting the immediate and subsequent effects of commercials on product valuation using EEG and deep learning

Neuromarketing mainly seeks to enhance the prediction of marketing stimuli success, such as commercials and movie trailers, by integrating neurophysiological measures with traditional behavioral measures. In the current study, the authors tested whether neural activity could predict consumer valuation and how preferences change after watching commercials, both immediately and over time. Participants (n=161) watched images of products followed by commercials advertising those products while their neural activity was recorded using electroencephalograph (EEG). They watched the product images again a week later without EEG recordings. Immediately after each stimulus exposure, participants stated their willingness to pay (WTP) for the product and how much they liked the commercial. Standard EEG measures showed weak and inconsistent relationships with behavior and yielded near-chance predictions. In contrast, deep learning models applied to the raw neural data achieved substantially higher predictive accuracy, successfully predicting both immediate and delayed WTP and ad liking. Importantly, the authors were able to successfully predict preferences for new participants and/or new products the models were not trained on. However, accuracy declined as generalization demands increased. Moreover, prediction performance declined as value differences narrow. Together, these findings show that neural responses carry reliable and temporally persistent information about consumer valuation and its evolution over time.

neuroscience↗

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases

MotivationEpigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. ResultsWe developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG-searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. Availability and implementationThe eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

genetics↗

SETD6-mediated methylation of PPARγ establishes a transcriptional feedback circuit promoting lipid accumulation in liver-derived cells

Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) is a key transcriptional regulator of genes mediating adipogenesis (fat-cell differentiation) and lipid storage in several cell types like hepatocytes. As such, its regulation is crucial for cell and organismal physiology. Indeed, PPAR{gamma}s activity is regulated by multiple mechanisms, including post-transcriptional modifications, which, when dys-coordinated, may contribute to the pathogenesis of various states, including obesity, insulin resistance, and fatty liver disease. Here, we demonstrate that SETD6 binds to, and methylates PPAR{gamma} at lysine 170 (K170) both in vitro and in liver-derived cells. This methylation event, in turn, is required for PPAR{gamma}-mediated activation of SETD6 transcription via promoter binding, forming a positive feedback regulatory loop. RNA sequencing revealed that both SETD6 and PPAR{gamma} methylation at K170 are required for full induction of lipid metabolism genes expression, manifesting functionally in lipid droplet biogenesis in liver-derived cells. Together, our findings uncover a novel role for lysine methylation of PPAR{gamma} in the regulation of lipid synthesis and lipid droplet biogenesis, thereby identifying putative new therapeutic targets for lipid over-production diseases, including MAFLD (Metabolic dysfunction-associated fatty liver disease) and obesity.

cell biology↗

Genetic Impacts on Variability of Body Fat Distribution Uncover Gene-Environment and Gene-Gene Interactions

Body fat distribution is a strong predictor of cardiometabolic disease risk. Gene-environment and gene-gene interactions can affect body fat distribution, resulting in differential phenotypic variance across genotype groups that can be detected through variance quantitative trait loci (vQTLs). Using UK Biobank MRI data in conjunction with genetic data, we explored evidence for vQTLs for body fat distribution phenotypes aiming to uncover potential genetic interactions. We identified three vQTLs for liver fat distribution, including rs738408 (PNPLA3), rs4293458 (APOE), and rs58542926 (TM6SF2), and one vQTL region (FTO) for abdominal subcutaneous adipose tissue. To dissect putative gene-environment and gene-gene interactions underlying these signals, we identified multiple vQTL-environment interactions and one epistatic effect (rs58542926*rs429358) for liver fat. The vQTLs and interaction results were validated in multiple UK Biobank and external replication cohort datasets (Framingham Heart Study, All of Us, and TwinsUK), showing replication of the three liver vQTLs with the greatest reproducibility for vQTL rs738408. Our findings uncover vQTLs and underlying interaction effects on body fat distribution, especially liver fat, that may be useful for the development of precision medicine approaches.

genetics↗

NW-flex: flexible-block sequence alignment for short tandem repeats

Aligning sequencing reads to short tandem repeats (STRs) is challenging: the number of repeat copies in a read often differs from the reference, and small changes inside and around the repeat can lead to many competing alignments. We introduce NW-flex, a simple extension of classical sequence alignment that addresses this problem. NW-flex takes a reference with a designated internal block and, while allowing that block to contract to any shorter substring, identifies the best-scoring alignment. Apart from this substring choice, the alignment obeys the usual substitution scoring and gap constraints. For STRs, we design the flexible block with enough repeat copies to accommodate any expected repeat count. The alignment then contracts the reference to match the read while the unique flanks remain fully constrained. NW-flex requires a small modification to the Needleman-Wunsch/Gotoh algorithm, adds minimal computational overhead, and preserves optimality with respect to classical scoring. We provide open-source Python and Cython implementations, a set of worked examples, and notebooks that reproduce the figures and validate correctness against baseline alignments.

bioinformatics↗

Meningeal macrophages exhibit diverse calcium signaling at steady-state and in response to aberrant cortical hyperexcitability in awake mice

The meninges, which envelop and protect the brain, host a dense network of resident macrophages with diverse roles in regulating homeostasis and neuroinflammation. Despite their importance, we have a limited understanding of their behavior in vivo. Many dynamic cellular functions of macrophages involve intracellular Ca2+ signaling. However, virtually nothing is known about the spatiotemporal Ca2+ dynamics of meningeal macrophages in vivo. We developed a chronic intravital two-photon imaging approach and related computational analysis tools to interrogate meningeal macrophage Ca2+ dynamics, at subcellular resolution, in a novel Pf4Cre:TIGRE2.0GCaMP6s/wt reporter mouse model. Using imaging in awake mice, we characterized Ca2+ activity in meningeal macrophages at steady state and in response to cortical spreading depolarization (CSD), an aberrant pro-inflammatory brain hyperexcitability event implicated in migraine, traumatic brain injury, and stroke. In homeostatic meninges, macrophages in the dural perivascular niche exhibited several Ca2+ dynamic features, including event duration and signal frequency spectrum, distinct from those of localized to the interstitial, non-perivascular niche. Simultaneous tracking of macrophage Ca2+ dynamics and local vasomotion revealed a subset of dural perivascular macrophages whose activity was coupled to locomotion-driven diameter fluctuations of their associated vessels. Most perivascular and non-perivascular meningeal macrophages displayed propagating intracellular Ca2+ activity and synchronized intercellular Ca2+ elevations, potentially driven by extrinsic factors. In response to CSD, the majority of perivascular and non-perivascular meningeal macrophages showed a persistent decrease in Ca2+ activity, while a smaller subset displayed Ca2+ elevations. Mechanistically, CGRP/RAMP1 signaling mediated the increase but not the decrease in CSD-mediated Ca2+ signaling. Collectively, our results highlight a previously unknown diversity of Ca2+ dynamics in meningeal macrophages at steady state and in response to an aberrant brain hyperexcitability event linked to neuroinflammation.

neuroscience↗

A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Controlling Transcriptome Integrity and Diversity

BackgroundMany functional features of mammalian genomic sequences remain poorly defined, especially how sequence motifs and genetic variants within non-coding regions (NCRs) regulate transcriptome integrity and diversity. We have shown that G-tracts unusually positioned between the polypyrimidine tract and 3' AG repress usage of the AG and are enriched at cryptic splice sites in cancer cells but their broader role across the extensive NCRs of mammalian genomes is unknown. ResultsHere, we identify a widely evolved genomic signature, G-tract-AG motifs consisting of guanine tracts closely upstream of AG dinucleotides, which is significantly associated with single-nucleotide variants (SNVs) identified in genome-wide association studies, particularly within NCRs. Approximately 9,000 such G-tracts within human genes are disrupted by variants of the cis-splicing quantitative trait loci in the Genotype-Tissue Expression project. Functionally, G-tracts repress splicing at the adjacent 3' AG, primarily by stalling the second transesterification step. Disruption of G-tracts by SNVs relieves this repression, enabling splicing and generating novel transcript isoforms. These G-tract-disrupting SNVs are in cis across the majority of protein-coding genes and are among thousands of rare variants causing genetic diseases. ConclusionsG-tract-AG signatures are widespread bipartite motifs with dual functions: G-tracts repress AG usage to safeguard transcriptome integrity, while SNV-induced disruption releases AGs for splicing to promote transcriptome diversity. Our findings provide mechanistic insights into the regulation of transcriptome integrity and diversity by a mammalian genomic signature, particularly for NCR SNVs associated with diverse traits and a new framework for their functional annotation.

genetics↗

SETD6 Mediates Selective Interaction and Genomic Occupancy of BRD4 and MITF in Melanoma cells

Aberrant transcriptional programs mediate malignant transformation of melanoma, the most aggressive form of skin cancer. The lysine methyltransferase SETD6 has been implicated in regulating transcription, cell adhesion, migration, and other processes in various cancers, however its role in melanoma remains unexplored. We recently reported that SETD6 mono-methylates the BRD4 at K99 to selectively regulate transcription of genes involved in mRNA translation. Here, we observed that BRD4 methylation at K99 by SETD6 occurs in melanoma cells. Knockout of SETD6 or a point mutation at BRD4-K99 disrupts BRD4 genomic occupancy. In addition, we show that SETD6 interacts with MITF, a master transcription factor in melanocytes and melanoma, and influences the genomic distribution of MITF. Mechanistically, we uncover a novel chromatin-localized interaction between BRD4 and MITF in melanoma. Our data suggest that BRD4 binds MITF in melanoma cells and that this interaction is dependent on both SETD6-mediated methylation of BRD4 and MITF acetylation. This chromatin complex plays a pivotal role in selective recruitment of BRD4 and MITF to different genomic loci in melanoma cells.

molecular biology↗

RAD18 Methylation by the Methyltransferase SETD6 Attenuates DNA Breaks

This study investigated the interaction between the SETD6 lysine methyltransferase and RAD18, a key protein in the DNA damage repair pathway. SETD6 belongs to the SET-domain-containing family of proteins, which are known to catalyze protein methylation, a post-translational modification that plays a critical role in regulating protein function, stability, and interactions. Using protein microarray technology, we identified RAD18 as an interactor and substrate of SETD6. We confirmed this interaction through ELISA and immunoprecipitation assays, demonstrating that SETD6 directly binds and methylates RAD18. Using mass spectrometry and site-directed mutagenesis, we identified that RAD18 undergoes mono-methylation at the K73 and K406 residues. Furthermore, we found that RAD18 methylation affects its nuclear localization. Specifically, SETD6 KO cells exhibited increased nuclear RAD18 levels, suggesting that methylation status influences RAD18s shuttling between the cytoplasm and nucleus. Notably, depletion of SETD6 led to elevated markers of DNA damage ({gamma}H2AX) and increased DNA breaks, as evidenced by comet assays. Restoring SETD6 activity significantly reduced DNA damage, while a catalytic inactive mutant did not have this effect, underscoring the importance of SETD6s enzymatic function. Overall, our results demonstrate that SETD6-mediated methylation of RAD18 is essential for attenuating DNA breaks, thereby regulating its cellular localization and function in maintaining genomic integrity.

molecular biology↗

Genetically-programmed Hypervesiculation of Lactiplantibacillus plantarum Increases Production of Bacterial Extracellular Vesicles with Therapeutic Efficacy in a Preclinical Inflammatory Bowel Disease Model

Inflammatory bowel diseases (IBD) affect over 6 million people globally and current treatments achieve only 10-20% rates of durable disease remission. Bacterial extracellular vesicles (BEVs) from probiotic lactic acid bacteria (LAB) are a promising novel therapeutic with mechanisms holding potential to drive increased rates of durable disease remission, including immunomodulation and intestinal epithelial tissue repair. However, translation of these cell-secreted nanovesicles is limited by long standing biomanufacturing hurdles, especially low production yields due to low biogenesis rates from cells. Here, our goal was to identify a candidate probiotic LAB that produces BEVs effective in a preclinical mouse model of IBD, and then genetically engineer the LAB for at least 10-fold increased production yields of BEVs, thereby passing a critical production threshold. We identified Lactiplantibacillus plantarum as a candidate LAB producing BEVs effective in treating acute dextran sulfate sodium (DSS)-induced murine colitis, and with greater efficacy than BEVs from probiotic Escherichia coli Nissle 1917. We then genetically engineered a hypervesiculating L. plantarum strain by inducible expression of a peptidoglycan-modifying enzyme, resulting in a 66-fold increase in BEV productivity. Finally, we confirmed hypervesiculating L. plantarum BEVs were therapeutically effective in the acute DSS mouse model of colitis and found these BEVs were superior in reducing mucosal tissue damage compared to live L. plantarum cells. These findings demonstrate that BEVs from genetically engineered hypervesiculating strain of L. plantarum are a promising preclinical therapeutic candidate for IBD that overcomes historical biomanufacturing limitations of BEV therapeutics.

bioengineering↗

Millisecond bidirectional protein translocation by a HSP100 machine

How biological machines harness ATP to drive mechanical work remains a crucial question. Structural studies of protein-translocating AAA+ machines proposed a coupled and sequential translocation process, whereby ATP hydrolysis events lead to short threading steps. Yet, direct real-time observation of these events remains elusive. Here, we employ single-molecule FRET spectroscopy to track substrate translocation through ClpB, a quality control AAA+ machine. We isolate ClpB and its substrate within lipid vesicles and find that translocation events, while dependent on ATP, take milliseconds, much faster than ATP hydrolysis times. Surprisingly, the translocation rate depends weakly on temperature and ATP concentration. Using three-color FRET experiments, we find that translocation events can occur bidirectionally but are not always complete. Replacing ATP with the slowly hydrolysable analog ATP{gamma}S abolishes both rapid translocation and directionality. These results indicate a fast, stochastic Brownian-motor-like mechanism, redefining how ATP is coupled with mechanical action in AAA+ machines.

biophysics↗

Cortical astrocyte activation triggers meningeal nociception and migraine-like pain

Migraine attacks are believed to originate in the brain, but the exact mechanisms by which the brain generates peripheral nociceptive signals that drive migraine pain remain unclear. Sensory cortex hyperexcitability has been observed consistently across different migraine subtypes. Astrocytes detect aberrant increases in cortical activity via their Gq-coupled receptors and respond by releasing gliotransmitters and other factors with proinflammatory and nociceptive properties. In the present study, we used a rat model to investigate whether heightened cortical astrocyte Gq-coupled signaling is sufficient to drive peripheral trigeminal meningeal nociceptive responses linked to the generation of migraine headaches. We used an AAV-based chemogenetic approach that allows selective activation of cortical astrocyte Gq-GPCR signaling. We targeted astrocytes in the visual cortex as hyperexcitability in this region has been implicated in migraine. Furthermore, the meninges overlying the visual cortex are densely innervated by nociceptive fibers. We combined this chemogenetic approach with in vivo single-unit recording of meningeal nociceptors to assess changes in their ongoing activity and mechanosensitivity, along with testing of migraine-like behaviors. We further targeted calcitonin gene-related peptide (CGRP), using a monoclonal antibody (anti-CGRP mAb), to assess the relevance of cortical astrocyte activation to migraine. We discovered that heightened activation of Gq-coupled signaling in visual cortex astrocytes drives persistent discharge and increased mechanosensitivity of meningeal nociceptors. Cortical astrocytic activation also generated cephalic mechanical pain hypersensitivity, reduced exploratory behavior, and anxiety-like behaviors linked to migraine headaches. Blocking calcitonin gene-related peptide signaling suppressed astrocyte-mediated increases in meningeal nociceptor discharge and alleviated associated migraine-related behaviors. Our findings reveal a previously unappreciated role for augmented visual cortex astrocyte signaling as a triggering factor sufficient to generate meningeal nociception and migraine pain and greatly expand our understanding of migraine pathophysiology.

neuroscience↗

Reflection Knockoffs via Householder Reflection: Applications in Proteomics and Genetic Fine Mapping

We present a novel knockoff construction method, and demonstrate its superior performance in two applications: identifying proteomic signatures of age and genetic fine mapping. Both applications involve datasets of highly correlated features, but they differ in the abundance of driver associations. Our primary contribution is the invention of the reflection knockoff, which is constructed from mirror images - obtained via Householder reflection - of the original features. The reflection knockoffs substantially outperform Model-X knockoffs in feature selection, particularly when features are highly correlated. Our secondary contribution is a simple method to aggregate multiple sets of identically distributed knockoff statistics to improve the consistency of knockoff filters. In the study of proteomic signatures of age, single feature tests showed overly abundant proteomic association with age. Knockoff filters using reflection knockoffs and aggregation, however, revealed that a majority of these associations are hitchhikers instead of drivers. When applied to genetic fine mapping, knockoff filters using reflection knockoffs and aggregation outperform a state-of-the-art method. We discuss a potentially exciting application of reflection knockoffs: sharing genetic data without raising concerns about privacy and regulatory violations.

bioinformatics↗

AuroraB-kinase methylation by SETD6 regulates cytokinesis and protects cells from chromosomal instability

SETD6 is a non-histone lysine methylatransferase, previously shown to participate in several housekeeping signaling pathways such as the NFkB pathway, Wnt signaling pathway, mitosis and more. In the current study we show evidence that SETD6 methylation is involved in the regulation of cytokinesis - the final process that divides cell contents into two daughter cells. SETD6 depleted HeLa cells presented high levels of chromatin bridges and actin patches, which are commonly observed following chromosomal segregation errors. In a proteomic screen we identified Aurora-B as a novel SETD6 substrate. Aurora-B kinase is an essential regulator of cytokinesis, known to actively delay cytokinesis as a response to the presence of chromatin in the midzone. We found that SETD6 binds and methylates Aurora-B on two adjacent lysine residues. Upon replication stress, Aurora-B methylation by SETD6 increases but is abolished when the two lysine methylation targets are substituted. In addition, replication stress led to a high tendency of SETD6 depleted cells to multinucleate, a major chromosomal-instability (CIN) phenotype. We detected a significant reduction in the Aurora-B kinase activity during cytokinesis in SETD6 knockout cells upon replication stress, which could be the mechanism underlying the accumulation of CIN phenotypes in these cells. CIN is a hallmark of cancer and is associated with tumor cell malignancy. Our findings suggest that Aurora-B methylation by SETD6 carries meaningful implications on tumorigenic cellular pathways.

cell biology↗

Single-molecule FRET reveals how urea paradoxically increases the activity of an enzyme

Proteins often harness extensive motions of domains and subunits to promote their function. Deciphering how these movements impact activity is key for understanding lifes molecular machinery. The enzyme adenylate kinase is an intriguing example for this relationship; it ensures efficient catalysis by large- scale domain motions that lead to the enclosure of the bound substrates ATP and AMP. At high concentrations, AMP also operates as an allosteric inhibitor of the protein. Surprisingly, the enzyme is activated by urea, a compound commonly acting as a denaturant. Combining single-molecule FRET spectroscopy and enzymatic activity studies, we find that urea interferes with two key mechanisms that contribute to enzyme efficacy. First, urea promotes the open conformation of the enzyme, aiding the proper positioning of the substrates. Second, urea decreases AMP affinity, paradoxically facilitating a more efficient progression towards the catalytically active complex. These results signify the important interplay between conformational dynamics and chemical steps, including binding, in the activity of enzymes. State-of-the-art tools, such as single-molecule fluorescence spectroscopy, offer new insights into how enzymes balance different conformations to regulate activity.

biophysics↗

Abundant Parent-of-origin Effect eQTL in Humans: The Framingham Heart Study

Parent-of-origin effect (POE) is a phenomenon whereby an alleles effect on a phenotype depends both on its allelic identity and parents gender from whom the allele is inherited, as exemplified by the polar overdominance in the ovine callypyge locus and the human obesity DLK1 locus. Systematic studies of POE of expression quantitative trait loci (eQTL) are lacking. In this study we use trios among participants in the Framingham Heart Study to examine to what extend POE exists for gene expression of whole blood using whole genome sequencing and RNA sequencing. For each gene and the SNPs in cis, we performed eQTL analysis using genotype, paternal, maternal, and joint models, where the genotype model enforces the identical effect sizes on paternal and maternal alleles, and the joint model allows them to have different effect sizes. We compared models using Bayes factors to identify paternal, maternal, and opposing eQTL, where paternal and maternal effects have opposite directions. The resultant variants are collectively called POE eQTL. The highlights of our study include: 1) There are more than 2, 000 genes harbor POE eQTL and majority POE eQTL are not in the vicinity of known imprinted genes; 2) Among 180 genes harboring opposing eQTL, 99 harbor exclusively opposing eQTL, and 58 of the 99 are phosphoprotein coding genes, reflecting significant enrichment; 3) Paternal eQTL are enriched with GWAS hits, and genes harboring paternal eQTL are enriched with drug targets. Our study demonstrates the abundance of POE in gene expression, illustrates the complexity of gene expression regulation, and provides a resource that is complementary to existing resources such as GTEx. We revisited two previous POE findings in light of our POE results. A SNP residing in KCNQ1 that is maternally associated with diabetes is a maternal eQTL of CDKN1C, not KCNQ1. A SNP residing in DLK1 that showed paternal polar overdominance for human obesity is a maternal eQTL of MEG3, offering an explanation for the baseline risk of homozygous samples through association between MEG3 expression and obesity. Finally, we advised caution on conducting Mendelian randomization using gene expression as the exposure.

genetics↗

EARLY NEUTROPHIL ACTIVATION AND NETs RELEASE IN THE PRISTANE-INDUCED LUPUS MICE MODEL

BackgroundNETosis is recognized as an important source of autoantigens. Therefore, we hypothesized whether the pristane-induced lupus mice model shows early activation of neutrophils, the presence of low-density granulocytes (LDGs), and neutrophil extracellular traps (NETs) release, which could contribute to the development of a lupus phenotype. MethodsTwelve female wild-type Balb/c mice were intraperitoneally injected with pristane (n=6; pristane group) or saline (n=6; control group). Five days after the injection, blood, peritoneal lavage, bone marrow, and spleen samples were collected for flow cytometry analyses of activated neutrophils (Ly6G+CD11b+), LDGs (CD15+CD14low), and NETs release (Sytox Green+). ResultsThe pristane-induced mice group had a significantly increased number of blood activated neutrophils and LDGs as well as NETs released by these cells compared to the saline-injected control group and the basal values determined 12 days before the injection. The pristane group also had a significantly increased number of activated neutrophils, LDGs, and NETs released compared to the control group for the peritoneal lavage, bone marrow, and spleen. ConclusionsWe demonstrated early changes in the innate immune response such as an increased number of activated neutrophils and LDGs and mainly increased NETosis in the pristane-induced mice model which may be considered as the primary event triggering lupus development.

immunology↗

Bayes factor for linear mixed model in genetic association studies

Bayes factor has advantages over p-value as test statistics for association, particularly when comparing multiple non-nested alternative models. An efficient method to compute Bayes factor for linear mixed model in the context of genetic association studies is lacking. In this study, we transform the standard linear mixed model to a Bayesian linear regression by substituting the random effect with fixed effects, where the covariates of the fixed effects are eigenvectors of the genetic relatedness matrix and their respective prior effect sizes are proportional to the corresponding eigenvalues. Using conjugate normal inverse gamma priors on regression parameters, Bayes factors can be computed in a closed form. We demonstrate numerically the known relationship between Bayes factors and p-values for the linear mixed model. We then show that predictions based on the transformed Bayesian linear regression are identical to those of the best linear unbiased prediction (BLUP) of the standard linear mixed model. Our results provided a new perspective and derivation to a known connection between BLUP and Bayesian estimates. Methods described in this note are implemented in the software IDUL as two new functionalities: computing Bayes factors and residuals for the linear mixed model. IDUL and its source code are freely available at https://github.com/haplotype/idul.

bioinformatics↗