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Ramirez, L.

Publications and source records attributed to Ramirez, L..

At least 19 recordsLinked to original sources

Functional temporal diversity in the fly reflects natural motion statistics

As animals move through the world, their visual input can change gradually or shift rapidly, spanning a broad range of temporal frequencies. Visual circuits therefore face the challenge of encoding inputs with an inherently multiscale temporal structure. From insects to vertebrates, peripheral visual neurons exhibit striking temporal diversity, yet the principles underlying this organization remain unclear. Here, we show that temporal diversity in the fly visual system supports efficient coding of natural motion by distributing encoding across complementary timescales. Using well-characterized fly motion-detection pathways as a model, we show that temporal filters within and across visual hierarchies occupy a low-dimensional feature space defined by filter polarity and characteristic timescale. Within an efficient-coding framework constrained by natural motion statistics, circuits that combine temporally distinct filters encode naturalistic inputs more efficiently than circuits composed of more similar filters, an advantage that largely disappears when changing the stimulus statistics. Measured filters of fly visual cell types closely match the optimal solutions predicted for natural motion, and these optima map onto both circuit architecture and function. Finally, extending beyond the motion pathway, we identify distinct correlation structures in circuits within and outside the motion pathway. Together, we identify temporal diversity in response filters as a circuit-level strategy for encoding natural motion, shaped by the multiscale statistics of the environment. Significance statementNeuronal diversity is ubiquitous across sensory systems, yet its functional role remains poorly understood. We investigate a prominent form of diversity: the wide temporal response profile of visual neurons, from transient detectors to slow integrators. Using the fly visual system, we uncover a coding function of temporal diversity. Neurons with complementary temporal properties span the multiscale structure of natural motion, achieving coding efficiency that no single neuron type can implement alone. Predictions from an efficient coding framework grounded in natural motion statistics closely match fly visual circuit organization, from cell-type response properties to anatomical wiring. Because similar temporal diversity exists in the vertebrate retina, we suggest this distributed temporal coding is a conserved design principle shaped by natural scene statistics.

neuroscience↗

Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters

Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage {Phi}KL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta, during in vitro growth. However, {Phi}KL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that {Phi}KL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.

microbiology↗

Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2

Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta-induced IFN-{gamma} production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research. HIGHLIGHTSO_LI27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota. C_LIO_LIFemale-enriched species are associated with MS risk and severity. C_LIO_LIFemale-enriched Eggerthella lenta exacerbates the EAE model. C_LIO_LIE. lenta impacts neuroinflammation via toll-like receptor 2. C_LI

microbiology↗

Comprehensive Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2

Determining the proteins interacting with sequence-defined chromatin segments is a critical step in understanding gene expression and developing experimental interventions in the process. We used genetically targeted proximity labeling with dCas9-APEX2 to specifically biotinylate the promoter proximal proteome of the single copy locus FOXP2 in live HEK293 cells. To identify labeled proteins in a discovery-based manner, we utilized quantitative mass spectrometry. Specifically, online 2D-LC coupled directly to a tribrid mass spectrometer to enable real-time database searching synchronous precursor selection MS3 provided deep proteome coverage and accurate quantitation via isobaric tandem mass tags. We inferred 6,039 proteins from our sample using Proteome Discoverer and performed bioinformatic analysis on quantified proteins to identify 373 significantly enriched proteins at the active promoter (Storey-q<.05, FC>1.2). These proteins were enriched for transcription factors and components of the spliceosome. To validate our candidate transcriptional regulators, we utilized computationally predicted transcription factor binding and the >200 ChIP-Seq experiments performed in HEK293 cells by ENCODE. In addition to validating several candidate transcription factors as binders of the targeted genomic locus, we identify IRF2BP2 as a negative regulator of FOXP2 transcription.

genetics↗

Endothelial-pericyte interactions regulate angiogenesis via VEGFR2 signaling during retinal development and disease

Pericytes stabilize the microvasculature by enhancing endothelial barrier integrity, resulting in functional networks. During retinal development, pericyte recruitment is crucial for stabilizing nascent angiogenic vasculature. However, in adulthood, disrupted endothelial-pericyte interactions lead to vascular dropout and pathological angiogenesis in ocular microvascular diseases, and strategies to stabilize the retinal vasculature are lacking. We demonstrate that direct endothelial-pericyte contact downregulates pVEGFR2 in endothelial cells, which enhances pericyte migration and promotes endothelial cell barrier function. Intravitreal injection of a VEGFR2 inhibitor in mouse models of the developing retina and oxygen-induced retinopathy increased pericyte recruitment and aided vascular stability. The VEGFR2 inhibitor further rescued ischemic retinopathy by enhancing vascularization and tissue growth while reducing vascular permeability. Our findings offer a druggable target to support the growth of functional and mature microvasculature in ocular microvascular diseases and tissue regeneration overall.

cell biology↗

Derivation of functional retinal endothelial cells from human pluripotent stem cells for therapeutics and modeling

Retinal microvascular diseases involve a compromised inner blood-retina barrier (iBRB), which remains poorly understood. A renewable source of human iBRB endothelium is thus vital for advancing eye research and treatment development. Here, we differentiated human iPSCs into retinal endothelial cells (iRECs) via the Wnt/{beta}-catenin pathway, namely Norrin/Frizzled4 signaling. These iRECs show genetic, protein, and functional fidelity and unique retinal features. When injected into oxygen-induced retinopathy mice, iRECs integrated into the host vascular network and revascularized the ischemic eye, rescuing the tissue. Within microphysiological models, iRECs form perfusable microvascular networks that mimic the iBRBs morphology and phenotype in both health and diabetic retinopathy conditions while also interacting and organizing physiologically with iPSC-derived retinal pericytes. Our studies establish functional human iRECs and microphysiological iBRB models that facilitate mechanistic studies aimed at identifying therapeutic targets and promoting the revascularization of injured retinas, thereby supporting treatment advancement.

bioengineering↗

IsoformMapper: A Web Application for Protein-Level Comparison of Splice Variants through Structural Community Analysis

Alternative splicing (AS) plays a key role in numerous cellular processes by enabling the existence of different protein isoforms with potentially different functions and fine-tuning isoform abundance. However, despite its biological importance, tools to compare the domain composition of AS-derived protein isoforms have lagged as they require both structural data and an appropriate methodology for isoform comparison. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, have made accurate structural determination of splicing isoforms easily accessible, paving the way for new tools to compare their structures and asses the functional consequences of AS at the protein structure level. Here, we present IsoformMapper, a web resource that enables researchers to study alternative splicing at the protein structural level using protein network community analysis, which captures 3D physical interactions between protein regions often missed by traditional domain analysis, allowing comparisons of isoforms across any biological system. As a proof of concept, we used our tool to a case study, in which we studied how GENOMES UNCOUPLED1 (GUN1) dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, we demonstrate that GUN1 regulates the expression of specific spliceosome components, consequently modifying alternative splicing of key genes encoding components essential for establishing of photosynthesis. Additionally, the gun1 mutant showed altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool revealed that these isoforms have significantly different protein community structures, illustrating the impact of AS on protein function and demonstrating the practical value of the tool. (247 words) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/641708v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@c006dcorg.highwire.dtl.DTLVardef@1025b07org.highwire.dtl.DTLVardef@1a64bf6org.highwire.dtl.DTLVardef@c512af_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO IsoformMapper enables structural comparison of protein isoforms through a multi-step analysis pipeline. Starting with AlphaFold2 protein structure predictions of splice variants, the method generates weighted network representations for each isoform. The web application processes multiple AlphaFold predictions per isoform, with the conformational variability between predictions represented as weighted edges in the network representation. These networks are then analyzed using the InfoMap community detection algorithm to identify structural communities, ultimately allowing visualization and comparison of protein isoform structures through interactive network displays and alluvial diagrams. The method is applicable to protein isoforms from any biological system, providing comprehensive analysis of alternative splicing consequences at the protein level by examining structural domains as integrated units. This holistic approach enables users to evaluate potential functional differences between isoforms based on their structural organization. C_FIG

bioinformatics↗

Undoing of firing rate adaptation enables invariant population codes

Neural adaptation supports coding efficiency by tuning responses to prevailing stimulus statistics. However, when information is represented by neural populations, adaptation of individual units could degrade behaviorally relevant signals. Here we investigate how the fly olfactory system implements adaptation in Olfactory Receptor Neurons (ORNs) and the consequences for combinatorial coding in downstream circuits. We show that adaptation of ORN firing rate is compensated at the axon terminal, where calcium transients remain background-invariant through inhibitory presynaptic feedback. Background invariance requires an adaptation strategy that shifts ORN response amplitude rather than sensitivity, diverging from efficient coding principles in single neurons. This property supports contrast encoding in ORN populations necessary for background compensation across the glomeruli. Downstream, the modulation of presynaptic Unc13 proteins maintains postsynaptic projection neurons responses to ON stimuli background invariant. We identify a new coding strategy where olfactory neuronal populations encode asymmetrically contrast information by implementing circuit computations that compensate peripheral firing rate adaptation.

neuroscience↗

Mixed outcomes in recombination rates after domestication: Revisiting theory and data

The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesized to indirectly select for increases in recombination rate. This hypothesis is consistent with theory on the evolution of recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilize population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domestic goats compared to bezoars, but more mixed results in chicken, and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in recombination with domestication.

evolutionary biology↗

Neural pathways and computations that achieve stable contrast processing tuned to natural scenes

Natural scenes are highly dynamic, challenging the reliability of visual processing. Yet, humans and many animals perform accurate visual behaviors, whereas computer vision devices struggle with changing environments. How does animal vision achieve this? Here, we reveal the algorithms and mechanisms of rapid luminance gain control in Drosophila, resulting in stable visual processing. We identify the dendrites of specific third order neurons, Tm1 and Tm9, as the site of luminance gain control. The circuitry further involves neurons with wide-field properties, matching computational predictions that local spatial pooling can drive optimal contrast processing in natural scenes where light conditions change rapidly. Experiments and theory argue that a spatially pooled luminance signal achieves luminance gain control via divisive normalization. This process relies on shunting inhibition using the glutamate-gated chloride channel GluCl. Our work describes computationally, algorithmically, and mechanistically, how visual circuits robustly process visual information in dynamically changing, natural scenes.

neuroscience↗

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity

Diet can protect from autoimmune disease; however, whether diet acts via the host and/or microbiome remains unclear. Here, we use a ketogenic diet (KD) as a model to dissect these complex interactions. A KD rescued the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis in a microbiota-dependent fashion. Dietary supplementation with a single KD-dependent host metabolite ({beta}-hydroxybutyrate, {beta}HB) rescued EAE whereas transgenic mice unable to produce {beta}HB in the intestine developed more severe disease. Transplantation of the {beta}HB-shaped gut microbiota was protective. Lactobacillus sequence variants were associated with decreased T helper 17 (Th17) cell activation in vitro. Finally, we isolated a L. murinus strain that protected from EAE, which was phenocopied by the Lactobacillus metabolite indole lactic acid. Thus, diet alters the immunomodulatory potential of the gut microbiota by shifting host metabolism, emphasizing the utility of taking a more integrative approach to study diet-host-microbiome interactions.

microbiology↗

Cytochrome P450 and Epoxide Hydrolase Metabolites in Aβ and tau-induced Neurodegeneration: Insights from Caenorhabditis elegans

This study aims to uncover potent cytochrome P450 (CYP) and epoxide hydrolase (EH) metabolites implicated in A{beta} and/or tau-induced neurodegeneration, independent of neuroinflammation, by utilizing Caenorhabditis elegans (C. elegans) as a model organism. Our research reveals that A{beta} and/or tau expression in C. elegans disrupts the oxylipin profile, and epoxide hydrolase inhibition alleviates the ensuing neurodegeneration, likely through elevating the epoxy-to-hydroxy ratio of various CYP-EH metabolites. In addition, our results indicated that the A{beta} and tau likely affect the CYP-EH metabolism of PUFA through different mechanism. These findings emphasize the intriguing relationship between lipid metabolites and neurodegenerations, in particular, those linked to A{beta} and/or tau aggregation. Furthermore, our investigation sheds light on the crucial and captivating role of CYP PUFA metabolites in C. elegans physiology, opening up possibilities for broader implications in mammalian and human contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/560527v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@8fd3fdorg.highwire.dtl.DTLVardef@a6c4e1org.highwire.dtl.DTLVardef@c7a5a7org.highwire.dtl.DTLVardef@14c8ce2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Cancer Prevalence Across Vertebrates

Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Petos Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Statement of SignificanceEvolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.

cancer biology↗

A genome-wide atlas of recurrent repeat expansions in human cancer

Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs (STRs), a phenomenon termed microsatellite instability (MSI); however larger repeat expansions have not been systematically analyzed in cancer. Here, we identified TR expansions in 2,622 cancer genomes, spanning 29 cancer types. In 7 cancer types, we found 160 recurrent repeat expansions (rREs); most of these (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with an enrichment near candidate cis-regulatory elements, suggesting a role in gene regulation. One rRE located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, targeting cells harboring this rRE with a rationally designed, sequence-specific DNA binder led to a dose-dependent decrease in cell proliferation. Overall, our results demonstrate that rREs are an important but unexplored source of genetic variation in human cancers, and we provide a comprehensive catalog for further study.

genomics↗

Sex differences in early and term placenta are conserved in adult tissues

BackgroundPregnancy complications vary based on the fetuss genetic sex, which may, in part, be modulated by the placenta. Further, developmental differences early in life can have lifelong health outcomes. Yet, sex differences in gene expression within the placenta at different time points throughout pregnancy and comparisons to adult tissues remains poorly characterized. MethodsHere, we collect and characterize sex differences in gene expression in term placentas ( [&ge;] 36.6 weeks; 23 male XY and 27 female XX). These are compared with sex differences in previously collected first trimester placenta samples and 42 non-reproductive adult tissues from GTEx. ResultsWe identify 268 and 53 sex differentially expressed genes in the uncomplicated late first trimester and term placentas, respectively. Of the 53 sex differentially expressed genes observed in the term placentas, 31 are also sex differentially expressed genes in the late first trimester placentas. Furthermore, sex differences in gene expression in term placentas are highly correlated with sex differences in the late first trimester placentas. We found that sex differential gene expression in the term placenta is significantly correlated with sex differences in gene expression in 42 non-reproductive adult tissues (correlation coefficient ranged from 0.892 to 0.957), with the highest correlation in brain tissues. Sex differences in gene expression were largely driven by gene expression on the sex chromosomes. We further show that some gametologous genes (genes with functional copies on X and Y) will have different inferred sex differences if the X-linked gene expression in females is compared to the sum of the X-linked and Y-linked gene expression in males. ConclusionsWe find that sex differences in gene expression are conserved in late first trimester and term placentas and that these sex differences are conserved in adult tissues. We demonstrate that there are sex differences associated with innate immune response in late first trimester placentas but there is no significant difference in gene expression of innate immune genes between sexes in healthy full term placentas. Finally, sex differences are predominantly driven by expression from sex-linked genes. HighlightsO_LISex differences in gene expression in late first trimester placentas are positively correlated with sex differences in gene expression in full term placentas; sex differences develop early and are maintained. C_LIO_LISex differences in gene expression on the sex chromosomes in the placenta are correlated to sex differences in adult tissues. C_LIO_LISex-linked gametolog genes require additional methodological approaches for accurate quantification. C_LI

genomics↗

Data-driven models of optimal chromatic coding in the outer retina

The functional properties of the outermost retinal circuits involved in color discrimination are not well understood. Recent experimental work on zebrafish has elucidated the in-vivo activity of photoreceptors and horizontal cells as a function of the stimulus spectrum, highlighting the appearance of chromatic-opponent signals at the first synaptic connection between cones and horizontal cells. These findings, together with the observed lack of gap junctions, suggest that the mechanism yielding early color-opponency in zebrafish is dominated by inhibitory feedback. We discuss the observed neuronal activity in the context of efficient codification of chromatic information, hypothesizing that opponent chromatic signals provide optimal codification, minimizing signal redundancy. We examine whether these functional properties are general across species by studying the dynamic properties of dichromatic and trichromatic outer retinal networks. Our findings show that dominant inhibitory feedback mechanisms provide an unambiguous codification of chromatic stimuli, whereas this property is not guaranteed in networks with strong excitatory inter-cone connections, for example via gap junctions. This provides a plausible explanation for the absence of gap junctions observed in the outermost zebrafish retinal layers. In addition, our study suggests that the simplest zebrafish-like network with dominant inhibitory feedback capable of optimally codifying chromatic information requires at least two successive inhibitory feedback layers. Finally, we contrast the chromatic codification performance of zebrafish-inspired retinal networks with networks having different opsin combinations. We find that optimal combinations lead to a chromatic codification improvement of only 13% compared with zebrafish opsins, suggesting that the zebrafish retina performs nearly optimal codification of chromatic information in its habitat. 2 Author summaryRecent experimental work has evidenced that outer neuronal circuits in the zebrafish retina use color-opponent mechanisms to codify and transmit chromatic information at the first synaptic contact between cones and horizontal cells. Inspired by these findings, we propose a data-driven model to study physiological and dynamical properties of outer retinal networks and their implications for color codification across vertebrate retinal circuits. We first study our model in a large parameter space, finding that the primary biological mechanism leading to color-opponent signals is mediated by dominant inhibitory feedback, e.g., via horizontal cell synaptic connections. In contrast, strong coupling among cones leads to ambiguous chromatic codification, undesirable in the outer retina. Then, we parameterize the model using zebrafish experimental data and quantify its chromatic codification performance. Our results suggest that trichromatic retinas with inhibitory feedback are highly efficient and capture most of the chromatic information variance typical from zebrafish environments. More specifically, a comparison among zebrafish-inspired retinal networks suggests that zebrafish retinal circuits are near-optimal chromatic codification of their natural chromatic information.

biophysics↗

Fast weight recovery, metabolic rate adjustment and gene-expression regulation define responses of cold-stressed honey bee brood

ABSTRACTIn temperate climates, low ambient temperatures in late winter and in spring can result in cold stress conditions in brood areas of weakened honey bee colonies, leading to increased levels of developmental interruptions and death of the brood. Very little is known about the physiological and molecular mechanisms that regulate honey bee brood responses to acute cold-stress. Here, we hypothesized that central regulatory pathways mediated by insulin/insulin-like peptide signalling (IIS) and adipokinetic hormone (AKH) are linked to metabolic changes in cold-stressed honey bee brood. A. mellifera brood reared at suboptimal temperatures showed diminished growth rate and arrested development progress. Notably, cold-stressed brood rapidly recovers the growth in the first 24 h after returning at control rearing temperature, sustained by the induction of compensatory mechanisms. We determined fast changes in the expression of components of IIS and AKH pathways in cold-stressed brood supporting their participation in metabolic events, growth and stress responses. We also showed that metabolic rate keeps high in brood exposed to stress suggesting a role in energy supply for growth and cell repair. Additionally, transcript levels of the uncoupling protein MUP2 were elevated in cold-stressed brood, suggesting a role for heat generation through mitochondrial decoupling mechanisms and/or ROS attenuation. Physiological, metabolic and molecular mechanisms that shape the responses to cold-stress in honey bee brood are addressed and discussed.View Full Text

physiology↗

RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Gene regulatory regions contain short and degenerated DNA sites recognized by transcription factors (TFs). When such regions harbor SNPs, the DNA motifs where TFs bind may be affected, thereby altering the transcriptional regulation of the target genes. Such regulatory SNPs have been implicated as causal variants in GWAS studies. In this study, we describe the application of the programs Var-tools designed to predict regulatory variants, and present four case studies to illustrate their usage and applications. In brief, Var-tools facilitate i) obtaining variation information, ii) interconversion of variation file formats, iii) retrieval of sequences surrounding variants, and iv) calculating the change on predicted TF affinity scores between alleles, using motif scanning approaches. Notably, the tools support the analysis of haplotypes. The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa and ten plant genomes. Vart-tools can also be used in command-line with any locally-installed Ensembl genome. Users can input personal collections of variants and motifs, providing flexibility in the analysis.

bioinformatics↗