Repertoire ≈ Repertoire
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HMMER web server: 2015 update Open
This FAIRsharing record describes: The profile hidden Markov Model (HMM) calculated from multiple sequence alignment data in this service is stored in Profile HMM save format (usually with ".hmm" extension). It is an ASCII file containing …
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Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data Open
Summary: Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic diversity of the Ig repertoire presents challenges for biologi…
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The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota Open
SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matte…
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A cell atlas of human thymic development defines T cell repertoire formation Open
Thymus development, cell by cell The human thymus is the organ responsible for the maturation of many types of T cells, which are immune cells that protect us from infection. However, it is not well known how these cells develop with a ful…
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VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires Open
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide ran…
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VDJdb: a curated database of T-cell receptor sequences with known antigen specificity Open
The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translati…
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Gender and entrepreneurship research: A review of methodological approaches Open
This article presents the findings of a systematic literature review (SLR) of the gender and entrepreneurship literature published in 18 journals over a 30-year period. The SLR sought to identify methodological trends in the field of gende…
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A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome Open
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclat…
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The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs Open
RNA-binding proteins (RBPs) exert a broad range of biological functions. To explore the scope of RBPs across eukaryotic evolution, we determined the in vivo RBP repertoire of the yeast Saccharomyces cerevisiae and identified 678 RBPs from …
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The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions Open
Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strik…
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The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis Open
The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformat…
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Not a First Language but One Repertoire: Translanguaging as a Decolonizing Project Open
Translanguaging has opened up spaces to recognize the dynamic multilingualism of students in classrooms taught in dominant languages, and problematized concepts such as ‘additive bilingualism’. This article aims to further explore two issu…
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Sentiment Analysis: An Overview from Linguistics Open
Sentiment analysis is a growing field at the intersection of linguistics and computer science that attempts to automatically determine the sentiment contained in text. Sentiment can be characterized as positive or negative evaluation expre…
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The continuous expansion of citizen participation: a new taxonomy Open
The repertoire of political participation in democratic societies is expanding rapidly and covers such different activities as voting, demonstrating, volunteering, boycotting, blogging, and flash mobs. Relying on a new method for conceptua…
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Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses Open
The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I 'interferome' have…
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Naive T Cell Maintenance and Function in Human Aging Open
In studies of immune aging, naive T cells frequently take center stage. Describing the complexity of the human naive T cell repertoire remains a daunting task; however, emerging data suggest that homeostatic mechanisms are robust enough to…
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Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation Open
Significance A hyperinflammatory syndrome reminiscent of toxic shock syndrome (TSS) is observed in severe COVID-19 patients, including children with Multisystem Inflammatory Syndrome in Children (MIS-C). TSS is typically caused by pathogen…
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Decoding the Human Immunoglobulin G-Glycan Repertoire Reveals a Spectrum of Fc-Receptor- and Complement-Mediated-Effector Activities Open
Glycosylation of the immunoglobulin G (IgG)-Fc tail is required for binding to Fc-gamma receptors (FcγRs) and complement-component C1q. A variety of IgG1-glycoforms is detected in human sera. Several groups have found global or antigen-spe…
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Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences Open
The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to g…
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Hydrophobic Fragmental Constant Open
The evolution that has taken place in medicinal chemistry practice as a result of major advances in genomics and molecular biology arising from the Human Genome Project has carried with it an extensive additional working vocabulary that ha…
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Teaching English through pedagogical translanguaging Open
Teaching English has traditionally been associated with a monolingual bias and the exclusive use of English in the classroom is highly recommended in different countries. Nowadays English is widely used to teach academic content and this s…
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High-throughput immune repertoire analysis with IGoR Open
High-throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis, and interpretation of…
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From regions to connections and networks: new bridges between brain and behavior Open
Connections and interactions among distributed brain areas are increasingly recognized as the basis for cognitive operations and a diverse repertoire of behaviors. Analytic advances have allowed for brain connectivity to be represented and…
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Corrigendum: Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Open
Olfactory receptors (ORs) detect odors in the environment, and OR genes constitute the largest multigene family in mammals. Numbers of OR genes vary greatly among species--reflecting the respective species' lifestyles--and this variation i…
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Motor Learning and the Cerebellum Open
Although our ability to store semantic declarative information can nowadays be readily surpassed by that of simple personal computers, our ability to learn and express procedural memories still outperforms that of supercomputers controllin…
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Gene family innovation, conservation and loss on the animal stem lineage Open
Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poo…
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Sensory Repertoire of Bacterial Chemoreceptors Open
SUMMARY Chemoreceptors in bacteria detect a variety of signals and feed this information into chemosensory pathways that represent a major mode of signal transduction. The five chemoreceptors from Escherichia coli have served as traditiona…
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TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: An Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence Open
Genomic intratumor heterogeneity (ITH) may be associated with postsurgical relapse of localized lung adenocarcinomas. Recently, mutations, through generation of neoantigens, were shown to alter tumor immunogenicity through T-cell responses…
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Predictability and hierarchy in <i>Drosophila</i> behavior Open
Significance How an animal chooses to order its activities—moving, grooming, resting, and so on—is essential to its ability to survive, adapt, and reproduce. Here we investigate the temporal pattern of behaviors performed by fruit flies, f…
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Aged neutrophils contribute to the first line of defense in the acute inflammatory response Open
Key Points Aged neutrophils exhibit a distinct, highly reactive phenotype that depends on age-related changes in their molecular repertoire. This specific phenotype of aged neutrophils enables them to serve as “first responders” in inflamm…