Annotation extension

DNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and progression of a tumor represents a significant challenge.

11p vibransone 28-03-2024 2 2   Download

Ebook "Calcium in human health" have had great success because each volume has the consistent overriding mission of providing health professionals with texts that are essential because each includes (1) a synthesis of the state of the science; (2) timely, in-depth reviews by the leading researchers in their respective fields; (3) extensive, - to-date fully annotated reference lists; (4) a detailed index; (5) relevant tables and figures; (6) identification of paradigm shifts and the consequences; (7) virtually no overlap of information between chapters, but targeted, interchapter referrals; ...

442p manmanthanhla0201 27-02-2024 5 2   Download

Continued part 1, part 2 of ebook "PHPUnit manual: Release latest" provides readers with contents including: logging; extending PHPUnit; assertions; annotations; the XML configuration file; write custom assertions;...

98p tieulangtran 28-09-2023 1 1   Download

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results.

14p viaristotle 29-01-2022 11 0   Download

To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validated driver fusions including internal tandem duplications and other noncanonical events in 170 pediatric cancer transcriptomes.

18p viarchimedes 26-01-2022 11 0   Download

The first comprehensive checklist of mayflies (Ephemeroptera) of Georgia is provided based on literature data supplemented by our unpublished data, including extensive samples in 2013–2017, works with the collections and types, faunistic observations, and taxonomical contributions. Records of 75 species are provided, with one species reported as a new finding for the country. Notes about the taxonomic status of several species are given. The present contribution represents the first publication of this kind for mayflies within the whole Caucasus area.

11p dolomite36 30-12-2021 9 0   Download

The CBL-interacting protein kinase (CIPK) gene family plays important roles in plant growth, development, and responses to abiotic stresses. To date, the CIPKs have been extensively identified and characterized in various plants. However, there have been few studies on CIPKs in Dimocarpus longan Lour (D. longan). In this study we identified eight putative CIPKs in D. longan (DlCIPKs) according to RNA-seq data.

13p tudichquannguyet 29-11-2021 5 1   Download

Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria.

11p vitzuyu2711 29-09-2021 9 1   Download

Mycobacterium tuberculosis (MTB) is a common bacterium causing tuberculosis and remains a major pathogen for mortality. Although the MTB genome has been extensively explored for two decades, the functions of 27% (1051/3906) of encoded proteins have yet to be determined and these proteins are annotated as hypothetical proteins.

10p visilicon2711 20-08-2021 7 1   Download

The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments.

6p viwyoming2711 16-12-2020 6 0   Download

The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data.

11p vikentucky2711 26-11-2020 11 1   Download

With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant calling, it has been found that a non-negligible proportion of the identified indel variants might be false positives due to sequencing errors, artifacts caused by ambiguous alignments, and annotation errors.

10p vikentucky2711 26-11-2020 11 0   Download

Biological data has grown explosively with the advance of nextgeneration sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function prediction can help wet labs formulate biological hypotheses and prioritize experiments.

16p vikentucky2711 24-11-2020 12 2   Download

Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms.

13p vioklahoma2711 19-11-2020 11 1   Download

Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools.

7p vioklahoma2711 19-11-2020 11 1   Download

Analysis of large genomic datasets along with their accompanying clinical information has shown great promise in cancer research over the last decade. Such datasets typically include thousands of samples, each measured by one or several high-throughput technologies (‘omics’) and annotated with extensive clinical information.

10p vicolorado2711 23-10-2020 11 1   Download

This paper describes POS tagging experiments with semi-supervised training as an extension to the (supervised) averaged perceptron algorithm, first introduced for this task by (Collins, 2002). Experiments with an iterative training on standard-sized supervised (manually annotated) dataset (106 tokens) combined with a relatively modest (in the order of 108 tokens) unsupervised (plain) data in a bagging-like fashion showed significant improvement of the POS classification task on typologically different languages, yielding better than state-of-the-art results for English and Czech (4.

9p bunthai_1 06-05-2013 37 1   Download

We describe the ongoing construction of a large, semantically annotated corpus resource as reliable basis for the largescale acquisition of word-semantic information, e.g. the construction of domainindependent lexica. The backbone of the annotation are semantic roles in the frame semantics paradigm. We report experiences and evaluate the annotated data from the first project stage. On this basis, we discuss the problems of vagueness and ambiguity in semantic annotation.

8p bunbo_1 17-04-2013 42 2   Download

This paper defines a generative probabilistic model of parse trees, which we call PCFG-LA. This model is an extension of PCFG in which non-terminal symbols are augmented with latent variables. Finegrained CFG rules are automatically induced from a parsed corpus by training a PCFG-LA model using an EM-algorithm. Because exact parsing with a PCFG-LA is NP-hard, several approximations are described and empirically compared. In experiments using the Penn WSJ corpus, our automatically trained model gave a per40 formance of 86.

8p bunbo_1 17-04-2013 35 2   Download

This paper presents recent extensions to Poliqarp, an open source tool for indexing and searching morphosyntactically annotated corpora, which turn it into a tool for indexing and searching certain kinds of treebanks, complementary to existing treebank search engines. In particular, the paper discusses the motivation for such a new tool, the extended query syntax of Poliqarp and implementation and efficiency issues.

4p hongvang_1 16-04-2013 39 1   Download