A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Ensembl Genomes 2016: more genomes, more complexity
2015
Nucleic Acids Research
Preserved Fulltext
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context ...
of the Ensembl project (http://www.ensembl. org). ...
This model, of specialized sites with a focus on specific domains linked to Ensembl and Ensembl Genomes through integrated search and comparative genomics, is likely to become more common as certain domains ...
doi:10.1093/nar/gkv1209
pmid:26578574
pmcid:PMC4702859
fatcat:n3oewab7gvei5fbg6wfrx2ydaa
Ensembl comparative genomics resources
2016
Database: The Journal of Biological Databases and Curation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here ...
The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. ...
We also thank the rest of the Ensembl team, especially the members of Ensembl Outreach for supporting the users and helping with the documentation and tutorials. ...
doi:10.1093/database/baw053
pmid:27141089
pmcid:PMC4852398
fatcat:sluvrnnct5dpxmd7grm3z76m3y
LEARNING PARSIMONIOUS ENSEMBLES FOR UNBALANCED COMPUTATIONAL GENOMICS PROBLEMS
2016
Biocomputing 2017
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
eukaryotic genomes. ...
We develop three RL-based strategies for constructing ensembles and analyze their results on two unbalanced computational genomics problems, namely the prediction of protein function and splice sites in ...
We thank the Icahn Institute for Genomics and Multiscale Biology and the Minerva supercomputing team for their financial and technical support. We also thank Om P. ...
doi:10.1142/9789813207813_0028
pmid:27896983
pmcid:PMC5147733
fatcat:t6fvnhzmmfdl7j2tthc27lssbm
The Ensembl Variant Effect Predictor
2016
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. ...
The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs. ...
A variant may have more than one alternative nonreference allele and may overlap more than one transcript or regulatory region. ...
doi:10.1186/s13059-016-0974-4
pmid:27268795
pmcid:PMC4893825
fatcat:lziduun2xnhpteudwo3utn4nyi
Interpretable per case weighted ensemble method for cancer associations
2016
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Bayesian hierarchical mixtures of experts takes a more similar approach, but the method is complex, and it has a high time complexity to train the architecture of the hierarchy [8] . ...
Conclusions Machine learning has become more and more popular in many real world scenarios for making sense of large collections of facts. ...
doi:10.1186/s12864-016-2647-9
pmid:27435615
pmcid:PMC4952276
fatcat:d4u2uyhvabgmfb6igsedh6kxoi
Ensemble Feature Learning of Genomic Data Using Support Vector Machine
2016
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
This paper introduces an ensemble SVM-Recursive Feature Elimination (ESVM-RFE) for gene selection that follows the concepts of ensemble and bagging used in random forest but adopts the backward elimination ...
Ensemble and bagging methods have been shown to work effectively in the process of gene selection and classification. ...
To bolster our methodology, we employ SVD for visual analytic with a goal to interrogate this complex and voluminous genomic data. ...
doi:10.1371/journal.pone.0157330
pmid:27304923
pmcid:PMC4909287
fatcat:uv4ksekyf5f25ehkunb5gz237y
Genome-Scale Classification of Recombinant and Non-Recombinant HIV-1 Sequences Using Artificial Neural Network Ensembles
2016
Current Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
This article presents ensemble models of artificial neural network for the classification of recombinant and non-recombinant sequences of HIV-1 genome. ...
Genetic recombination and high rate of mutations in the HIV-1 genome increase the diversity of HIV-1, which allows viruses to escape more easily from host immune system or develop resistance for antiretroviral ...
It can be envisioned that phylogenetic analysis based on whole genomes is more trustworthy than those based on small segments of the HIV-1 genome. ...
doi:10.18520/cs/v111/i5/853-860
fatcat:yyv6kkg3kzgwdlu6lafrqpzcqe
Orchestrating the Selection and Packaging of Genomic RNA by Retroviruses: An Ensemble of Viral and Host Factors
2016
Viruses
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
and the possible subcellular sites of genomic RNA dimerization and selection by Gag. ...
Infectious retrovirus particles contain two copies of unspliced viral RNA that serve as the viral genome. ...
Gag and the vRNA may first interact: (1) in the nucleus;
© 2016 by the authors; licensee MDPI, Basel, Switzerland. ...
doi:10.3390/v8090257
pmid:27657110
pmcid:PMC5035971
fatcat:qmakgtqm35aa5pzbu5pcpv47ha
A Stacking Ensemble Learning Framework for Genomic Prediction
2021
Frontiers in Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
To improve the genomic predictions, we constructed a stacking ensemble learning framework (SELF), integrating three machine learning methods, to predict genomic estimated breeding values (GEBVs). ...
Except for the milk fat percentage (MFP) traits, of the German Holstein dairy cattle dataset, SELF was more robust than BayesB in all remaining traits. ...
Therefore, the exploration of more robust genomic prediction methods is a well-identified searched by breeders. ...
doi:10.3389/fgene.2021.600040
pmid:33747037
pmcid:PMC7969712
fatcat:772jktwrrbg2fhwligpow6t6ju
Stable feature selection based on the ensemble L 1 -norm support vector machine for biomarker discovery
2016
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Owing to the presence of high-throughput technologies, genomic data, such as microarray data and RNA-seq, have become widely available. ...
We apply an ensemble L 1 -norm support vector machine to efficiently reduce irrelevant features, considering the stability of features. ...
Declarations This article has been published as part of BMC Genomics Volume 17 Supplement 3, 2016: 15th International Conference On Bioinformatics (INCOB 2016). ...
doi:10.1186/s12864-016-3320-z
pmid:28155664
pmcid:PMC5260053
fatcat:ozzax5x4jzebldcstgtizfl45a
An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA
2016
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. ...
The modeling and simulation results assuming synergistic mode of binding obtained from this subset were used to train an ensemble micro neural network. ...
Simulation studies for the same sample set affirm stability for complexes with higher binding affinity and more negative docking score [34] . ...
doi:10.1186/s12864-016-3323-9
pmid:28155662
pmcid:PMC5260015
fatcat:zwm7smpcjjf4fdqi547hhysugy
Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
[article]
2016
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. ...
Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA sequencing ...
The copyright holder for this preprint . http://dx.doi.org/10.1101/087239 doi: bioRxiv preprint first posted online Nov. 11, 2016; genomes, more complexity. Nucleic Acids Res., 44, D574-D580. . ...
doi:10.1101/087239
fatcat:td5frmusmfal5pa56hjnonv44u
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
2017
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl ...
These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. ...
NEW AND IMPROVED GENOME ASSEMBLIES Ensembl Genomes has continued to grow in 2016 and 2017 (see Table 1 ). ...
doi:10.1093/nar/gkx1011
pmid:29092050
pmcid:PMC5753204
fatcat:mmgammsp3fcrpdfrwprhsxl4g4
Ancestral state reconstruction of metabolic pathways across pangenome ensembles
2020
Microbial Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny. ...
The method is evaluated with a selected benchmark set of pathways against collections of genome sequences from key data resources. ...
Overall, this case signifies the challenge of exact pathway detection in complex pangenomes and the need for more accurate, taxonspecific values for the threshold of detection. ...
doi:10.1099/mgen.0.000429
pmid:32924924
fatcat:wcwho3jxlzavnlkafvoncc7kjy
SHARP: hyper-fast and accurate processing of single-cell RNA-seq data via ensemble random projection
2020
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Particularly, for large-size data sets (more than 40,000 cells), SHARP runs faster than other competitors while maintaining high clustering accuracy and robustness. ...
To process large-scale single-cell RNA-sequencing (scRNA-seq) data effectively without excessive distortion during dimension reduction, we present SHARP, an ensemble random projection-based algorithm that ...
; Goolam et al. 2016; Wang et al. 2016; 10x Genomics 2017; Enge et al. 2017; Montoro et al. 2018; Park et al. 2018) . ...
doi:10.1101/gr.254557.119
pmid:31992615
pmcid:PMC7050522
fatcat:6fxq73c3szf5lpcfu6efxhjw6q
« Previous
Showing results 1 — 15 out of 22,082 results