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Ensembl Genomes 2016: more genomes, more complexity

Paul Julian Kersey, James E. Allen, Irina Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay Humphrey, Arnaud Kerhornou (+26 others)
2015 Nucleic Acids Research  
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

Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha (+2 others)
2016 Database: The Journal of Biological Databases and Curation  
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


2016 Biocomputing 2017  
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

William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
2016 Genome Biology  
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

Adrin Jalali, Nico Pfeifer
2016 BMC Genomics  
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

Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole, Ali Braytee, Paul J. Kennedy, Bin Liu
2016 PLoS ONE  
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

Ashok Kumar Dwivedi, Usha Chouhan
2016 Current Science  
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

Rebecca Kaddis Maldonado, Leslie Parent
2016 Viruses  
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

Mang Liang, Tianpeng Chang, Bingxing An, Xinghai Duan, Lili Du, Xiaoqiao Wang, Jian Miao, Lingyang Xu, Xue Gao, Lupei Zhang, Junya Li, Huijiang Gao
2021 Frontiers in Genetics  
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

Myungjin Moon, Kenta Nakai
2016 BMC Genomics  
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

Shayoni Dutta, Spandan Madan, Harsh Parikh, Durai Sundar
2016 BMC Genomics  
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]

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates (+2 others)
2016 bioRxiv   pre-print
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 . 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

Paul Julian Kersey, James E Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu (+34 others)
2017 Nucleic Acids Research  
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

Fotis E. Psomopoulos, Jacques van Helden, Claudine Médigue, Anastasia Chasapi, Christos A. Ouzounis
2020 Microbial Genomics  
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

Shibiao Wan, Junil Kim, Kyoung Jae Won
2020 Genome Research  
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
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