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Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns

H. Nagasaki, M. Arita, T. Nishizawa, M. Suwa, O. Gotoh
2006 Bioinformatics  
Motivation: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms  ...  splicing patterns on demand.  ...  Japan and by Institute for Bioinformatics Research and Development (BIRD) of Japan Science and Technology Agency (JST).  ... 
doi:10.1093/bioinformatics/btl067 pmid:16500940 fatcat:wd4h5aulrndeti5cvtetfwatwu

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town
2005 BMC Biology  
Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified  ...  Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories.  ...  Acknowledgements We would like to thank all past members of the Arabidopsis annotation group at TIGR, the IT group led by Vadim Sapiro, the database managers Michael Heaney and Susan Lo, and many members  ... 
doi:10.1186/1741-7007-3-7 pmid:15784138 pmcid:PMC1082884 fatcat:jw5tyx6eubea7fb5yczxnc4ynq

Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events

Dirk Holste, Uwe Ohler
2008 PLoS Computational Biology  
Citation: Holste D, Ohler U (2008) Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PLoS Comput Biol 4(1): e21.  ...  Abbreviations: 39ss, 39 splice site; 59ss, 59 splice site; A5E, alternative 59ss exon; A3E, alternative 39ss exon; AS, alternative splicing or alternatively spliced; cDNA, complementary DNA; ESE (ESS),  ...  Yeo and M. Stadler for helpful comments on the manuscript. Author contributions. DH and UO wrote the paper. Funding.  ... 
doi:10.1371/journal.pcbi.0040021 pmid:18225947 pmcid:PMC2217580 fatcat:kic2crv6fnghvaldx2v3j2xjde

The importance of identifying alternative splicing in vertebrate genome annotation

Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer Harrow
2012 Database: The Journal of Biological Databases and Curation  
While alternative splicing (AS) can potentially expand the functional repertoire of vertebrate genomes, relatively few AS transcripts have been experimentally characterized.  ...  We use information about the predicted functional potential and structural properties of every AS transcript annotated at a protein-coding or non-coding locus to place them into one of eleven subclasses  ...  Introduction The alternative splicing (AS) of RNA transcripts can produce multiple mature transcripts from a single locus and the vast majority of human multi-exon loci are subject to AS (1, 2) .  ... 
doi:10.1093/database/bas014 pmid:22434846 pmcid:PMC3308168 fatcat:26zcrc2mijfvvbmk5ar3l4nqre

Exploration of predictive and prognostic alternative splicing signatures in lung adenocarcinoma using machine learning methods

Qidong Cai, Boxue He, Pengfei Zhang, Zhenyu Zhao, Xiong Peng, Yuqian Zhang, Hui Xie, Xiang Wang
2020 Journal of Translational Medicine  
Background Alternative splicing (AS) plays critical roles in generating protein diversity and complexity. Dysregulation of AS underlies the initiation and progression of tumors.  ...  The splicing network constructed of survival-related SFs and ASEs depicts regulatory relationships between them.  ...  Acknowledgements The authors thank Professor Yongguang Tao for helpful comments and suggestions.  ... 
doi:10.1186/s12967-020-02635-y pmid:33287830 fatcat:rv37rudtdzhcri23xhrgvzoy6y

Genomewide comparative analysis of alternative splicing in plants

B.-B. Wang, V. Brendel
2006 Proceedings of the National Academy of Sciences of the United States of America  
We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at͞ASIP). exon skipping  ...  ͉ intron retention ͉ non-sense-mediated decay ͉ spliced alignment ͉ conserved alternative splicing Conflict of interest statement: No conflicts declared.  ...  We thank Wei Huang for help with statistical analysis and Robert Fluhr, Qunfeng Dong, Yuanbin Ru, and Michael Sparks for critical reading of the manuscript.  ... 
doi:10.1073/pnas.0602039103 pmid:16632598 pmcid:PMC1459036 fatcat:kw7eioonxncwla3hxrol7qnoju

A hitchhiker's guide to expressed sequence tag (EST) analysis

S. H. Nagaraj, R. B. Gasser, S. Ranganathan
2006 Briefings in Bioinformatics  
An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping.  ...  Extensive computational strategies have been developed to organize and analyse both small-and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as  ...  Acknowledgements Partial funding from Genetic Technologies Limited and the Australian Research Council (LP0667795), and the award of a Macquarie University research scholarship to S.H.N. is acknowledged  ... 
doi:10.1093/bib/bbl015 pmid:16772268 fatcat:wmumdszmnjalhnw5doqjzicxue

Algorithms For Next-Generation Sequencing Data [chapter]

Costas S. Iliopoulos, Solon P. Pissis
2013 Biological Knowledge Discovery Handbook  
(TBoN), 828 Tokenization of biomedical knowledge, 843 divide natural language texts, 843 process of breaking text, 843 tokens, 843 Transcript-initial cassette (TIC) exons, 24, 25 Transcription, 5, 379  ...  , see Genome data visualization major structure patterns, sequence, 1078 number of leucines on a 20-amino-acid, ELAND, SOAP, FM and MAQ indexes, 253 multiplex polony sequencing protocol, 252 partitioning  ...  Random access memory, 232, 994, 1018 , 1055 analysis , alternative, 9 correlation of input transcript numbers and, 27 databases, 12-14 genomic and transcriptomic sequence analyses, 12 mechanism, 10  ... 
doi:10.1002/9781118617151.ch11 fatcat:khmmb6ga6zctjdflhlf764ri6u

PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

Steven Verbruggen, Elvis Ndah, Wim Van Criekinge, Siegfried Gessulat, Bernhard Kuster, Mathias Wilhelm, Petra Van Damme, Gerben Menschaert
2019 Molecular & Cellular Proteomics  
frames, 5' and 3' extended and truncated proteoforms, single amino acid variants, splice variants and translation products of so-called noncoding regions.  ...  Some of the most important upgrades include P-site offset calculation during mapping, comprehensive data pre-exploration, the introduction of two alternative proteoform calling strategies and extended  ...  It illustrates the benefit of including alternative splice isoforms in the search space.  ... 
doi:10.1074/mcp.ra118.001218 pmid:31040227 pmcid:PMC6692777 fatcat:2dcxmgxfnffh7hfexjnfaerqbe

Functional analysis by minigene assay of putative splicing variants found in Bardet-Biedl syndrome patients

María Álvarez-Satta, Sheila Castro-Sánchez, Guillermo Pousada, Diana Valverde
2017 Journal of Cellular and Molecular Medicine  
Functional studies of variants identified in BBS and ALMS patients are essential for their proper classification and subsequent genetic counselling and could also be the start point for new therapeutic  ...  We found discordance between bioinformatics analysis and experimental data when comparing wild-type and mutant constructs.  ...  Acknowledgements We fully appreciate the ongoing cooperation of patients with BBS and their families in our research projects, and also the collaboration of all colleagues that provided us with reagents  ... 
doi:10.1111/jcmm.13147 pmid:28502102 pmcid:PMC5618670 fatcat:5ry3vtjplbgsvgsnxbp3tdyxya

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Girum Fitihamlak Ejigu, Jaehee Jung
2020 Biology  
We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation.  ...  This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology9090295 pmid:32962098 pmcid:PMC7565776 fatcat:gdaxbwygqnaapiqisyf56ajpea

Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning

Guishan Zhang, Yiyun Deng, Qingyu Liu, Bingxu Ye, Zhiming Dai, Yaowen Chen, Xianhua Dai
2020 Frontiers in Genetics  
Experiments on public and our constructed datasets show that the proposed algorithms outperform the available state-of-the-art methods. circLGB is available at  ...  transcriptional regulation.  ...  In addition, circRNAs can also be involved in transcriptional regulation (TR) and alternative splicing (Zhang et al., 2013; Conn et al., 2017) . circRNAs may even have translation potential . circRNAs  ... 
doi:10.3389/fgene.2020.00655 pmid:32849764 pmcid:PMC7396586 fatcat:sgre27znyrasddkjhkfhdpy3oe

The functional modulation of epigenetic regulators by alternative splicing

Sergio Lois, Noemí Blanco, Marian Martínez-Balbás, Xavier de la Cruz
2007 BMC Genomics  
Third, because of the availability, in public databases, of a large amount of unexplored information on alternative splicing patterns of chromatinmodifying enzymes is available in public databases.  ...  Due to the different procedures followed in the different databases to obtain alternative splicing information we expect a complementary coverage of the alternative splicing patterns.  ...  Most of the data were obtained after querying the ENSEMBL [44] and NCBI Gene databases [43] .  ... 
doi:10.1186/1471-2164-8-252 pmid:17651478 pmcid:PMC1949830 fatcat:fzwwgwlfwzcnziowvvngb2tgba

C. elegans network biology: a beginning

Fabio Piano
2006 WormBook  
Tiling arrays -now in use for human (Bertone et al., 2004 ), Drosophila (Stolc et al., 2004 , and Arabidopsis (Yamada et al., 2003) -should soon reveal alternative splicing patterns and expressed non-coding  ...  Recently a formal classification system linked to an automated image analysis system was developed that is capable of automatically gathering many behavioral and gross morphological phenotypic parameters  ... 
doi:10.1895/wormbook.1.118.1 pmid:18050437 fatcat:sryljpplivctfiwxvvmjuzwgf4

Influenza Research Database: An integrated bioinformatics resource for influenza virus research

Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken (+16 others)
2016 Nucleic Acids Research  
predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype  ...  The Influenza Research Database (IRD) is a U.S.  ...  M42 and NS3 have very rare and strict alternative splicing, and are therefore only found in 0.2% and 0.1% of influenza strains, respectively.  ... 
doi:10.1093/nar/gkw857 pmid:27679478 pmcid:PMC5210613 fatcat:5e2dsqkibbe63dbu3epmgzgeja
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