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A general approach for discriminative de novo motif discovery from high-throughput data
2013
Nucleic Acids Research
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Here, we propose Dimont, a general approach for fast and accurate de-novo motif discovery from high-throughput data. ...
Since the emergence of high-throughput techniques like ChIP-seq, ChIP-exo, and protein binding microarrays (PBMs), the focus of de-novo motif discovery has shifted to runtime and accuracy on large data ...
doi:10.1093/nar/gkt831
pmid:24057214
pmcid:PMC3834837
fatcat:bgtukeej75hu5ddkzhfa3itqnq
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
2014
BMC Genomics
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The large amount of data produced by high-throughput sequencing poses new computational challenges. ...
SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences and (iii) an easy-to-use web-server interface. ...
We also acknowledge support from the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017' (SEV-2012-0208). ...
doi:10.1186/1471-2164-15-925
pmid:25341390
pmcid:PMC4223730
fatcat:ywfaywlgmjfgfjhpu3hyivbufi
Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors
[chapter]
2010
Msphere
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In this chapter we review the tools, workflow, and common pitfalls of such analyses, and recommend strategies for effective motif discovery from these data. ...
Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis ...
After identification of bound regions from the experiment, motif hypotheses are generated using de novo motif discovery algorithms or assembled from databases. ...
doi:10.1007/978-1-60761-854-6_11
pmid:20827592
pmcid:PMC3922641
fatcat:u4e3puf5p5av3fcxb27rl6ltei
Conquering computational challenges of omics data and post-ENCODE paradigms
2013
Genome Biology
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Tools for effi cient and accurate analysis of newly generated high-throughput data are continuing to be developed. ...
Henry CM Leung (Th e University of Hong Kong, China) described a de novo RNA-seq assembler, IDBA-tran, designed to remove assembly paths of de Bruijn graphs associated with sequencing errors and for merging ...
Acknowledgements This work has been supported in part by the University of Illinois Cancer Center, the University of Illinois CCTS (UL1TR000050) and The Institute for Interventional Health Informatics. ...
doi:10.1186/gb-2013-14-8-310
pmid:23998801
pmcid:PMC4053832
fatcat:csdndkvprrf7fea2ybljmgezfe
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS
2004
Drug Discovery Today
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Tandem mass spectrometry has been used increasingly for high-throughput analysis of complex protein samples. ...
A major challenge lies in the consistent, objective and transparent analysis of the large amounts of data generated by such experiments and in their dissemination and publication. ...
Acknowledgements This work was funded in part by Federal funds from the National Heart, Lung and Blood Institute at the National Institutes of Health (contract number N01-HV-28179). ...
doi:10.1016/s1359-6446(03)02978-7
pmid:14960397
fatcat:nra3rzyzl5atlcrsudldfrftca
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data
2017
Briefings in Bioinformatics
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The purpose of this study is to review existing motif-finding methods for ChIP-seq data from an algorithmic perspective and provide new computational insight into this field. ...
to specific biological demands, including discriminative motif finding and cofactor motifs analysis. ...
It provides high-throughput motif signals and allows genomescale discovery in a cell. ...
doi:10.1093/bib/bbx026
pmid:28334268
fatcat:m4kvr736ojfz3jtwgxh6euisua
GimmeMotifs: an analysis framework for transcription factor motif analysis
[article]
2018
bioRxiv
pre-print
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Using our de novo motif discovery pipeline we find large differences in performance between de novo motif finders on ChIP-seq data. ...
It now includes tools for de novo motif discovery, motif scanning and sequence analysis, motif clustering, calculation of performance metrics and visualization. ...
New approaches and algorithms for de novo motif discovery continue to be published, however, many of them are not tested on more than a few datasets. ...
doi:10.1101/474403
fatcat:a4rzr4ti2rf3tpi2yub3pyjt6e
Discriminative motif analysis of high-throughput dataset
2013
Computer applications in the biosciences : CABIOS
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Lastly, we demonstrate discovery of key TF motifs involved in tissue specification by examination of high-throughput DNase accessibility data. ...
Motivation: High-throughput ChIP-seq studies typically identify thousands of peaks for a single transcription factor (TF). ...
ACKNOWLEDGEMENTS The authors thank Yi Cao, Deepayan Sarkar and Michael Lawrence for helpful discussion. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btt615
pmid:24162561
pmcid:PMC3957073
fatcat:5ctlxbuziza6jhuqzmkrtuwznm
AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses
2011
PLoS ONE
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Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIPchip/seq experiments. ...
We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous. ...
Elisabeth Tillier for the helpful discussion and critical reading of the manuscript. ...
doi:10.1371/journal.pone.0024576
pmid:21931761
pmcid:PMC3171486
fatcat:zpin7d2mtvf2jkozoo7zhkepqe
A comprehensive library of canonical and non-canonical MHC class I antigens for cancer vaccine development
[article]
2022
bioRxiv
pre-print
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Here we release COD-dipp, a cancer vaccine toolkit as a web-application (www.proteogenomics.ca/codipp) and open-source high-throughput resource (upon peer-review). ...
We suggest a vaccine design approach using 140,966 highly immune-visible regions of the genome annotated by their expression and haplotype frequency in the human population. ...
Acknowledgments The International Centre for Cancer Vaccine Science project is carried out within the International Research Agendas programme of the Foundation for Polish Science co-financed by the European ...
doi:10.1101/2022.01.13.475872
fatcat:oqfnbu6t4rcoln2wdxwwt2nu7q
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications
2017
Briefings in Bioinformatics
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Cross-Linking Immunoprecipitation associated to high-throughput sequencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell ...
In this review, we summarize and discuss the most recent computational methods for CLIP-seq analysis, and discuss their impact on Ago2/miRNA-binding site identification and prediction with a regard toward ...
Funding The FRM (grant #DEQ20140329551) and ANR through the 'Investments for the Future' # ANR-11-LABX-0028-01 (LABEX SIGNALIFE) (to M.T.). The FRM (ING20140129224) (to E.R.). ...
doi:10.1093/bib/bbx063
pmid:28605404
fatcat:ea6kui4cwravzdizlw6vcphri4
De novo assembly of transcriptome from next-generation sequencing data
2016
Quantitative Biology
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A multi-k-mer strategy balancing efficiency and sensitivity is discussed and highly recommended for de novo transcriptome assembly. ...
Reconstruction of transcriptome by de novo assembly from next generation sequencing (NGS) short-sequence reads provides an essential mean to catalog expressed genes, identify splicing isoforms, and capture ...
Strategies for preprocessing and filtering sequence reads High-throughput sequencing data are often contaminated with artificial elements, generated from library construction and/or PCR amplification. ...
doi:10.1007/s40484-016-0069-y
fatcat:zo2zm2adifdaddnfth6aks5hua
Integrative analysis identifies bHLH transcription factors as contributors to Parkinson's disease risk mechanisms
2021
Scientific Reports
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The involvement of transcriptional networks was explored in neurons of the superior temporal cortex based on the location of candidate transcription factor motifs identified by two de novo motif discovery ...
Our findings show that cortical neurons are likely mediators of genetic risk for PD. ...
Acknowledgements We thank the investigators and participants who have contributed to the generation of data made accessible in publicly available resources that was analysed in this study. ...
doi:10.1038/s41598-021-83087-2
pmid:33568722
pmcid:PMC7875985
fatcat:iz6674y3sfewto7mveugvx35l4
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
2014
GigaScience
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from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. ...
To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long ...
Acknowledgements We wish to recognize BGI-Shenzhen's sequencing platform for generating the data in this study. We thank the faculty and staff at BGI-Shenzhen who contributed to this project. ...
doi:10.1186/2047-217x-3-34
pmid:25671094
pmcid:PMC4322599
fatcat:2bmmyvjnqjhthozkd5pnnyqgge
PacBio Sequencing and Its Applications
2015
Genomics, Proteomics & Bioinformatics
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The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. ...
In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. ...
Acknowledgments We would like to thank Jason Weirather and Eno-Abasi Augustine-Akpan for critical reading of the manuscript. ...
doi:10.1016/j.gpb.2015.08.002
pmid:26542840
pmcid:PMC4678779
fatcat:4rymtez34nd45dgvnw3gia7wsu
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