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A general approach for discriminative de novo motif discovery from high-throughput data

Jan Grau, Stefan Posch, Ivo Grosse, Jens Keilwagen
2013 Nucleic Acids Research  
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

Federico Agostini, Davide Cirillo, Riccardo Ponti, Gian Tartaglia
2014 BMC Genomics  
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]

Kenzie D. MacIsaac, Ernest Fraenkel
2010 Msphere  
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

Yves A Lussier, Haiquan Li, Mark Maienschein-Cline
2013 Genome Biology  
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

Alexey I Nesvizhskii, Ruedi Aebersold
2004 Drug Discovery Today  
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

Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
2017 Briefings in Bioinformatics  
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]

Niklas Bruse, Simon J. van Heeringen
2018 bioRxiv   pre-print
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

Zizhen Yao, Kyle L. MacQuarrie, Abraham P. Fong, Stephen J. Tapscott, Walter L. Ruzzo, Robert C. Gentleman
2013 Computer applications in the biosciences : CABIOS  
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

Jiantao Shi, Wentao Yang, Mingjie Chen, Yanzhi Du, Ji Zhang, Kankan Wang, Ashok Aiyar
2011 PLoS ONE  
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]

Georges Bedran, Tongjie Wang, Dominika Pankanin, Kenneth Weke, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Catia Pesquita, Hakan Axelson, Ajitha Rajan, David J. Harrison, Aleksander Palkowski (+11 others)
2022 bioRxiv   pre-print
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

Silvia Bottini, David Pratella, Valerie Grandjean, Emanuela Repetto, Michele Trabucchi
2017 Briefings in Bioinformatics  
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

Xuan Li, Yimeng Kong, Qiong-Yi Zhao, Yuan-Yuan Li, Pei Hao
2016 Quantitative Biology  
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

Victoria Berge-Seidl, Lasse Pihlstrøm, Mathias Toft
2021 Scientific Reports  
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

Hongzhi Cao, Alex R Hastie, Dandan Cao, Ernest T Lam, Yuhui Sun, Haodong Huang, Xiao Liu, Liya Lin, Warren Andrews, Saki Chan, Shujia Huang, Xin Tong (+6 others)
2014 GigaScience  
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

Anthony Rhoads, Kin Fai Au
2015 Genomics, Proteomics & Bioinformatics  
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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