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Exact Transcript Quantification Over Splice Graphs

Cong Ma, Hongyu Zheng, Carl Kingsford, Nadia Pisanti
2020 Workshop on Algorithms in Bioinformatics  
This new approach is useful for modeling scenarios where reference transcriptome is incomplete or not available and can be further used in transcriptome assembly or alternative splicing analysis.  ...  The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts.  ...  Guillaume Marçais, Xiangrui Zeng and Dr. Jose Lugo-Martinez for insightful comments on the manuscript. C.K. is a co-founder of Ocean Genomics, Inc.  ... 
doi:10.4230/lipics.wabi.2020.12 dblp:conf/wabi/MaZK20 fatcat:vditzbzcunb2retszcfri3kvfa

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia

N. S. Watson-Haigh, C. A. Shang, M. Haimel, M. Kostadima, R. Loos, N. Deshpande, K. Duesing, X. Li, A. McGrath, S. McWilliam, S. Michnowicz, P. Moolhuijzen (+4 others)
2013 Briefings in Bioinformatics  
Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics.  ...  Nathan S.Watson-Haigh is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery.  ...  Acknowledgements We would like to thank all those who have provided much assistance during the course of running the workshops. In  ... 
doi:10.1093/bib/bbt022 pmid:23543352 pmcid:PMC3771231 fatcat:efbjg73oanew3k37kwdqunyxk4

Evaluation of SMP Shared Memory Machines for Use with In-Memory and OpenMP Big Data Applications

Andrew J. Younge, Christopher Reidy, Robert Henschel, Geoffrey C. Fox
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
Symmetric Multiprocessor Systems (SMPs) have become increasingly important recently among a wide array of disciplines, ranging from Bioinformatics to astrophysics, and beyond.  ...  With the increase in big data computing, the size and scope of traditional commodity server systems is often outpaced.  ...  The authors would also like to acknowledge the FutureSystems team for their help with system setup, and Susan J. Miller for her help in formulating the Trinity de novo assembly data sets.  ... 
doi:10.1109/ipdpsw.2016.133 dblp:conf/ipps/YoungeRHF16 fatcat:czrbuv6etrhodakrpjwbrgqzva

Meeting report: a workshop on Best Practices in Genome Annotation

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme, P. Lamesch, L. I. Hannick
2010 Database: The Journal of Biological Databases and Curation  
Illumina) is used to sequence the transcriptome (known as RNA-Seq). Sequences obtained from RNA-Seq experiments are mapped onto the genome based on uniqueness.  ...  Examples of data that have become available on a larger scale in the last couple of years include proteomics data in the form of Mass Spec and transcriptomics data in the form of RNA-Seq.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

A Scalable Pipeline for Transcriptome Profiling Tasks with On-Demand Computing Clouds

Shayan Shams, Nayong Kim, Xiandong Meng, Ming Tai Ha, Shantenu Jha, Zhong Wang, Joohyun Kim
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
We introduce a pilot-based approach with which scalable data analytics essential for a large RNA-seq data set are efficiently carried out.  ...  method for large-scale RNA-seq data analysis, particularly maximizing merits of Infrastructure as a Service (IaaS) clouds.  ...  We thank Colin Dewey and his group member for helping us for the use of DETONATE. This research was supported in part by the funding from NIH P20 GM103458-10.  ... 
doi:10.1109/ipdpsw.2016.129 dblp:conf/ipps/ShamsKMHJWK16 fatcat:dh6z5bslu5btpcvk6knddcfklu

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes

Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso
2019 BMC Bioinformatics  
Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics.  ...  The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event.  ...  This work performs a detailed multi-omics analysis of large volumes of RNA-seq and DNA methylation data, primarily generated by the SysCol project and published in previous publication [32] .  ... 
doi:10.1186/s12859-019-2681-0 fatcat:xydnzbuhubfctof3vo47gom2ea

Interactive Analysis, Exploration, and Visualization of RNA-Seq Data with SeqCVIBE

Efthimios Bothos, Pantelis Hatzis, Panagiotis Moulos
2022 Methods and Protocols  
Although a large variety of RNA-Seq data analysis software packages has emerged, both open-source and commercial, most fail to simultaneously address the above challenges, while they lack obvious functionalities  ...  The large data sets and the continually expanding applications for which they can be mined, such as the investigation of alternative splicing and others, have created novel challenges for data management  ...  Acknowledgments: The author would like to thank Alexandros Galaras from BSRC 'Alexander Fleming' and Antonis Giakountis, University of Thessaly, for testing SeqCVIBE and useful suggestions.  ... 
doi:10.3390/mps5020027 pmid:35314664 pmcid:PMC8938808 fatcat:6rilbwqyqzfcddfzt6owqxdqkm

Parallelization of the Trinity Pipeline for De Novo Transcriptome Assembly

V. Sachdeva, C.S. Kim, K.E. Jordan, M.D. Winn
2014 2014 IEEE International Parallel & Distributed Processing Symposium Workshops  
By enabling the use of multi-node clusters, this implementation is a significant step towards making de novo transcriptome assembly feasible for ever bigger transcriptome datasets.  ...  This paper details a distributed-memory implementation of Chrysalis, part of the popular Trinity workflow used for de novo transcriptome assembly.  ...  ACKNOWLEDGMENT We would like to thank Brian Haas of the Broad Institute for his advice on Trinity software and source code, as well as providing the datasets for the validation of the hybrid parallelized  ... 
doi:10.1109/ipdpsw.2014.67 dblp:conf/ipps/SachdevaKJW14 fatcat:zntr64pnk5d73pxx7kxdhf4ojq

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

Eliah G. Overbey, Amanda M. Saravia-Butler, Zhe Zhang, Komal S. Rathi, Homer Fogle, Willian A. da Silveira, Richard J. Barker, Joseph J. Bass, Afshin Beheshti, Daniel C. Berrios, Elizabeth A. Blaber, Egle Cekanaviciute (+33 others)
2021 iScience  
Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments.  ...  With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight.  ...  The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care.  ... 
doi:10.1016/j.isci.2021.102361 pmid:33870146 pmcid:PMC8044432 fatcat:6hbtuoun5vgd3bw3rsq2mkwdjm

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data [article]

Eliah G Overbey, Amanda M Saravia-Butler, Zhe Zhang, Komal S Rathi, Homer Fogle, Willian A da Silveira, Richard J Barker, Joseph J Bass, Afshin Beheshti, Daniel C Berrios, Elizabeth A Blaber, Egle Cekanaviciute (+33 others)
2020 biorxiv/medrxiv   pre-print
Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments.  ...  With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight.  ...  The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care.  ... 
doi:10.1101/2020.11.06.371724 fatcat:paiesrg5bnfznl3tbzz7ezr5yu

SITC 2018 workshop report: Immuno-Oncology Biomarkers: State of the Art

Lisa H. Butterfield, on behalf of the Society for Immunotherapy of Cancer Immuno-Oncology Biomarkers: State of the Art workshop speakers, Mary L. Disis, Bernard A. Fox, David R. Kaufman, Samir N. Khleif, Ena Wang
2018 Journal for ImmunoTherapy of Cancer  
Topics discussed included challenges in handling biospecimens, identification and validation of new biomarkers, data sharing, and collaborating across disciplines to advance biomarker development.  ...  To address recent progress and hurdles around cancer biomarker development and utilization, the Society for Immunotherapy of Cancer (SITC) convened a workshop, "Immuno-Oncology Biomarkers: State of the  ...  Availability of data and materials Not applicable.  ... 
doi:10.1186/s40425-018-0453-4 fatcat:ihybil7iwzeafd7pbwimvmytyq

Data Standards for Omics Data: The Basis of Data Sharing and Reuse [chapter]

Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone, Christian J. Stoeckert, Chris F. Taylor, Ronald Taylor, Catherine A. Ball
2011 Msphere  
Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.  ...  The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards.  ...  results from such data and others.  ... 
doi:10.1007/978-1-61779-027-0_2 pmid:21370078 pmcid:PMC4152841 fatcat:5633yzznv5bijnxtw33dwtm7ne

transPLANT Resources for Triticeae Genomic Data

Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M. Bolser, Kai C. Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer (+17 others)
2016 The Plant Genome  
integration of data from distributed resources.  ...  Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting  ...  EBI acknowledges funding from the United Kingdom Biotechnology and Biological Sciences Research Council grants BB/ I008071/1 and BB/J00328X/1, and grant 52930112 from the United States National Science  ... 
doi:10.3835/plantgenome2015.06.0038 pmid:27898761 fatcat:qbt3ggpfgvbz3okorau7zvsnca

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
We used an existing gene expression atlas (right) to link single-cell RNA-seq data (left) from cells extracted from the developing brain of P. dumerilii (top left) with the spatial coordinates.  ...  expression modules and cell states from the new flood of single cell RNA-sequencing data.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability

Bastian Schiffthaler, Myrto Kostadima, Nicolas Delhomme, Gabriella Rustici, Francis Ouellette
2016 PLoS Computational Biology  
Embarking on developing new training materials is challenging for many reasons.  ...  The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for  ...  Acknowledgments The authors wish to thank Matt Drew, from The Genome Analysis Centre (TGAC), and Cathy Hemmings, from the Department of Genetics of the University of Cambridge, for the support with the  ... 
doi:10.1371/journal.pcbi.1004937 pmid:27309738 pmcid:PMC4910983 fatcat:tqu3o5qzizddxgezlvq7glbksu
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