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GenomeGems: evaluation of genetic variability from deep sequencing data

Sharon Ben-Zvi, Adi Givati, Noam Shomron
2012 BMC Research Notes  
As such, via automatic, clear and accessible presentation of processed Deep Sequencing data, our tool aims to facilitate ranking of genomic SNP calling.  ...  Detection of disease-causing mutations using Deep Sequencing technologies possesses great challenges.  ...  Algorithms were developed for a simple comparison using graphs and tables of data produced from a number of samples, and for a wide and detailed visualization of the Deep Sequencing pre-processed data.  ... 
doi:10.1186/1756-0500-5-338 pmid:22748151 pmcid:PMC3499170 fatcat:bedz7il7krg6ffsufgtzlwytfe

Scientific Visualizations Based on Integrated Model of Text and Picture Comprehension via Eye-tracking

Azam Majooni, Mona Masood, Amir Akhavan
2015 Procedia - Social and Behavioral Sciences  
Analysis of the gaze data and the percentage of the correct answers to the questions indicate that the sequence of picture and text and use of color in the visualizations results in reduction of the cognitive  ...  This study investigates the "color combination effect" and the "sequence of pictures and text effect" in the "Integrated Model of Text and Picture Comprehension" (ITPC) on the formation of the mental model  ...  Acknowledgements This research is supported by the Center for Instructional Technology and Multimedia and the Research University Grant awarded by Universiti Sains Malaysia.  ... 
doi:10.1016/j.sbspro.2015.01.443 fatcat:s6c45dyrgfbk7ojyhpma7kz42a

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system

D. Bannasch
2004 Nucleic Acids Research  
The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation.  ...  We have implemented LIFEdb ( LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on  ...  ACKNOWLEDGEMENTS We thank Patricia McCabe and Lee Bergman for critical reading of the manuscript and Stefanie Bechtel, Anni Duda, Kerstin Hettler and Heike Wilhelm for suggestions on the internal interface  ... 
doi:10.1093/nar/gkh022 pmid:14681468 pmcid:PMC314201 fatcat:jju2pzdgzndn3k4tiiengf4xaa

MVIP: multi-omics portal of viral infection

Zhidong Tang, Weiliang Fan, Qiming Li, Dehe Wang, Miaomiao Wen, Junhao Wang, Xingqiao Li, Yu Zhou
2021 Nucleic Acids Research  
We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc.  ...  We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc.  ...  ACKNOWLEDGEMENTS The authors thank the members in Zhou lab for insightful discussions during the process of this investigation.  ... 
doi:10.1093/nar/gkab958 pmid:34718748 pmcid:PMC8689837 fatcat:c6zabbruprei5dk6ap5wge4k2y

Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation

Caroline Barretto, Cristian Rincón, Anne-Catherine Portmann, Catherine Ngom-Bru
2021 Genes  
However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions.  ...  Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years.  ...  data analysis and reliable results interpretation in the context of whole genome sequencing applied to pathogen source tracking in food industry.  ... 
doi:10.3390/genes12020275 pmid:33671973 pmcid:PMC7919020 fatcat:rz4afnr7kbh3vi2nut4bifiedm

The Translational Genomics Core at Partners Personalized Medicine: Facilitating the Transition of Research towards Personalized Medicine

Ashley Blau, Alison Brown, Lisa Mahanta, Sami Amr
2016 Journal of Personalized Medicine  
The interaction of the TGC with various components of PPM provides it with a unique infrastructure that allows for greater IT and bioinformatics opportunities, such as sample tracking and data analysis  ...  , diverse investigator needs, and high staff turnover.  ...  Author Contributions: Ashley Blau drafted sections 1-4 including tables and graphs, Alison Brown drafted sections 6-7, and all authors contributed to revision and editing of the manuscript.  ... 
doi:10.3390/jpm6010010 pmid:26927185 pmcid:PMC4810389 fatcat:ryiv27zha5c53hao7a3o4ogdgq

Enhort: a platform for deep analysis of genomic positions

Michael Menzel, Peter Koch, Stefan Glasenhardt, Andreas Gogol-Döring
2019 PeerJ Computer Science  
Enhort provides comprehensive yet easy-to-use methods for statistical analysis, visualization, and the adjustment of background models according to experimental conditions and scientific questions.  ...  However, there is no specialized software to investigate integration site profiles of virus integration or transcription factor binding sites by correlating the sites with the diversity of available genomic  ...  Our aim is to accelerate and simplify the data analysis process as well as to standardize it in order to increase reproducibility.  ... 
doi:10.7717/peerj-cs.198 pmid:33816851 pmcid:PMC7924414 fatcat:4ghiamqehngnrpozahhnfdbefu

Dynamic integrity measurement and attestation

Lucas Davi, Ahmad-Reza Sadeghi, Marcel Winandy
2009 Proceedings of the 2009 ACM workshop on Scalable trusted computing - STC '09  
To mitigate return-oriented programming attacks, we propose new runtime integrity monitoring techniques that use tracking instrumentation of program binaries based on taint analysis and dynamic tracing  ...  But they only provide integrity at load-time and are not able to prevent or detect runtime attacks.  ...  The process of the program is then started and the tracking code stores tracking data in the data segment. The tracking code will dynamically update tracking data as tracking events occur.  ... 
doi:10.1145/1655108.1655117 dblp:conf/ccs/DaviSW09 fatcat:4bmgql34zrhwhawj4wk5epth5i

MycoCosm portal: gearing up for 1000 fungal genomes

Igor V. Grigoriev, Roman Nikitin, Sajeet Haridas, Alan Kuo, Robin Ohm, Robert Otillar, Robert Riley, Asaf Salamov, Xueling Zhao, Frank Korzeniewski, Tatyana Smirnova, Henrik Nordberg (+2 others)
2013 Nucleic Acids Research  
MycoCosm is a fungal genomics portal (http://jgi., developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences  ...  MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data.  ...  ACKNOWLEDGEMENTS We thank MycoCosm users for valuable feedback, members of JGI portal group for development of software modules used in MycoCosm and Byoungnam Min for technical assistance.  ... 
doi:10.1093/nar/gkt1183 pmid:24297253 pmcid:PMC3965089 fatcat:rw7f4asps5gu7mu7x2yjiwjph4

Large Scale Audio-Visual Video Analytics Platform for Forensic Investigations of Terroristic Attacks [article]

Alexander Schindler, Martin Boyer, Andrew Lindley, David Schreiber, Thomas Philipp
2018 arXiv   pre-print
Visual object detection and tracking are used to index the content according to relevant concepts.  ...  The platform integrates analytical modules for different input-modalities on a scalable architecture. Videos are analyzed according their acoustic and visual content.  ...  SEC-740754 and the project FLORIDA, FFG Kooperative F&E Projekte 2015, project no. 854768.  ... 
arXiv:1811.11623v1 fatcat:k2uxr3djhrefpmtxt4wi376eyq

New Products

2013 Science  
HUMAN RNA SEQUENCING DATA ANALYSIS The Ingenuity iReport now supports analysis and interpretation of human isoform-level RNA sequencing data.  ...  studies to 3-D investigations.  ... 
doi:10.1126/science.340.6130.382-a fatcat:yrpyqn4bdnbujaqilizf47pqwe

Integrated Genome Browser: visual analytics platform for genomics [article]

Nowlan H. Freese, David C. Norris, Ann E. Loraine
2015 bioRxiv   pre-print
To demonstrate, we describe example visualizations and analyses of data sets from RNA-Seq, ChIP-Seq, and bisulfite sequencing experiments.  ...  discovery process.  ...  Acknowledgements We thank the many developers, testers, and designers who contributed to IGB,  ... 
doi:10.1101/026351 fatcat:rpz3i6u4sbgl7h672rsmp4disy

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

David B Burdick, Chris C Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John Boyle
2010 BMC Bioinformatics  
We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms.  ...  However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.  ...  Authors' contributions SR and DB developed the initial ChIPSeq analysis, and translated that work into a pipeline.  ... 
doi:10.1186/1471-2105-11-377 pmid:20630057 pmcid:PMC2916924 fatcat:woblcip2nrc6nftjxljh4bwori

Path Mapping of Shape Drawings Using Double Integration Technique

Ching Yee Yong, Rubita Sudirman, Nasrul Humaimi Mahmood, Kim Mey Chew
2014 Information Engineering Research Institute procedia  
PCA and double integration technique were used to process and analyze the data. The tracking path was mapped and presented in GUI developed by MATLAB.  ...  A preliminary path tracking experiment was done and a mapping system was developed in this study. Data collection of human activities in this study was focused on different shape of hand drawings.  ...  Acknowledgements The authors would like to express our gratitude to the Universiti Teknologi Malaysia for supporting and funding this study under Research University Grant (Q.J130000.2523.05H37) and MyPhD  ... 
doi:10.1016/j.ieri.2014.09.090 fatcat:6fpuqzwhpbdyvgktbgjzf4v3aa

Neural Integration of Stimulus History Underlies Prediction for Naturalistically Evolving Sequences

Brian Maniscalco, Jennifer L. Lee, Patrice Abry, Amy Lin, Tom Holroyd, Biyu J. He
2018 Journal of Neuroscience  
Here, we studied predictive processing in the human brain using auditory tone sequences that exhibit temporal statistical regularities similar to those found in natural stimuli.  ...  We further show that neural response to a given tone in the sequence reflects integration over the preceding tone sequence and that this history dependence forms the foundation for prediction.  ...  We investigated this question using the following analysis.  ... 
doi:10.1523/jneurosci.1779-17.2017 pmid:29311143 pmcid:PMC5815353 fatcat:73ay4qqnlbcmjj7pcaafvflebu
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