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Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data
2006
Bioinformatics
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Its primary application is in normalization of array data as well as subsequent identification of 'enriched targets', e.g. differentially expressed genes in expression profiling arrays and enriched sites ...
We show how to accommodate the unique characteristics of ChIP-on-chip data, where the set of 'enriched targets' is large, asymmetric and whose proportion to the whole data varies locally. ...
Terry Papoutsakis and Carles Paredes for their help in interpreting the data appearing in their original paper on pSOL1 genes; James Glimm and Jacob Schwartz for commenting on earlier versions of this ...
doi:10.1093/bioinformatics/btl606
pmid:17164284
fatcat:4rhr7wj4gbhmzp64ixlne3njmm
Multiscale representation of genomic signals
2014
Nature Methods
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We developed a multiscale framework to analyze and visualize the information content of genomic signals. ...
(ChIP-seq) measurements and we observed that gene expression differences in colorectal cancer are not most strongly related to gene body methylation, but rather to methylation patterns that extend beyond ...
ChIP-seq data was produced by T. Stolyar, G. S. ...
doi:10.1038/nmeth.2924
pmid:24727652
pmcid:PMC4040162
fatcat:bpldem7ywveqphuwpf2af6dw7u
HiGlass: web-based visual exploration and analysis of genome interaction maps
2018
Genome Biology
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We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks ...
HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform. ...
Availability of data and materials This paper used data from two published studies, the data for which are on GEO. Note that the data from Rao et al. ...
doi:10.1186/s13059-018-1486-1
pmid:30143029
pmcid:PMC6109259
fatcat:ifl7dumnfje4zkfcex7gyo4qfa
BioCyBig: A Cyberphysical System for Integrative Microfluidics-Driven Analysis of Genomic Association Studies
2016
IEEE Transactions on Big Data
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This framework will be based on the integration of CPS with microfluidic biochips and cloud computing. ...
A case study from cancer research is discussed to explain the significance of our framework in promoting coordinated genomic studies. ...
Biological Pathway of Gene Expression and Omic Data Genomic association mechanisms and the associated omic data are linked to different stages of the gene-expression pathway. ...
doi:10.1109/tbdata.2016.2643683
fatcat:u5ws25dwdnbmbj4bb4qyppbl2a
HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps
[article]
2017
bioRxiv
pre-print
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We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks ...
HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform. ...
We thank Geoffrey Fudenberg for feedback on the manuscript. We also acknowledge important suggestions and feedback from members of the Park Lab at Harvard Medical School, the Mirny Lab at MIT, and the ...
doi:10.1101/121889
fatcat:os4kibst4rbcvdfdp3w2wvu7au
MUSIC: Identification of Enriched Regions in ChIP-Seq Experiments using a Mappability-Corrected Multiscale Signal Processing Framework
2014
Genome Biology
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In particular, analysis of RNA polymerase II data reveals a clear distinction between the stalled and elongating forms of the polymerase. ...
We present MUSIC, a signal processing approach for identification of enriched regions in ChIP-Seq data, available at music.gersteinlab.org. ...
Acknowledgements We thank Akdes Serin Harmanci for constructive comments and discussions on the study and experimental design. This study was supported by grants from the NIH. ...
doi:10.1186/preaccept-9116006401338101
pmid:25292436
pmcid:PMC4234855
fatcat:gsohvpx4evf2zf3lnjq7p4f344
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework
2014
Genome Biology
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In particular, analysis of RNA polymerase II data reveals a clear distinction between the stalled and elongating forms of the polymerase. ...
We present MUSIC, a signal processing approach for identification of enriched regions in ChIP-Seq data, available at music.gersteinlab.org. ...
Acknowledgements We thank Akdes Serin Harmanci for constructive comments and discussions on the study and experimental design. This study was supported by grants from the NIH. ...
doi:10.1186/s13059-014-0474-3
pmid:25292436
pmcid:PMC4234855
fatcat:mxjcbrwfc5bypburixlr4qpxdu
Computational Systems Bioinformatics and Bioimaging for Pathway Analysis and Drug Screening
2008
Proceedings of the IEEE
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In this paper, we describe pathway reconstruction and target validation based on the proposed systems biologic approach and show selected application examples for pathway analysis and drug screening. ...
The former methods provide the profiles of genes, proteins, and metabolites, whereas the latter techniques generate objective, quantitative phenotypes correlating to the molecular profiles and interactions ...
His research theme has been focused on the application of advanced technology to pragmatic biomedical problems and is based on the belief that problems of importance involve the interplay between theory ...
doi:10.1109/jproc.2008.925440
pmid:20011613
pmcid:PMC2790217
fatcat:lqqa3pfffjet5gpstqndjsz4la
Radiogenomic Analysis of Oncological Data: A Technical Survey
2017
International Journal of Molecular Sciences
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This survey is aimed to review the state-of-the-art techniques employed in radiomics and genomics with special focus on analysis methods based on molecular and multimodal probes. ...
Radiogenomics integrates both aspects, investigating the relationship between imaging features and gene expression. ...
Radiogenomic Data Analysis Once both radiomic and genomic features are extracted for each subject, radiogenomic analysis are performed on a population dataset, including the clinical outcome related to ...
doi:10.3390/ijms18040805
pmid:28417933
pmcid:PMC5412389
fatcat:xcpjv3mbhvdrvkjt5jblfm6uzu
MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
[article]
2018
bioRxiv
pre-print
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Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. ...
Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the ...
This work was supported by NIH U54DK107977 to BR and MH and R01HL129132 to YL. ...
doi:10.1101/411835
fatcat:ht3xotwhg5gwfl4parnlq3mzou
Machine-assisted cultivation and analysis of biofilms
2019
Scientific Reports
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We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy ...
The system is operable under oxic and anoxic conditions, allowing for different gases and nutrients as feeding sources and it offers high spatiotemporal resolution in the analysis of metabolites and biofilm ...
Acknowledgements We acknowledge financial support of this work by the Helmholtz program BioInterfaces in Technology and Medicine. ...
doi:10.1038/s41598-019-45414-6
pmid:31222095
pmcid:PMC6586868
fatcat:raajfps6gjalxircru7wagpcj4
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
2020
Science Advances
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Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ...
ChIA-PIPE also supports the analysis of other related chromatin-mapping data types. ...
Reifsnyder for artistic improvement of the figures; and the legacy ...
doi:10.1126/sciadv.aay2078
pmid:32832596
pmcid:PMC7439456
fatcat:zo2jnuxap5csnlfypsyapnpare
Integrative analysis from the epigenome through translation exposes patterns of dominant nuclear regulation during transient stress
[article]
2018
bioRxiv
pre-print
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Gene regulation is modulated from chromatin to translation. ...
to hypoxia and reoxygenation. ...
Expanded overview of the multiscale chromatin and RNA gene regulatory analyses. a Schematic of library types and data analysis performed on 7-day-old seedlings subjected to control (normoxic) (2NS, 9NS ...
doi:10.1101/479980
fatcat:h2mfbavaobhijllksxiabp6bae
CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data
[article]
2018
bioRxiv
pre-print
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Moreover, CaSpER discovers gene expression signatures of CNV sub-clones, performs gene ontology (GO) enrichment analysis and identifies potential therapeutic targets for the sub-clones. ...
CaSpER uses Hidden Markov Models (HMM) to assign copy number states to regions. The multiscale nature of CaSpER enables comprehensive analysis of focal and large-scale CNVs and LOH segments. ...
Although we have focused only on RNA-sequencing data, the analysis framework that CaSpER utilizes can be extended to other functional genomics datasets such as ChIP-Sequencing, which are currently not ...
doi:10.1101/426122
fatcat:mwilqxwqanhtdiduu7vf474woy
Machine-assisted cultivation and analysis of biofilms
[article]
2017
bioRxiv
pre-print
Preserved Fulltext
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We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy ...
Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. ...
Acknowledgements We acknowledge financial support of this work by the Helmholtz program BioInterfaces in Technology and Medicine.
Author Contributions ...
doi:10.1101/210583
fatcat:tiwpaxjmnfbjvadk7nc7pjlogq
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