Filters








545 Hits in 8.3 sec

Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data

G. Lerman, J. McQuown, A. Blais, B. D. Dynlacht, G. Chen, B. Mishra
2006 Bioinformatics  
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

Theo A Knijnenburg, Stephen A Ramsey, Benjamin P Berman, Kathleen A Kennedy, Arian F A Smit, Lodewyk F A Wessels, Peter W Laird, Alan Aderem, Ilya Shmulevich
2014 Nature Methods  
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

Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee (+5 others)
2018 Genome Biology  
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

Mohamed Ibrahim, Krishnendu Chakrabarty, Jun Zeng
2016 IEEE Transactions on Big Data  
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]

Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee (+5 others)
2017 bioRxiv   pre-print
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

Arif Harmanci, Joel Rozowsky, Mark Gerstein
2014 Genome Biology  
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

Arif Harmanci, Joel Rozowsky, Mark Gerstein
2014 Genome Biology  
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

Xiaobo Zhou, S. Wong
2008 Proceedings of the IEEE  
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

Mariarosaria Incoronato, Marco Aiello, Teresa Infante, Carlo Cavaliere, Anna Grimaldi, Peppino Mirabelli, Serena Monti, Marco Salvatore
2017 International Journal of Molecular Sciences  
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]

Ivan Juric, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yuchen Yang, Yun Li, Bing Ren, Ming Hu
2018 bioRxiv   pre-print
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

Silla H. Hansen, Tobias Kabbeck, Carsten P. Radtke, Susanne Krause, Eva Krolitzki, Theo Peschke, Jannis Gasmi, Kersten S. Rabe, Michael Wagner, Harald Horn, Jürgen Hubbuch, Johannes Gescher (+1 others)
2019 Scientific Reports  
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

Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed Abbas, Chia-Lin Wei, Yijun Ruan (+1 others)
2020 Science Advances  
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]

Travis A Lee, Julia Bailey-Serres
2018 bioRxiv   pre-print
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]

Akdes Serin Harmanci, Arif O Harmanci, Xiaobo Zhou
2018 bioRxiv   pre-print
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]

Silla H. Hansen, Tobias Kabbeck, Carsten P. Radtke, Susanne Krause, Eva Krolitzki, Theo Peschke, Jannis Gasmi, Kersten S. Rabe, Michael Wagner, Harald Horn, Juergen Hubbuch, Johannes Gescher (+1 others)
2017 bioRxiv   pre-print
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
« Previous Showing results 1 — 15 out of 545 results