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FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

Malte Mader, Ronald Simon, Stefan Kurtz
2014 Journal of Clinical Bioinformatics  
Results: We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research.  ...  One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.  ...  Acknowledgements This work was supported by a grant from the Monika-Kutzner-Stiftung to SK. We thank Ole Eigenbrod for performing the analysis of SNP and expression data.  ... 
doi:10.1186/2043-9113-4-5 pmid:24684958 pmcid:PMC4230720 fatcat:zc7pwesthngshlqwit6ejh3qea

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
Results: We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context.  ...  The FISH Oracle application and an installed demo web server are available at  ...  Acknowledgements This work was supported by a grant from the Werner-Otto-Stiftung to SK and RS (# 6/73) and a grant from the Federal Ministry of Education and Research (BMBF), Germany to RS (# FKZ 01GS08189  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

Systems biology visualization tools for drug target discovery

Tianxiao Huan, Xiaogang Wu, Jake Y Chen
2010 Expert Opinion on Drug Discovery  
Department of Defense (DOD) Breast Cancer Research Program (BCRP) Concept Award (W81XWH-08-1-0623) to J Chen.  ...  Acknowledgments The authors thank M Grobe of the Pervasive Technology Institute at Indiana University for proofreading the manuscript. 650 Declaration of interest This work is partly supported by the  ...  GraphWeb [44] is a web server for biological network 300 analysis and module discovery with visualization capabilities, all of which help users discover network modules in their data sets and link network  ... 
doi:10.1517/17460441003725102 pmid:22823128 fatcat:3gumecrgwjafrkgzxcn753sbhu

Internet-based Profiler system as integrative framework to support translational research

Robert Kim, Francesca Demichelis, Jeffery Tang, Alberto Riva, Ronglai Shen, Doug F Gibbs, Vasudeva Mahavishno, Arul M Chinnaiyan, Mark A Rubin
2005 BMC Bioinformatics  
TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability.  ...  We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler.  ...  Acknowledgements Martina Schweitzer-Storz for extensive discussion related to TMA technology application. Matt van de Rijn for his thoughtful comments and review of the manuscript.  ... 
doi:10.1186/1471-2105-6-304 pmid:16364175 pmcid:PMC1343596 fatcat:wypuwdeha5fdhgosv5ed5ratnq

A database system for comparative genomic hybridization analysis

D. Berrar, W. Dublizky, S. Solinas-Toldo, S. Buloshevska, M. Granzow, C. Conrad, J. Kalla, P. Lichter, R. Eils
2001 IEEE Engineering in Medicine and Biology Magazine  
The CGH approach is used in cancer research to identify over-and under-representations of chromosomal regions [1-3].  ...  C omparative genomic hybridization (CGH) is a molecular cytogenetic analysis method that allows the detection of chromosomal imbalances in entire genomes.  ...  Acknowledgments We acknowledge the contribution of Michael Baudis at an early stage of this project.  ... 
doi:10.1109/51.940052 pmid:11494773 fatcat:cxipjduzujgnpj5vl5soe4wmiq

Structural Proteomics: Methods in Deriving Protein Structural Information and Issues in Data Management

Shankari E. Mylvaganam, Muthuchidambram Prabhakaran, Suresh S. Tudor, Saied Moezzi, Kalyanaraman Ramnarayan
2002 BioTechniques  
We have developed an extensive collection of three-dimensional protein structures from sequence data and have implemented a relational architecture for data management.  ...  A key component of this research sector is accessing the threedimensional structures of protein targets by both experimental and theoretical methods.  ...  On the integration side, we will also be seeing the linking of pathways data, proteomics analysis data (like 2-D gel analysis), and small molecule data in one common platform.  ... 
doi:10.2144/mar0206 fatcat:nl56fhkrbzg3vom3c5zvuw7zz4

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation  ...  As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data  ...  Figure 2 . 2 Genome Browser image of interspersed repeat (IR) annotation on a short region of the human assembly hg38 using the new visualization track. ).  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

Challenges in Small Screening Laboratories: Implementing an On-Demand Laboratory Information Management System

Vance P. Lemmon, Yuanyuan Jia, Yan Shi, S. Douglas Holbrook, John L. Bixby, William Buchser
2011 Combinatorial chemistry & high throughput screening  
For academic laboratories generating large data sets from experiments using thousands of perturbagens, a laboratory information management system (LIMS) is the data tracking solution of choice.  ...  The article discusses this application in detail, and how the system was selected and integrated into the laboratory. The advantages of SaaS are described.  ...  In this new model, the vendor or a third party data center hosts the LIMS server. This is likely to be a virtual server instead of a physical device.  ... 
doi:10.2174/138620711796957161 pmid:21631415 pmcid:PMC3289069 fatcat:k5inbavx75dvnoc7uicmbwhplq


2015 Laboratory Investigation  
SNP microarrays also have the added advantage of identifying regions of LOH which play a very important role in the 2 hit hypothesis in somatic cancers.  ...  Design: We created CGA (Clinical Genome Analytics), an automated data analysis pipeline that is implemented using Civet, an in-house engineered XML-based framework for building analytical pipelines for  ...  Results: A total of 1251 cases were submitted for telepathology consultations, including 144 cases in 2012, 614 in 2013, and 493 in the first 8 months of 2014.  ... 
doi:10.1038/labinvest.2015.17 fatcat:74eygyy7o5gkrhizoootoyfol4

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
Apache Tomcat web server.  ...  Whenever a JavaServer page is opened in a web browser, a request is sent from the client to the server.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
Apache Tomcat web server.  ...  Whenever a JavaServer page is opened in a web browser, a request is sent from the client to the server.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
We will extend our work on cancer genomics as a part of the pan-cancer project of the ICGC, in which we are co-leading the transcriptomics/genomics integration working group that aims to study aberrant  ...  We also developed a Fourier-Shell-Correlation server and a tilt-pair-validation server, and added new types of images (e.g. rotationally averaged power spectra and central slices) to the visual-analysis  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Genomics of complex disorders I

2008 Genomic Medicine  
of IGVdb While the putative association between individual genetic polymorphisms and cancer risk remains uncertain, current data strongly suggest that relating it with epidemiological factors such as  ...  Genetic predisposition is a major determinant in the development of renal complications of diabetes.  ...  It is a searchable, client-server, relational database application, developed on the Windows TM platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script.  ... 
doi:10.1007/s11568-009-9104-7 pmid:19466586 pmcid:PMC2694889 fatcat:z7p2zq7hjnewfox4mstdv7mpee


2014 Modern Pathology  
While many DHS are present only in a few samples, a set of 20,201 DHS are present in all fetal kidney tissues analyzed (Fig. 2) .  ...  Background: Synoptic reporting for cancer has increased the consistency, completeness of reporting, ease of interpretation and creating of discrete value reporting that allows for ease in data mining.  ...  , and federating caTissue Suite with other research databases, such as cancer genomics and other multidimensional data-rich molecular repositories.  ... 
doi:10.1038/modpathol.2014.19 fatcat:knorze3lwbeyve4pif5exhufe4

The Fourth Paradigm – Data-Intensive Scientific Discovery [chapter]

Tony Hey
2012 Communications in Computer and Information Science  
The F o u r T H Data-In t e n s I v e scIen t I f I c DIs c o v e r y P a r a d i g m MiCroSoF T reSe arCH REDMOND, WASHINGTON  ...  very helpful discussion on a draft of this material. to all the contributors to this book for sharing their visions within the Fourth Paradigm.  ...  Acknowledgments My thanks to the participants at the April 24, 2009, Buckland-Lynch-Larsen "Friday Seminar" on information access at the University of California, Berkeley, School of Information for a  ... 
doi:10.1007/978-3-642-33299-9_1 fatcat:etue636ubrandga5corvkx3d7u
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