Difference between revisions of "Template:Article of the week"

From LIMSWiki
Jump to navigationJump to search
(Updated article of the week text.)
(Updated article of the week text)
(232 intermediate revisions by the same user not shown)
Line 1: Line 1:
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig3 Dander BMCBioinformatics2014 15.jpg|220px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig4 Auer CytometryPartA2018 93-7.jpg|240px]]</div>
'''"[[Journal:Personalized Oncology Suite: Integrating next-generation sequencing data and whole-slide bioimages|Personalized Oncology Suite: Integrating next-generation sequencing data and whole-slide bioimages]]"'''
'''"[[Journal:ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis|ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis]]"'''
 
Cancer immunotherapy has recently entered a remarkable renaissance phase with the approval of several agents for treatment. [[Cancer informatics|Cancer treatment platforms]] have demonstrated profound tumor regressions including complete cure in patients with metastatic cancer. Moreover, technological advances in next-generation sequencing (NGS) as well as the development of devices for scanning whole-slide bioimages from tissue sections and [[Bioimage informatics|image analysis software]] for quantitation of tumor-infiltrating lymphocytes (TILs) allow, for the first time, the development of personalized cancer immunotherapies that target patient specific mutations. However, there is currently no [[bioinformatics]] solution that supports the integration of these heterogeneous datasets.
 
We have developed a bioinformatics platform – Personalized Oncology Suite (POS) – that integrates clinical data, NGS data and whole-slide bioimages from tissue sections. POS is a web-based platform that is scalable, flexible and expandable. The underlying database is based on a data warehouse schema, which is used to integrate [[information]] from different sources. POS stores clinical data, [[Genomics|genomic]] data (SNPs and INDELs identified from NGS analysis), and scanned whole-slide images. ('''[[Journal:Personalized Oncology Suite: Integrating next-generation sequencing data and whole-slide bioimages|Full article...]]''')<br />


Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex [[wikipedia:Fluorescence in situ hybridization|fluorescence ''in situ'' hybridization]] (M‐FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse [[wikipedia:Karyotype|karyotypes]], for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publicly available open-source software that combines flexibility and customizable functionalities is needed. Here we present such a tool, called “ChromaWizard,” which is based on popular scientific image analysis libraries (OpenCV, scikit‐image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster (''Cricetulus griseus'') fibroblasts metaphase spreads and on Chinese hamster ovary cell lines, known for their large number of chromosomal rearrangements.  ('''[[Journal:ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis|Full article...]]''')<br />
<br />
<br />
''Recently featured'': [[Journal:Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations|Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations]], [[Journal:Requirements for data integration platforms in biomedical research networks: A reference model|Requirements for data integration platforms in biomedical research networks: A reference model]], [[Journal:4273π: Bioinformatics education on low cost ARM hardware|4273π: Bioinformatics education on low cost ARM hardware]]
''Recently featured'':
: ▪ [[Journal:Haves and have nots must find a better way: The case for open scientific hardware|Haves and have nots must find a better way: The case for open scientific hardware]]
: ▪ [[Journal:CytoConverter: A web-based tool to convert karyotypes to genomic coordinates|CytoConverter: A web-based tool to convert karyotypes to genomic coordinates]]
: ▪ [[Journal:Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry|Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry]]

Revision as of 22:58, 24 February 2020

Fig4 Auer CytometryPartA2018 93-7.jpg

"ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis"

Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex fluorescence in situ hybridization (M‐FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse karyotypes, for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publicly available open-source software that combines flexibility and customizable functionalities is needed. Here we present such a tool, called “ChromaWizard,” which is based on popular scientific image analysis libraries (OpenCV, scikit‐image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster (Cricetulus griseus) fibroblasts metaphase spreads and on Chinese hamster ovary cell lines, known for their large number of chromosomal rearrangements. (Full article...)

Recently featured:

Haves and have nots must find a better way: The case for open scientific hardware
CytoConverter: A web-based tool to convert karyotypes to genomic coordinates
Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry