<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26571?offset=140 https://bioinformaticsonline.com/bookmarks/view/29284/genebreak-a-tool-to-systematically-identify-genes-recurrently-affected-by-the-genomic-location-of-chromosomal-cna-associated-breaks-by-a-genome-wide-approach Sat, 01 Oct 2016 15:15:29 -0500 https://bioinformaticsonline.com/bookmarks/view/29284/genebreak-a-tool-to-systematically-identify-genes-recurrently-affected-by-the-genomic-location-of-chromosomal-cna-associated-breaks-by-a-genome-wide-approach <![CDATA[GeneBreak: a tool to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach]]> Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).

 

Address of the bookmark: http://www.bioconductor.org/packages/release/bioc/html/GeneBreak.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30234/last Mon, 19 Dec 2016 14:07:53 -0600 https://bioinformaticsonline.com/bookmarks/view/30234/last <![CDATA[LAST]]> LAST can:

  • Handle big sequence data, e.g:
    • Compare two vertebrate genomes
    • Align billions of DNA reads to a genome
  • Indicate the reliability of each aligned column.
  • Use sequence quality data properly.
  • Compare DNA to proteins, with frameshifts.
  • Compare PSSMs to sequences
  • Calculate the likelihood of chance similarities between random sequences.
  • Do split and spliced alignment.
  • Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

]]> Bulbul https://bioinformaticsonline.com/researchlabs/view/2002/ibl-laboratory Mon, 12 Aug 2013 02:02:29 -0500 <![CDATA[IBL laboratory]]> The IBL laboratory focuses on the multi-disciplinary analyses of the global responses of model microorganisms, cyanobacteria (mainly Synechocystis PCC6803) and yeasts (mainly Saccharomyces cerevisae) to environmental stresses triggered by oxidative agents, heavy metals, or drastic changes in nutrients availability. The genome-wide responses studied with the "omics" techniques (transcriptomics, proteomics, metabolomics and genetics) generate a wealth of experimental data, which are processed, archived, integrated and represented as working models through bioinformatics and mathematics.

Link : http://www-dsv.cea.fr/en/instituts/institut-de-biologie-et-de-technologies-de-saclay-ibitec-s/unites-de-recherche/service-de-biologie-integrative-et-genetique-moleculaire-sbigem/laboratoire-de-biologie-integrative-lbi/presentation__1

]]> https://bioinformaticsonline.com/researchlabs/view/914/welch-lab Mon, 15 Jul 2013 18:21:13 -0500 <![CDATA[Welch Lab]]> They are based in the Department of Genetics at the University of Cambridge.

The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly evolutionary inference from genome sequence data.

Links @ http://www.gen.cam.ac.uk/research/welch/GroupPage/Home.html

]]> https://bioinformaticsonline.com/researchlabs/view/32629/bienko-and-crosetto-labs Fri, 12 May 2017 07:42:15 -0500 <![CDATA[Bienko and Crosetto Labs]]> We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation to gene expression regulation. The Crosetto group engineers new molecular methods for single-cell and spatially resolved omic measurements of DNA, RNA, and proteins, with a strong focus on tumor heterogeneity. By sharing ideas and resources, we work synergistically towards a more quantitative understanding of life’s processes in healthy and diseased conditions.

https://bienkocrosettolabs.org/

]]> https://bioinformaticsonline.com/videolist/watch/4003/personalised-medicine-animation Tue, 27 Aug 2013 10:07:24 -0500 https://bioinformaticsonline.com/videolist/watch/4003/personalised-medicine-animation <![CDATA[Personalised Medicine - Animation]]> Two animated case scenarios set now and in the future. These highlight potential differences in the way patients are treated now, and how they might be treated as healthcare becomes more tailored.]]> https://bioinformaticsonline.com/researchlabs/view/40945/the-clark-lab Fri, 07 Feb 2020 13:57:24 -0600 <![CDATA[The Clark Lab]]> Study the process of Adaptive Evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology.

More at http://clark.genetics.utah.edu/

]]> https://bioinformaticsonline.com/opportunity/view/41905/research-associate-bioinformatics-in-iisc-recruitment-2020 Tue, 23 Jun 2020 21:53:34 -0500 <![CDATA[Research Associate Bioinformatics in IISc Recruitment 2020]]> Research Associate Bioinformatics in IISc Recruitment 2020

Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.

Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.

Desirable Qualifications (Research Associate/s): i) Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment).

ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv) Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.

The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.

Emoluments: As per DST, GOI norms and commensurate with experience.

More at https://www.iisc.ac.in/positions-open/

]]> https://bioinformaticsonline.com/opportunity/view/4653/human-genome-meeting-2014-geneva-switzerland Fri, 20 Sep 2013 12:36:44 -0500 <![CDATA[Human Genome Meeting 2014, Geneva, Switzerland]]> The spectacular advances of the last few years resulted in the rapid analysis of the genome sequence of each individual. The biomedical world is now faced with the enormous challenges of assigning pathogenicity to each genomic variant, the functional analysis of the genome of each individual, and the accurate and detailed phenotypic characterization. Advances in these challenges are likely to fundamentally change the medical practice in a global scale.

This 2014 HUGO Meeting in Geneva will be a Forum for discussions on innovative approaches, and proposals to tackle the anticipated challenges.

Time : 27 April 2014 - 30 April 2014

For enquiries, please email hugo2014@mci-group.com or visit www.hugo-international.org

More at http://www.hgm2014-geneva.org/

]]> https://bioinformaticsonline.com/videolist/watch/5380/04-informatics-approach-to-cancer-interview-with-dr-joel-saltz Mon, 07 Oct 2013 14:35:43 -0500 https://bioinformaticsonline.com/videolist/watch/5380/04-informatics-approach-to-cancer-interview-with-dr-joel-saltz <![CDATA[04- Informatics Approach to Cancer - Interview with Dr. Joel Saltz]]> For additional information visit http://www.cancerquest.org/joel-saltz-interview. Dr. Joel Saltz is a Professor in the Departments of Pathology, Biostatistics and Bioinformatics, and Mathematics and Computer Science at Emory University. Dr. Saltz's research on bioinformatics spans several disciplines.  One project involves applying computer analysis to medical imaging to yield better results for patients.  As an example, a computer program may able to help doctors detect small cancers in a CT scan or mammogram. In this interview segment, Dr. Saltz discusses the informatics approach to cancer. To learn more about cancer and watch additional interviews, please visit the CancerQuest website at http://www.cancerquest.org.]]>