BOL: Related items

Evolution and Cancer

Fri, 27 Sep 2013 11:28:49 -0500

Air date: Wednesday, January 04, 2012, 3:00:00 PM Time displayed is Eastern Time, Washington DC Local Category: Wednesday Afternoon Lectures Description: There is a broad consensus that cancer is the result of somatic cells having serially gained, by a series of mutations, the ability to grow independently, to recruit resources from the circulation and the stroma, to invade local tissues, and to found anatomically distant metastases, ultimately killing the host. From the point of view of the cancer-causing somatic cell population, this is evolution driven by mutation and selection. Genomics has resulted in a parallel consensus that the central functions of all eukaryotes are highly conserved, not only at the level of individual protein functions, but also complex biological pathways and systems. These ideas motivated a comparison between results of molecular genetic studies of experimental evolution in yeast and the molecular genetic phenomena associated with tumorigenesis and tumor progression. We find some very striking similarities, including recurring genomic rearrangements, alterations of the regulation of specific growth-promoting genes, population-genetic features that affect the fitness trajectories of growth rate variants in evolving populations, and physiological and metabolic similarities derived from the conservation of the basic plan of growth and cell multiplication among all eukaryotes. It is hoped that some of the insights from yeast will aid the interpretation of sequence changes found in tumors, especially in the urgent necessity to distinguish 'driver' from 'passenger' mutations." David Botstein's fundamental contributions to modern genetics include the development of genetic methods for understanding biological functions and the discovery of the functions of many yeast and bacterial genes. In 1980, Botstein and three colleagues proposed a method for mapping human genes that laid the groundwork for the Human Genome Project. The basic principle of the mapping scheme was to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms when hybridized to restriction digests, or specific fragments, of an individual's DNA. The method was used in subsequent years to identify several human disease genes, such as Huntington's and BRCA1. Variations of this method enabled the sequencing phase of the Human Genome Project. In the 1990s Botstein, having moved to Stanford University School of Medicine, collaborated with Patrick O. Brown of Stanford in exploiting DNA microarrays to study genome-wide gene expression patterns in yeast and in human cancers. This required developing a new statistical method and graphical interface, widely used today to interpret genomic data. Botstein also has helped to create, with Michael Ashburner and Gerald Rubin, a bioinformatics initiative to unify the representation of gene and gene product attributes across all species, called Gene Ontology. He graduated from Harvard College and earned his doctorate from the University of Michigan. He worked at Massachusetts Institute of Technology from 1967 to 1988; served as vice president for science at Genentech from 1988 to 1990; chaired the Department of Genetics at the Stanford University School of Medicine from 1990 to 2003; and joined the Princeton University faculty in 2003. He has sat on numerous editorial boards and was the founding editor of Molecular Biology of the Cell. Among recent major awards, Bostein won the Peter Gruber Foundation Prize in Genetics in 2003, the Apple Science Innovator Award in 2008, and the Albany Medical Center Prize in 2010. The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. For more information, visit: The NIH Director's Wednesday Afternoon Lecture Series Author: Dr. David Botstein, Princeton University Runtime: 00:59:58 Permanent link: http://videocast.nih.gov/launch.asp?17046

Yau Group

Tue, 15 Oct 2013 13:05:15 -0500

Yau Group are a new research group based at the Wellcome Trust Centre for Human Genetics and the Department of Statistics at the University of Oxford.

Yau Group develops statistical and computational methods for the analysis of genomic datasets with a particular interest in cancer sequencing applications and the use of Bayesian Statistics.

Yau Group are currently have projects in somatic mutation analysis of heterogeneous cancers, data fusion or integration techniques and single cell genomics.

More @ http://www.well.ox.ac.uk/~cyau/index.html

Postdoc in Comparative Single Cell Genomics at University of Basel

Fri, 06 Dec 2024 23:41:20 -0600

A fully funded 4-year Postdoc position is available in the lab of Patrick
Tschopp at the University of Basel, Switzerland, study the molecular and
tissue-scale dynamics during the embryonic formation of the vertebrate
skeleton and compare it across different vertebrate species with distinct
habitats.

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Patrick Tschopp

MATHomics Lab

Tue, 19 Nov 2013 18:17:32 -0600

Mathomics is a collaborative research group of the Center for Mathematical Modeling and the Center for Genome Regulation at University of Chile, created to play a central role in the development of biotechnological projects, providing state of the art bioinformatics and mathematical modeling tools, allowing to face these problems from the point of view of Systems Biology.

Lab page @ http://www.mathomics.cl/

Bioinformatics and Sequencing Courses and Workshops

Rahul Agarwal — Sat, 24 Aug 2013 16:41:26 -0500

Swiss Institute of Bioinformatics (SIB) organises lots of bioinformatics courses covering wide range of topics:

http://www.isb-sib.ch/education/training-courses.html

Canadian bioinformatics also organises various bioinformatics and sequencing courses:

http://bioinformatics.ca/workshops

In addition to above two, EMBI Europe, EMBO Europe, Cold Spring Harbour USA, Wellcome Trust UK and NOVA Europe also organise bioinformatics and sequencing courses annually:

http://www.embl.de/training/events/index.php?p_outstation=ALL

http://www.embo.org/funding-awards/courses-workshops

http://meetings.cshl.edu/courses.html

http://www.wellcome.ac.uk/Education-resources/Courses-and-conferences/Advanced-Courses-and-Scientific-Conferences/Advanced-Courses/index.htm

http://www.nova-university.org/pagetop.cfm?MenySidorTop_id=2&open=7

BOKU Lab

Wed, 08 Jan 2014 19:33:12 -0600

We are interested in the study of complex systems in living organisms. Novel views augmenting the classical gene by gene approaches are required to overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes. We therefore combine work to establish improved quantitative experimental assays, such as microarrays or differential in-gel electrophoresis, and development of modern computational methods, such as hierarchical probabilistic models or integration of heterogeneous data sources, focussed by biological studies in our laboratory and collaborations.

Highlights of our research include:

Optimization of microarray design, probe signal interpretation
Advanced models and tools for expression profiling
State-of-the-art applications and integrated analyses

Lab page @ http://bioinf.boku.ac.at/

Computational Methods for the Analysis of the Diversity and Dynamics of Genomes

Sat, 09 Nov 2013 20:19:02 -0600

The German-Canadian international research training group

"Computational Methods for the Analysis of the Diversity and Dynamics of Genomes"

has currently open positions for graduate students, to study at Simon Fraser University (Vancouver, Canada) and
Bielefeld University (Germany), starting in the fall 2014.

This international graduate program is a close cooperation of:

Bielefeld University, Germany: Graduate progam "DiDy"
Simon Fraser University (SFU), Vancouver, Canada: Graduate program "MADD-Gen"

The available positions include six PhD positions at Bielefeld University, as well as PhD and MSc positions at SFU.

Application deadline: December 31st, 2013
Webpage: http://wiki.techfak.uni-bielefeld.de/didy/Announcement

Bioinformatics job in Genotypic Tech, India

Mon, 07 Apr 2014 08:20:54 -0500

Genotypic Technology, the first Genomics Company of India is poised to become the next generation life sciences company. We are hiring professionals for our high end Genomics Labs (Molecular Biology/ Microarray/NGS) and Bioinformatics groups.

Apply to Genotypic Technology if you are a PhD in Life Sciences/ Molecular Biology/ Biotechnology/ Human Genetics/ Bioinformatics with minimum 4-5 years post doctoral experience as well as publications in peer reviewed journals.

Source: http://www.genotypic.co.in/Careers/2/Current-Openings.aspx

The genome factory !!!

Madhvan Reddy — Thu, 16 Jan 2014 02:09:31 -0600

Illumina, Inc. announced Tuesday that its new HiSeq X Ten Sequencing System has broken the “sound barrier” of human genomics by enabling the $1,000 genome. “This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab,” Illumina stated.

Initial customers for the HiSeq X Ten System, which will ship in Q1 2014, include Macrogen, based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, and the Garvan Institute of Medical Research in Sydney, Australia.

“For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”

“The HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease,” Illumina stated. “It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.”

HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before — generating a 10x increase in daily throughput when compared to current HiSeq 2500 performance.

The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year. Illumina says the $1,000 includes typical instrument depreciation, DNA extraction, library preparation, and estimated labor.

17 Marie Curie PhD position available immediately

Tue, 23 Jun 2015 06:52:06 -0500

Kindly look into following webpage:
http://medhealth.leeds.ac.uk/info/1450/scholarships/1795/marie_curie_phd_training_network

The closing date for application will be 26 June 2015.