BOL: Related items

Computer Theory & Genetics: George Chao at TEDxUMNSalon

Thu, 15 Aug 2013 22:08:10 -0500

George Chao is an undergraduate senior studying Genetics and Computer Science at the University of Minnesota. Having started genetics research as soon as he entered the university, he has worked in labs spanning multiple disciplines as well as in Japan. Some of these researches include developmental genetics in Drosophila, computational techniques for analyzing protein interactions, and helping with the development of algorithms to analyze motion capture data of patients with neck pain. During this time, George steadily developed a fascination with the field of bioinformatics, the study of using computational techniques to learn from genetic data. He would like to go into a career of research into the application of bioinformatics in various fields. ---- The individuals involved with TEDxUMN have a passion for bringing together the great thinkers at the University of Minnesota and giving them the opportunity to share their ideas worth spreading and to discuss our shared future. We provide these great people the opportunity to share these ideas on a global stage and with an incredibly diverse audience. We believe in the power of ideas to change attitudes, lives and ultimately the world. Check out TEDxUMN at http://www.TEDxUMN.com/ In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

'What is Life? A 21st Century Perspective' by Dr Craig Venter

Mon, 26 Aug 2013 17:09:17 -0500

One of the landmark events of 20th century science was celebrated and reinterpreted for the 21st century in Trinity College Dublin on 12 July 2012 as part of the Science in the City programme of ESOF2012. Dr Craig Venter, one of the leaders of the Human Genome Project in the 1990s and a pioneer of synthetic biology delivered a lecture entitled, 'What is Life? A 21st century perspective' recreating the Irish event that inspired the discovery of the structure of DNA. In February, 1943 one of the most distinguished scientists of the 20th Century, Erwin Schrödinger, delivered a seminal lecture, entitled 'What is Life?', under the auspices of the Dublin Institute for Advanced Studies, in Trinity College Dublin. The lecture presented far-sighted ideas on how hereditary information could be encoded in a chemical structure (aperiodic crystal) in living cells. Schrödinger's book (1944) of the same title is considered to be a scientific classic. The book was cited by Crick and Watson as one of the inspirations which ultimately led them to unravel the structure of DNA in 1953, a breakthrough which won them the Nobel prize.

Giovanni Parmigiani Lab

Fri, 20 Sep 2013 13:21:41 -0500

Scientific Interests:

Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

Statistical methods for comparative effectiveness research: comprehensive models for lifetime history of chronic disease outcomes; Bayesian meta-analysis; Bayesian causal inference; decision analysis.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design and their application to adaptive and multistage studies in clinical and epidemiological research.

http://bcb.dfci.harvard.edu/~gp/index.html

http://scholar.google.com/citations?user=OlpYP3UAAAAJ&hl=en

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

University of California, Irvine - Center for Complex Biological Systems

Mon, 04 Nov 2013 17:10:29 -0600

The University of California Irvine's Center for Complex Biological Systems got its start just as there was a revolution in biology. Systems Biology requires that scientists work across many disciplines including engineering, physics and mathematics. The Center specializes in helping form the kinds of teams that will propel biological research into the future. It is also proud to be able to train students in the new interdisciplinary approach. http://ccbs.uci.edu

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/

Oldest Hominin DNA Sequenced

Surajeet — Fri, 27 Dec 2013 19:58:31 -0600

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy

Tue, 11 Feb 2014 08:06:47 -0600

We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889

The Best Bioinformatics / Computational Biology Quotes

Jit — Wed, 26 Feb 2014 17:50:59 -0600

Bioinformatician are not anti-social; We are just genome friendly.

Bioinformatician would love to change the biological world, but they won't give us the genetic code :P

If at first you don't succeed; call it version 1.0

The glass is neither half-full nor half-empty: it's actually have several genomes.

I'm BioGeek.

Fedup with LIPS, try God script.

Idiot, Go ahead, make my data!

Thank god, my genome just compiled.

Error message: "Out of space on genome drive:"

Shut up mobile elements, or i'll flush you out.

Never underestimate the internet bandwidth, u gotta incomplete.

Applied fuzzy logic to understand God's logic?

Warning! Overflow, delete chromosome !

Be nice to the BioGeek, for all you know they might be the next curator!

Beware of computational biologist they screw genes and protein.

Warning! Your genome is full of garbage, delete it !

Bad or missing mouse genome. Spank the cat? (Y/N)

Genome make very fast, very accurate mistakes.

Let's BLAST it.

Some genome never has transposons. It just develops random features.

Go watch CINEMA and have BLAST.