Subscribe: Blogging the biotechnology revolution
Added By: Feedage Forager Feedage Grade B rated
Language: English
bioinformatics  biology  conference  expression  interesting  nature  networks  paper  papers  science  systems biology  systems  talks  work 
Rate this Feed
Rate this feedRate this feedRate this feedRate this feedRate this feed
Rate this feed 1 starRate this feed 2 starRate this feed 3 starRate this feed 4 starRate this feed 5 star

Comments (0)

Feed Details and Statistics Feed Statistics
Preview: Blogging the biotechnology revolution

Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk

Updated: 2018-03-06T06:52:08.890-08:00




Something interesting in my mail today:A British bioinformatician wants to open discussion about the greatest biological discovery made possible by bioinformatics. He has just launched a "brainstorming competition" with a small cash prize to stoke discussion. Kaggle is hosting the "brainstorming competition" at:



Recently the Boone group published a short report concerning the generation of systematic gene deletion for another strain of yeast: Genotype to phenotype: a complex problem. Its amazing how much work went into this short reports, but this is the first study to show that genes required for growth can be significantly different between closely related strains of the same species. The article from



Were at ICSB this year and heard about a very interesting paper from Tobias Meyer. Using an intricate assay for wound healing in 96 well plates and automated microscopy, Tobias Meyer's lab looked for signaling components which could effect would healing. In this very clever approach they were able to track single cells as they migrated in response to a wound on a glass plate, in response to



This paper in Nature from Ian Taylor and Jeff Wrana from U. Toronto present a compelling method for the discrimination and diagnosis of disease states based on the disruption of co-expression patterns with neighbors in a protein interaction network. Typically, the search for cancer biomarkers involves searching for differentially expressed genes which alone can discriminate between different



Genetics meets social networks! In a paper today in PNAS Fowler et al compare the topological characteristics of the social networks of MZ and DZ twins and find that some network properties are heritable. This is expanding on some previous work that showed that the −G1438A polymorphism within the promoter region of the 5-HT2A serotonin receptor gene is associated with



I just ran across an interesting paper in Nature on the genetic basis of tumor susceptibility and skin inflammation. The authors use backcrossed mice to identify eQTLs and mapped these onto a network for co-expression based on various skin expression profiles. The expression profiles highlighted skin specific networks such as keratins. Their analysis suggests to me that using a generic


2008-09-04T12:44:38.792-07:00 released its 2008 salary survey today. There are some interesting tools in there to find out the average pay for professors of different rank in different states (Avg pay for tenured faculty in California is 150K). Somewhat disturbing is the observation that women at the same rank make significantly less than men (23% less pay for women full professors vs men).Check it out:



ISMB 2008 Toronto, ON- Any other bloggers/readers out there attending this conference want to have an informal meetup? Just give me a shout!



BIO2008 is in town this week in San Diego, where ive been given a press pass. The conference is huge so i'll expect to be attending random sessions, but there are definately a few that are very interesting including algal biofuels, therapeutic gene silencing and personalized medicine. Of course what would any high profile biology conference do without a keynote from Craig Venter. This is by far



La Jolla Bioinformatics Conference 2008. This conference features a blend of speakers from both academia and industry with a focus on systems biology/bioinformatics. Because ive talked about most of the academic researchers speaking, ill focus on Industry in bioinformatics.Steven Hofstadler, VP of research at Ibis Biosciences.Presented the companies work in determining the identity of an unknown



I usually dont post on tools, but I find the Journal/Author Name Estimator extremely useful! The paper in bioinformatics describes the method, but the lithmus test is that the recommendation engine works! You can upload your title and/or abstract and it can recommend Journals that would be the best fit or authors that can serve as experts (reviewers really) on that particular topic. Give it a



RECOMB satellite systems biology in La Jolla, CA.Thanks to Rohith and Han-yu for blogging the talks at this conference! This conference brings together the systems biology community with selected papers published in Molecular Systems Biology.The keynotes:Trey Ideker - Comparative Genomics Vista rears its ugly head as Trey's talk is postponed due to technical difficulties! And we're off. The



Blog Hijacking - Sorry to all those that were subject to a couple weeks of spam associated with this blog. Apparently theres some bug that lets people take your domain and generally they use it to post inappropriate spam. Ive got my domain back after contacting with Either way, if your reading this thanks for sticking with it. Ill try to make sure it doesnt happen again.



I just ran into Phil Bourne who was talking about a pretty cool project he has been working on called SciVee. Which is basically a youtube for scientists. How it works is that authors of papers create video talks of their papers basically telling the story of the paper instead of people just reading an abstract. Its a pretty good concept - and has a social networking aspect to it, youg scientists



Confirmation of Organized Modularity in the Yeast Interactome. From Vidal, Roth and colleagues is a rebuttal to a recent paper that there isn't dynamic modularity in the yeast (and other) interactomes which was a rebuttal of a Vidal Nature paper on date and party hubs and a Fraser Science paper on Evolutionary rate and Hubs. Basically the debate is that one group accused the other of using an



Clustering by Passing Messages Between Data Points. Brendan Frey and Delbert Dueck, Science Jan 2007. This paper firstly caught my eye as a pure CS paper in Science! They propose a method of clustering that uses message passing. In this framework each node get as input messages from each other node how much they think that the particular node is an exemplar (or best representative of the cluster)



A few days ago I stumbled on Lee Hood's commemorative lecture upon recieving the 2002 Kyoto Prize.In the lecture he talks about his childhood (its no surprise he excelled in school and pretty much every other area), grad school (bieng invited for talks in his second year), getting his MD (MD/Phd), and leaving caltech for UW and then again forming ISB.Along the way he gives some good advice that



RECOMB Satellite Conferences on Systems Biology and Computational Proteomics was also this weekend here at UCSD. Although I will not outline all the talks, they were very good and had a number of very prominent and interesting speakers.Daphne Koller, Stanford. Genetic Variation and Regulatory Networks: Mechanisms and Complexity. Her lab was looking at Yeast variation and gene expression data



Algorithmic biology conference is at UCSD today and RECOMB Satellites tommorow. I will give a summary of keynote talks from Manolis Kellis, Ron Shamir, David Haussler and Serafim Batzoglou.Manolis Kellis MIT "Interpreting the human genome"Sequence signatures of highly accurate synteny alignments between human, mouse, worm, rat and fly to discover, refine, and refute (annotation errors) genes in



Systems Biology Paper WatchThere is now a community page whose aim is to maintain a list ofupcoming relevant papers in systems biology. a viewer feel free to bookmark it or subscribe to its RSS feed.Even better would be if you are interested in contributing to itssuccess. It is fairly simple and requires you to register and email your



Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling by Li et. al in PLOS Biology uses boolean models to predict the modulators of Guard Cell closure in plants based on Abscisic Acid.Guard Cells are the cells on the surface of plants that open and close for gas exchange. Here the authors use literature to build a boolean model of



Science annual Life Science Salary SurveyIn the report , they report an all around in increase in salaries this year compared to last(whether this is just becuase of some sampling bias is unclear, it seems odd to me that there was an increase of around 5% in salaries in just about every field they looked into). The mean salaried for academics rose to $78K and in industry to $116K. Postdoc



"How to get a paper in Nature" Dr. Angela Eggleston, Senior Editor, NatureTalk on the UCSD CampusThe talk "how to publish in nature" was rather misadvertised. Infact, when we got there, the host said he chose the title to getpeople to come (it worked), but the talk was more about the editor,how she came to be an editor at Nature, and what NPG is like. On topof that, 90% of what she said was



The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease Lamb et. al. Including Lander E.S. and Golub T.R. Science Sept 29th 2006 this work this team exploits the information from 564 human affy microarrays in the profiling of 164 different drugs. They find some drugs work similarly as well as



Applied Biosystems makes file formats open sourceBack when I was outside the academic sector I remember the groans and moans over working with the ubiquitous ABI sequencing/genotyping/rt-pcr machines and their crazy proprietary file formats. We had to invent ways to get around the restrictions imposed by the software that we had to use because of their almost monopolistic hold of the market share