tag:blogger.com,1999:blog-195268752012-01-24T09:57:30.346-08:00Blogging the biotechnology revolutionSystems 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 <a href="http://bioinf.ucsd.edu/~sbandyop/papers.html">systems biology paper watch</a>
Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: <a href='mailto:bioinfblog@gmail.com'>bioinfblog@gmail.com</a> and get the word out!The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.comBlogger661100tag:blogger.com,1999:blog-19526875.post-83994648454854733862010-06-17T15:08:00.000-07:002010-06-17T15:11:32.325-07:00Something 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: http://kaggle.com/blog/2010/06/17/%EF%BB%Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com21tag:blogger.com,1999:blog-19526875.post-62012710158598856362010-05-17T13:01:00.000-07:002010-05-17T13:06:26.243-07:00Recently 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 Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-69438655360322247122009-08-31T15:57:00.000-07:002009-08-31T16:00:27.791-07:00Were 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 Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com28tag:blogger.com,1999:blog-19526875.post-32693269865447664752009-03-25T17:34:00.000-07:002009-03-25T17:38:37.513-07:00This 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 Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-48767400572792895592009-02-13T12:24:00.000-08:002009-02-13T12:31:36.074-08:00Genetics 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 Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-72330693378210696372009-01-15T11:59:00.000-08:002009-01-15T12:07:19.687-08:00I 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 Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-32913473730930594642008-09-04T12:35:00.000-07:002008-09-04T12:44:38.792-07:00The-scientist.com 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: Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-17328578989767420332008-07-15T16:30:00.001-07:002008-07-15T16:32:21.451-07:00ISMB 2008 Toronto, ON- Any other bloggers/readers out there attending this conference want to have an informal meetup? Just give me a shout!Souravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-84369764810873579022008-06-16T10:24:00.000-07:002008-06-18T11:07:05.340-07:00BIO2008 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 farSouravhttp://www.blogger.com/profile/12944952532807242591noreply@blogger.com8tag:blogger.com,1999:blog-19526875.post-4852264883079822822008-04-04T11:38:00.000-07:002008-04-04T16:31:47.677-07:00La 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 unknownThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com51tag:blogger.com,1999:blog-19526875.post-75566037385364899862008-02-20T11:13:00.000-08:002008-02-20T11:17:55.735-08:00I 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-35365512658056206822007-12-03T08:01:00.000-08:002007-12-03T08:14:02.336-08:00RECOMB 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-11490715413253909412007-10-03T10:51:00.000-07:002007-10-03T10:54:05.311-07:00Blog 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 Blogger.com Either way, if your reading this thanks for sticking with it. Ill try to make sure it doesnt happen again.The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-28228196089523447332007-08-21T19:10:00.000-07:002007-08-21T19:16:28.946-07:00I 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 scientistsThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-29996188948349469762007-06-15T12:37:00.001-07:002007-06-15T15:05:07.109-07:00Confirmation 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-38146617463224051682007-03-13T16:07:00.000-07:002007-03-13T16:21:46.882-07:00Clustering 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)The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-42806327559042509102007-01-12T11:16:00.000-08:002007-01-12T11:24:09.600-08:00A 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1165260113172171412006-12-04T11:01:00.000-08:002007-03-12T13:55:04.489-07:00RECOMB 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com6tag:blogger.com,1999:blog-19526875.post-1164917414485687102006-11-30T12:01:00.000-08:002007-03-12T13:56:24.675-07:00 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com31tag:blogger.com,1999:blog-19526875.post-1164674571564160962006-11-27T16:41:00.000-08:002006-11-27T16:43:06.930-08:00Systems Biology Paper WatchThere is now a community page whose aim is to maintain a list ofupcoming relevant papers in systems biology.http://bioinf.ucsd.edu/~sbandyop/papers.htmlAs 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 atconnotea.org and email your The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-1164223740366751042006-11-22T11:15:00.000-08:002006-11-22T11:34:04.786-08:00Predicting 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1162840045973507772006-11-06T11:01:00.000-08:002006-11-06T11:07:51.546-08:00Science 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-1162250166035125772006-10-30T15:12:00.000-08:002006-10-30T15:26:44.900-08:00"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 Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com5tag:blogger.com,1999:blog-19526875.post-1159564021995933532006-09-29T13:20:00.000-07:002006-09-29T15:41:24.993-07:00The 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 http://web.mit.edu/newsoffice/2006/drugs.htmlIn 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 The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1156918352058733492006-08-29T23:06:00.000-07:002006-08-29T23:12:32.070-07:00Applied 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 shareThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com79tag:blogger.com,1999:blog-19526875.post-1155599402913421192006-08-14T16:31:00.000-07:002006-08-14T16:59:23.773-07:00Systems Biology companiesLately ive been hearing gripes that there are no bioinformatics/systems biology companies and that within industry the only jobs you can hope for are within a progressive big pharma company. Recently i read an interview with the CEO of GeneStruct Keith Ellison who talked about tools, strategies and companies driving systems biology. Here he mentions that this new The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com5tag:blogger.com,1999:blog-19526875.post-1155077829709122582006-08-08T15:55:00.000-07:002006-08-08T16:01:37.053-07:00Few papers that have come out recently that are of interest (some to be reviewed later)A yeast-one-hybrid approach for mapping p-dna binding in vitro in elegans ( specied where chip/chip doesnt work)A gene-centered C. elegans protein-DNA interaction network. Cell 2006This one talks about the stability of using arrays for classificationReliable gene signatures for microarray classification: The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1154114456390806132006-07-28T12:12:00.000-07:002006-07-28T12:23:51.953-07:00Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Gupta A, Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NWNature 2006 May 31Ive alyways wondered about how many viruses stay latent within the body and then activate upon certain stimulus (HIV is the prime example). This paper is remarkable in that it finds that a single gene is expressed during latencyThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1146116966856814142006-04-26T22:18:00.000-07:002006-04-30T17:09:47.613-07:00Genome-wide survey for biologically functional pseudogenes by Orjan Svensson, Lars Arvestad, and Jens Lagergren, PLoS computational biology, early online releaseA pseudogene is a piece of noncoding DNA very similar in sequence to a normal "true" gene but containing disablements that prevent its expression into a functional protein. Pseudogenes were long thought to be relatives of functional Flehmen Responsenoreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1145746003351423162006-04-22T15:45:00.000-07:002006-04-22T15:48:36.326-07:005th Annual Systems Biology Symposium will be webcast around the world!From Lee Hood:Dear colleagues,I have the exciting opportunity to announce that we will be conducting alive webcast during this years symposium this Sunday and Monday, April 23and 24. The free webcast will be available to viewers both inside andoutside ISB.To register for the webcast please go tohttp://www.systemsbiology.org/The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1144262684686218632006-04-05T11:18:00.000-07:002006-04-06T03:10:54.813-07:00Bioinf PhD program rankingsFor the first time since 2002, U.S. News also surveyed Ph.D. programs in the sciences. This is the first time that Genetics/Genomics/Bioinformatics was included in the study. The results are not terribly surprising, but should give people thinking about graduate school something to think about. Here are the top 10, including links to their bioinformatics or similar The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1144132824272856942006-04-03T23:35:00.000-07:002006-04-03T23:43:31.680-07:00 Stochastic protein expression in individual cells at the single molecule level. Cai, Friedman, Xie in Nature March 16, 2006. Stochasticity in gene expression is a well known phenomenon, and mechanisms by which cells attenuate stochastic fluxuations to achieve deterministic outcomes is a topic of current research. Here for the first time, Cai, Friedman and Xie characterize the magnitude and The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3tag:blogger.com,1999:blog-19526875.post-1143660688334389512006-03-29T11:09:00.000-08:002006-03-29T19:10:11.560-08:00Sean Eddy - Washington University - St. Louis: "Biological Sequence Analysis with Probabilistic Models." Talk at the UCSD Bioinformatics SymposiumSean Eddy had a very interesting talk, obviously departing from his normal presentation to one that addressed the history of his career in science. It was very interesting to hear from a pioneer in the field of probabilistic models in bioinformatics.He The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1143318418822340692006-03-25T12:06:00.000-08:002006-03-28T08:13:03.786-08:00Ruben Abagyan - The Scripps Research Institute: "Structures, Drugs and Computing". Talk at the UCSD Bioinformatics SymposiumThe focus of this symposium was "most important open problems in bioinformatics." Dr. Abagyan represented the structure community and discussed docking and modeling.He apparently has an affinity for -omes. There is a need to characterize the "pocketome", meaning a method forThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1141681240571457422006-03-06T13:28:00.000-08:002006-03-06T15:47:12.856-08:00There are two special features in this month's issue of Science about careers in systems biology. One is "Working the Systems" by Jim Kling and the other "A Meeting of Minds, Expertise, and Imagination" by Anne Forde.Both articles say that the burgeoning field of systems biology is so new and unique that people haven't been able to really get their heads around it. Although the definition of theThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3tag:blogger.com,1999:blog-19526875.post-1140823755551704952006-02-24T15:23:00.000-08:002006-02-24T15:43:24.210-08:00Symposium announcement: The Most Important Open Problems in BioinformaticsSaturday March 25, 2006 CalIT2 auditorium, UCSD, La Jolla, CA.If you are going to be in the area around this time I would suggest checking out this symposium coordinated by the UCSD Bioinformatics Graduate Program [full disclosure: this author is a member of this program]. The symposium is to be a survey of the big problemsThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1140389556735248402006-02-19T14:48:00.000-08:002006-02-19T15:42:39.720-08:00A simple physical model for scaling in protein-protein interaction networks. by Deeds, Ashenberg, Shakhnovich in Jan 2006 PNAS.I've been sitting on this review for a few days because I wanted to really think about what the authors are saying in this paper and figure out the best way to convey it. What this paper posits is that the touted scale free property of protein-protein interaction networksThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com11tag:blogger.com,1999:blog-19526875.post-1139540610911705492006-02-09T18:53:00.000-08:002006-02-16T19:14:30.683-08:00Information Theory & Applications Inaugural Workshop at UCSDPanel discussion: Robert Calderbank, Dave Forney, Michael Luby, Pavel Pevzner, Martin Vetterli, Andrew Viterbi, and Jacob Ziv.Unfortunately, most of this discussion by premier information theorists was over my head. Robert Calderbank, the moderator, started off by asking the rest of the panel what the greatest triumphs and failures of Flehmen Responsenoreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-1139261281224810592006-02-06T13:26:00.000-08:002006-02-19T15:25:35.686-08:00The metabolic world of Escherichia coli is not small, by M Arita (2004) PNAS. This brief communication illustrates that analyses of biological network topologies must always be cognizant of how the networks are constructed. By extracting atomic fluxes between metabolites from a genome-scale model of metabolism in E. coli, Arita concludes that the average distance between any two metabolites is The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-1138146636945438692006-01-24T15:32:00.000-08:002006-01-25T09:59:53.046-08:00Oncogenic pathway signatures in human cancers as a guide to targeted therapies in this month's Nature by Bild et al. describes a fairly comprehensive report on how the signature of expression of a group of genes (rather than genes acting individually as has been done in the past) can predict outcomes and subtypes of various cancers. Really here 'pathways' seem to be groups of genes whose The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com12tag:blogger.com,1999:blog-19526875.post-1137011266159010732006-01-11T12:24:00.000-08:002006-01-11T14:52:04.343-08:00Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers, by Green and Karp in NAR, is crucial reading for people in the bioinformatics community. It highlights (in the context of pathway databases) two errors which are potential pitfalls for bioinformaticians: erroneously interpreting other researchers' data and not fully understanding data types when makingThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3tag:blogger.com,1999:blog-19526875.post-1136928408152991202006-01-10T13:26:00.000-08:002006-01-11T14:47:38.560-08:00PSB 2006Eric Meslin, "The Moral Status of U.S. Science and Science Policy: Lessons from the Stem Cell Research Wars"The scheduling of this talk was actually quite lucky considering things going on in Korea right now over the faked papers. They are now saying that all papers concerning human stem cells by Hwang Woo-suk were faked. However, Dr. Meslin really skirted this subject besides pretty muchThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-1136451666501303222006-01-05T00:46:00.000-08:002006-01-05T12:04:27.603-08:00PSB 2006 Michael Ashburner, "Ontologies for biologists - A community model for the annotation of genomic data"One of the originators of the GO ontology, Dr. Ashburner talked about the intial planning and development of the GO ontology and how it (and everything in bioinformatics) should follow the "Manifesto of liberation of bioinformatics":-Be open source.-Use open standards.-Make data and code The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-1136318887149966942006-01-03T12:04:00.000-08:002006-01-03T12:14:24.236-08:00Stay tuned this week as bioinfblog reports from the Pacific Symposium on Biocomputing 2006 (PSB site) from gorgeous Maui! There are keynotes from Dr. Michael Ashburner who is credited with setting up the GO ontology and Gene Ontology consortium as well as Dr. Eric M. Meslin who will speak about the effects of the U.S. policy on stem cell research. The talk from Dr. Melsin should be interesting The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1136007121049009932005-12-30T21:24:00.000-08:002006-02-19T15:26:30.100-08:00"An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets" by Daniel Schwartz and Steven Gygi, Gygi lab at Harvard Medical School, published in Nature Biotechnology on November 4, 2005.[Historical Digression] Edwin Krebs and Edmond Fischer, Nobel Laureates for discovering the regulatory role of protein phosphorylation in the 1950s. Flehmen Responsenoreply@blogger.com21tag:blogger.com,1999:blog-19526875.post-1134805134785236932005-12-16T23:37:00.000-08:002005-12-30T21:19:11.976-08:00 "A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis" by Janes et al. from the Lauffenburger and Yaffe groups at MIT published in Science December 9, 2005. This work explores the pathways to cytokine induced apoptosis by perturbing the inputs (in this case TNF, EGF, and insulin) to the well characterized apoptotic pathway. By perturbing the inputs and The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133936522395256932005-12-06T22:20:00.000-08:002005-12-11T21:35:47.550-08:00Sydney Brenner, The Salk Institute"What is a Gene"Sydney Brenner has been called "the Thomas Jefferson of molecular biology," with good reason.Much of his talk described the hurdles that the pioneers of genome sequencing had to overcome. It is hard to grasp the progress this field has made in merely 50 years since the double helix. In the beginning, when they met to discuss the sequencing of The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3tag:blogger.com,1999:blog-19526875.post-1133930658690763802005-12-06T20:41:00.000-08:002005-12-06T21:44:19.453-08:00J. Craig Venter, J. Craig Venter Institute"From Reading to Writing the Genetic Code"Talked about the Sargasso gene sequencing in the beginning. So many sequences make genbank look small in comparison!Trying to design the minimal cell based on mycoplasma genitalium (smallest genome).Got so far as to reconstruct viruses, using plasmid-based cassette synthesis. The paper was in PNAS.But to get The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133849565424787262005-12-05T22:10:00.000-08:002005-12-06T23:02:53.796-08:00J. Craig Venter looking craftyFlehmen Responsenoreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1133833468289027912005-12-05T17:40:00.000-08:002005-12-07T12:59:02.536-08:00Tomorrow the bioinfblog team will be at the Venter meeting "Celebrating a decade of genome sequencing" here at UCSD. There are many notable speakers, including Lucy Shapiro, Tony Hunter, Sydney Brenner, and of course Craig Venter. Hopefully we will be able to get some pictures to share!Check out the details at: http://pkr.sdsc.edu/venter/index.phpThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133725692848549862005-12-04T11:45:00.000-08:002005-12-04T11:48:12.850-08:00Manolis Kellis, MIT"Regulatory network discovery and evolution"First part of the talk was comparative genomics techniques for short regulatory motifs. Since motifs are small ~8bp and degenerate this is hard without comparative techniques.Genome wide motif discovery by looking for over represented n-mers. They did an apparently simple counting technique that seemed to work well.Promoter motifs areThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com5tag:blogger.com,1999:blog-19526875.post-1133725491715918962005-12-04T11:43:00.000-08:002005-12-04T11:44:51.726-08:00Michael G. Rosenfeld, UCSD"Coactivator and Corepressor Networks Integrated Transcriptional Response Programs"Transcriptional regulation is done by exchange of activators and co-repressors on the binding sites.Uses a variation of chip-chip called chip-dsl-chip where they biotinynlate the RNA and use 40 mer primers to ligate small fragments that can be detected on a chip (this avoids the random The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133676990020454562005-12-03T22:15:00.000-08:002005-12-03T22:17:16.263-08:00Keith Elliston, Genestruct"What is the significance of Systems Biology and Regulatory Genomics to industry?"Its clear from vioxx etc that drug companies dont know the molecular action of their drugs, this is where sys biology can helpThere is a 'cognitive barrier' that so much is known that people cant get their head around it. SYstems biology is to filter al that is known to 'actionable' items The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1133676857337910042005-12-03T22:13:00.000-08:002005-12-03T22:14:17.336-08:00Mike Levine, UC Berkeley"Genome regulatory network controlling gastrulation of the Drosophila embryo"His group found 10 noncoding genes regulated by the dorsal gradient in fly and half are miRNAs.orientation of the enhancer is important, if you reverse it you see disrupted effects.Ciona (sea squirt) notochord development network mapped out using a electroporation transgene systemMost of this talkThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133676738153718132005-12-03T22:10:00.000-08:002005-12-03T22:12:18.153-08:00Robert Waterston, University of Washington"Automated Gene Expression Profiling in C. elegans with Continuous Single Cell Resolution"There are exactly 959 cells in an embyro in c. elegans. Theres a complete lineage (the path of how they divided and came to be) of cells by Sulston et al 1983. They did GFP tag of the nuclei to monitor the lineage of each cell using microscopy. Software automaticallyThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1133676556283180392005-12-03T22:08:00.000-08:002005-12-03T22:09:16.283-08:00Stuart Kim, Stanford"Systems Biology of Aging"Coexpression from a compendium of gene expression profiles. They use a comparative approach for orthologs in different organisms to monitor coexpression. Found a cluster in c. elegans that is regulated by aging. Which started his group on the search for the regulatory program of aging.He views aging as a process of the deterioration of robust gene The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1133676376076891582005-12-03T22:05:00.000-08:002005-12-03T22:06:58.796-08:00Eric Davidson, California Institute of Technology (CalTech)"Functional properties of the gene regulatory network for early sea urchin development"Uses BioTapestry software to visualize networks~50 genes with knockout and expression measurements in sea urchin come up with a detailed regulatory network.looked at network evolution between starfish and sea urchin. the cell differentiation topology isThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133676297546035432005-12-03T22:03:00.000-08:002005-12-03T22:05:30.463-08:00David Gifford, MIT"Embryonic Stem Cell Regulatory Networks"This is prety much an explanation of their cell paper earlier this year. However hey shows how they use the approach of joint binding deconvolution (JBD) to discern binding to 50bp Resolution outperforms other methods. Using this they can get a positional prior for motif searching and use that as a seed for motif searching. find that it The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133597665798578522005-12-03T00:13:00.000-08:002005-12-03T00:14:25.800-08:00Leroy Hood, Institute for Systems Biology"An Analysis of Gene Regulatory and Protein Networks in Halobacteria"Halobacter is involved in bio-energy and bio-remediation. Discussed how the study of halobacteria drives the development of new computational tools at ISB.The acidic nature of Halobacter makes it easier to do ab initio protein folding (using rosetta). Does anyone know why that is?Used The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133566347508650112005-12-02T15:32:00.000-08:002005-12-03T00:09:20.563-08:00David Dill, SRI International"The Pathalyzer: a tool for visualization and analysis of signal transduction pathways"Petri Nets as a method for monitoring signal transduction pathways. This group developed software to find active pathways in a network of reactions. Encoded in Maude language layed out using Dot. A query (can gene x,y,z be activated), is known as the reachability problem, and can beThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com1tag:blogger.com,1999:blog-19526875.post-1133565596914799242005-12-02T15:15:00.000-08:002005-12-02T15:41:42.180-08:00Satoru Miyano, University of Toyko"Gene Networks for Drug Target Gene Discovery"Uses knockout/knockdowns and microarray data and bayesian network and nonparametric regression to establish gene links. Optimize parameters to an approximating function using both microarray and the DAG of the bayesian network.Data set of 521 genes from 120 micrarrays each with about 1800 genes each. To compute the The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3tag:blogger.com,1999:blog-19526875.post-1133565103782661832005-12-02T15:09:00.000-08:002005-12-02T15:40:57.903-08:00Edda Klipp, Max Planck Institute for Molecular Genetics"Dynamic modeling of yeast cell stress response"Uses differential equations to define reactions in the system. Handles lack of parameters using a combination of interaction data , text mining, and parameter estimation/optimization approaches. Models the osmotic stress response pathway. The complete model is very complex and includes input The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133564545242614702005-12-02T14:26:00.000-08:002005-12-02T15:40:15.540-08:00Aviv Regev, Harvard University"Trees and Forests: How do molecular networks accommodate change?"Studied the evolution of functional modules from gene expression data in various yeasts. Using a definition of modules as reciprocal best blast hits. Using co-expression from cerevisiae and pombe infer these modules in ~20 other yeast related species.Also tries to reconstruct evolutionary history of The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com4tag:blogger.com,1999:blog-19526875.post-1133562054586174612005-12-02T14:20:00.000-08:002005-12-02T15:38:41.083-08:00Richard Karp, Berkeley"An integrated approach to the reconstruction of molecular networks"Mentioned the flow cytometry approach of lauffenbeger an emerging way to measure abundances accutaely in single cells. Currently can only do up to 13 proteins at once. Using this data they are trying to reconstruct the networks.sAt the end of the talk showed evidence that the netowrk topology (arrows) are The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com0tag:blogger.com,1999:blog-19526875.post-1133561737306883712005-12-02T14:07:00.000-08:002005-12-02T15:39:42.500-08:00Douglas Lauffenburger, MIT"Multivariate Cue/Signal/Response Analysis of Cell Decision Processes" Talked about interesting methods for the survey of signal transduction. Looks at temporal (dynamic) activation over short time points using protein abundance as wall as kinase activity all on a chip. They find that different phosphorylation sites are activated at different times. This is done using aThe Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com2tag:blogger.com,1999:blog-19526875.post-1133560590810563742005-12-02T13:47:00.000-08:002005-12-02T13:59:52.480-08:00This is SB from the 2005 RECOMB Satellite workshop on Systems Biology and Regulatory Genomics in La Jolla, CA. This blog is expose everyone to contents of talks and emerging papers in the field of bioinformatics and systems biology. Guest reports are always welcome and encouraged!Anyway the atmosphere is electric and bionformaitcs is in the air! More to come!Conference web page: http://The Bioinformatics Bloghttp://www.blogger.com/profile/00301576226357844501noreply@blogger.com3