Buried Treasure

"Q: What is Ontology? A: It Depends on What the Meaning of “Is” Is."

Tue, 24 Nov 2009 17:24:49 +0100

“Q: What is Ontology? A: It Depends on What the Meaning of “Is” Is.”

- Clay Shirky

35th FEBS Congress, Gothenburg, Sweden, June 26–July 1, 2010

Tue, 22 Sep 2009 17:41:33 +0200

35th FEBS Congress, Gothenburg, Sweden, June 26–July 1, 2010

"Favor moves that increase options; shy away from moves that end well but require cutting off..."

Mon, 24 Aug 2009 11:28:31 +0200

“Favor moves that increase options; shy away from moves that end well but require cutting off choices; work from strong positions that have many adjoining strong positions. Balance looking ahead to really paying attention to what’s happening now on the whole board.”

- Kevin Kelly

Metagenomic methods for gut bacterial genomics and biofuel production

Fri, 21 Aug 2009 08:25:00 +0200

Jian Xu presenting approaches to use meta-genomics, -transcriptomics, and -metabolomics for studying the gut microbiota as well as organisms useful for the production of biofuels.

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

Fri, 21 Aug 2009 05:36:00 +0200

Francesca Ciccarelli gives a short presentation of how a unified tree
of life was constructed based on concatenated protein alignments.

The impact of Orthology, Paralogy and Homology assignments

Fri, 21 Aug 2009 05:32:00 +0200

Roland Krause explains how to identify orthologous genes and why it is important to discriminate between orthologs and homologs.

Phylogenetic tree reconstruction

Fri, 21 Aug 2009 05:26:00 +0200

Shamil Sunyaev gives a great overview on the many different algorithms and tools for reconstruction of phylogenetic trees.

Estimation of Genomic Instability with Ultradeep Sequencing

Fri, 21 Aug 2009 05:12:00 +0200

Francesca Ciccarelli presents a new database called “Network of Cancer Genes” that contains information on the evolution and interactions of cancer genes (http://bio.ifom-ieo-campus.it/ncg/).

Global Mapping of Copy-Number Variants in Humans by Next-Generation Sequencing

Fri, 21 Aug 2009 04:44:00 +0200

Jan Korbel gives a beautiful example of how even high-resolution maps can be flawed. This old map of the world is pretty accurate except from Australia being absent.

Bridging from molecular simulation to biochemical networks

Fri, 21 Aug 2009 04:40:00 +0200

Rebecca Wade explaining how molecular simulations can be used to estimate parameters needed for modeling of biological systems.

Learning about rates and mechanisms of mutations from functional genomics

Thu, 20 Aug 2009 08:13:00 +0200

Shamil Sunyaev asking the question that I think many researchers should ask themselves more often: why bother?

Evolution of protein complexes

Thu, 20 Aug 2009 08:11:00 +0200

Roland Krause explaining the theoretical foundations for how protein complexes can be derived from tandem-affinity purification data.

Towards systems biology of Mycoplasma pneunomiae

Thu, 20 Aug 2009 08:07:00 +0200

Peer Bork presenting exciting unpublished results. I cannot share the rest of his slides with you, but watch for high-impact papers from his hand in the near future.

Computational analysis of metagenomics data: from oceans to the human body

Thu, 20 Aug 2009 08:04:00 +0200

Jeroen Raes explaining how to find correlations between the functional contents of metagenomes and environmental factors.

Whole-body Systems Approaches for Gut-Microbiota Targeted, Preventive Healthcare

Thu, 20 Aug 2009 02:50:00 +0200

Liping Zhao presenting nice analogies between traditional Chinese medicine, systems biology, and engineering.

Guru Meditation #00000008.00000340

Wed, 19 Aug 2009 07:13:00 +0200

Opening slide from the symposium that takes place in conjunction with the EMBO World Practical Course in Shanghai.

Computational analysis of metagenomics data: basic analyses and why they are not so basic

Tue, 18 Aug 2009 06:23:00 +0200

Jeroen Raes giving an excellent summary of the many challenges in analysis of metagenomics data. In many cases statistically significant differences are do to “something else”: differences in sampling methods (e.g. filter sizes used for ocean samples), sequencing technologies (e.g. differences in read length), and sequence processing (e.g. algorithms used for assembly and gene finding) can all have a major impact on the final results. The details of how each sample was produced and analyzed really matter if you want to compare metagenomes.

Integration of external datasets with metagenomics data: focus environmental variation data

Tue, 18 Aug 2009 04:37:00 +0200

Liping Zhao giving a very interesting introduction to how the gut microbiome interacts with the human body. Gut bacteria are not only crucial for performing metabolic processes in the gut but can also regulate the expression of metabolic proteins encoded by the human genome and thereby cause obesity.

Protein domains in the pre-, post-, and meta-genomics era

Tue, 18 Aug 2009 04:17:00 +0200

Francesca Ciccarelli gave an overview of the definition of protein domains, how to identify them, and domain databases that can be used to scan genomes or metagenomes for protein domains.

Our beloved leader Peer Bork gives us priceless advice at the Yu Garden

Mon, 17 Aug 2009 17:09:00 +0200

I wonder if his advice also applies to posting this photo ;-)