Archive by category | Genomics

[Research highlight] Mycoplasma rebooted

Upshot of a series of four papers published over the last years (Gibson et al, 2010, Lartigue et al, 2009, Gibson et al, 2008, Lartigue et al, 2007), J. Craig Venter’s team now reports the successful transplantation of a chemically synthesized genome into a host bacterial cell (Gibson et al, 2010). As proof of principle, a slightly altered Mycoplasma mycoides genome (JCVI-syn1.0) was synthesized, assembled and transplanted into M. capricolum recipient cells.  Read more

SciFoo: scientific fireworks

SciFoo: scientific fireworks

In his list of eight ‘generative’ values (Better Than Free), Kevin Kelly includes ’embodiment’–the actual physical realization of an item or event which could be otherwise freely distributed over the web. While we are all ‘hyperlinked’ on the Internet, the value of those unique qualities that cannot be generated or “copied” on the web is dramatically increased. The type of intense emulation and shared excitement sparked at the recent Science Foo Camp (SciFoo 2008), organized by Nature, Google and O’Reilly, gave a wonderful example of the unique value of direct human exchange during an exclusive event bringing together roughly 200 top scientists, ‘geeks’ and other technologists at the Googleplex in Mountain View, California.  Read more

Top-down mapping of gene regulatory pathways

Top-down mapping of gene regulatory pathways

In a very recent lecture (see full video from NIH VideoCasting) given for the NIH Systems Biology Special Interest Group, Trey Ideker presents a great overview of the various strategies his group has been developing in the recent years in order to integrate multiple types of large scale datasets. While one of the most pervasive ‘meme’ about high-throughput measurement is that they are “notoriously unreliable” (see Hakes et al, 2008, for a recent example), Trey beautifully illustrates how predictive computational models and novel biological insights can be generated by sophisticated data integration strategies. Three types of applications are presented in his talk:  … Read more

Personal genomics for a fistful of dollars

Personal genomics for a fistful of dollars

The wave of personal genomics is progressing rapidly. A string of four papers appeared recently (Porreca et al, 2007, Albert et al, 2007, Okou et al 2007, Hodges et al, 2007) reporting on microarrray-based technologies that enable the enrichment of selected genomic fragments in a single massively multiplexed reaction, thus greatly facilitating subsequent resequencing of pre-defined portions of the human genome (eg all coding exons). These technologies are expected to reduce dramatically the cost of targeted resequencing of individual genomes.  Read more

The broken double helix

The broken double helix

Contrary to what Charlotte Hunt-Grubbe predicted in her interview published in the Sunday Times (The elementary DNA of Dr Watson), James Watson did not “enthusiastically counter the inevitable criticisms” that arose from his unacceptable comments on racial differences in intelligence. After being suspended, he apologized and finally resigned yesterday as Chancellor of Cold Spring Harbor Laboratory (Watson’s statement).  Read more

J Craig Venter’s Genome

J Craig Venter’s Genome

Many others have abundantly commented on the publication of Craig Venter’s genome this week in PLOS Biology (Levy et al, 2007). The sequence of his full diploid genome (HuRef) reveals that the degree of genetic variability between maternal and paternal chromosomes is much higher (0.5%) than expected. Part of this variability is due to insertion/deletions (indels represent only 22% of variant events but amount to up to 75% of the variant nucleotides), alterations that are typically missed by SNP genotyping (SNPs represent 78% of the variants). Copy number variations (62, amounting to 10Mb) are also reported, albeit not determined by sequencing but via microarray genomic hybridization. With regard to variability in gene exons, the analysis shows that at least 44% of the genes are in the heterozygous state.  Read more

E. coli counts in base 117

E. coli counts in base 117

Finding general laws on the organization principle of living organisms is a particularly difficult task in biology but certainly a central one in systems biology. Part of the difficulty in this endeavor is probably linked to the fact that “by its very nature, life is both contingent and particular, each organism the product of eons of tinkering, of building on what had accumulated over the course of a particular evolutionary trajectory” (Keller, 2007, see also our post). Such laws are thus particularly significant when they emerge from evolutionary constraints alone. In a recent paper published in PNAS, Matthew Wright and colleagues may well provide such an example by looking at the “”http://dx.doi.org/10.1073/pnas.0610776104″>chromosomal periodicity of evolutionarily conserved gene pairs” (Wright et al, 2007).  Read more

The Human (Genetic) Disease Network

The Human (Genetic) Disease Network

The relationship between genetic mutations and human diseases is often complex and ambiguous: a given disease can be associated with mutations in distinct genes and, conversely, mutations in a given gene can be associated with several diseases. Can this many-to-many relationship be exploited to construct a human disease network and extract information on the human disease landscape?  Read more