In this week's Science, four articles discuss the genomics of cancer. A team from the Johns Hopkins Kimmel Cancer Center suggests that grouping cancer-associated genes by their function can help simplify the complexity of data from genome studies, while a University of North Carolina at Chapel Hill researcher discusses ways to use whole-genome sequencing data diagnostically and in the development of personalized therapies. A Harvard Medical School team presents an overview of epigenetic regulation of cellular fates and the shared mechanisms of differentiation of healthy and cancerous cells. Finally, a University of Helsinki duo "call[s] for the international development of standards to facilitate the clinical use of germline information arising from diagnostic cancer genome sequencing."

Also in Science, researchers from Stanford University report on the development of a new genetic circuit based on changing the structure of DNA. The team created a three-terminal device architecture that uses bacteriophage serine integrases to "control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA-encoding transcription terminators or a promoter modulate transcription rates," as they write in their paper. The researchers say that the work enables the engineering of amplifying logic gates to control transcription rates within and across various organisms.

Eagle Genomics has released a new version of its Elements of Bioinformatics table, a periodic table-like representation of all the currently available software for bioinformaticians as well as the years they became available.

Much like the chemical periodic table, each tool has a two-letter acronym. Each tool type — aligner, assembler, genome browser, and so on — is assigned a color and tools that fall into that category are grouped together. Clicking on the acronyms opens up a brief description of the software along with information about how to download it and what operating systems to use.

Other features of the table include a slider that allows you to go back to 1970 and see what tools were available back then, and compare the progress that has been made in bioinformatics through the 1970s, 1980s, 1990s, 2000s and right up to the present day.

Finally, the table also distinguishes between open source software, tools that are free for academics, and those that are sold commercially.

The same tools you use for looking up cat videos might also offer scientists new insights into cancer, Jason Bittel writes this week in Slate.

Highlighting a recent paper in the journal Cancer Research, Bittel describes how researchers at the University of Southern California are using an algorithm "similar to Google PageRank" to better understand patterns of lung cancer metastases.

Using data from old lung cancer autopsy reports, the researchers are using Markov chains to work backwards from this data to develop models of how metastatic lung cancer spreads.

As USC researcher Paul Newton tells Bittel: "Basically we're doing the inverse of what Google does. They know the transition probabilities and compute the steady-state, we know the steady-state and compute the transition probabilities."

Using this Markov chain-based analysis, the team has identified regions of the body – such as the liver, lymph nodes, and bones – that appear to trap and halt the spread of metastases, and regions – such as the kidneys and adrenal glands – that appear to promote their proliferation. Bittel notes that these findings could offer "a new way to target treatments and lessen or prevent the spread of cancer."

In Nature this week, a multinational team reported the draft genome of the wheat A-genome progenitor Triticum urartu, or bread wheat, one of the most widely consumed food crops in the world. They identified protein-coding gene models, performed genome structure analyses, and assessed the potential for the draft sequence’s use in studying agronomically important genes and molecular marker development.

Also in Nature, researchers, including those involved in the bread wheat study, published a draft genome of the wild diploid grass Aegilops tauschii, which hybridized with the cultivated tetraploid wheat Triticum turgidum thousands of years ago to give rise to hexaploid wheat. Whole-genome analysis uncovered gene family expansion in Ae. tauschii of “agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance, and grain quality.” The findings give insights into the environmental adaptation of bread wheat and can help in “defining large and complicated genomes of wheat species.”

The New York Times highlights a number of omics tests that are on the horizon to supplement the PSA test that is currently the standard of care for prostate cancer screening.

As the Times notes, the PSA test picks up a large number of cancers that are harmless, so many men with positive test results end up undergoing unnecessary surgery or radiation treatment. Indeed, the US Preventive Services Task Force has recommended against PSA-based screening for prostate cancer because "many men are harmed as a result of prostate cancer screening and few, if any, benefit."

The Times reports that more than a dozen companies are either marketing or plan to launch tests that measure multiple genes or other markers in order to more accurately detect prostate cancer.

Among these firms are a number of companies who will be familiar to GenomeWeb readers, including GenomeDx Biosciences, Metamark Genetics, Hologic, MDxHealth, Mitomics, Opko Health, Beckman Coulter, and Metabolon.

But the "biggest battle" in the market is likely to be between Myriad Genetics and Genomic Health, the Times says, noting that both firms plan to build on their success in the breast cancer testing market. Myriad's Prolaris test is already available and Genomic Health plans to launch its test later this year.

The Netherlands Cancer Institute's Bas van Steensel leads a team tracking nuclear lamina interactions with the genome in individual human cells for a study published in Cell. The researchers came up with a system in which adenine bases became methylated when they come in contact with lamin proteins that line the inner nuclear envelope. With this so-called 'molecular contact memory' method, investigators followed nuclear lamina-genome interactions in human fibrosarcoma cell lines, getting a look at the lamina-associated genome domains making contact with the nuclear lamina at different points of the cell cycle and in relation to histone methylation profiles. "Contact of individual [lamina-associated domains] with the [nuclear lamina] is linked to transcriptional repression and [histone] H3K9 dimethylation in single cells," they found, noting that this process is mediated, in part, by an H3K9 methyltransferase enzyme.

In Cell's annual special review issue, researchers tackle topics pertaining to the organization, dynamics, and function of the nucleus. This look at the genomic DNA-containing organelle includes several reviews focused on the genome — from chromosomal organization and genome stability to epigenetics and transcriptional regulation. In the same issue, a primer article considers the criteria used to define chromothripsis events in cancer genomes and the National Cancer Institute's Tom Misteli muses on the nuclear environment's role in genome function in his essay on the cell biology of genomes.

Researchers based in Japan, the US, and Austria report on findings from an influenza study suggesting that the influenza A virus may be susceptible to a lipid mediator known as protectin D1, or PD1. The group used a bioactive lipid screen in influenza-infected human lung epithelial cells to find PD1, a derivative of omega-3 polyunsaturated fatty acid. Through this screen and subsequent experiments, the investigators determined that PD1 not only curbs influenza A virus replication, but that it could also improve the survival of mice infected with the flu virus — even those with late-stage flu infections.