Emma Hill

Show me the data

![Graphic][1] ©cartoonbank.com. All Rights Reserved. The integrity of data, and transparency about their acquisition, are vital to science. The impact factor data that are gathered and sold by Thomson Scientific (formerly the Institute of Scientific Information, or ISI) have a strong

Metadata matters: access to image data in the real world

Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.

Being positive about selection.

Detecting positive selection at the molecular level has recently become easier and editors of PLoS Biology face the challenge of identifying standards of excellence in the face of burgeoning interest in this field.

Irreproducible Results—a Response to Thomson Scientific

Thomson Scientific has posted a response (1) to our editorial on the reliability of their impact factor data (2). In it, they claim that our interpretation of the communication between our office and their Research Services Group was “misleading and inaccurate.” We have already published some excerpts from these communications in our previous editorial. For proprietys sake, however, we have refrained from publishing internal Thomson Scientific e-mails, sent to us accidentally, which substantiate our claim that they could not provide us with the original data underlying the published 2006 impact factor calculations.

Show me the data.

The integrity of data, and transparency about their acquisition, are vital to science. The impact factor data that are gathered and sold by Thomson Scientific (formerly the Institute of Scientific Information, or ISI) have a strong influence on the scientific community, affecting decisions on where to publish, whom to promote or hire,1 the success of grant applications,2 and even salary bonuses.3 Yet, members of the community seem to have little understanding of how impact factors are determined, and, to our knowledge, no one has independently audited the underlying data to validate their reliability.

Protein structure prediction.

Protein structure prediction has matured over the past few years to the point that even fully automated methods can provide reasonably accurate three-dimensional models of protein structures. However, until now it has not been possible to develop programs able to perform as well as human experts, who are still capable of systematically producing better models than automated servers. Although the precise details of protein structure prediction procedures are different for virtually every protein, this chapter describes a generic procedure to obtain a three-dimensional protein model starting from the amino acid sequence. This procedure takes advantage both of programs and servers that have been shown to perform best in blind tests and of the current knowledge about evolutionary relationships between proteins, gained from detailed analyses of protein sequence, structure, and functional data.

Super-coil me: Sizing up centromeric nucleosomes

Every chromosome needs a centromere for proper segregation during cell division. Centromeric chromatin wraps around histones, providing an anchor for kinetochore proteins and spindle attachment. It is clear why cells need centromeres, but how they form and what they look like is less so. Recent reports extend our understanding of chaperones involved in centromere formation. And other accounts of half-sized, right-handed nucleosomes have created an unexpected twist.

You Wrote It; You Own It!

Authors of papers published in Rockefeller University Press journals (The Journal of Cell Biology, The Journal of Experimental Medicine, or The Journal of General Physiology) now retain copyright to their published work. This permits authors to reuse their own work in any way, as long as they attribute it to the original publication. Third parties may use our published materials under a Creative Commons license, six months after publication.

You wrote it; you own it!

Authors of papers published in Rockefeller University Press journals (The Journal of Cell Biology, The Journal of Experimental Medicine, or The Journal of General Physiology) now retain copyright to their published work. This permits authors to reuse their own work in any way, as long as they attribute it to the original publication. Third parties may use our published materials under a Creative Commons license, six months after publication.

Marsupial genome sheds light on the evolution of immunity.

All organisms need defense systems to ward off infection. These defenses typically mobilize in response to antigens, bits of protein fragments derived from a pathogen. Vertebrates have a superbly efficient system of adaptive immunity that uses proteins to recognize and bind billions of different antigens via a process known as antigen presentation. Ultimately, this process leads to removal of the antigen. Antigen binding proteins are encoded within one large genomic region known as the major histocompatibility complex (MHC). The high level of polymorphism, or variation, in this genomic region allows the adaptive immune system to keep pace with an ever-changing array of antigens.