Showing papers by "Philip E. Bourne published in 2014"

Ten Simple Rules for Better Figures

Abstract: Scientific visualization is classically defined as the process of graphically displaying scientific data. However, this process is far from direct or automatic. There are so many different ways to represent the same data: scatter plots, linear plots, bar plots, and pie charts, to name just a few. Furthermore, the same data, using the same type of plot, may be perceived very differently depending on who is looking at the figure. A more accurate definition for scientific visualiza- tion would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface; rather, see [1,2] for introductory work. Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.

Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine

Abstract: Genome-Wide Association Studies (GWAS), whole genome sequencing, and high-throughput omics techniques have generated vast amounts of genotypic and molecular phenotypic data. However, these data have not yet been fully explored to improve the effectiveness and efficiency of drug discovery, which continues along a one-drug-one-target-one-disease paradigm. As a partial consequence, both the cost to launch a new drug and the attrition rate are increasing. Systems pharmacology and pharmacogenomics are emerging to exploit the available data and potentially reverse this trend, but, as we argue here, more is needed. To understand the impact of genetic, epigenetic, and environmental factors on drug action, we must study the structural energetics and dynamics of molecular interactions in the context of the whole human genome and interactome. Such an approach requires an integrative modeling framework for drug action that leverages advances in data-driven statistical modeling and mechanism-based multiscale modeling and transforms heterogeneous data from GWAS, high-throughput sequencing, structural genomics, functional genomics, and chemical genomics into unified knowledge. This is not a small task, but, as reviewed here, progress is being made towards the final goal of personalized medicines for the treatment of complex diseases.

Ten simple rules for writing a PLOS ten simple rules article.

Abstract: Would Newton retweet your post on Twitter? How would Einstein view open source software? How would Darwin have handled a Wikipedia edit war? The way we do science is changing almost as fast as the volume of our data. Advice is needed; however, advice on leading a successful scientific life is usually confined to outdated memoirs, unrecorded weekly lab meetings, neglected blogs, or casual conversations at a conference. When we are faced with the challenges of how to be the best scientist we can, our instinctive reaction is to follow our usual pattern of inquiry—search the literature. This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner. Many topics cover the professional (or “soft”) skills that are necessary for a modern scientific career, but are not part of a formal scientific education. [PB: Sad but true—teaching such skills should be a no-brainer.] These articles represent an invaluable chance to pass on advice and knowledge in a way that can be widely distributed, formally recognised, and—as an added benefit—cited. If (like us) you have read some articles in the Ten Simple Rules collection and appreciated their value, you may feel the urge to write one of your own. The collection provides a succinct and engaging format for advice on these skills. However, coming up with an article on soft skills need not be hard. Perhaps you have some insight, experience, or wisdom to impart. How would you do that? Is there practical advice for contributing to the Ten Simple Rules collection already available? What can we learn from the existing articles in the collection? If only there was an article with ten simple rules for writing a PLOS Ten Simple Rules article. If only that article could be peppered with insightful comments from the founder of the collection: Philip E. Bourne. This is that article.

A turn-key approach for large-scale identification of complex posttranslational modifications.

Abstract: The conjugation of complex post-translational modifications (PTMs) such as glycosylation and Small Ubiquitin-like Modification (SUMOylation) to a substrate protein can substantially change the resulting peptide fragmentation pattern compared to its unmodified counterpart, making current database search methods inappropriate for the identification of tandem mass (MS/MS) spectra from such modified peptides. Traditionally it has been difficult to develop new algorithms to identify these atypical peptides because of the lack of a large set of annotated spectra from which to learn the altered fragmentation pattern. Using SUMOylation as an example, we propose a novel approach to generate large MS/MS training data from modified peptides and derive an algorithm that learns properties of PTM-specific fragmentation from such training data. Benchmark tests on data sets of varying complexity show that our method is 80–300% more sensitive than current state-of-the-art approaches. The core concepts of our method are readily applicable to developing algorithms for the identifications of peptides with other complex PTMs.

Ten simple rules for approaching a new job.

Abstract: At some point in your professional career, you will be faced with a job interview. This may range from visiting a graduate school where you already have a placement should you want it, to interviewing for a very high-profile position in industry, government, or academia where there is significant competition for that job. Thinking both as a job applicant and a job interviewer about how I have approached job situations over the years before, during, and after the interview and how those situations have turned out, I can offer the following ten simple rules as you prepare. Where appropriate, I conclude a rule with an illustrative scenario for a junior- and/or senior-level position since while the general principles are universal, how they are applied depends somewhat on the seniority of the position.