ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction.

Motivation: The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions.

A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondence.

Background: Liquid chromatography-mass spectrometry is a popular technique for high-throughput protein, lipid, and metabolite comparative analysis. Such statistical comparison of millions of data points requires the generation of an inter-run correspondence. Though many techniques for generating this correspondence exist, few if any, address certain well-known run-to-run LC-MS behaviors such as elution order swaps, unbounded retention time swaps, missing data, and significant differences in abundance.

Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view.

Background: For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress towards solving any of these disparate problems depends upon overcoming the common challenge of interpreting the large data sets generated. Despite interim successes, many data interpretation problems in mass spectrometry are still challenging.

LC-MS alignment in theory and practice: a comprehensive algorithmic review.

Liquid chromatography-mass spectrometry is widely used for comparative replicate sample analysis in proteomics, lipidomics and metabolomics. Before statistical comparison, registration must be established to match corresponding analytes from run to run. Alignment, the most popular correspondence approach, consists of constructing a function that warps the content of runs to most closely match a given reference sample.

Controlling for confounding variables in MS-omics protocol: why modularity matters.

As the field of bioinformatics research continues to grow, more and more novel techniques are proposed to meet new challenges and improvements upon solutions to long-standing problems. These include data processing techniques and wet lab protocol techniques. Although the literature is consistently thorough in experimental detail and variable-controlling rigor for wet lab protocol techniques, bioinformatics techniques tend to be less described and less controlled.

Rubabel: wrapping open Babel with Ruby.

Background: The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose. Although high-level language wrappers have been implemented, more can be done to leverage the intuitiveness of object-orientation, the paradigms of high-level languages, and the extensibility of languages such as Ruby.

Statistical agglomeration: peak summarization for direct infusion lipidomics.

Motivation: Quantification of lipids is a primary goal in lipidomics. In direct infusion/injection (or shotgun) lipidomics, accurate downstream identification and quantitation requires accurate summarization of repetitive peak measurements. Imprecise peak summarization multiplies downstream error by propagating into species identification and intensity estimation.

A general model for continuous noninvasive pulmonary artery pressure estimation.

Elevated pulmonary artery pressure (PAP) is a significant healthcare risk. Continuous monitoring for patients with elevated PAP is crucial for effective treatment, yet the most accurate method is invasive and expensive, and cannot be performed repeatedly. Noninvasive methods exist but are somewhat inaccurate, expensive, and cannot be used for continuous monitoring.

Phylogenetic search through partial tree mixing.

Background: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

Noninvasive diagnosis of pulmonary hypertension using heart sound analysis.

Right-heart catheterization is the most accurate method for measuring pulmonary artery pressure (PAP). It is an expensive, invasive procedure, exposes patients to the risk of infection, and is not suited for long-term monitoring situations. Medical researchers have shown that PAP influences the characteristics of heart sounds.