Perceived quality of care and choice of healthcare provider in informal settlements.

When a person chooses a healthcare provider, they are trading off cost, convenience, and a latent third factor: "perceived quality". In urban areas of lower- and middle-income countries (LMICs), including slums, individuals have a wide range of choice in healthcare provider, and we hypothesised that people do not choose the nearest and cheapest provider. This would mean that people are willing to incur additional cost to visit a provider they would perceive to be offering better healthcare.

Div-BLAST: diversification of sequence search results.

Sequence similarity tools, such as BLAST, seek sequences most similar to a query from a database of sequences. They return results significantly similar to the query sequence and that are typically highly similar to each other. Most sequence analysis tasks in bioinformatics require an exploratory approach, where the initial results guide the user to new searches.

Smolign: a spatial motifs-based protein multiple structural alignment method.

Availability of an effective tool for protein multiple structural alignment (MSTA) is essential for discovery and analysis of biologically significant structural motifs that can help solve functional annotation and drug design problems. Existing MSTA methods collect residue correspondences mostly through pairwise comparison of consecutive fragments, which can lead to suboptimal alignments, especially when the similarity among the proteins is low. We introduce a novel strategy based on: building a contact-window based motif library from the protein structural data, discovery and extension of common alignment seeds from this library, and optimal superimposition of multiple structures according to these alignment seeds by an enhanced partial order curve comparison method.

MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs.

Background: Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing.

Integrated search and alignment of protein structures.

Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing.

An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories.

Background: Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them.

CellTrack: an open-source software for cell tracking and motility analysis.

Motivation: Cell motility is a critical part of many important biological processes. Automated and sensitive cell tracking is essential to cell motility studies where the tracking results can be used for diagnostic or curative decisions and where mathematical models can be developed to deepen our understanding of the mechanisms underlying cell motility.

Results: We have developed CellTrack: a self-contained, extensible, and cross-platform software package for cell tracking and motility analysis.

Enhanced partial order curve comparison over multiple protein folding trajectories.

Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them.

Predicting the binding affinity of MHC class II peptides.

MHC (Major Histocompatibility Complex) proteins are categorized under the heterodimeric integral membrane proteins. The MHC molecules are divided into 2 subclasses, class I and class II. Two classes differ from each other in size of their binding pockets.

LFM-Pro: a tool for detecting significant local structural sites in proteins.

Motivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.