IEEE/ACM Transactions on Computational Biology and Bioinformatics

We present the results of the BioCreative II.5 evaluation in association with the FEBS Letters experiment, where authors created Structured Digital Abstracts to capture information about protein-protein interactions. The BioCreative II.5 challenge ...

We participated (as Team 9) in the Article Classification Task of the Biocreative II.5 Challenge: binary classification of full-text documents relevant for protein-protein interaction. We used two distinct classifiers for the online and offline ...

The interactor normalization task (INT) is to identify genes that play the interactor role in protein-protein interactions (PPIs), to map these genes to unique IDs, and to rank them according to their normalized confidence. INT has two subtasks: gene ...

The selection of protein interaction documents is one important application for biology research and has a direct impact on the quality of downstream BioNLP applications, i.e., information extraction and retrieval, summarization, QA, etc. The ...

This paper describes a Biological Literature Miner (BioLMiner) system and its implementation. BioLMiner is a text mining system for biological literature, whose purpose is to extract useful information from biological literature, including gene and ...

Currently, relation extraction (RE) and event extraction (EE) are the two main streams of biological information extraction. In 2009, the majority of these RE and EE research efforts were centered around the BioCreative II.5 Protein-Protein Interaction (...

The team at the University of Wisconsin-Milwaukee developed an information retrieval and machine learning framework. Our framework requires only the standardized training data and depends upon minimal external knowledge resources and minimal parsing. ...

We introduce a system developed for the BioCreative II.5 community evaluation of information extraction of proteins and protein interactions. The paper focuses primarily on the gene normalization task of recognizing protein mentions in text and mapping ...

We describe a system for the detection of mentions of protein-protein interactions in the biomedical scientific literature. The original system was developed as a part of the OntoGene project, which focuses on using advanced computational linguistic ...

Proteins and their interactions govern virtually all cellular processes, such as regulation, signaling, metabolism, and structure. Most experimental findings pertaining to such interactions are discussed in research papers, which, in turn, get curated ...

We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alignment and three-way sequence alignment (or median), both with affine gap costs,...

Haplotype data play a relevant role in several genetic studies, e.g., mapping of complex disease genes, drug design, and evolutionary studies on populations. However, the experimental determination of haplotypes is expensive and time-consuming. This ...

Motifs are overrepresented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein function. When motifs are located in short sequence fragments, as in ...

As a well-established feature selection algorithm, principal component analysis (PCA) is often combined with the state-of-the-art classification algorithms to identify cancer molecular patterns in microarray data. However, the algorithm's global feature ...

This paper integrates the signal, context, and structure features for genome-wide human promoter recognition, which is important in improving genome annotation and analyzing transcriptional regulation without experimental supports of ESTs, cDNAs, or ...

Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be ...

We show that subtree prune and regraft (uSPR) distance on unrooted trees is fixed parameter tractable with respect to the distance. We also make progress on a conjecture of Steel [9] on the preservation of uSPR distance under chain reduction, improving ...