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Article
Open AccessCo-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features
Antimicrobial peptides (AMPs) are oligopeptides that act as crucial components of innate immunity, naturally occur in all multicellular organisms, and are involved in the first line of defense function. Recent...
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Article
Open AccessGSAlign: an efficient sequence alignment tool for intra-species genomes
Personal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Though m...
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Chapter and Conference Paper
KIDER: Knowledge-Infused Document Embedding Representation for Text Categorization
Advancement of deep learning has improved performances on a wide variety of tasks. However, language reasoning and understanding remain difficult tasks in Natural Language Processing (NLP). In this work, we co...
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Article
Open AccessN-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding
N-linked glycosylation is one of the predominant post-translational modifications involved in a number of biological functions. Since experimental characterization of glycosites is challenging, glycosite predi...
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Article
Open AccessStatistical principle-based approach for gene and protein related object recognition
The large number of chemical and pharmaceutical patents has attracted researchers doing biomedical text mining to extract valuable information such as chemicals, genes and gene products. To facilitate gene and...
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Article
Open AccessHierarchical and programmable one-pot synthesis of oligosaccharides
The programmable one-pot oligosaccharide synthesis method was designed to enable the rapid synthesis of a large number of oligosaccharides, using the software Optimer to search Building BLocks (BBLs) with defi...
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Chapter and Conference Paper
An Ensemble Neural Network Model for Benefiting Pregnancy Health Stats from Mining Social Media
Extensive use of social media for communication has made it a desired resource in human behavior intensive tasks like product popularity, public polls and more recently for public health surveillance tasks suc...
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Article
A semantic frame-based intelligent agent for topic detection
Detecting the topic of documents can help readers construct the background of the topic and facilitate document comprehension. In this paper, we propose a semantic frame-based topic detection (SFTD) that simul...
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Article
Open AccessAn expanded evaluation of protein function prediction methods shows an improvement in accuracy
A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their rel...
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Chapter and Conference Paper
A Frame-Based Approach for Reference Metadata Extraction
In this paper, we propose a novel frame-based approach (FBA) and use reference metadata extraction as a case study to demonstrate its advantages. The main contributions of this research are three-fold. First, ...
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Chapter and Conference Paper
An Interaction Pattern Kernel Approach for Protein-Protein Interaction Extraction from Biomedical Literature
Discovering the interactions between proteins mentioned in biomedical literature is one of the core topics of text mining in the life sciences. In this paper, we propose an interaction pattern generation appro...
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Chapter and Conference Paper
Semantic Frame-Based Natural Language Understanding for Intelligent Topic Detection Agent
Detecting the topic of documents can help readers construct the background of the topic and facilitate document comprehension. In this paper, we proposed a semantic frame-based method for topic detection that ...
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Article
Open AccessLipid exposure prediction enhances the inference of rotational angles of transmembrane helices
Since membrane protein structures are challenging to crystallize, computational approaches are essential for elucidating the sequence-to-structure relationships. Structural modeling of membrane proteins requir...
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Article
Open AccessConstruction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension
Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous invol...
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Chapter and Conference Paper
A Composite Kernel Approach for Detecting Interactive Segments in Chinese Topic Documents
Discovering the interactions between persons mentioned in a set of topic documents can help readers construct the background of a topic and facilitate comprehension. In this paper, we propose a rich interactiv...
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Article
Open AccessPrediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing
Identification of subcellular localization in proteins is crucial to elucidate cellular processes and molecular functions in a cell. However, given a tremendous amount of sequence data generated in the post-ge...
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Article
Open AccessLabel-free quantitative proteomics of CD133-positive liver cancer stem cells
CD133-positive liver cancer stem cells, which are characterized by their resistance to conventional chemotherapy and their tumor initiation ability at limited dilutions, have been recognized as a critical targ...
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Chapter and Conference Paper
FISER: An Effective Method for Detecting Interactions between Topic Persons
Discovering the interactions between the persons mentioned in a set of topic documents can help readers construct the background of the topic and facilitate document comprehension. To discover person interacti...
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Article
Open AccessMeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature
DNA methylation is regarded as a potential biomarker in the diagnosis and treatment of cancer. The relations between aberrant gene methylation and cancer development have been identified by a number of recent ...
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Article
Open AccessImproving protein secondary structure prediction based on short subsequences with local structure similarity
When characterizing the structural topology of proteins, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures because it represents the local conformation of a...
