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Using distant supervision to augment manually annotated data for relation extraction

Conceptualization: Gang Li, K. Vijay-Shanker. Data curation: Peng Su, Gang Li. Formal analysis: Peng Su, K. Vijay-Shanker. Funding acquisition: Cathy Wu, K. Vijay-Shanker. Methodology: Peng Su, Gang Li, K. Vijay ... -Shanker. Software: Peng Su, Gang Li. Writing ? original draft: Peng Su, Cathy Wu, K. Vijay-Shanker. Writing ? review & editing: Peng Su, Gang Li, Cathy Wu, K. Vijay-Shanker. 15 / 17 10. 11. Peng Y, Gupta

eGARD: Extracting associations between genomic anomalies and drug responses from text

Samir Gupta for helping with typing of phrases. Author Contributions Conceptualization: A. S. M. Ashique Mahmood, Shruti Rao, Peter McGarvey, Cathy Wu, Subha Madhavan, K. Vijay-Shanker. Data curation ... : A. S. M. Ashique Mahmood, Shruti Rao, Peter McGarvey. 16 / 19 Funding acquisition: Peter McGarvey, Cathy Wu, Subha Madhavan, K. Vijay-Shanker. Investigation: A. S. M. Ashique Mahmood, Shruti Rao

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse...

Safety and efficacy of paliperidone extended-release in Chinese patients with schizophrenia: a 24-week, open-label extension of a randomized, double-blind, placebo-controlled study

Huafang Li,2 Yanning Liu,3 Cathy Wu,3 Qingqi Wu,3 Isaac Nuamah,4 Jianguo Shi,5 Shiping Xie,6 Gang Wang,7 Srihari Gopal4 1Peking University 6th Hospital, Peking University Institute of Mental Health, Key ... and medical research O r i g i N a l r e s e a r c h hongyan Zhang 1 huafang li 2 Yanning liu 3 cathy Wu 3 Qingqi Wu3 isaac Nuamah 4 Jianguo shi 5 shiping Xie 6 gang Wang 7 srihari gopal 4

Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We...

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

Background The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a characterized function and are annotated as hypothetical or uncharacterized. While homology-based methods are useful, and work well for sequences with sequence identities...

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a characterized function and are annotated as hypothetical or uncharacterized. While homology-based methods are useful, and work well for sequences with sequence identities above 50...

Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map

Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI), leading to over one million abstracts associated with “MI” and “Cardiovascular Diseases” in PubMed. Accumulation of the research results imposed a challenge to integrate and interpret these results. To address this problem and better understand how the left ventricle...

A framework for biomedical figure segmentation towards image-based document retrieval

The figures included in many of the biomedical publications play an important role in understanding the biological experiments and facts described within. Recent studies have shown that it is possible to integrate the information that is extracted from figures in classical document classification and retrieval tasks in order to improve their accuracy. One important observation...

Elevated FGF21 secretion, PGC-1α and ketogenic enzyme expression are hallmarks of iron–sulfur cluster depletion in human skeletal muscle

Iron–sulfur (Fe-S) clusters are ancient enzyme cofactors found in virtually all life forms. We evaluated the physiological effects of chronic Fe-S cluster deficiency in human skeletal muscle, a tissue that relies heavily on Fe-S cluster-mediated aerobic energy metabolism. Despite greatly decreased oxidative capacity, muscle tissue from patients deficient in the Fe-S cluster...

Update on genome completion and annotations: Protein Information Resource

The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt -- the Universal Protein Resource -- which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (SuperFamily) classification system is central to the PIR/UniProt functional annotation of proteins, providing...

The representation of protein complexes in the Protein Ontology (PRO)

Background Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these...

BioThesaurus: a web-based thesaurus of protein and gene names

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase. Currently covering more than two million proteins, BioThesaurus consists of over 2.8 million names extracted from multiple molecular biological databases according to the database cross-references in iProClass. The BioThesaurus...

Proteomic Analysis of Pathways Involved in Estrogen-Induced Growth and Apoptosis of Breast Cancer Cells

Background Estrogen is a known growth promoter for estrogen receptor (ER)-positive breast cancer cells. Paradoxically, in breast cancer cells that have been chronically deprived of estrogen stimulation, re-introduction of the hormone can induce apoptosis. Methodology/Principal Findings Here, we sought to identify signaling networks that are triggered by estradiol (E2) in isogenic...

Back-propagation and counter-propagation neural networks for phylogenetic classification of ribosomal RNA sequences

A neural network system has been developed for rapid and accurate classification of ribosomal RNA sequences according to phylogenetic relationship. The molecular sequences are encoded into neural input vectors using an n-gram hashing method. A SVD (singular value decomposition) method is used to compress and reduce the size of long and sparse ngram input vectors. The neural...

Neural networks for full-scale protein sequence classification: Sequence encoding with singular value decomposition

A neural network classification method has been developed as an alternative approach to the search/organization problem of protein sequence databases. The neural networks used are three-layered, feed-forward, back-propagation networks. The protein sequences are encoded into neural input vectors by a hashing method that counts occurrences ofn-gram words. A new SVD (singular value...

Neural Networks for Full-Scale Protein Sequence Classification: Sequence Encoding with Singular Value Decomposition

A neural network classification method has been developed as an alternative approach to the search/organization problem of protein sequence databases. The neural networks used are three-layered, feed-forward, back-propagation networks. The protein sequences are encoded into neural input vectors by a hashing method that counts occurrences of n-gram words. A new SVD (singular value...

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

associations. The Skate (Leucoraja erinacea) genome database, presented by Cathy Wu, has employed a different approach to community engagement, through workshops and annotation jamborees (3). This approach ... Sobral, Virginia Bioinformatics Institute, USA; Granger G. Sutton, JCVI, USA; Cathy Wu, Protein Information Resource, USA; Jasmine Young, PDB, USA. The local arrangement committee provided excellent