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HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach.
Nucleic acids research , 2004 | Pubmed ID: 15448186
HYPROSP II--a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.
Bioinformatics (Oxford, England) Aug, 2005 | Pubmed ID: 15932901
GANA--a genetic algorithm for NMR backbone resonance assignment.
Nucleic acids research , 2005 | Pubmed ID: 16093550
A new similarity measure among protein sequences.
Proceedings. IEEE Computer Society Bioinformatics Conference , 2003 | Pubmed ID: 16452810
Various criteria in the evaluation of biomedical named entity recognition.
BMC bioinformatics Feb, 2006 | Pubmed ID: 16504116
Multi-Q: a fully automated tool for multiplexed protein quantitation.
Journal of proteome research Sep, 2006 | Pubmed ID: 16944945
HYPLOSP: a knowledge-based approach to protein local structure prediction.
Journal of bioinformatics and computational biology Dec, 2006 | Pubmed ID: 17245815
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition.
BMC bioinformatics Dec, 2006 | Pubmed ID: 17254295
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).
BMC bioinformatics Feb, 2007 | Pubmed ID: 17326819
Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function.
Computational systems bioinformatics. Computational Systems Bioinformatics Conference , 2006 | Pubmed ID: 17369623
Protein subcellular localization prediction based on compartment-specific biological features.
Computational systems bioinformatics. Computational Systems Bioinformatics Conference , 2006 | Pubmed ID: 17369650
The Multi-Q web server for multiplexed protein quantitation.
Nucleic acids research Jul, 2007 | Pubmed ID: 17553828
BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features.
BMC bioinformatics Sep, 2007 | Pubmed ID: 17764570
Protein subcellular localization prediction based on compartment-specific features and structure conservation.
BMC bioinformatics Sep, 2007 | Pubmed ID: 17825110
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function.
Journal of proteome research Feb, 2008 | Pubmed ID: 18081245
PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis.
Proteins Aug, 2008 | Pubmed ID: 18260102
Bioinformatics research in the Asia Pacific: a 2007 update.
BMC bioinformatics , 2008 | Pubmed ID: 18315840
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles.
BMC bioinformatics , 2008 | Pubmed ID: 18315856
BIOSMILE web search: a web application for annotating biomedical entities and relations.
Nucleic acids research Jul, 2008 | Pubmed ID: 18515840
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.
Bioinformatics (Oxford, England) Dec, 2008 | Pubmed ID: 18974075
Emerging strengths in Asia Pacific bioinformatics.
BMC bioinformatics Dec, 2008 | Pubmed ID: 19091008
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation.
BMC bioinformatics Dec, 2008 | Pubmed ID: 19091017
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information.
BMC bioinformatics Dec, 2008 | Pubmed ID: 19091029
Triplet supertree heuristics for the tree of life.
BMC bioinformatics Jan, 2009 | Pubmed ID: 19208181
A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data.
Bioinformatics (Oxford, England) Apr, 2009 | Pubmed ID: 19237446
Predicting helix-helix interactions from residue contacts in membrane proteins.
Bioinformatics (Oxford, England) Apr, 2009 | Pubmed ID: 19244388
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.
Nucleic acids research Jul, 2009 | Pubmed ID: 19528069
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.
Molecular & cellular proteomics : MCP Jan, 2010 | Pubmed ID: 19752006
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach.
BMC bioinformatics Dec, 2009 | Pubmed ID: 19958518
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features.
BMC bioinformatics Dec, 2009 | Pubmed ID: 19958519
Automated generic analysis tools for protein quantitation using stable isotope labeling.
Methods in molecular biology (Clifton, N.J.) , 2010 | Pubmed ID: 20013376
An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion.
Journal of proteome research Nov, 2010 | Pubmed ID: 20815410
Improving protein secondary structure prediction based on short subsequences with local structure similarity.
BMC genomics Dec, 2010 | Pubmed ID: 21143813
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins.
Nucleic acids research Jan, 2011 | Pubmed ID: 21177659
Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas.
PloS one , 2011 | Pubmed ID: 21637843
Comparative proteomic analysis of proteins involved in the tumorigenic process of seminal vesicle carcinoma in transgenic mice.
International journal of proteomics , 2010 | Pubmed ID: 22084680
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.
PloS one , 2011 | Pubmed ID: 22163274
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature.
BMC bioinformatics Dec, 2011 | Pubmed ID: 22168213
Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.
PloS one , 2012 | Pubmed ID: 22457753
Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures.
PloS one , 2012 | Pubmed ID: 22496884
Coreference resolution of medical concepts in discharge summaries by exploiting contextual information.
Journal of the American Medical Informatics Association : JAMIA Sep-Oct, 2012 | Pubmed ID: 22556185
Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.
PloS one , 2012 | Pubmed ID: 22701576
Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.
PloS one , 2012 | Pubmed ID: 22848404
Label-free quantitative proteomics of CD133-positive liver cancer stem cells.
Proteome science Nov, 2012 | Pubmed ID: 23170877
Decoding the disease-associated proteins encoded in the human chromosome 4.
Journal of proteome research Jan, 2013 | Pubmed ID: 23256888
Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing.
BMC bioinformatics , 2012 | Pubmed ID: 23282098
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes.
Database : the journal of biological databases and curation , 2013 | Pubmed ID: 23406793
Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.
Journal of proteome research May, 2013 | Pubmed ID: 23560440
Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension.
BMC genomics Jul, 2013 | Pubmed ID: 23879630
TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries.
Journal of biomedical informatics Dec, 2013 | Pubmed ID: 24060600
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.
BMC bioinformatics Oct, 2013 | Pubmed ID: 24112406
Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.
PloS one , 2013 | Pubmed ID: 24146760
CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.
PloS one , 2014 | Pubmed ID: 24897343
LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations.
Database : the journal of biological databases and curation , 2014 | Pubmed ID: 25168057
Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information.
Analytical chemistry Feb, 2015 | Pubmed ID: 25543920
MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS² approach.
Analytical chemistry Feb, 2015 | Pubmed ID: 25629585
A context-aware approach for progression tracking of medical concepts in electronic medical records.
Journal of biomedical informatics Dec, 2015 | Pubmed ID: 26432355
Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics.
Journal of proteome research Dec, 2015 | Pubmed ID: 26549055
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.
Nucleic acids research Jan, 2016 | Pubmed ID: 26590260
iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination.
PloS one , 2016 | Pubmed ID: 26784691
MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.
Nucleic acids research Jul, 2016 | Pubmed ID: 27084943
MET network in PubMed: a text-mined network visualization and curation system.
Database : the journal of biological databases and curation , 2016 | Pubmed ID: 27242035
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.
Database : the journal of biological databases and curation , 2016 | Pubmed ID: 27524807
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database : the journal of biological databases and curation , 2016 | Pubmed ID: 27589962
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Genome biology 09, 2016 | Pubmed ID: 27604469
Kart: a divide-and-conquer algorithm for NGS read alignment.
Bioinformatics (Oxford, England) Aug, 2017 | Pubmed ID: 28379292
DART - a fast and accurate RNA-seq mapper with a partitioning strategy.
Bioinformatics (Oxford, England) 09, 2017 | Pubmed ID: 28968831
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.
Nucleic acids research Jan, 2018 | Pubmed ID: 29126174
iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm.
Analytical chemistry 12, 2017 | Pubmed ID: 29165996
LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task.
Database : the journal of biological databases and curation 01, 2018 | Pubmed ID: 30346607
Hierarchical and programmable one-pot synthesis of oligosaccharides.
Nature communications 12, 2018 | Pubmed ID: 30523255
Statistical principle-based approach for gene and protein related object recognition.
Journal of cheminformatics Dec, 2018 | Pubmed ID: 30560325
Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.
Database : the journal of biological databases and curation 01, 2019 | Pubmed ID: 30809637
WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline.
Analytical chemistry Aug, 2019 | Pubmed ID: 31305071
Medical knowledge infused convolutional neural networks for cohort selection in clinical trials.
Journal of the American Medical Informatics Association : JAMIA Aug, 2019 | Pubmed ID: 31390470