POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability

The miRNA: a small but powerful RNA for COVID-19

(2021) Song Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Pharmacometabonomics: data processing and statistical analysis

(2021) Jianbo Fu et al.   BRIEFINGS IN BIOINFORMATICS

Machine learning-based prognostic modeling using clinical data and quantitative radiomic features from chest CT images in COVID-19 patients

(2021) Isaac Shiri et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multi-omics Data

(2021) Zhiao Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection

(2021) Matee Ullah et al.   BRIEFINGS IN BIOINFORMATICS

Biolabel-led research pattern positions the effects and mechanisms of Sophorae Tonkinensis radix et rhizome on lung diseases: A novel strategy for computer-aided herbal medicine research based on omics and bioinformatics

(2021) Shuai-nan Zhang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Hybrid dilation and attention residual U-Net for medical image segmentation

(2021) Zekun Wang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

CytomegaloVirusDb: Multi-omics knowledge database for cytomegaloviruses

(2021) Taimoor Khan et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Feature, Function, and Information of Drug Transporter Related Databases

(2021) Jiayi Yin et al.   DRUG METABOLISM AND DISPOSITION

Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction

(2021) Li-Hsin Cheng et al.   Scientific Reports

Feature selection methods on gene expression microarray data for cancer classification: A systematic review

(2021) Esra'a Alhenawi et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach

(2021) Mei Sze Tan et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Deep learning based pipelines for Alzheimer's disease diagnosis: A comparative study and a novel deep-ensemble method

(2021) Andrea Loddo et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A deep learning framework with an embedded-based feature selection approach for the early detection of the Alzheimer's disease

(2021) Nivedhitha Mahendran et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A novel ensemble learning method using multiple objective particle swarm optimization for subject-independent EEG-based emotion recognition

(2021) Rui Li et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Optimization of metabolomic data processing using NOREVA

(2021) Jianbo Fu et al.   Nature Protocols

SYNBIP: synthetic binding proteins for research, diagnosis and therapy

(2021) Xiaona Wang et al.   NUCLEIC ACIDS RESEARCH

VARIDT 2.0: structural variability of drug transporter

(2021) Tingting Fu et al.   NUCLEIC ACIDS RESEARCH

ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures

(2021) Jacob L. Steenwyk et al.   Microbiology Resource Announcements

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

(2020) Fengcheng Li et al.   JOURNAL OF MOLECULAR BIOLOGY

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

MetaFS: Performance assessment of biomarker discovery in metaproteomics

(2020) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel

(2020) Yue Zhang et al.   Journal of Chemical Information and Modeling

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

High glucose‐ROS conditions enhance the progression in cholangiocarcinoma via upregulation of MAN2A2 and CHD8

(2020) Unchalee Thonsri et al.   CANCER SCIENCE

Biomarker discovery by feature ranking: Evaluation on a case study of embryonal tumors

(2020) Matej Petković et al.   COMPUTERS IN BIOLOGY AND MEDICINE

MMEASE: Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis

(2020) Qingxia Yang et al.   Journal of Proteomics

Investigation of Temperature and Feature Size Effects on Deformation of Metals by Superplastic Nanomolding

(2019) Ze Liu   PHYSICAL REVIEW LETTERS

Ensemble feature selection for high-dimensional data: a stability analysis across multiple domains

(2019) Barbara Pes   NEURAL COMPUTING & APPLICATIONS

Revelation of the metabolic pathway of hederacoside C using an innovative data analysis strategy for dynamic multiclass biotransformation experiments

(2019) Laura Peeters et al.   JOURNAL OF CHROMATOGRAPHY A

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

(2019) Yang Zhang et al.   ACS Chemical Neuroscience

Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

(2019) Jing Tang et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and validation of a prognostic proteomic signature for tuberculosis progression: A prospective cohort study

(2019) Adam Penn-Nicholson et al.   PLOS MEDICINE

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

(2019) Daniel P. Donnelly et al.   NATURE METHODS

Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection

(2019) Alejandro Lopez-Rincon et al.   BMC BIOINFORMATICS

Proteomics of Melanoma Response to Immunotherapy Reveals Mitochondrial Dependence

(2019) Michal Harel et al.   CELL

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Inflammation-related biomarkers in major psychiatric disorders: a cross-disorder assessment of reproducibility and specificity in 43 meta-analyses

(2019) Ning Yuan et al.   Translational Psychiatry

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies

(2019) Qingxia Yang et al.   BRIEFINGS IN BIOINFORMATICS

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

Research Techniques Made Simple: Feature Selection for Biomarker Discovery

(2019) Rodrigo Torres et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

(2019) Vera Ignjatovic et al.   JOURNAL OF PROTEOME RESEARCH

Machine learning algorithm validation with a limited sample size

(2019) Andrius Vabalas et al.   PLoS One

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

(2018) Tingting Fu et al.   ACS Chemical Neuroscience

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Relief-Based Feature Selection: Introduction and Review

(2018) Ryan J. Urbanowicz et al.   JOURNAL OF BIOMEDICAL INFORMATICS

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Loss-of-function of IFT88 determines metabolic phenotypes in thyroid cancer

(2018) Junguee Lee et al.   ONCOGENE

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

(2018) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Dealing with Confounders in Omics Analysis

(2018) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

(2018) Feng Zhu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

A proteomic landscape of diffuse-type gastric cancer

(2018) Sai Ge et al.   Nature Communications

A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models

(2018) Shayan Tabe-Bordbar et al.   Scientific Reports

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis

(2018) Sen Liang et al.   Computational and Structural Biotechnology Journal

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

On developing an automatic threshold applied to feature selection ensembles

(2018) B. Seijo-Pardo et al.   Information Fusion

Statistical analysis of proteomics data: A review on feature selection

(2018) Marta Lualdi et al.   Journal of Proteomics

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Robust clinical marker identification for diabetic kidney disease with ensemble feature selection

(2018) Xing Song et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

(2018) Ying Hong Li et al.   BRIEFINGS IN BIOINFORMATICS

Ensembles for feature selection: A review and future trends

(2018) Verónica Bolón-Canedo et al.   Information Fusion

Exploiting the ensemble paradigm for stable feature selection: A case study on high-dimensional genomic data

(2017) Barbara Pes et al.   Information Fusion

Ensemble feature selection: Homogeneous and heterogeneous approaches

(2017) B. Seijo-Pardo et al.   KNOWLEDGE-BASED SYSTEMS

Statistical and integrative system-level analysis of DNA methylation data

(2017) Andrew E. Teschendorff et al.   NATURE REVIEWS GENETICS

Cross-validation failure: Small sample sizes lead to large error bars

(2017) Gaël Varoquaux   NEUROIMAGE

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

Trisomy 21 causes changes in the circulating proteome indicative of chronic autoinflammation

(2017) Kelly D. Sullivan et al.   Scientific Reports

Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry

(2017) Etienne Caron et al.   Cell Reports

Feature Selection Based on Structured Sparsity: A Comprehensive Study

(2017) Jie Gui et al.   IEEE Transactions on Neural Networks and Learning Systems

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

EFS: an ensemble feature selection tool implemented as R-package and web-application

(2017) Ursula Neumann et al.   BioData Mining

Comparative proteomic profiling of the serum differentiates pancreatic cancer from chronic pancreatitis

(2017) Mayank Saraswat et al.   Cancer Medicine

Secretome protein signature of human pancreatic cancer stem-like cells

(2016) Jessica Brandi et al.   Journal of Proteomics

Feature selection methods for big data bioinformatics: A survey from the search perspective

(2016) Lipo Wang et al.   METHODS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics

(2016) Ute Distler et al.   Nature Protocols

A novel features ranking metric with application to scalable visual and bioinformatics data classification

(2016) Quan Zou et al.   NEUROCOMPUTING

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

(2016) Ying Hong Li et al.   PLoS One

Proteomic maps of breast cancer subtypes

(2016) Stefka Tyanova et al.   Nature Communications

Molecular Signatures of Immune Activation and Epithelial Barrier Remodeling Are Enhanced during the Luteal Phase of the Menstrual Cycle: Implications for HIV Susceptibility

(2015) Kenzie Birse et al.   JOURNAL OF VIROLOGY

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Feature Selection Based on the SVM Weight Vector for Classification of Dementia

(2015) Esther E. Bron et al.   IEEE Journal of Biomedical and Health Informatics

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

The Differentiation of Pancreatic Tumor-Initiating Cells by Vitronectin Can Be Blocked by Cilengitide

(2013) Stephanie M. Cabarcas et al.   PANCREAS

STATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS DATA

(2013) Jörg Bartel et al.   Computational and Structural Biotechnology Journal

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

Diabetes mellitus and cancer risk: Review of the epidemiological evidence

(2012) Kentaro Shikata et al.   CANCER SCIENCE

The serum anion gap is altered in early kidney disease and associates with mortality

(2012) Matthew K. Abramowitz et al.   KIDNEY INTERNATIONAL

A Critical Assessment of Feature Selection Methods for Biomarker Discovery in Clinical Proteomics

(2012) Christin Christin et al.   MOLECULAR & CELLULAR PROTEOMICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

A hybrid feature selection method for DNA microarray data

(2011) Li-Yeh Chuang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Generalizability and Simplicity as Criteria in Feature Selection: Application to Mood Classification in Music

(2011) Pasi Saari et al.   IEEE Transactions on Audio Speech and Language Processing

Aliskiren and the calcium channel blocker amlodipine combination as an initial treatment strategy for hypertension control (ACCELERATE): a randomised, parallel-group trial

(2011) Morris J Brown et al.   LANCET

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting

(2011) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating Stability and Comparing Output of Feature Selectors that Optimize Feature Subset Cardinality

(2010) Petr Somol et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes

(2009) Min Zhang et al.   BIOINFORMATICS

Entropy-Based Optimization of Wavelet Spatial Filters

(2008) D. Farina et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Feature Selection with Kernel Class Separability

(2008) Lei Wang   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE