MetaFS: Performance assessment of biomarker discovery in metaproteomics

Assessing the Effectiveness of Direct Data Merging Strategy in Long-Term and Large-Scale Pharmacometabonomics

(2019) Xuejiao Cui et al.   Frontiers in Pharmacology

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

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

Shifts in diversity and function of the bacterial community during the manufacture of Fu brick tea

(2019) Qin Li et al.   FOOD MICROBIOLOGY

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach

(2019) Stefano Levi Mortera et al.   Journal of Proteomics

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Taxonomy dimension reduction for colorectal cancer prediction

(2019) Kaiyang Qu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

iMetaLab 1.0: a web platform for metaproteomics data analysis

(2018) Bo Liao et al.   BIOINFORMATICS

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

(2018) Sheng-Yong Niu et al.   BRIEFINGS IN BIOINFORMATICS

A Novel Approach based on Bipartite Network to Predict Human Microbe-Disease Associations

(2018) Lei Wang et al.   Current Bioinformatics

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

(2018) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

(2018) Xu Zhang et al.   Nature Communications

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

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs` Species Origin, Druglikeness, Target and Pathway

(2018) Xiaofeng Li et al.   Anti-Cancer Agents in Medicinal Chemistry

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

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

Integrated proteomic and metabolomic analysis of a reconstructed three-species microbial consortium for one-step fermentation of 2-keto-l-gulonic acid, the precursor of vitamin C

(2018) Qian Ma et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Statistical analysis of proteomics data: A review on feature selection

(2018) Marta Lualdi et al.   Journal of Proteomics

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

Meta-path methods for prioritizing candidate disease miRNAs

(2017) Xuan Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein–Protein Interaction Network

(2017) Shiheng Lu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein–Protein Interactions from Protein Sequences

(2017) Yanbin Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Challenges and perspectives of metaproteomic data analysis

(2017) Robert Heyer et al.   JOURNAL OF BIOTECHNOLOGY

Novel common variants associated with body mass index and coronary artery disease detected using a pleiotropic cFDR method

(2017) Wan-Qiang Lv et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks

(2017) Bruno Tilocca et al.   Microbiome

Identification of Bone Metastasis-associated Genes of Gastric Cancer by Genome-wide Transcriptional Profiling

(2017) Mingzhe Lin et al.   Current Bioinformatics

A New Approach of Outlier-robust Missing Value Imputation for Metabolomics Data Analysis

(2017) Nishith Kumar et al.   Current Bioinformatics

A Novel Strategy for Large-Scale Metabolomics Study by Calibrating Gross and Systematic Errors in Gas Chromatography–Mass Spectrometry

(2016) Yanni Zhao et al.   ANALYTICAL CHEMISTRY

Power Analysis and Sample Size Determination in Metabolic Phenotyping

(2016) Benjamin J. Blaise et al.   ANALYTICAL CHEMISTRY

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

(2016) R. Heyer et al.   Biotechnology for Biofuels

Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach

(2016) Xiao Wei et al.   BMC GASTROENTEROLOGY

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

(2016) Quan Zou et al.   BMC Systems Biology

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

(2016) Claudia Manzoni et al.   BRIEFINGS IN BIOINFORMATICS

Indexing and encoding based image feature representation with bin overlapped similarity measure for CBIR applications

(2016) S.G. Shaila et al.   JOURNAL OF VISUAL COMMUNICATION AND IMAGE REPRESENTATION

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

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

(2016) Quan Zou et al.   NEUROCOMPUTING

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

(2016) Xu Zhang et al.   Microbiome

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

(2016) Bo Li et al.   Scientific Reports

The effect of microbial colonization on the host proteome varies by gastrointestinal location

(2015) Joshua S Lichtman et al.   ISME Journal

Optimization of Statistical Methods Impact on Quantitative Proteomics Data

(2015) Anna Pursiheimo et al.   JOURNAL OF PROTEOME RESEARCH

A Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections (CAUTIs)

(2015) Christian Lassek et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimal consistency in microRNA expression analysis using reference-gene-based normalization

(2015) Xi Wang et al.   Molecular BioSystems

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Metaproteomic analysis using the Galaxy framework

(2015) Pratik D. Jagtap et al.   PROTEOMICS

A comparison of parametric and non-parametric statistical tests

(2015) P. Sedgwick   BMJ-British Medical Journal

A comparison of parametric and non-parametric statistical tests

(2015) P. Sedgwick   BMJ-British Medical Journal

Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

(2014) F. Bastida et al.   Journal of Proteomics

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Analysis of Glossina palpalis gambiensis and Glossina tachinoides from two distant locations in Burkina Faso using MALDI TOF MS

(2013) Antje Hoppenheit et al.   PARASITOLOGY RESEARCH

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

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

Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface

(2011) Laura L. Presley et al.   INFLAMMATORY BOWEL DISEASES

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY