Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

Hierarchical pattern recognition in milking parameters predicts mastitis prevalence

(2018) Esmaeil Ebrahimie et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates

(2018) Ibrahim O. Alanazi et al.   GENE

A large-scale study of indicators of sub-clinical mastitis in dairy cattle by attribute weighting analysis of milk composition features: highlighting the predictive power of lactose and electrical conductivity

(2018) Esmaeil Ebrahimie et al.   JOURNAL OF DAIRY RESEARCH

Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle

(2018) Somayeh Sharifi et al.   PLoS One

Transcription factors network in root endosymbiosis establishment and development

(2018) Issa Diédhiou et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process

(2018) Mohammad Farhadian et al.   Frontiers in Genetics

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K + Deprivation

(2017) Kevin Garcia et al.   PLANT PHYSIOLOGY

A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

(2017) Mario Fruzangohar et al.   PLoS One

Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments

(2016) Fatemeh Kargarfard et al.   BMC GENOMICS

Symbiotic Fungi Control Plant Root Cortex Development through the Novel GRAS Transcription Factor MIG1

(2016) Carolin Heck et al.   CURRENT BIOLOGY

DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins

(2016) Ali Akbar Jamali et al.   DRUG DISCOVERY TODAY

Unravelling evolution of Nanog, the key transcription factor involved in self-renewal of undifferentiated embryonic stem cells, by pattern recognition in nucleotide and tandem repeats characteristics

(2016) Maryam Pashaiasl et al.   GENE

Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis

(2016) Maryam Pashaiasl et al.   MOLECULAR BIOLOGY REPORTS

Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process

(2016) Ibrahim O. Alanazi et al.   MOLECULAR BIOTECHNOLOGY

The phosphate transporters LjPT4 and MtPT4 mediate early root responses to phosphate status in non mycorrhizal roots

(2016) Veronica Volpe et al.   PLANT CELL AND ENVIRONMENT

Intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor

(2016) S. R. Rasmussen et al.   Scientific Reports

NIN Is Involved in the Regulation of Arbuscular Mycorrhizal Symbiosis

(2016) Bruno Guillotin et al.   Frontiers in Plant Science

Minimizing the cost of translocation failure with decision-tree models that predict species’ behavioral response in translocation sites

(2015) Mehregan Ebrahimi et al.   CONSERVATION BIOLOGY

Knowledge discovery and sequence-based prediction of pandemic influenza using an integrated classification and association rule mining (CBA) algorithm

(2015) Fatemeh Kargarfard et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis

(2015) Roohollah Shamloo-Dashtpagerdi et al.   JOURNAL OF THEORETICAL BIOLOGY

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

(2015) Mark M Pomerantz et al.   NATURE GENETICS

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

(2015) Jianguo Xia et al.   Nature Protocols

A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease

(2014) Layla K Mahdi et al.   BMC GENOMICS

New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase

(2014) Zahra Zinati et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology

(2014) Mohammad Reza Bakhtiarizadeh et al.   JOURNAL OF THEORETICAL BIOLOGY

MTGD: The Medicago truncatula Genome Database

(2014) Vivek Krishnakumar et al.   PLANT AND CELL PHYSIOLOGY

TheMedicago truncatulahypermycorrhizal B9 mutant displays an altered response to phosphate and is more susceptible toAphanomyces euteiches

(2014) HOAI-NAM TRUONG et al.   PLANT CELL AND ENVIRONMENT

Understanding the Underlying Mechanism of HA-Subtyping in the Level of Physic-Chemical Characteristics of Protein

(2014) Mansour Ebrahimi et al.   PLoS One

Determining the Most Important Physiological and Agronomic Traits Contributing to Maize Grain Yield through Machine Learning Algorithms: A New Avenue in Intelligent Agriculture

(2014) Avat Shekoofa et al.   PLoS One

SoybeanSAT1(Symbiotic Ammonium Transporter 1) encodes a bHLH transcription factor involved in nodule growth and NH4+transport

(2014) David M. Chiasson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline

(2013) Lun-Ching Chang et al.   BMC BIOINFORMATICS

Underlying functional genomics of fat deposition in adipose tissue

(2013) Mohammad Reza Bakhtiarizadeh et al.   GENE

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network

(2013) Batool Hosseinpour et al.   GENE

Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue

(2013) Mohammad Reza Bakhtiarizadeh et al.   Genes & Genomics

Combined phosphate and nitrogen limitation generates a nutrient stress transcriptome favorable for arbuscular mycorrhizal symbiosis inMedicago truncatula

(2013) Laurent Bonneau et al.   NEW PHYTOLOGIST

INMEX—a web-based tool for integrative meta-analysis of expression data

(2013) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Comparative GO: A Web Application for Comparative Gene Ontology and Gene Ontology-Based Gene Selection in Bacteria

(2013) Mario Fruzangohar et al.   PLoS One

A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae

(2013) Layla K. Mahdi et al.   PLoS One

NODULE INCEPTION Directly Targets NF-Y Subunit Genes to Regulate Essential Processes of Root Nodule Development in Lotus japonicus

(2013) Takashi Soyano et al.   PLoS Genetics

A GRAS-Type Transcription Factor with a Specific Function in Mycorrhizal Signaling

(2012) Enrico Gobbato et al.   CURRENT BIOLOGY

Comprehensive literature review and statistical considerations for microarray meta-analysis

(2012) George C. Tseng et al.   NUCLEIC ACIDS RESEARCH

Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses

(2012) Alexandre Tromas et al.   PLoS One

Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses

(2012) Tahereh Deihimi et al.   SpringerPlus

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

Strigolactone Biosynthesis in Medicago truncatula and Rice Requires the Symbiotic GRAS-Type Transcription Factors NSP1 and NSP2

(2011) W. Liu et al.   PLANT CELL

Laser Microdissection Unravels Cell-Type-Specific Transcription in Arbuscular Mycorrhizal Roots, Including CAAT-Box Transcription Factor Gene Expression Correlating with Fungal Contact and Spread

(2011) C. Hogekamp et al.   PLANT PHYSIOLOGY

Prediction of Thermostability from Amino Acid Attributes by Combination of Clustering with Attribute Weighting: A New Vista in Engineering Enzymes

(2011) Mansour Ebrahimi et al.   PLoS One

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Comparison study of microarray meta-analysis methods

(2010) Anna Campain et al.   BMC BIOINFORMATICS

Weighted Distance Weighted Discrimination and Its Asymptotic Properties

(2010) Xingye Qiao et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A basic introduction to fixed-effect and random-effects models for meta-analysis

(2010) Michael Borenstein et al.   Research Synthesis Methods

Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction

(2009) Chunrong Cheng et al.   BIOINFORMATICS

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis

(2009) Kengo Kinoshita et al.   BIOINFORMATICS

A-MADMAN: Annotation-based microarray data meta-analysis tool

(2009) Andrea Bisognin et al.   BMC BIOINFORMATICS

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

(2008) Andrew H Sims et al.   BMC Medical Genomics

Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age

(2008) Yohan Lee et al.   BMC Medical Genomics

Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets

(2008) Adaikalavan Ramasamy et al.   PLOS MEDICINE