Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

Ets1-Mediated Acetylation of FoxO1 Is Critical for Gluconeogenesis Regulation during Feed-Fast Cycles

(2019) Kai Li et al.   Cell Reports

PGC1A regulates the IRS1:IRS2 ratio during fasting to influence hepatic metabolism downstream of insulin

(2019) Aurèle Besse-Patin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle

(2019) Brian A Hodge et al.   eLife

Carbohydrate Sensing Through the Transcription Factor ChREBP

(2019) Paula Ortega-Prieto et al.   Frontiers in Genetics

An association analysis for 14 candidate genes mapping to meat quality quantitative trait loci in a Duroc pig population reveals that the ATP 1A2 genotype is highly associated with muscle electric conductivity

(2019) E. Mármol‐Sánchez et al.   ANIMAL GENETICS

MicroRNA-30e promotes hepatocyte proliferation and inhibits apoptosis in cecal ligation and puncture-induced sepsis through the JAK/STAT signaling pathway by binding to FOSL2

(2018) Lan Ling et al.   BIOMEDICINE & PHARMACOTHERAPY

The Wnt antagonist and secreted frizzled-related protein 5: implications on lipid metabolism, inflammation, and type 2 diabetes mellitus

(2018) Ling-Bin Liu et al.   BIOSCIENCE REPORTS

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Defining the Transcriptional Targets of Leptin Reveals a Role forAtf3in Leptin Action

(2018) Margaret B. Allison et al.   DIABETES

Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously

(2018) Chenchen Ma et al.   BMC BIOINFORMATICS

Role of AMPK signalling pathway during compensatory growth in pigs

(2018) Maria Ballester et al.   BMC GENOMICS

MicroRNA-17 impairs glucose metabolism in insulin-resistant skeletal muscle via repressing glucose transporter 4 expression

(2018) Dan Xiao et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Regulation of microRNA function in animals

(2018) Luca F. R. Gebert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

(2018) Xiaoyong Pan et al.   PLoS One

Myogenin promotes myocyte fusion to balance fibre number and size

(2018) Massimo Ganassi et al.   Nature Communications

Analysing the Expression of Eight Clock Genes in Five Tissues From Fasting and Fed Sows

(2018) Tainã Figueiredo Cardoso et al.   Frontiers in Genetics

Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs

(2018) María Muñoz et al.   Frontiers in Genetics

Increased expression of thyroid hormone responsive protein (THRSP) is the result but not the cause of higher intramuscular fat content in cattle

(2017) Lisa Schering et al.   International Journal of Biological Sciences

Diurnal Variation in PDK4 Expression Is Associated With Plasma Free Fatty Acid Availability in People

(2017) Shintaro Yamaguchi et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Definition and identification of small RNA sponges: Focus on miRNA sequestration

(2017) Mélodie Migault et al.   METHODS

C10ORF10/DEPP-mediated ROS accumulation is a critical modulator of FOXO3-induced autophagy

(2017) S. Salcher et al.   Molecular Cancer

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq

(2017) Di Ran et al.   NUCLEIC ACIDS RESEARCH

TXNIP overexpression suppresses proliferation and induces apoptosis in SMMC7221 cells through ROS generation and MAPK pathway activation

(2017) Jian Li et al.   ONCOLOGY REPORTS

A Bach2-Cebp Gene Regulatory Network for the Commitment of Multipotent Hematopoietic Progenitors

(2017) Ari Itoh-Nakadai et al.   Cell Reports

RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles

(2017) T. F. Cardoso et al.   Scientific Reports

microRNAs in lipoprotein metabolism and cardiometabolic disorders

(2016) Noemi Rotllan et al.   ATHEROSCLEROSIS

The Pentose Phosphate Pathway Regulates the Circadian Clock

(2016) Guillaume Rey et al.   Cell Metabolism

From Nutrient to MicroRNA: a Novel Insight into Cell Signaling Involved in Skeletal Muscle Development and Disease

(2016) Yong Zhang et al.   International Journal of Biological Sciences

Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig

(2016) Cunling Jia et al.   PLoS One

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

(2015) Pau Bellot et al.   BMC BIOINFORMATICS

miR-22 as a prognostic factor targets glucose transporter protein type 1 in breast cancer

(2015) Bo Chen et al.   CANCER LETTERS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels

(2015) Leigh Goedeke et al.   NATURE MEDICINE

Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis

(2015) Alexandre Wagschal et al.   NATURE MEDICINE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Characterization of the mammalian miRNA turnover landscape

(2015) Yanwen Guo et al.   NUCLEIC ACIDS RESEARCH

On the availability of microRNA-induced silencing complexes, saturation of microRNA-binding sites and stoichiometry

(2015) Vinay K. Mayya et al.   NUCLEIC ACIDS RESEARCH

miR-148a is Associated with Obesity and Modulates Adipocyte Differentiation of Mesenchymal Stem Cells through Wnt Signaling

(2015) Chunmei Shi et al.   Scientific Reports

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism

(2015) Miriam Ayuso et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

(2014) Cristina Óvilo et al.   BMC GENOMICS

microRNA regulation of lipoprotein metabolism

(2014) Leigh Goedeke et al.   CURRENT OPINION IN LIPIDOLOGY

The pivotal role of pyruvate dehydrogenase kinases in metabolic flexibility

(2014) Shuai Zhang et al.   Nutrition & Metabolism

Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition

(2014) Anna Puig-Oliveras et al.   PLoS One

Argonaute 2 in Cell-Secreted Microvesicles Guides the Function of Secreted miRNAs in Recipient Cells

(2014) Zhiyuan Lv et al.   PLoS One

Nuclear receptor Rev-erbα: up, down, and all around

(2014) Logan J. Everett et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Hypothalamic ATF3 is involved in regulating glucose and energy metabolism in mice

(2013) Y.-S. Lee et al.   DIABETOLOGIA

Bach2 Regulates Homeostasis of Foxp3+ Regulatory T Cells and Protects against Fatal Lung Disease in Mice

(2013) E. H. Kim et al.   JOURNAL OF IMMUNOLOGY

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

(2013) Kenneth A. Dyar et al.   Molecular Metabolism

Beyond differential expression: the quest for causal mutations and effector molecules

(2012) Nicholas J Hudson et al.   BMC GENOMICS

MicroRNA-7 inhibits tumor growth and metastasis by targeting the phosphoinositide 3-kinase/Akt pathway in hepatocellular carcinoma

(2012) YuXiang Fang et al.   HEPATOLOGY

FOSL2 promotes leptin gene expression in human and mouse adipocytes

(2012) Christiane D. Wrann et al.   JOURNAL OF CLINICAL INVESTIGATION

FOXO1-mediated upregulation of pyruvate dehydrogenase kinase-4 (PDK4) decreases glucose oxidation and impairs right ventricular function in pulmonary hypertension: therapeutic benefits of dichloroacetate

(2012) Lin Piao et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Novel Foxo1-dependent transcriptional programs control Treg cell function

(2012) Weiming Ouyang et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Glucose-Induced Down Regulation of Thiamine Transporters in the Kidney Proximal Tubular Epithelium Produces Thiamine Insufficiency in Diabetes

(2012) James R. Larkin et al.   PLoS One

Kruppel-like factor 15 regulates skeletal muscle lipid flux and exercise adaptation

(2012) S. M. Haldar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay between gene expression noise and regulatory network architecture

(2012) Guilhem Chalancon et al.   TRENDS IN GENETICS

A regulatory circuit of miR-148a/152 and DNMT1 in modulating cell transformation and tumor angiogenesis through IGF-IR and IRS1

(2012) Qing Xu et al.   Journal of Molecular Cell Biology

Transcriptional Regulation of Pyruvate Dehydrogenase Kinase

(2012) Ji Yun Jeong et al.   Diabetes & Metabolism Journal

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method

(2011) S.M. Nalaila et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis

(2011) Laure-Emmanuelle Zaragosi et al.   GENOME BIOLOGY

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data

(2010) Antonio Reverter et al.   BIOINFORMATICS

Patterns of human gene expression variance show strong associations with signaling network hierarchy

(2010) Kakajan Komurov et al.   BMC Systems Biology

Emerging Roles for Natural MicroRNA Sponges

(2010) Margaret S. Ebert et al.   CURRENT BIOLOGY

Mammalian target of rapamycin regulates miRNA-1 and follistatin in skeletal myogenesis

(2010) Yuting Sun et al.   JOURNAL OF CELL BIOLOGY

MiR-322/424 and -503 Are Induced during Muscle Differentiation and Promote Cell Cycle Quiescence and Differentiation by Down-Regulation of Cdc25A

(2010) Sukumar Sarkar et al.   MOLECULAR BIOLOGY OF THE CELL

Differential regulation of microRNA stability

(2010) S. Bail et al.   RNA

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches

(2009) N. S. Watson-Haigh et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The transcription factors Egr1 and Egr2 have opposing influences on adipocyte differentiation

(2009) K B Boyle et al.   CELL DEATH AND DIFFERENTIATION

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

microRNA-7 Inhibits the Epidermal Growth Factor Receptor and the Akt Pathway and Is Down-regulated in Glioblastoma

(2008) B. Kefas et al.   CANCER RESEARCH