Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue

Increased Hemodynamic Load in Early Embryonic Stages Alters Endocardial to Mesenchymal Transition

(2017) Madeline Midgett et al.   Frontiers in Physiology

A multi-model statistical approach for proteomic spectral count quantitation

(2016) Owen E. Branson et al.   Journal of Proteomics

Gene expression profiles reveal effect of a high-fat diet on the development of white and brown adipose tissues

(2015) Hyeng-Soo Kim et al.   GENE

Granulocyte/Macrophage Colony-stimulating Factor-dependent Dendritic Cells Restrain Lean Adipose Tissue Expansion

(2015) Nathalie Pamir et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes

(2015) J Huan et al.   LEUKEMIA

2016 update of the PRIDE database and its related tools

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

Macrophage Metalloelastase (MMP12) Regulates Adipose Tissue Expansion, Insulin Sensitivity, and Expression of Inducible Nitric Oxide Synthase

(2014) Jung-Ting Lee et al.   ENDOCRINOLOGY

Effect of age on bovine subcutaneous fat proteome: Molecular mechanisms of physiological variations during beef cattle growth1

(2014) J. M. Romao et al.   JOURNAL OF ANIMAL SCIENCE

Integrative Analysis of Transcriptomics, Proteomics, and Metabolomics Data of White Adipose and Liver Tissue of High-Fat Diet and Rosiglitazone-Treated Insulin-Resistant Mice Identified Pathway Alterations and Molecular Hubs

(2014) David Meierhofer et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

(2014) Ville-Petteri Mäkinen et al.   PLoS Genetics

Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates

(2013) Michael W. Senko et al.   ANALYTICAL CHEMISTRY

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Macrophages, fat, and the emergence of immunometabolism

(2013) Anthony W. Ferrante   JOURNAL OF CLINICAL INVESTIGATION

Protein Sets Define Disease States and PredictIn VivoEffects of Drug Treatment

(2013) David Meierhofer et al.   MOLECULAR & CELLULAR PROTEOMICS

Short-term, high fat feeding-induced changes in white adipose tissue gene expression are highly predictive for long-term changes

(2013) Anja Voigt et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Deficiency of lymphotoxin-α does not exacerbate high-fat diet-induced obesity but does enhance inflammation in mice

(2012) Nathalie Pamir et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Time-course microarrays reveal early activation of the immune transcriptome and adipokine dysregulation leads to fibrosis in visceral adipose depots during diet-induced obesity

(2012) Eun-Young Kwon et al.   BMC GENOMICS

Body Fat Distribution and Risk of Cardiovascular Disease

(2012) Jean-Pierre Després   CIRCULATION

Mouse Betaine-HomocysteineS-Methyltransferase Deficiency Reduces Body Fat via Increasing Energy Expenditure and Impairing Lipid Synthesis and Enhancing Glucose Oxidation in White Adipose Tissue

(2012) Ya-Wen Teng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Food Intake, Energy Balance, and Body Fat Mass: Implications for the Pathogenesis and Treatment of Obesity

(2012) Stephan J. Guyenet et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Differential responses of white adipose tissue and brown adipose tissue to caloric restriction in rats

(2012) Naoyuki Okita et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

(2012) I.-M. Wang et al.   Molecular Systems Biology

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

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

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

Diabetes promotes an inflammatory macrophage phenotype and atherosclerosis through acyl-CoA synthetase 1

(2012) J. E. Kanter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A distinct adipose tissue gene expression response to caloric restriction predicts 6-mo weight maintenance in obese subjects

(2011) David M Mutch et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort

(2011) D. M. Greenawalt et al.   GENOME RESEARCH

Inflammatory links between obesity and metabolic disease

(2011) Carey N. Lumeng et al.   JOURNAL OF CLINICAL INVESTIGATION

Protein Database and Quantitative Analysis Considerations when Integrating Genetics and Proteomics to Compare Mouse Strains

(2011) Suzanne S. Fei et al.   JOURNAL OF PROTEOME RESEARCH

Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction

(2011) William C. Hallows et al.   MOLECULAR CELL

COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

(2011) Craig D. Wenger et al.   PROTEOMICS

Differential expression of adipose tissue proteins between obesity-susceptible and -resistant rats fed a high-fat diet

(2011) Jeong In Joo et al.   PROTEOMICS

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Macrophages, Inflammation, and Insulin Resistance

(2010) Jerrold M. Olefsky et al.   Annual Review of Physiology

Coordinated up-regulation of cyclooxygenase-2 and microsomal prostaglandin E synthase 1 transcription by nuclear factor kappa B and early growth response-1 in macrophages

(2010) Manuel D. Díaz-Muñoz et al.   CELLULAR SIGNALLING

Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver

(2010) X. Yang et al.   GENOME RESEARCH

Identification of Genes and Networks Driving Cardiovascular and Metabolic Phenotypes in a Mouse F2 Intercross

(2010) Jonathan M. J. Derry et al.   PLoS One

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

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

Neutrophil-specific deletion of Syk kinase results in reduced host defense to bacterial infection

(2009) J. A. Van Ziffle et al.   BLOOD

Correlations between RNA and protein expression profiles in 23 human cell lines

(2009) Marcus Gry et al.   BMC GENOMICS

SIRT5 Deacetylates Carbamoyl Phosphate Synthetase 1 and Regulates the Urea Cycle

(2009) Takashi Nakagawa et al.   CELL

Proteome Differences between Brown and White Fat Mitochondria Reveal Specialized Metabolic Functions

(2009) Francesca Forner et al.   Cell Metabolism

A Branched-Chain Amino Acid-Related Metabolic Signature that Differentiates Obese and Lean Humans and Contributes to Insulin Resistance

(2009) Christopher B. Newgard et al.   Cell Metabolism

Receptors for Tumor Necrosis Factor-α Play a Protective Role against Obesity and Alter Adipose Tissue Macrophage Status

(2009) Nathalie Pamir et al.   ENDOCRINOLOGY

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Mice lacking angiotensin-converting enzyme have increased energy expenditure, with reduced fat mass and improved glucose clearance

(2008) A. P. Jayasooriya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Transcript Profiles of Fat in Monozygotic Twins Discordant for BMI: Pathways behind Acquired Obesity

(2008) Kirsi H Pietiläinen et al.   PLOS MEDICINE