Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats

Effect of high amylose resistant starch (HAM-RS2) supplementation on biomarkers of inflammation and oxidative stress in hemodialysis patients: a randomized clinical trial

(2018) Hamid Tayebi Khosroshahi et al.   Hemodialysis International

Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing

(2017) Elena Herrmann et al.   Frontiers in Microbiology

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

(2017) Dmitry A. Ravcheev et al.   Frontiers in Genetics

Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)

(2017) Marco Fernandes et al.   Scientific Reports

Nuclear receptor NR5A2 is involved in the calreticulin gene regulation during renal fibrosis

(2016) Eleni Arvaniti et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

(2016) Roi Avraham et al.   Nature Protocols

Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases

(2016) Eleni Arvaniti et al.   Scientific Reports

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

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

The Unipept metaproteomics analysis pipeline

(2015) Bart Mesuere et al.   PROTEOMICS

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

(2015) Özgün C O Umu et al.   Microbiome

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Expansion of Urease- and Uricase-Containing, Indole- and p-Cresol-Forming and Contraction of Short-Chain Fatty Acid-Producing Intestinal Microbiota in ESRD

(2014) Jakk Wong et al.   AMERICAN JOURNAL OF NEPHROLOGY

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Lacking alignments? The next-generation sequencing mapper segemehl revisited

(2014) Christian Otto et al.   BIOINFORMATICS

High Amylose Resistant Starch Diet Ameliorates Oxidative Stress, Inflammation, and Progression of Chronic Kidney Disease

(2014) Nosratola D. Vaziri et al.   PLoS One

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Non-Immunologic Actions of Calcineurin Inhibitors in Proteinuric Kidney Diseases

(2014) Robert Frank Spurney   Frontiers in Endocrinology

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

(2013) Mikel Esnaola et al.   BMC BIOINFORMATICS

Urine haptoglobin levels predict early renal functional decline in patients with type 2 diabetes

(2013) Nishant M. Bhensdadia et al.   KIDNEY INTERNATIONAL

Mitochondrial impairment in the five-sixth nephrectomy model of chronic renal failure: proteomic approach

(2013) Larisa V Fedorova et al.   BMC Nephrology

Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses

(2012) Wayne Young et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CKD impairs barrier function and alters microbial flora of the intestine

(2012) Nosratola D. Vaziri   CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION

The intestinal microbiota in aged mice is modulated by dietary resistant starch and correlated with improvements in host responses

(2012) Sybille Tachon et al.   FEMS MICROBIOLOGY ECOLOGY

An overview of the chemistry and biology of reactive aldehydes

(2012) Kristofer S. Fritz et al.   FREE RADICAL BIOLOGY AND MEDICINE

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

(2012) Bart Mesuere et al.   JOURNAL OF PROTEOME RESEARCH

Chronic kidney disease alters intestinal microbial flora

(2012) Nosratola D. Vaziri et al.   KIDNEY INTERNATIONAL

CUBN as a Novel Locus for End-Stage Renal Disease: Insights from Renal Transplantation

(2012) Anna Reznichenko et al.   PLoS One

Plasma membrane repair and cellular damage control: The annexin survival kit

(2011) Annette Draeger et al.   BIOCHEMICAL PHARMACOLOGY

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Chronic kidney disease-related atherosclerosis - proteomic studies of blood plasma

(2011) Magdalena Luczak et al.   Proteome Science

Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease

(2009) Simona Granata et al.   BMC GENOMICS

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

(2009) Z. Gao et al.   DIABETES

Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa

(2009) Steven A. L. W. Vanhoutvin et al.   PLoS One

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags

(2008) Loïc Dayon et al.   ANALYTICAL CHEMISTRY