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List of works by Daniel Figeys

18O Labeling: a tool for proteomics ⬇️

scientific article published on January 1, 2001

A Regulatory Network Involving β-Catenin, e-Cadherin, PI3k/Akt, and Slug Balances Self-Renewal and Differentiation of Human Pluripotent Stem Cells In Response to Wnt Signaling ⬇️

scientific article published on May 2015

A charge-suppressing strategy for probing protein methylation.

scientific article published on 29 March 2016

A differential phosphoproteomic analysis of retinoic acid-treated P19 cells.

scientific article

A microfabricated device for rapid protein identification by microelectrospray ion trap mass spectrometry

scientific article published on 01 August 1997

A new chemical probe for phosphatidylinositol kinase activity.

scientific article published on 21 May 2014

A novel proteomics approach for the discovery of chromatin-associated protein networks

scientific article published on 22 December 2008

A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts.

scientific article published on 6 March 2012

APols-aided protein precipitation: a rapid method for concentrating proteins for proteomic analysis.

scientific article

Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm. Effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis.

scientific article published in October 1994

Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast.

scientific article

Activity-based profiling of the proteasome pathway during hepatitis C virus infection

scientific article published on 28 August 2015

Advancements in top-down proteomics.

scientific article

Advancing functional and translational microbiome research using meta-omics approaches

scientific article published on 06 December 2019

Amyloid-beta42 signals tau hyperphosphorylation and compromises neuronal viability by disrupting alkylacylglycerophosphocholine metabolism.

scientific article

An Integrated Microfluidics-Tandem Mass Spectrometry System for Automated Protein Analysis ⬇️

scientific article published on September 15, 1998

An autocrine inflammatory forward-feedback loop after chemotherapy withdrawal facilitates the repopulation of drug-resistant breast cancer cells

scientific article published on 13 July 2017

An enhanced chemically defined SILAC culture system for quantitative proteomics study of human embryonic stem cells ⬇️

scientific article published on August 31, 2011

Analysis of human serum phosphopeptidome by a focused database searching strategy

scientific article published on 16 October 2012

Analysis of low-abundance proteins using the proteomic reactor with pH fractionation.

scientific article

Analytical aspects of proteomics: 2009-2010.

scientific article published on 28 April 2011

Assessing the impact of protein extraction methods for human gut metaproteomics

article

Associations Between Soluble LDLR and Lipoproteins in a White Cohort and the Effect of PCSK9 Loss-of-Function

scientific article published on 01 September 2018

BAG2 Gene-mediated Regulation of PINK1 Protein Is Critical for Mitochondrial Translocation of PARKIN and Neuronal Survival

scientific article

Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes

scientific article published on 06 May 2020

Biomarker assay translation from discovery to clinical studies in cancer drug development: quantification of emerging protein biomarkers.

scientific article published on January 2007

Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology

scientific article

Capillary electrophoresis of peptides and proteins at neutral pH in capillaries covalently coated with polyethyleneimine

scientific article published on 01 July 1997

Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation

scientific article published on 20 December 2019

Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis

scientific article published on 01 October 2012

Combining different 'omics' technologies to map and validate protein-protein interactions in humans.

scientific article published on February 2004

DJ-1 interacts with and regulates paraoxonase-2, an enzyme critical for neuronal survival in response to oxidative stress.

scientific article

Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase.

scientific article

Deep Metaproteomics Approach for the Study of Human Microbiomes.

scientific article published on 27 July 2017

Defining the budding yeast chromatin‐associated interactome ⬇️

scientific article published on December 21, 2010

Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures.

scientific article

Detecting protein-protein interactions/complex components using mass spectrometry coupled techniques

scientific article published on 01 January 2014

Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis.

scientific article published on 12 May 2016

Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification

scientific article published on 14 December 2015

Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions

scientific article published on 10 May 2011

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

scientific article published on 09 March 2020

Differential proteomic screen to evidence proteins ubiquitinated upon mitotic exit in cell-free extract of Xenopus laevis embryos.

scientific article published on 30 September 2008

Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design.

scientific article published on 18 December 2014

Dynamic proteins: changes in structures, activities and networks.

scientific article

Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes.

scientific article published on July 1998

Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach.

scientific article published on 13 November 2017

Evaluating live microbiota biobanking using an <i>ex vivo</i> microbiome assay and metaproteomics

scientific article published on 01 January 2022

Exploring the yeast acetylome using functional genomics

scientific article

Fine tuning of proteomic technologies to improve biological findings: advancements in 2011-2013.

scientific article

From cells to peptides: "one-stop" integrated proteomic processing using amphipols.

scientific article

Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity.

scientific article

GRK2 Fine-Tunes Circadian Clock Speed and Entrainment via Transcriptional and Post-translational Control of PERIOD Proteins

scientific article published on 12 August 2015

Gelsolin regulates cisplatin sensitivity in human head-and-neck cancer.

scientific article

Glycoproteomic reactor for human plasma.

scientific article published in February 2009

High sensitivity analysis of proteins and peptides by capillary electrophoresis-tandem mass spectrometry: recent developments in technology and applications.

scientific article published in May 1998

High sensitivity identification of proteins by electrospray ionization tandem mass spectrometry: initial comparison between an ion trap mass spectrometer and a triple quadrupole mass spectrometer

scientific article published on 01 March 1997

High throughput solid phase microextraction: A new alternative for analysis of cellular lipidome?

scientific article published on 29 September 2016

Highly sensitive detection of S-nitrosylated proteins by capillary gel electrophoresis with laser induced fluorescence.

scientific article

Human Proteinpedia enables sharing of human protein data

scientific article

Identification and quantitation of changes in the platelet activating factor family of glycerophospholipids over the course of neuronal differentiation by high-performance liquid chromatography electrospray ionization tandem mass spectrometry.

scientific article published on 20 October 2007

Identification of flow-dependent endothelial nitric-oxide synthase phosphorylation sites by mass spectrometry and regulation of phosphorylation and nitric oxide production by the phosphatidylinositol 3-kinase inhibitor LY294002

scientific article published on 01 October 1999

Identification of lysophosphatidylcholine (LPC) and platelet activating factor (PAF) from PC12 cells and mouse cortex using liquid chromatography/multi-stage mass spectrometry (LC/MS3).

scientific article

Identification of protein-protein interactions by mass spectrometry coupled techniques.

scientific article published on January 2008

Identification of proteins by capillary electrophoresis-tandem mass spectrometry. Evaluation of an on-line solid-phase extraction device

scientific article published on 01 February 1997

Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor

scientific article

Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach

scientific article published on 21 September 2011

In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics.

scientific article published in June 2016

Integrative proteomics.

scientific article published in April 2013

Labeling of double-stranded DNA by ROX-dideoxycytosine triphosphate using terminal deoxynucleotidyl transferase and separation by capillary electrophoresis

scientific article published on 01 December 1994

Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method

scientific article published on 23 August 2014

Large-scale mapping of human protein-protein interactions by mass spectrometry

scientific article

Large-scale screening on small scale

scientific article published on 01 September 2000

Lipidomics era: accomplishments and challenges.

scientific article

Lipin — The bridge between hepatic glycerolipid biosynthesis and lipoprotein metabolism ⬇️

scientific article published on 06 August 2010

Lyso-form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids

scientific article published on 01 January 2011

MFG-E8 Is Critical for Embryonic Stem Cell-Mediated T Cell Immunomodulation.

scientific article published on 6 October 2015

Mapping the human protein interactome.

scientific article published on July 2008

Mass spectrometric analysis reveals remnants of host-pathogen molecular interactions at the starch granule surface in wheat endosperm.

scientific article

Mass spectrometry for the study of protein-protein interactions.

scientific article published in July 2001

MetaLab: an automated pipeline for metaproteomic data analysis

scientific article

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

scientific article

Metabolic Reprogramming by Hexosamine Biosynthetic and Golgi N-Glycan Branching Pathways

scientific article

Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

scientific article published on 31 July 2019

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

scientific article published in Nature Communications

Methylmercury can induce Parkinson's-like neurotoxicity similar to 1-methyl-4- phenylpyridinium: a genomic and proteomic analysis on MN9D dopaminergic neuron cells

scientific article published on January 2015

Microsome-associated lumenal lipid droplets in the regulation of lipoprotein secretion.

scientific article published on April 2013

Mucosal–luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis

scientific article published on 12 March 2018

Myosin phosphatase modulates the cardiac cell fate by regulating the subcellular localization of Nkx2.5 in a Wnt/Rho-associated protein kinase-dependent pathway.

scientific article published on 20 November 2012

N-Glycopeptide Reduction with Exoglycosidases Enables Accurate Characterization of Site-Specific N-Glycosylation.

scientific article published on 3 November 2016

Nanoflow Gradient Generator Coupled with μ-LC−ESI-MS/MS for Protein Identification

scientific article published on 01 March 2001

Nanoflow Solvent Gradient Delivery from a Microfabricated Device for Protein Identifications by Electrospray Ionization Mass Spectrometry ⬇️

scientific article published on September 15, 1998

New ammunition for the proteomic reactor: strong anion exchange beads and multiple enzymes enhance protein identification and sequence coverage

scientific article published on 03 June 2010

Nonsynonymous mutations within APOB in human familial hypobetalipoproteinemia: evidence for feedback inhibition of lipogenesis and postendoplasmic reticulum degradation of apolipoprotein B

scientific article

Of proteins and DNA--proteomic role in the field of chromatin research.

scientific article published on 03 September 2009

On-line strong cation exchange μ-HPLC-ESI-MS/MS for protein identification and process optimization

scientific article published on 01 July 2003

Optimization of solid phase microextraction ‐ capillary zone electrophoresis ‐ mass spectrometry for high sensitivity protein identification ⬇️

scientific article published on October 1, 1998

PCSK4-null sperm display enhanced protein tyrosine phosphorylation and ADAM2 proteolytic processing during in vitro capacitation

scientific journal article

PINK1-mediated phosphorylation of LETM1 regulates mitochondrial calcium transport and protects neurons against mitochondrial stress

scientific article published on 9 November 2017

Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data.

scientific article

Perspective and Guidelines for Metaproteomics in Microbiome Studies

scientific article published on 26 April 2019

Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus.

scientific article published on 22 March 2017

Phosphoproteome analysis of an early onset mouse model (TgCRND8) of Alzheimer's disease reveals temporal changes in neuronal and glia signaling pathways ⬇️

scientific article published on April 2, 2013

Pink1 regulates FKBP5 interaction with AKT/PHLPP and protects neurons from neurotoxin stress induced by MPP

scientific article published on 02 April 2019

Platelet activating factors are associated with depressive symptoms in coronary artery disease patients: a hypothesis-generating study

scientific article

Platelet-activating factors are associated with cognitive deficits in depressed coronary artery disease patients: a hypothesis-generating study.

scientific article

Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine.

scientific article

Profiling Kinase Activity during Hepatitis C Virus Replication Using a Wortmannin Probe

scientific article published on 20 August 2015

Protein identification by capillary zone electrophoresis/microelectrospray ionization-tandem mass spectrometry at the subfemtomole level

scientific article published on 01 June 1996

Protein identification by solid phase microextraction—capillary zone electrophoresis—microelectrospray—tandem mass spectrometry ⬇️

scientific article published on November 1, 1996

Proteome analysis: biological assay or data archive?

scientific article

Proteome profiling reveals regional protein alteration in cerebrum of common marmoset (Callithrix jacchus) exposed to methylmercury

scientific article published on 21 March 2016

Proteomic Analysis of Cerebellum in Common Marmoset Exposed to Methylmercury.

scientific article published on 25 March 2015

Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2

scientific article published on 01 October 2011

Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC

scientific article published on 23 May 2016

Proteomic analysis of minute amount of colonic biopsies by enteroscopy sampling

scientific article

Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry.

scientific article published on November 2005

Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions.

scientific article

Proteomic reactors and their applications in biology.

scientific article published on 06 September 2011

Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-Luminal Interface

scientific article published on 24 June 2020

Proteomics in 2002: a year of technical development and wide-ranging applications.

scientific article

Proteomics technology in systems biology.

scientific article published on 27 June 2006

Proteomics: from gel based to gel free.

scientific article published in June 2005

Proteomics: from technology developments to biological applications.

scientific article published on June 2009

Pseudo-coulometric loading in capillary electrophoresis DNA sequencing

scientific article published on 01 September 1996

Purification of trypsin for mass spectrometric identification of proteins at high sensitivity.

scientific article

Quantitative phosphoproteomics reveals involvement of multiple signaling pathways in early phagocytosis by the retinal pigmented epithelium.

scientific article published on 4 October 2017

Quantitative proteomic analysis of Dunaliella salina upon acute arsenate exposure.

scientific article published on 10 December 2015

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

scientific article published on 11 March 2020

Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation.

scientific article published on 8 June 2010

Recent developments in mass spectrometry-based quantitative phosphoproteomics.

scientific article published on April 2008

Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4

scientific article

Regulation of the VHL/HIF-1 pathway by DJ-1

scientific article

Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein.

scientific article

Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC-MS/MS

scientific article published on 08 April 2014

Skeletal myosin light chain kinase regulates skeletal myogenesis by phosphorylation of MEF2C

scientific article

Spatial and temporal depletion of ions from noncrosslinked denaturing polyacrylamide in capillary electrophoresis

scientific article published on 01 December 1994

Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics

scientific article published on 30 November 2020

Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry

scientific article published on March 2008

Targeted lipidomics - advances in profiling lysophosphocholine and platelet-activating factor second messengers

scientific article

Techniques for the optimization of proteomic strategies based on head column stacking capillary electrophoresis.

scientific article published on July 2000

The Achilles' heel of proteomics

scientific article published on 01 December 2000

The functional diversity of protein lysine methylation

scientific article

The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus.

scientific article published on 26 April 2013

The precursor to the germ cell-specific PCSK4 proteinase is inefficiently activated in transfected somatic cells: evidence of interaction with the BiP chaperone.

scientific article published on 16 November 2010

The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes.

scientific article

The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells

scientific article

The reproducible acquisition of comparative liquid chromatography/tandem mass spectrometry data from complex biological samples.

scientific article

Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer's Disease Mouse Model

scientific article published on 06 August 2019

Time-of-day- and light-dependent expression of ubiquitin protein ligase E3 component N-recognin 4 (UBR4) in the suprachiasmatic nucleus circadian clock

scientific article

Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression

scientific article

Uncovering the proteome response of the master circadian clock to light using an AutoProteome system.

scientific article published on 22 August 2011

Using neurolipidomics to identify phospholipid mediators of synaptic (dys)function in Alzheimer's Disease.

scientific article

Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass.

scientific article published on 18 November 2012

Web surfing in yeast: a network of proteins

scientific article published on 01 March 2001

Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease

scientific article published on 17 August 2020

iMetaLab 1.0: a web platform for metaproteomics data analysis

scientific article published on 01 November 2018

mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases ⬇️

scientific article published on April 9, 2013

miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock

scientific article published in April 2017

β-Catenin and NF-κB co-activation triggered by TLR3 stimulation facilitates stem cell-like phenotypes in breast cancer

scientific article

β-Estradiol results in a proprotein convertase subtilisin/kexin type 9-dependent increase in low-density lipoprotein receptor levels in human hepatic HuH7 cells

scientific article published on 18 May 2015

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