Publication results omics@VIB program

Meléndez-Rodríguez F, Urrutia AA, Lorendeau D, Rinaldi G, Roche O, Böğürcü-Seidel N, Ortega Muelas M, Mesa-Ciller C, Turiel G, Bouthelier A, Hernansanz-Agustín P, Elorza A, Escasany E, Li QOY, Torres-Capelli M, Tello D, Fuertes E, Fraga E, Martínez-Ruiz A, Pérez B, Giménez-Bachs JM, Salinas-Sánchez AS, Acker T, Sánchez Prieto R, Fendt SM, De Bock K, Aragonés J 
HIF1alpha suppresses tumor cell proliferation through inhibition of aspartate biosynthesis.
Cell Rep 26, 2257-2265e4, 2019
Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E
Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation.
Mol Cell Mol Cell Proteomics 18, 909-922, 2019

Rambow F, Marine JC, Goding CR
Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities.
Genes Dev 33, 1295-1318, 2019

Fonteyne S., Muylle H., Lootens P., Kerchev P., Van den Ende W., Staelens A., Reheul D., Roldán-Ruiz I.
Physiological basis of chilling tolerance and early-season growth in miscanthus.
Ann Bot-London  121, 281-295,2018

Dabrafenib plus trametinib in BRAF K601E-mutant melanoma
Brit J Dermatol  e-pub, 2018

Proteomics reveals scope of mycolactone-mediated Sec61 blockade and distinctive stress signature
Mol Cell Proteomics  e-pub, 2018 

Goemans C.V., Beaufay F., Wahni K., Van Molle I., Messens J., Collet J.F.
An essential thioredoxin is involved in the control of the cell cycle in the bacterium Caulobacter crescentus.
J Biol Chem  293, 3839-3848, 2018.
Mora N., Oliva C., Fiers M., Ejsmont R., Soldano A., Zhang T.T.N.V., Yan J., Claeys A., De Geest N., Hassan B.A.
A Temporal Transcriptional Switch Governs Stem Cell Division, Neuronal Numbers, and Maintenance of Differentiation.
Dev Cell  45, 53-66 e55,2018.

The Endosomal Protein CEMIP Links WNT Signaling to MEK1-ERK1/2 Activation in Selumetinib-Resistant Intestinal Organoids.
Cancer Res  78, 4533-4548,2018.

Toward Minimal Residual Disease-Directed Therapy in Melanoma.
Cell  174, 843-855 e819,2018.

Codon-specific translation reprogramming promotes resistance to targeted therapy.
Nature  558, 605-609,2018.

Sustained SREBP-1-dependent lipogenesis as a key mediator of resistance to BRAF-targeted therapy.
Nat Commun  9, 2500,2018.


Wendrich J.R., Boeren S., Möller B.K., Weijers D., De Rybel B.
In vivo identification of plant protein complexes using IP-MS/MS.
Methods Mol Biol 1497, 147-158, 2017.
The tumour suppressor, miR-137, inhibits malignant melanoma migration by targetting the TBX3 transcription factor.
Cancer Lett  405, 111-119,2017.

Dual loss of succinate dehydrogenase (SDH) and complex I activity is necessary to recapitulate the metabolic phenotype of SDH mutant tumors
Metab Eng  43, 187-197, 2017.

Considine M.J., Diaz-Vivancos P., Kerchev P., Signorelli S., Agudelo-Romero P., Gibbs D.J., Foyer C.H.
Learning to breathe: developmental phase transitions in oxygen status.
Trends Plant Sci, 22, 140-153, 2017.​

Species-function relationships shape ecological properties of the human gut microbiome.
Nat Microbiol  1, 16088,2016. 

Dippel S., Kollmann M., Oberhofer G., Montino A., Knoll C., Krala M., Rexer K.H., Frank S., Kumpf R., Schachtner J., Wimmer E.A.
Morphological and Transcriptomic Analysis of a Beetle Chemosensory System Reveals a Gnathal Olfactory Center.
BMC Biol  14, 90, 2016.

SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions.
Plant Cell  28, 1844-1859,2016.

Breast Cancer-Derived Lung Metastases Show Increased Pyruvate Carboxylase-Dependent Anaplerosis.
Cell Rep  17, 837-848,2016.

Regulation of Drosophila Brain Wiring by Neuropil Interactions via a Slit-Robo-RPTP Signaling Complex.
Dev Cell  39, 267-278, 2016.

Population-level analysis of gut microbiome variation.
Science  352, 560-564, 2016.

Sulfur Denitrosylation by an Engineered Trx-like DsbG Enzyme Identifies Nucleophilic Cysteine Hydrogen Bonds as Key Functional Determinant.
J Biol Chem  291, 15020-15028,2016.

Chemical Genetics Uncovers Novel Inhibitors of Lignification, Including p-Iodobenzoic Acid Targeting CINNAMATE-4-HYDROXYLASE.
Plant Physiol  172, 198-220,2016

Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages.
Immunity  44, 755-768,2016.

The allelochemical MDCA inhibits lignification and affects auxin homeostasis.
Plant Physiol  172, 874-888, 2016.

Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis.
Plant Physiol  171, 1704-1719,2016.

J Clin Invest  126, 68-84,2016.

The ROS Wheel: Refining ROS Transcriptional Footprints.
Plant Physiol  171, 1720-1733,2016.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Science  352, 565-569,2016.

The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE.
Chem Commun  52, 10293-10296,2016.

Chromatin-Bound MDM2 Regulates Serine Metabolism and Redox Homeostasis Independently of p53.
Mol Cell  62, 890-902,2016.

Towards biome-specific analysis of meta-omics data.
Isme J  10, 1025-1028,2016.

Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system.
Nat Commun  7, 10239,2016.
Nature  535, 376-381,2016.

Design principles involving protein disorder facilitate specific substrate selection and degradation by the ubiquitin-proteasome system.
J Biol Chem  291, 6723-6731,2016

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.
PLoS One  11, e0153294,2016.

Melanoma addiction to the long non-coding RNA SAMMSON.
Nature  531, 518-522,2016.

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD.
Gut  65, 1681-1689,2016.

Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae.
Biotechnol Biofuels  9, 5,2016.

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity.
Nat Med  22, 861-868,2016.

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination.
Proc Natl Acad Sci U S A  113, E4639-E4647,2016.

Regulation of melanoma progression through the TCF4/miR-125b/NEDD9 cascade.
J Invest Dermatol  136, 1229-1237,2016.

Meta-omics in IBD research: applications, challenges and guidelines.
J Crohns Colitis 10, 735-746,2016.

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.
Gut  65, 57-62,2016.

Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis.
Science  351, 384-387,2016.

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root.
Proc Natl Acad Sci U S A  113, 1447-1452,2016.

Melanoma addiction to the long non-coding RNA SAMMSON.
Nature  53, 518-522,2016.
Toll-like Receptor 4 Engagement on Dendritic Cells Restrains Phago-Lysosome Fusion and Promotes Cross-Presentation of Antigens.
Immunity  43, 1087-1100,2015.
Bioinformatics Approaches for Predicting Disordered Protein Motifs.
Adv Exp Med Biol  870, 291-318,2015.
Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins.
J Am Chem Soc  137, 13807-13817,2015.
AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling.
BMC Plant Biol  15, 270,2015.
NF-kappaB-Independent Role of IKKalpha/IKKbeta in Preventing RIPK1 Kinase-Dependent Apoptotic and Necroptotic Cell Death during TNF Signaling.
Mol Cell  60, 63-76,2015.
Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine.
Annu Rev Microbiol  69, 305-321,2015.
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Nature  528, 262-266,2015.
SnapShot: Intrinsic Structural Disorder.
Cell  161, 1230-1230 e1231,2015.
Redox Strategies for Crop Improvement.
Antioxid Redox Sign  23, 1186-1205,2015.
Kerchev P., Muhlenbock P., Denecker J., Morreel K., Hoeberichts F.A., Van Der Kelen K., Vandorpe M., Nguyen L., Audenaert D., Van Breusegem F.
Activation of auxin signalling counteracts photorespiratory H2O2-dependent cell death.
Plant Cell Environ  38, 253-265,2015.
Developing 3D SEM in a broad biological context.
J Microsc-Oxford  259, 80-96,2015.
The root cap: a short story of life and death.
J Exp Bot  66, 5651-5662,2015.
Metabolic control of signalling pathways and metabolic auto-regulation.
Biol Cell  107, 251-272,2015.
How informative is the mouse for human gut microbiota research?
Dis Model Mech  8, 1-16,2015.
A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.
Plant Physiol  169, 2684-2699,2015.
Autism Spectrum Disorders: Translating human deficits into mouse behavior.
Neurobiol Learn Mem  124, 71-87,2015.
The Corynebacterium glutamicum mycothiol peroxidase is a reactive oxygen species-scavenging enzyme that shows promiscuity in thiol redox control.
Mol Microbiol  96, 1176-1191,2015.
Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants.
Curr Opin Plant Biol  23, 116-123,2015.
Corynebacterium diphtheriae Methionine Sulfoxide Reductase A Exploits a Unique Mycothiol Redox Relay Mechanism.
J Biol Chem  290, 11365-11375,2015.
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.
BMC Bioinformatics  16, 153,2015.
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.
PLoS One  10, e0139731,2015.
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.
Nat Commun  6, 6683,2015.
Transcriptome dynamics of the microRNA inhibition response.
Nucleic Acids Res  43, 6207-6221,2015.
Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root.
Curr Biol  25, 1381-1388,2015.
The Alzheimer Disease Protective Mutation A2T Modulates Kinetic and Thermodynamic Properties of Amyloid-beta (Abeta) Aggregation.
J Biol Chem  289, 30977-30989,2014.
Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?
ACS Med Chem Lett  5, 23-28,2014.
The Little Fly that Could: Wizardry and Artistry of Drosophila Genomics.
GENES-BASEL  5, 385-414,2014.
Programmed Cell Death Controlled by ANAC033/SOMBRERO Determines Root Cap Organ Size in Arabidopsis.
Curr Biol  24, 931-940,2014.
Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.
J Med Chem  57, 8657-8663,2014.
A quiescent path to plant longevity.
Trends Cell Biol  24, 443-448,2014.
Necroptosis, in vivo detection in experimental disease models.
Semin Cell Dev Biol  35, 2-13,2014.
Polar delivery in plants; commonalities and differences to animal epithelial cells.
Open Biol  4, 140017,2014.
Mitochondrial perturbation negatively affects auxin signaling.
Mol Plant  7, 1138-1150,2014.
The ASH1-RELATED3 SET-Domain Protein Controls Cell Division Competence of the Meristem and the Quiescent Center of the Arabidopsis Primary Root.
Plant Physiol  166, 632-643,2014.
The unfolded-protein-response sensor IRE-1alpha regulates the function of CD8alpha+ dendritic cells.
Nat Immunol  15, 248-257,2014.
Learning and behavioral deficits associated with the absence of the fragile X mental retardation protein: what a fly and mouse model can teach us.
Learn Memory  21, 543-555,2014.
Mutation of the Inducible ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE2 Alters Lignin Composition and Improves Saccharification.
Plant Physiol  166, 1956-1971,2014.
A click chemistry strategy for visualization of plant cell wall lignification.
Chem Commun  50, 12262-12265,2014.
Regulated necrosis: the expanding network of non-apoptotic cell death pathways.
Nat Rev Mol Cell Biol  15, 135-147,2014.
A20 controls intestinal homeostasis through cell-specific activities.
Nat Commun  5, 5103,2014.
Sulfenome mining in Arabidopsis thaliana.
Proc Natl Acad Sci U S A  111, 11545-11550,2014.
Visualization of the exocyst complex dynamics at the plasma membrane of Arabidopsis thaliana.
Mol Biol Cell  24, 510-520,2013.
Intrinsic cleavage of receptor-interacting protein kinase-1 by caspase-6.
Cell Death Differ  20, 86-96,2013.
Exocyst complexes multiple functions in plant cells secretory pathways.
Curr Opin Plant Biol  16, 726-733,2013.
TRAIL induces necroptosis involving RIPK1/RIPK3-dependent PARP-1 activation.
Cell Death Differ  19, 2003-2014,2012.
FrVB/VEGREP/476: not available yet