Research Explorer

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Researcher

Steven Maere

Publications & Research Data

Awards & Distinctions

75 Results

2026

Inference and phylogenetic placement of whole-genome multiplications in plants

Cecilia SensalariSteven Maere

Smoppix : unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices

Stijn HawinkelXilan YangWard PoelmansHans MotteTom BeeckmanSteven Maere

A1 Journal Article in GENOME BIOLOGY

2025

A case for absolute gene expression estimates in microbiome studies using metatranscriptomics

Michiel PerneelHarriet AlexanderPascal I HablützelSteven Maere

Editorial material

Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science

Sonia García MéndezStien MertensArne TemmermanHelena Van den EyndeMargo VermeerschLena VlaminckOlivier BertelootJudith Van DingenenAlexander ClarysseAnnick De Keyser et al.

A1 Journal Article in ISME JOURNAL

Spatiotemporal metatranscriptomics of surface microeukaryotic plankton communities in the southern North Sea

Michiel PerneelSteven MaerePascal Hablützel

The endocycle regulators SIM and CCS52A1 control Arabidopsis root hair cell ploidy and expansion

Lei LiKlaus HerburgerIlse VercauterenDuncan ColemanQian WangSteven MaereJefri HeymanLieven De Veylder

A1 Journal Article in PLANT PHYSIOLOGY

2024

Analysis of maize growth under drought in an automated plant phenotyping platform

Lennart VerbraekenHilde NelissenSteven MaereDirk Inzé

Citizen science boosts fundamental and applied research for sustainable soybean cultivation in North‐Western Europe

Lena VlaminckBirgit Vanden BerghenStien MertensJurgen WuytsLiesbeth AertsJudith Van DingenenSofie BekaertSteven MaereLiesbet VrankenSofie Goormachtig

A1 Journal Article in PLANTS, PEOPLE, PLANET

Out-of-sample R2 : estimation and inference

Stijn HawinkelWillem WaegemanSteven Maere

A1 Journal Article in AMERICAN STATISTICIAN

Seasonal metabolic dynamics of microeukaryotic plankton : a year-long metatranscriptomic study in a temperate sea

Michiel PerneelRune LagaisseJonas MortelmansSteven MaerePascal I. Hablützel

A1 Journal Article in MBIO

Single-plant omics : a new methodology to gather knowledge in field conditions

Daniel Felipe Cruz GalvisSteven Maere

Studying single-plant responses to natural perturbations

Sam De MeyerSteven Maere

2023

Interspecies co‐expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis

Hans MotteBoris ParizotWei XuanQian ChenSteven MaereSandra BensmihenTom Beeckman

A1 Journal Article in PLANT JOURNAL

Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform

Stien MertensLennart VerbraekenHeike SprengerSam De MeyerKirin DemuynckBernard CannootJulie MerchieJolien De BlockJonathan T. VogelWesley Bruce et al.

A1 Journal Article in PLANT METHODS

Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression

Sam De MeyerDaniel Felipe Cruz GalvisTom De SwaefPeter LootensJolien De BlockKevin BirdHeike SprengerMichael Van de VoordeStijn HawinkelTom Van Hautegem et al.

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation

Ward DeveltereEvelien WaegneerKevin DebrayJonas De SaegerSabine Van GlabekeSteven MaereTom RuttinkThomas B. Jacobs

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2022

Ksrates : positioning whole-genome duplications relative to speciation events in KS distributions

Cecilia SensalariSteven MaereRolf Lohaus

A1 Journal Article in BIOINFORMATICS

SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation

Ward DeveltereEvelien WaegneerKevin DebraySabine Van GlabekeSteven MaereTom RuttinkThomas B. Jacobs

Spatial regression models for field trials : a comparative study and new ideas

Stijn HawinkelSam De MeyerSteven Maere

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2021

Drought affects the rate and duration of organ growth but not inter-organ growth coordination

Lennart VerbraekenNathalie WuytsStien MertensBernard CannootKatrien MaleuxKirin DemuynckJolien De BlockJulie MerchieStijn DhondtGustavo Bonaventure et al.

A1 Journal Article in PLANT PHYSIOLOGY

Proximal hyperspectral imaging detects diurnal and drought-induced changes in maize physiology

Stien MertensLennart VerbraekenHeike SprengerKirin DemuynckKatrien MaleuxBernard CannootJolien De BlockSteven MaereHilde NelissenGustavo Bonaventure et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2020

Current status of the multinational Arabidopsis community

Geraint ParryNicholas J. ProvartSiobhan M. BradyBaris UzildayGeert De JaegerSteven MaereMULTINATIONAL ARABIDOPSIS STEERING COMMITTEE

A1 Journal Article in PLANT DIRECT

Using single‐plant‐omics in the field to link maize genes to functions and phenotypes

Daniel Felipe Cruz GalvisSam De MeyerJoke AmpeHeike SprengerDorota HermanTom Van HautegemJolien De BlockDirk InzéHilde NelissenSteven Maere

A1 Journal Article in MOLECULAR SYSTEMS BIOLOGY

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

Jos WendrichBaojun YangNiels VandammeKevin VerstaenWouter SmetCelien Van de VeldeMax MinneBrecht WybouwEliana MorHelena Arents et al.

A1 Journal Article in SCIENCE

2019

Endoreplication as a potential driver of cell wall modifications

Rahul BhosaleSteven MaereLieven De Veylder

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Interspecific hybridization facilitates niche adaptation in beer yeast

Brigida GalloneJan SteenselsStijn MertensMaria C DzialoJonathan L GordonRuben WautersFlorian A TheßelingFrancesca BellinazzoVeerle SaelsBeatriz Herrera-Malaver et al.

A1 Journal Article in NATURE ECOLOGY & EVOLUTION

The impact of genome duplications on the dynamics of gene family evolution in plants

Setareh TasdighianSteven MaereYves Van de Peer

2018

A spatiotemporal DNA endoploidy map of the Arabidopsis root reveals roles for the endocycle in root development and stress adaptation

Rahul BhosaleVéronique BoudolfFabiola Cuevas BustamanteRan LuThomas EekhoutZhubing HuGert Van IsterdaelGeorgina M LambertFan XuMoritz Nowack et al.

A1 Journal Article in PLANT CELL

Comparative genomics of industrial yeasts

Brigida GalloneSteven MaereKevin J Verstrepen

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Fay-Wei LiPaul BrouwerLorenzo Carretero-PauletShifeng ChengJan de VriesPierre-Marc DelauxAriana EilyNils KoppersLi-Yaung KuoZheng Li et al.

A1 Journal Article in NATURE PLANTS

Origins, evolution, domestication and diversity of Saccharomyces beer yeasts

Brigida GalloneStijn MertensJonathan L GordonSteven MaereKevin J VerstrepenJan Steensels

A1 Journal Article in CURRENT OPINION IN BIOTECHNOLOGY

The Apicomplexa-specific glucosamine-6-phosphate N-acetyltransferase gene family encodes a key enzyme for glycoconjugate synthesis with potential as therapeutic target

Marta CovaBorja López-GutiérrezSara Artigas-JerónimoAida González-DíazGiulia BandiniSteven MaereLorenzo Carretero-PauletLuis Izquierdo

A1 Journal Article in SCIENTIFIC REPORTS

The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels

Hilde NelissenXiaohuan SunBart RymenYusuke JikumaruMikko KojimaYumiko TakebayashiRafael AbbeloosKirin DemuynckVeronique StormeMarnik Vuylsteke et al.

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

2017

Evolutionary context improves regulatory network predictions

Jonathan L GordonBrigida GalloneSteven MaereKevin J Verstrepen

Editorial material

Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity

Setareh TasdighianMichiel Van BelZhen LiYves Van de PeerLorenzo Carretero-PauletSteven Maere

A1 Journal Article in PLANT CELL

The origin of floral organ identity quartets

Philip RuelensZhicheng ZhangHilda van MourikSteven MaereKerstin KaufmannKoen Geuten

A1 Journal Article in PLANT CELL

2016

Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

Joke BauteDorota HermanFrederik CoppensJolien De BlockBram SlabbinckMatteo Dell'AcquaMario Enrico PeSteven MaereHilde NelissenDirk Inzé

A1 Journal Article in PLANT PHYSIOLOGY

Domestication and divergence of Saccharomyces cerevisiae beer yeasts

Brigida GalloneJan SteenselsTroels PrahlLeah SoriagaVeerle SaelsBeatriz Herrera-MalaverAdriaan MerlevedeMiguel RoncoroniKarin VoordeckersLoren Miraglia et al.

A1 Journal Article in CELL

Gene duplicability of core genes is highly consistent across all angiosperms

Zhen LiJonas DefoortSetareh TasdighianSteven MaereYves Van de PeerRiet De Smet

A1 Journal Article in PLANT CELL

Leaf growth response to mild drought : natural variation in Arabidopsis sheds light on trait architecture

Pieter ClauwFrederik CoppensArthur KorteDorota HermanBram SlabbinckStijn DhondtTwiggy Van DaeleLiesbeth De MildeMattias VermeerschKatrien Maleux et al.

A1 Journal Article in PLANT CELL

2015

A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development

Qian ChenYang LiuSteven MaereEunkyoung LeeGert Van IsterdaelZidian XieWei XuanJessica LucasValya VassilevaSaeko Kitakura et al.

A1 Journal Article in NATURE COMMUNICATIONS

A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants

Yadira Olvera CarrilloMichiel Van BelTom Van HautegemMatyas FendrychMarlies HuysmansMária Braun ŠimáškováMatthias Van DurmePierre BuscaillSusana RivasNuria S Coll et al.

A1 Journal Article in PLANT PHYSIOLOGY

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Joke BauteDorota HermanFrederik CoppensJolien De BlockBram SlabbinckMatteo Dell'AcquaMario Enrico PèSteven MaereHilde NelissenDirk Inzé

A1 Journal Article in GENOME BIOLOGY

2014

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Kevin VannesteGuy BaeleSteven MaereYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Deciphering the evolutionary impact of gen(om)e duplications through mechanistic modeling of the genotype-phenotype map

Jayson Arley Gutiérrez BetancurSteven Maere

Interview with Steven Maere

Editorial material

Modeling the evolution of molecular systems from a mechanistic perspective

Jayson Arley Gutiérrez BetancurSteven Maere

A1 Journal Article in TRENDS IN PLANT SCIENCE

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Kevin VannesteSteven MaereYves Van de Peer

A1 Journal Article in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The evolutionary significance of gene and genome duplications

Kevin VannesteYves Van de PeerSteven Maere

The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants

Astrid GadeyneClara Sánchez-RodríguezSteffen VannesteSimone Di RubboHenrik ZauberKevin VannesteJelle Van LeeneNancy De WinneDominique EeckhoutGeert Persiau et al.

A1 Journal Article in CELL

Transcriptome-based predictive modeling approaches in Arabidopsis thaliana

Rahul BhosaleSteven MaereLieven De Veylder

2013

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Riet De SmetKeith L AdamsKlaas VandepoeleMarc Van MontaguSteven MaereYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of genome duplications from age distributions revisited

Kevin VannesteYves Van de PeerSteven Maere

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

Rahul BhosaleJeremy B JewellJens HollunderAbraham JK KooMarnik VuylstekeTom MichoelPierre HilsonAlain GoossensGregg A HoweJohn Browse et al.

A1 Journal Article in PLANT CELL

Significance and biological consequences of polyploidization in land plant evolution

Jeffrey FawcettYves Van de PeerSteven Maere

Bookchapter in Physical structure, behaviour and evolution of plant genomes

2012

Expansive evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE gene family in Arabidopsis

Lies VandesteeneLorena Lopez GalvisKevin VannesteRegina FeilSteven MaereWillem LammensFilip RollandJohn E LunnNelson AvonceTom Beeckman et al.

A1 Journal Article in PLANT PHYSIOLOGY

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification

Dries VekemansSebastian ProostKevin VannesteHeleen CoenenTom ViaenePhilip RuelensSteven MaereYves Van de PeerKoen Geuten

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication

Karin VoordeckersChris A. BrownKevin VannesteElisa van der ZandeArnout VoetSteven MaereKevin J. Verstrepen

A1 Journal Article in PLOS BIOLOGY

2011

PiNGO: a cytoscape plugin to find candidate genes in biological networks

Michael SmootKeiichiro OnoTrey IdekerSteven Maere

A1 Journal Article in BIOINFORMATICS

2010

2R or not 2R is not the question anymore

Yves Van de PeerSteven MaereAxel Meyer

A1 Journal Article in NATURE REVIEWS GENETICS

Duplicate retention after small- and large-scale duplications

Steven MaereYves Van de Peer

Bookchapter in Evolution after gene duplication

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Jelle Van LeeneJens HollunderDominique EeckhoutGeert PersiauEveline Van De SlijkeHilde StalsGert Van IsterdaelAurine VerkestSandy NeirynckYelle Buffel et al.

A1 Journal Article in MOLECULAR SYSTEMS BIOLOGY

2009

Open-ended on-board evolutionary robotics for robot swarms

Guy BaeleNicolas BredecheEvert HaasdijkSteven MaereNico MichielsYves Van de PeerThomas SchmicklChristopher SchwarzerRonald Thenius

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

Jeffrey FawcettSteven MaereYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolutionary significance of ancient genome duplications

Yves Van de PeerSteven MaereAxel Meyer

A1 Journal Article in Nature Reviews Genetics

2008

Extracting expression modules from perturbational gene expression compendia

Steven MaerePatrick Van DijckMartin Kuiper

A1 Journal Article in BMC SYSTEMS BIOLOGY

2007

Integration of biological networks and gene expression data using Cytoscape

Melissa S ClineMichael SmootEthan CeramiAllan KuchinskyNerius LandysChris WorkmanRowan ChristmasIliana Avila-CampiloMichael CreechBenjamin Gross et al.

A1 Journal Article in NATURE PROTOCOLS

The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth

Delphine FleuryKristiina HimanenGerda CnopsHilde NelissenTommaso Matteo BoccardiSteven MaereGerrit BeemsterPia NeytSylvester AnamiPedro Robles et al.

A1 Journal Article in PLANT CELL

Validating module network learning algorithms using simulated data

Tom MichoelSteven MaereEric BonnetAnagha Madhusudan JoshiYvan SaeysTim Van den BulckeKoenraad Van LeemputPiet Van RemortelMartin KuiperKathleen Marchal et al.

A1 Journal Article in BMC BIOINFORMATICS

2006

Development of mathematical methods for modeling biological systems

Steven MaereDirk AeyelsMarc Zabeau

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

Tineke CasneufStefanie De BodtJeroen RaesSteven MaereYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

The gain and loss of genes during 600 million years of vertebrate evolution

Tine BlommeKlaas VandepoeleStefanie De BodtCedric SimillionSteven MaereYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

2005

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

Steven MaereKarel HeymansMartin Kuiper

A1 Journal Article in BIOINFORMATICS

Genome duplication and the origin of angiosperms

Stefanie De BodtSteven MaereYves Van de Peer

Editorial material

Modeling gene and genome duplications in eukaryotes

Steven MaereStefanie De BodtJeroen RaesTineke CasneufMarc Van MontaguMartin KuiperYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA