Ghent University Academic Bibliography

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Parameter estimation for models of chemical reaction networks from experimental data of reaction rates

Manvel Gasparyan (UGent) , Arnout Van Messem (UGent) and Shodhan Rao (UGent)

(2023) INTERNATIONAL JOURNAL OF CONTROL. 96(2). p.392-407
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Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

Fabricio De Almeida Silva (UGent) and Yves Van de Peer (UGent)

(2023) MOLECULAR BIOLOGY AND EVOLUTION. 40(7).
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Alzheimer’s disease : a systems view provides a unifying explanation of its development

Corlia Grobler, Marvi van Tongeren (UGent) , Jan Gettemans (UGent) , Douglas B. Kell and Etheresia Pretorius

(2023) JOURNAL OF ALZHEIMERS DISEASE. 91(1). p.43-70
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Ulva : an emerging green seaweed model for systems biology

Jonas Blomme (UGent) , Thomas Wichard, Thomas B. Jacobs (UGent) and Olivier De Clerck (UGent)

(2023) JOURNAL OF PHYCOLOGY. 59(3). p.433-440
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MINI-EX : integrative inference of single-cell gene regulatory networks in plants

Camilla Ferrari (UGent) , Nicolás Manosalva Pérez (UGent) and Klaas Vandepoele (UGent)

(2022) MOLECULAR PLANT. 15(11). p.1807-1824
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Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum

Sávio Siqueira Ferreira, Geert Goeminne (UGent) , Marcella Siqueira Simões, André Vicioli de Almeida Pina, Leydson Gabriel Alves de Lima, Jade Pezard, Ana Gutiérrez, Jorge Rencoret, Jenny C Mortimer, José C del Río, et al.

(2022) JOURNAL OF EXPERIMENTAL BOTANY. 73(18). p.6307-6333
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A systems radiation biology approach to unravel the role of chronic low-dose-rate gamma-irradiation in inducing premature senescence in endothelial cells

Gabriele Babini, Giorgio Baiocco, Sofia Barbieri, Jacopo Morini, Traimate Sangsuwan, Siamak Haghdoost, Ramesh Yentrapalli, Omid Azimzadeh, Charlotte Rombouts (UGent) , An Aerts, et al.

(2022) PLOS ONE. 17(3).
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Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes

Razgar Seyed Rahmani (UGent) , Tao Shi, Dongzhi Zhang, Xiaoping Gou, Jing Yi, Giles Miclotte (UGent) , Kathleen Marchal (UGent) and Jia Li

(2021) BMC GENOMICS. 22(1).
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Mechanist idealisation in systems biology

Dingmar van Eck (UGent) and Cory Wright

(2021) SYNTHESE. 199(1-2). p.1555-1575
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An automated model reduction method for biochemical reaction networks

Manvel Gasparyan (UGent) , Arnout Van Messem (UGent) and Shodhan Rao (UGent)

(2020) SYMMETRY-BASEL. 12(8).
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Inference of plant gene regulatory networks using data-driven methods : a practical overview

Shubhada Rajabhau Kulkarni and Klaas Vandepoele (UGent)

(2020) BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS. 1863(6).
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Compensatory guaiacyl lignin biosynthesis at the expense of syringyl lignin in 4CL1-knockout poplar

Chung-Jui Tsai, Peng Xu, Liang-Jiao Xue, Hao Hu, Batbayar Nyamdari, Radnaa Naran, Xiaohong Zhou, Geert Goeminne (UGent) , Ruili Gao, Erica Gjersing, et al.

(2020) PLANT PHYSIOLOGY. 183(1). p.123-136
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Drought resistance is mediated by divergent strategies in closely related Brassicaceae

Nora Marín‐de la Rosa, Chung‐Wen Lin, Yang Jae Kang, Stijn Dhondt (UGent) , Nathalie Gonzalez Sanchez (UGent) , Dirk Inzé (UGent) and Pascal Falter‐Braun

(2019) NEW PHYTOLOGIST. 223(2). p.783-797
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Hub protein controversy : taking a closer look at plant stress response hubs

Katy Vandereyken, Jelle Van Leene (UGent) , Barbara De Coninck and Bruno PA Cammue

(2018) FRONTIERS IN PLANT SCIENCE. 9.
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Best practices for analysing microbiomes

Rob Knight, Alison Vrbanac, Bryn C. Taylor, Alexander Aksenov, Chris Callewaert (UGent) , Justine Debelius, Antonio Gonzalez, Tomasz Kosciolek, Laura-Isobel McCall, Daniel McDonald, et al.

(2018) NATURE REVIEWS MICROBIOLOGY. 16(7). p.410-422
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Adjuvant-associated peripheral blood mRNA profiles and kinetics induced by the adjuvanted recombinant protein candidate tuberculosis vaccine M72/AS01 in Bacillus Calmette–Guérin-vaccinated adults

Robert A. van den Berg, Laurane De Mot, Geert Leroux-Roels (UGent) , Viviane Bechtold, Frédéric Clement (UGent) , Margherita Coccia, Erik Jongert, Thomas G. Evans, Paul Gillard and Robbert G. van der Most

(2018) FRONTIERS IN IMMUNOLOGY. 9.
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Precision medicine and drug development in Alzheimer's disease : the importance of sexual dimorphism and patient stratification

Harald Hampel, Andrea Vergallo, Filippo Sean Giorgi, Seung Hyun Kim, Herman Depypere (UGent) , Manuela Graziani, Amira Saidi, Robert Nistico and Simone Lista

(2018) FRONTIERS IN NEUROENDOCRINOLOGY. 50. p.31-51
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Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses

Nicolaas Van Renne (UGent) , Ruifang Wei (UGent) , Nathalie Pochet and Hans Nauwynck (UGent)

(2018) BMC GENOMICS. 19.
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Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1

Christy Grobbler, Bernardino Virdis, Amanda Nouwens, Falk Harnisch, Korneel Rabaey (UGent) and Philip L Bond

(2018) BIOELECTROCHEMISTRY. 119. p.172-179
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E-health beyond technology : analyzing the paradigm shift that lies beneath

Tania Moerenhout, Ignaas Devisch (UGent) and Gustaaf C Cornelis

(2018) MEDICINE HEALTH CARE AND PHILOSOPHY. 21(1). p.31-41
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Mechanism discovery and design explanation : where role function meets biological advantage function

Dingmar van Eck (UGent) and Julie Mennes (UGent)

(2018) JOURNAL FOR GENERAL PHILOSOPHY OF SCIENCE. 49(3). p.413-434
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Accurate detection of dysmorphic nuclei using dynamic programming and supervised classification

Marlies Verschuuren, Jonas De Vylder (UGent) , Hannes Catrysse, Joke Robijns, Wilfried Philips (UGent) and Winnok De Vos (UGent)

(2017) PLOS ONE. 12(1).
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Abscisic acid as pathogen effector and immune regulator

Laurens Lievens, Jacob Pollier (UGent) , Alain Goossens (UGent) , Rudi Beyaert (UGent) and Jens Staal (UGent)

(2017) FRONTIERS IN PLANT SCIENCE. 8.
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Kresoxim-methyl primes Medicago truncatula plants against abiotic stress factors via altered reactive oxygen and nitrogen species signalling leading to downstream transcriptional and metabolic readjustment

Panagiota Filippou, Chrystalla Antoniou, Toshihiro Obata, Katrien Van Der Kelen (UGent) , Vaggelis Harokopos, Loukas Kanetis, Vassilis Aidinis, Frank Van Breusegem (UGent) , Alisdair R Fernie and Vasileios Fotopoulos

(2016) JOURNAL OF EXPERIMENTAL BOTANY. 67(5). p.1259-1274
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The allelochemical MDCA inhibits lignification and affects auxin homeostasis

Ward Steenackers, Igor Cesarino (UGent) , Petr Klima, Mussa Quareshy, Ruben Vanholme (UGent) , Sander Corneillie (UGent) , Robert Kumpf (UGent) , Dorien Van de Wouwer (UGent) , Karin Ljung, Geert Goeminne (UGent) , et al.

(2016) PLANT PHYSIOLOGY. 172(2). p.874-888
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Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Sofie Van Landeghem (UGent) , Thomas Van Parys (UGent) , Marieke Dubois (UGent) , Dirk Inzé (UGent) and Yves Van de Peer (UGent)

(2016) BMC BIOINFORMATICS. 17.
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Molecular systems governing leaf growth: from genes to networks

Nathalie Gonzalez Sanchez (UGent) and Dirk Inzé (UGent)

(2015) JOURNAL OF EXPERIMENTAL BOTANY. 66(4). p.1045-1054
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Renal microRNA- and RNA-profiles in progressive chronic kidney disease

Michael Rudnicki, Paul Perco, Barbara D′haene, Johannes Leierer, Andreas Heinzel, Irmgard Mühlberger, Ninella Schweibert, Judith Sunzenauer, Heinz Regele, Andreas Kronbichler, et al.

(2015) EUROPEAN JOURNAL OF CLINICAL INVESTIGATION. 46(3). p.213-226
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New insights in molecular mechanisms involved in chronic kidney disease using high-resolution plasma proteome analysis

Griet Glorieux (UGent) , William Mullen, Flore Duranton, Szymon Filip, Nathalie Gayrard, Holger Husi, Eva Schepers (UGent) , Nathalie Neirynck (UGent) , Joost P Schanstra, Joachim Jankowski, et al.

(2015) NEPHROLOGY DIALYSIS TRANSPLANTATION. 30(11). p.1842-1852
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Proteomic biomarkers in kidney disease: issues in development and implementation

Harald Mischak, Christian Delles, Antonia Vlahou and Raymond Vanholder (UGent)

(2015) NATURE REVIEWS NEPHROLOGY. 11(4). p.221-232
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Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

Frederik van Parijs, Tom Ruttink (UGent) , Wout Boerjan (UGent) , Geert Haesaert (UGent) , SL Byrne, T Asp, Isabel Roldán-Ruiz (UGent) and H Muylle

(2015) PLANT BIOLOGY. 17(4). p.877-892
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From DNA- to NA-centrism and the conditions for gene-centrism revisited

Alexis De Tiège (UGent) , Koen Tanghe (UGent) , Johan Braeckman (UGent) and Yves Van de Peer (UGent)

(2014) BIOLOGY & PHILOSOPHY. 29(1). p.55-69
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Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry

Colin Ruprecht, Takayuki Tohge, Alisdair Fernie, Cara L Mortimer, Amanda Kozlo, Paul D Fraser, Norma Funke, Igor Cesarino (UGent) , Ruben Vanholme (UGent) , Wout Boerjan (UGent) , et al.

(2014) JOURNAL OF VISUALIZED EXPERIMENTS. 87.
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The proteome under translational control

Daria Fijalkowska (UGent) , Kris Gevaert (UGent) and Petra Van Damme (UGent)

(2014) PROTEOMICS. 14(23-24). p.2647-2659
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A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms

Bram Van de Poel (UGent) , Inge Bulens, Maarten LATM Hertog, Bart M Nicolaï and Annemie H Geeraerd

(2014) NEW PHYTOLOGIST. 202(3). p.952-963
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Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Vanessa Vermeirssen (UGent) , Inge De Clercq (UGent) , Thomas Van Parys (UGent) , Frank Van Breusegem (UGent) and Yves Van de Peer (UGent)

(2014) PLANT CELL. 26(12). p.4656-4679
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Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

Marc Vaudel, Albert Sickmann and Lennart Martens (UGent)

(2014) BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS. 1844(1A). p.12-20
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Gibberellins and DELLAs: central nodes in growth regulatory networks

Hannes Claeys (UGent) , Stefanie De Bodt (UGent) and Dirk Inzé (UGent)

(2014) TRENDS IN PLANT SCIENCE. 19(4). p.231-239
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The ABCC6 transporter : what lessons can be learnt from other ATP-binding cassette transporters?

Olivier Vanakker (UGent) , Mohammad Jakir Hosen (UGent) and Anne De Paepe (UGent)

(2013) FRONTIERS IN GENETICS. 4.
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CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data

Alex Van Moerkercke (UGent) , Michele Fabris (UGent) , Jacob Pollier (UGent) , Gino Baart (UGent) , Stephane Rombauts (UGent) , Ghulam Hasnain, Heiko Rischer, Johan Memelink, Kirsi-Marja Oksman-Caldentey and Alain Goossens (UGent)

(2013) PLANT AND CELL PHYSIOLOGY. 54(5). p.673-685
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ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours

Annica Wilzen, Cecilia Krona, Baldur Sveinbjornsson, Erik Kristiansson, Daniel Dalevi, Ingrid Ora, Katleen De Preter (UGent) , Raymond L Stallings, John Maris, Rogier Versteeg, et al.

(2013) MOLECULAR CANCER. 12.
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Directed module detection in a large-scale expression compendium

Qiang Fu, Karen Lemmens, Aminael Sánchez-Rodríguez, Inge M Thijs, Pieter Meysman, Hong Sun, Ana Carolina Fierro, Kristof Engelen and Kathleen Marchal (UGent)

(2012) Bacterial molecular networks : methods and protocols. In Methods in Molecular Biology 804. p.131-165
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Protein-protein interactions: network analysis and applications in drug discovery

Jennyfer Bultinck (UGent) , Sam Lievens (UGent) and Jan Tavernier (UGent)

(2012) CURRENT PHARMACEUTICAL DESIGN. 18(30). p.4619-4629
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Performance assessment of the anticipatory approach to optimal experimental design for model discrimination

Brecht Donckels (UGent) , Dirk De Pauw (UGent) , Peter A Vanrolleghem and Bernard De Baets (UGent)

(2012) CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS. 110(1). p.20-31
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Minimum information about a cardiac electrophysiology experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing

TA Quinn, S Granite, MA Allessie, C Antzelevitch, C Bollensdorff, G Bub, RAB Burton, E Cerbai, PS Chen, M Delmar, et al.

(2011) PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY. 107(1). p.4-10
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Proteomics in chronic kidney disease: the issues clinical nephrologists need an answer for

Goce Spasovski, Alberto Ortiz, Raymond Vanholder (UGent) and Meguid El Nahas

(2011) PROTEOMICS CLINICAL APPLICATIONS. 5(5-6). p.233-240
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Modelling gene and protein regulatory networks with answer set pogramming

Timur Fayruzov (UGent) , Jeroen Janssen (UGent) , Dirk Vermeir, Chris Cornelis (UGent) and Martine De Cock (UGent)

(2011) INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS. 5(2). p.209-229
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Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane

Jürgen Kleine-Vehn (UGent) , Krzysztof Wabnik (UGent) , Alexandre Martinière, Lukasz Langowski (UGent) , Katrin Willig, Satoshi Naramoto (UGent) , Johannes Leitner, Hirokazu Tanaka (UGent) , Stefan Jakobs, Stephanie Robert (UGent) , et al.

(2011) MOLECULAR SYSTEMS BIOLOGY. 7.
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Integration of 'omics' data: does it lead to new insights into host-microbe interactions?

Gwendoline Kint, Carolina Fierro, Kathleen Marchal (UGent) , Jos Vanderleyden and Sigrid CJ De Keersmaecker

(2010) FUTURE MICROBIOLOGY. 5(2). p.313-328
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Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Philippe De Backer (UGent) , Danny De Waele (UGent) and Linda Van Speybroeck (UGent)

(2010) ACTA BIOTHEORETICA. 58(1). p.15-49

Parameter estimation for models of chemical reaction networks from experimental data of reaction rates

Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

Alzheimer’s disease : a systems view provides a unifying explanation of its development

Ulva : an emerging green seaweed model for systems biology

MINI-EX : integrative inference of single-cell gene regulatory networks in plants

Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum

A systems radiation biology approach to unravel the role of chronic low-dose-rate gamma-irradiation in inducing premature senescence in endothelial cells

Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes

Mechanist idealisation in systems biology

An automated model reduction method for biochemical reaction networks

Inference of plant gene regulatory networks using data-driven methods : a practical overview

Compensatory guaiacyl lignin biosynthesis at the expense of syringyl lignin in 4CL1-knockout poplar

Drought resistance is mediated by divergent strategies in closely related Brassicaceae

Hub protein controversy : taking a closer look at plant stress response hubs

Best practices for analysing microbiomes

Adjuvant-associated peripheral blood mRNA profiles and kinetics induced by the adjuvanted recombinant protein candidate tuberculosis vaccine M72/AS01 in Bacillus Calmette–Guérin-vaccinated adults

Precision medicine and drug development in Alzheimer's disease : the importance of sexual dimorphism and patient stratification

Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses

Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1

E-health beyond technology : analyzing the paradigm shift that lies beneath

Mechanism discovery and design explanation : where role function meets biological advantage function

Accurate detection of dysmorphic nuclei using dynamic programming and supervised classification

Abscisic acid as pathogen effector and immune regulator

Kresoxim-methyl primes Medicago truncatula plants against abiotic stress factors via altered reactive oxygen and nitrogen species signalling leading to downstream transcriptional and metabolic readjustment

The allelochemical MDCA inhibits lignification and affects auxin homeostasis

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Molecular systems governing leaf growth: from genes to networks

Renal microRNA- and RNA-profiles in progressive chronic kidney disease

New insights in molecular mechanisms involved in chronic kidney disease using high-resolution plasma proteome analysis

Proteomic biomarkers in kidney disease: issues in development and implementation

Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

From DNA- to NA-centrism and the conditions for gene-centrism revisited

Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry

The proteome under translational control

A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms

Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

Gibberellins and DELLAs: central nodes in growth regulatory networks

The ABCC6 transporter : what lessons can be learnt from other ATP-binding cassette transporters?

CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data

ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours

Directed module detection in a large-scale expression compendium

Protein-protein interactions: network analysis and applications in drug discovery

Performance assessment of the anticipatory approach to optimal experimental design for model discrimination

Minimum information about a cardiac electrophysiology experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing

Proteomics in chronic kidney disease: the issues clinical nephrologists need an answer for

Modelling gene and protein regulatory networks with answer set pogramming

Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane

Integration of 'omics' data: does it lead to new insights into host-microbe interactions?

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?