Ghent University Academic Bibliography

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Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay Shiferaw, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Tim Van Den Bossche (UGent) , Elien Vandermarliere (UGent) , Lennart Martens (UGent) and Pieter-Jan Volders (UGent)

(2022) JOURNAL OF PROTEOME RESEARCH. 21(5). p.1365-1370
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Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

Morgane Boone (UGent) , Pathmanaban Ramasamy (UGent) , Jasper Zuallaert (UGent) , Robbin Bouwmeester (UGent) , Berre Van Moer (UGent) , Davy Maddelein (UGent) , Demet Turan (UGent) , Niels Hulstaert (UGent) , Hannah Eeckhaut (UGent) , Elien Vandermarliere (UGent) , et al.

(2021) NATURE COMMUNICATIONS. 12(1).
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The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis

Stephanie Smith, Shanshuo Zhu, Lisa Joos (UGent) , Ianto Roberts (UGent) , Natalia Nikonorova (UGent) , Lam Dai Vu (UGent) , Elisabeth Stes (UGent) , Hyunwoo Cho, Antoine Larrieu, Wei Xuan (UGent) , et al.

(2020) MOLECULAR & CELLULAR PROTEOMICS. 19(8). p.1248-1262
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- open access
Scop3P : a comprehensive resource of human phosphosites within their full context

Pathmanaban Ramasamy (UGent) , Demet Turan (UGent) , Natalia Tichshenko (UGent) , Niels Hulstaert (UGent) , Elien Vandermarliere (UGent) , Wim Vranken and Lennart Martens (UGent)

(2020) JOURNAL OF PROTEOME RESEARCH. 19(8). p.3478-3486
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- Journal Article
- A1
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COSS : a fast and user-friendly tool for spectral library searching

Genet Abay Shiferaw, Elien Vandermarliere (UGent) , Niels Hulstaert (UGent) , Ralf Gabriels (UGent) , Lennart Martens (UGent) and Pieter-Jan Volders (UGent)

(2020) JOURNAL OF PROTEOME RESEARCH. 19(7). p.2786-2793
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The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3

Sindisiwe G Buthelezi, Heini W Dirr, Ereck Chakauya, Rachel Chikwamba, Lennart Martens (UGent) , Tsepo L Tsekoa, Elien Vandermarliere (UGent) and Stoyan H Stoychev

(2018) PLOS ONE. 13(12).
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Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins

Sigrid Gouma, Tessa Vermeire, Steven Van Gucht, Lennart Martens (UGent) , Veronik Hutse, Jeroen Cremer, Paul A Rota, Geert Leroux-Roels (UGent) , Marion Koopmans, Rob van Binnendijk, et al.

(2018) SCIENTIFIC REPORTS. 8.
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- Journal Article
- A1
Cross-linked peptide identification : a computational forest of algorithms

Sule Yilmaz-Rumpf (UGent) , Genet Abay Shiferaw, Josep Rayo, Anastassios Economou, Lennart Martens (UGent) and Elien Vandermarliere (UGent)

(2018) MASS SPECTROMETRY REVIEWS. 37(6). p.738-749
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- Journal Article
- A2
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The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

Bram De Wilde (UGent) , Anneleen Beckers (UGent) , Sven Lindner, Kristina Althoff, Katleen De Preter (UGent) , Pauline Depuydt, Pieter Mestdagh (UGent) , Tom Sante (UGent) , Steve Lefever (UGent) , Falk Hertwig, et al.

(2018) ONCOTARGET. 9(9). p.8334-8349
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- Book Chapter
Methods to calculate spectrum similarity

Sule Yilmaz-Rumpf (UGent) , Elien Vandermarliere (UGent) and Lennart Martens (UGent)

(2017) Proteome bioinformatics. In Methods in Molecular Biology 1549. p.75-100
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- A1
The Lyssavirus glycoprotein : a key to cross-immunity

Sindisiwe G Buthelezi, Heini W Dirr, Ereck Chakauya, Rachel Chikwamba, Lennart Martens (UGent) , Tsepo L Tsekoa, Stoyan H Stoychev and Elien Vandermarliere (UGent)

(2016) VIROLOGY. 498. p.250-256
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- A1
Resolution of protein structure by mass spectrometry

Elien Vandermarliere (UGent) , Elisabeth Stes (UGent) , Kris Gevaert (UGent) and Lennart Martens (UGent)

(2016) MASS SPECTROMETRY REVIEWS. 35(6). p.653-665
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An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

Giel Vandemoortele, An Staes (UGent) , Giulia Gonnelli (UGent) , Noortje Samyn (UGent) , Delphine De Sutter (UGent) , Elien Vandermarliere (UGent) , Evy Timmerman (UGent) , Kris Gevaert (UGent) , Lennart Martens (UGent) and Sven Eyckerman (UGent)

(2016) SCIENTIFIC REPORTS. 6.
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- Journal Article
- A1
A pipeline for differential proteomics in unsequenced species

Sule Yilmaz-Rumpf (UGent) , Bjorn Victor, Niels Hulstaert (UGent) , Elien Vandermarliere (UGent) , Harald Barsnes, Sven Degroeve (UGent) , Surya Gupta (UGent) , Adriaan Sticker, Sarah Gabriël (UGent) , Pierre Dorny (UGent) , et al.

(2016) JOURNAL OF PROTEOME RESEARCH. 15(6). p.1963-1970
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- A1
Xilmass: a new approach toward the identification of cross-linked peptides

Sule Yilmaz-Rumpf (UGent) , Friedel Drepper, Niels Hulstaert (UGent) , Maša Černič, Kris Gevaert (UGent) , Anastassios Economou, Bettina Warscheid, Lennart Martens (UGent) and Elien Vandermarliere (UGent)

(2016) ANALYTICAL CHEMISTRY. 88(20). p.9949-9957
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- A1
Structural investigation of B-Raf paradox breaker and inducer inhibitors

Rohit Arora, Michela Di Michele (UGent) , Elisabeth Stes (UGent) , Elien Vandermarliere (UGent) , Lennart Martens (UGent) , Kris Gevaert (UGent) , Erika Van Heerde, Joannes TM Linders, Dirk Brehmer, Edgar Jacoby, et al.

(2015) JOURNAL OF MEDICINAL CHEMISTRY. 58(4). p.1818-1831
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- Journal Article
- A1
Limited proteolysis combined with stable isotope labeling reveals conformational changes in protein (pseudo)kinases upon binding small molecules

Michela Di Michele (UGent) , Elisabeth Stes (UGent) , Elien Vandermarliere (UGent) , Rohit Arora, Juan Astorga-Wells, Jonathan Vandenbussche (UGent) , Erika van Heerde, Roman Zubarev, Pascal Bonnet, Joannes TM Linders, et al.

(2015) JOURNAL OF PROTEOME RESEARCH. 14(10). p.4179-4193
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- Journal Article
- A1
Scop3D : three-dimensional visualization of sequence conservation

Tessa Vermeire, Stijn Vermaere, Bert Schepens (UGent) , Xavier Saelens (UGent) , Steven Van Gucht, Lennart Martens (UGent) and Elien Vandermarliere (UGent)

(2015) PROTEOMICS. 15(8). p.1448-1452
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- Journal Article
- A1
PepShell : visualization of conformational proteomics data

Elien Vandermarliere (UGent) , Davy Maddelein (UGent) , Niels Hulstaert (UGent) , Elisabeth Stes (UGent) , Michela Di Michele (UGent) , Kris Gevaert (UGent) , Edgar Jacoby, Dirk Brehmer and Lennart Martens (UGent)

(2015) JOURNAL OF PROTEOME RESEARCH. 14(4). p.1987-1990
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- A1
- open access
Ryanodine receptors are targeted by anti-apoptotic Bcl-X-L involving its BH4 domain and Lys87 from its BH3 domain

Tim Vervliet, Irma Lemmens (UGent) , Elien Vandermarliere (UGent) , Elke Decrock (UGent) , Hristina Ivanova, Giovanni Monaco, Vincenzo Sorrentino, Nael Nadif Kasri, Ludwig Missiaen, Lennart Martens (UGent) , et al.

(2015) SCIENTIFIC REPORTS. 5.
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- Conference Paper
- C3
A novel STAT1 mutation in a patient with pneumocystis jiroveci and chronic mucocutaneous candidiasis

Delfien Bogaert (UGent) , Melissa Dullaers (UGent) , Jens Staal (UGent) , Sarah Gerlo (UGent) , Elien Vandermarliere (UGent) , Veronique De Backer, Maria Bordon Cueto De Braem (UGent) , Kathleen De Waele (UGent) , Isabelle Meyts, Leen Moens, et al.

(2015) 43th Annual Meeting of the Belgian Society of Paediatrics, Abstracts.
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- Journal Article
- A1
Unraveling the specificities of the different human methionine sulfoxide reductases

Elien Vandermarliere (UGent) , Bart Ghesquière (UGent) , Veronique Jonckheere (UGent) , Kris Gevaert (UGent) and Lennart Martens (UGent)

(2014) PROTEOMICS. 14(17-18). p.1990-1998
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- Conference Paper
- C3
A novel Stat1 mutation leading to hyperphosphorylation in a patient with Pneumocystis jjiroveci and chronic mucocutaneous candidiasis

Melissa Dullaers (UGent) , Jens Staal (UGent) , Sarah Gerlo (UGent) , Elien Vandermarliere (UGent) , V Debacker, Maria Bordon Cueto De Braem (UGent) , K De Waele, I Meyts, L Moens, X Bossuyt, et al.

(2014) JOURNAL OF CLINICAL IMMUNOLOGY. 34(suppl. 2). p.S443-S444
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- Journal Article
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Protein structure as a means to triage proposed PTM sites

Elien Vandermarliere (UGent) and Lennart Martens (UGent)

(2013) PROTEOMICS. 13(6). p.1028-1035
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- Journal Article
- A1
Predicting tryptic cleavage from proteomics data using decision tree ensembles

Thomas Fannes, Elien Vandermarliere (UGent) , Leander Schietgat, Sven Degroeve (UGent) , Lennart Martens (UGent) and Jan Ramon

(2013) JOURNAL OF PROTEOME RESEARCH. 12(5). p.2253-2259
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- Journal Article
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Getting intimate with trypsin, the leading protease in proteomics

Elien Vandermarliere (UGent) , Michael Mueller and Lennart Martens (UGent)

(2013) MASS SPECTROMETRY REVIEWS. 32(6). p.453-465
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- Conference Paper
- C3
- open access
Vpr content of HIV-1 virions determines infection of resting peripheral blood CD4⁺ lymphocytes

Anouk Van Nuffel (UGent) , Francis Impens (UGent) , Ann Baeyens (UGent) , Stijn Vanhee (UGent) , Wojciech Witkowski (UGent) , Elien Vandermarliere (UGent) , Hanne Vanderstraeten (UGent) , Evelien Naessens (UGent) , Kathleen Van Landeghem (UGent) , Sophie Vermaut (UGent) , et al.

(2013) RETROVIROLOGY. 10(suppl. 1). p.S32-S33

Academic Bibliography

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis

Scop3P : a comprehensive resource of human phosphosites within their full context

COSS : a fast and user-friendly tool for spectral library searching

The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3

Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins

Cross-linked peptide identification : a computational forest of algorithms

The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

Methods to calculate spectrum similarity

The Lyssavirus glycoprotein : a key to cross-immunity

Resolution of protein structure by mass spectrometry

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

A pipeline for differential proteomics in unsequenced species

Xilmass: a new approach toward the identification of cross-linked peptides

Structural investigation of B-Raf paradox breaker and inducer inhibitors

Limited proteolysis combined with stable isotope labeling reveals conformational changes in protein (pseudo)kinases upon binding small molecules

Scop3D : three-dimensional visualization of sequence conservation

PepShell : visualization of conformational proteomics data

Ryanodine receptors are targeted by anti-apoptotic Bcl-X-L involving its BH4 domain and Lys87 from its BH3 domain

A novel STAT1 mutation in a patient with pneumocystis jiroveci and chronic mucocutaneous candidiasis

Unraveling the specificities of the different human methionine sulfoxide reductases

A novel Stat1 mutation leading to hyperphosphorylation in a patient with Pneumocystis jjiroveci and chronic mucocutaneous candidiasis

Protein structure as a means to triage proposed PTM sites

Predicting tryptic cleavage from proteomics data using decision tree ensembles

Getting intimate with trypsin, the leading protease in proteomics

Vpr content of HIV-1 virions determines infection of resting peripheral blood CD4⁺ lymphocytes

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