IMforFUTURE open access publications
Network members, including ESRs, have had many open access publications submitted and these are listed below. Publications that are not open access can be found at the bottom of the list.
- Intraspecies characterization of bacteria via evolutionary modeling of protein domains
Iva Budimir (ESR6) et al (including Enrico Giampieri, Daniel Remondini, Gastone Castellani & Claudia Sala)
Scientific Reports, 12, 16595 (2022)
https://doi.org/10.1038/s41598-022-21036-3
- Statistical integration of heterogeneous omics data: Probabilistic two-way partial least squares (PO2PLS)
Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Jeanine Houwing-Duistermaat
Journal of the Royal Statistical Society Series C, Volume 71, Issue 5, November 2022, Pages 1451-1470
https://doi.org/10.1111/rssc.12583
- PhD thesis: Antibody glycomics signatures of SARS-CoV-2 infection and vaccination
Tamas Pongracz (ESR1)
Leiden University Scholarly Publications 2022
https://hdl.handle.net/1887/3455304
- Genetic regulation of post-translational modification of two distinct proteins
Arianna Landini (ESR11) et al (including Frano Vuckovic, Yurii Aulchenko, Gordan Lauc, James Wilson, Lucija Klaric)
Nature Communications 13, 1586 (2022)
https://doi.org/10.1038/s41467-022-29189-5
- Immunoglobulin G1 Fc glycosylation as an early hallmark of severe COVID-19
Tamas Pongracz (ESR1) et al (including Manfred Wuhrer)
EBioMedicine Volume 78, April 2022, 103957
https://doi.org/10.1016/j.ebiom.2022.103957
- Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome
Zeng et al (including Azra Frkatović ESR4 and James Wilson)
EBioMedicine Volume 75, January 2022, Pages 103804
https://doi.org/10.1016/j.ebiom.2021.103730
- Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases
Tarozzi etl (including Gastone Castellani)
BMC Med Genomics 15, 26 (2022)
https://doi.org/10.1186/s12920-022-01173-4
- A Transient Expression System with Stably Integrated CRISPR-dCas9 Fusions for Regulation of Genes Involved in Immunoglobulin G Glycosylation
Mijakovac et al (including Gordan Lauc, Vlatka Zoldos, and Aleksandar Vojta)
The CRISPR journal, Volume: 5 Issue 2: April 19, 2022
https://doi.org/10.1089/crispr.2021.0089
- Multivariate functional partial least squares for classification using longitudinal data
Sonia Dembowska, Haiyan Liu, Jeanine Houwing-Duistermaat, Alex Frangi
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401007
- Nonparametric clustering for longitudinal functional data with the application to HNMR spectra of Kidney transplant patients : longitudinal functional data clustering
Minzhen Xie, Jeanine Houwing-Duistermaat, Haiyan Liu
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401003
- Estimation of the effect of surrogate multi-omic biomarkers
Angga M. Fuady, Jeanine Houwing-Duistermaat, Hae-Won Uh, Said El Bouhaddani
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401006
- Use of shared gamma frailty model in analysis of survival data in twins
Annah Mwikali Muli (ESR8), Jeanine Houwing-Duistermaat, Arief Gusnanto
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401005
- DNA methylation correlation structure of chromosome 21 in Down syndrome
Iva Budimir (ESR6), Claudia Sala, Gastone Castellani, Paolo Garagnani, Maria Giulia Bacalini
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401008
- Investigating the impact of Down syndrome on Methylation and Glycomics with two-stage PO2PLS
Zhujie Gu (ESR5), Hae-Won Uh, Jeanine Houwing-Duistermaat, Said El Bouhaddani
Theoretical Biology Forum 114, 1, 2021
https://doi.org/10.19272/202111401004
- Characterization and comparison of gene-centered human interactomes
Mosca et al (including Gastone Castellani)
Briefings in Bioinformatics, Volume 22, Issue 6, November 2021
https://doi.org/10.1093/bib/bbab153
- Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese
Meng et al (including Gordan Lauc)
Journal for Personalized Medicine 2021, 11(7), 614
(This article belongs to the Special Issue Personalized Medicine in Epidemics)
https://doi.org/10.3390/jpm11070614
- Estimage: a webserver hub for the computation of methylation age
Di Lena, Pietro, Claudia Sala, and Christine Nardini.
Nucleic Acids Research Volume 49, Issue W1, 2 July 2021, Pages W199–W206
DOI: https://doi.org/10.1093/nar/gkab426
- Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease
Angga Fuady, Willeke van Roon-Mom, Szymon Kiełbasa, Hae-Won Uh, Jeanine Houwing-Duistermaat
Biometrical Journal Volume 63, Issue 4, April 2021, Pages 745-760
DOI: https://doi.org/10.1002/bimj.201900235
- Statistical Integration of Multiple Omics Datasets Using GO2PLS
Zhujie Gu (ESR5), Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat, Hae-Won Uh
BMC Bioinformatics 22, Article number: 131 (2021)
DOI: https://doi.org/10.1186/s12859-021-03958-3
- Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain
Rahman et al (including Md Shafiqur Rahman ESR10, Yurii Aulchenko, Frances Williams)
Annals of the Rheumatic Diseases 2021; 80: 1227-1235
DOI: https://doi.org/10.1136/annrheumdis-2020-219624
- Effects of Estradiol on Immunoglobulin G Glycosylation: Mapping of the Downstream Signaling Mechanism
Mijakovac et al (including Azra Frkatović ESR4, Frano Vučković, Aleksandar Vojta, Vlatka, Zoldoš, Gordan Lauc)
Frontiers in Immunology 2021
DOI: https://doi.org/10.3389/fimmu.2021.680227
- Node Centrality Measures Identify Relevant Structural MRI Features of Subjects with Autism
Zanghieri et al (including Gastone Castellani)
Brain Sciences 2021, 11(4), 498
DOI: https://doi.org/10.3390/brainsci11040498
- Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes
Bersanelli et al (including Claudia Sala, Enrico Giampieri, Gastone Castellani)
Journal of Clinical Oncology 39, no. 11 (April 10, 2021) 1223-1233
DOI: https://doi.org/10.1200/JCO.20.01659
- WISDoM: Characterizing Neurological Time Series With the Wishart Distribution
Carlo Mengucci, Daniel Remondini, Enrico Giampieri
Frontiers in Neuroinformatics 14, article 611762 (2021)
DOI: https://doi.org/10.3389/fninf.2020.611762
- The structure and role of lactone intermediates in linkage-specific sialic acid derivatization reactions
Tamas Pongracz (ESR1), Aswin Verhoeven, Manfred Wuhrer & Noortje de Haan
Glycoconjugate journal 38, pages 157–166 (2021)
DOI: https://doi.org/10.1007/s10719-020-09971-7
- Impact of Concurrency on the Performance of a Whole Exome Sequencing Pipeline
Daniele Dall'Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone Castellani and Enrico Giampieri
BMC Bioinformatics 22, Article number: 60 (February 2021)
DOI: https://doi.org/10.1186/s12859-020-03780-3
- Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging
Claudia Sala, Enrico Giampieri, Silvia Vitali, Paolo Garagnani, Daniel Remondini, Armando Bazzani, Claudio Franceschi, Gastone C. Castellani
PLoS ONE 15(10): e0237207, October 2020.
DOI: https://doi.org/10.1371/journal.pone.0237207
- Prediction of vascular aging based on smartphone acquired PPG signals
Lorenzo Dall’Olio, Nico Curti, Daniel Remondini, Yosef Safi Harb, Folkert W. Asselbergs, Gastone Castellani & Hae‑Won Uh
Scientific Reports, 10:19756, 2020
DOI: https://doi.org/10.1038/s41598-020-76816-6
- Systematic evaluation of normalization methods for glycomics data based on performance of network inference
Elisa Benedetti et al (including Manfred Wuhrer and Gordan Lauc)
Metabolites, 10 (7) 271, 2020
DOI: https://doi.org/10.3390/metabo10070271
- A strategy to incorporate prior knowledge into correlation network cutoff selection
Elisa Benedetti et al (including Gordan Lauc)
Nature Communications, 11:5153 (2020)
DOI: https://doi.org/10.1038/s41467-020-18675-3
- Choosing proper normalization is essential for discovery of sparse glycan biomarkers
Hae-Won Uh, Lucija Klarić, Ivo Ugrina, Gordan Lauc, Age K. Smilde and Jeanine J. Houwing-Duistermaat
Molecular Omics, Issue 3, June 2020, 16, 231-242
DOI: https://doi.org/10.1039/C9MO00174C
- Plasma N-Glycans as Emerging Biomarkers of Cardiometabolic Risk: A Prospective Investigation in the EPIC-Potsdam Cohort Study
Wittenbecher et al (including Frano Vučković and Gordan Lauc)
Diabetes Care 2020 Mar; 43(3): 661-668
DOI: https://doi.org/10.2337/dc19-1507
- Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform
Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini
PLoS ONE, 10 March 2020
DOI: https://doi.org/10.1371/journal.pone.0229763
- Small extracellular vesicles deliver miR-21 and miR-217 as pro-senescence effectors to endothelial cells
Emanuela Mensà et al (including Claudia Sala, Iva Budimir (ESR6), Paolo Garagnani)
Journal of Extracellular Vesicles, 9:1, 18 February 2020
DOI: https://doi.org/10.1080/20013078.2020.1725285
- Decreased immunoglobulin G core fucosylation, a player in antibody-dependent cell-mediated cytotoxicity, is associated with autoimmune thyroid diseases
Tiphaine C Martin et al (including Gordan Lauc)
Molecular & Cellular Proteomics, February 5, 2020, mcp.RA119.001860
DOI: https://doi.org/10.1074/mcp.RA119.001860
- NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods
Maria Lorna A. de Leoz et al (including Gordan Lauc, Erdmann Rapp, Manfred Wuhrer)
Molecular and Cellular Proteomics, January 2020, vol. 19 no. 1 11-30
DOI: https://doi.org/10.1074/mcp.RA119.001677
- The Role of the Central Limit Theorem in the Heterogeneous Ensemble of Brownian Particles Approach
Silvia Vitali, Iva Budimir (ESR6), Claudio Runfola and Gastone Castellani
Mathematics 2019, 7, 1145, 23 November 2019
DOI: https://doi.org/10.3390/math7121145
(This article belongs to the Special Issue Advanced Mathematical Methods: Theory and Applications)
- Expanding the Reaction Space of Linkage-Specific Sialic Acid Derivatization
Tamas Pongracz (ESR1), Manfred Wuhrer, Noortje de Haan
Molecules, 24(19), 3617, October 2019
DOI: 10.3390/molecules24193617
- Altered N‐glycosylation profiles as potential biomarkers and drug targets in diabetes
Najda Rudman, Olga Gornik, Gordan Lauc
FEBS Letters, Volume 593, Issue 13 (Krakow Special Issue), July 2019, Pages 1598-1615
DOI: 10.1002/1873-3468.13495
- Low galactosylation of IgG associates with higher risk for future diagnosis of rheumatoid arthritis during 10 years of follow-up
Ivan Gudelj, Perttu P.Salo, Irena Trbojević-Akmačić, Malena Albers, Dragan Primorac, Markus Perola, and Gordan Lauc
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1864, Issue 6, Part A, June 2018, Pages 2034-2039
DOI: 10.1016/j.bbadis.2018.03.018
- Glycosylation Profile of Immunoglobulin G Is Cross-Sectionally Associated With Cardiovascular Disease Risk Score and Subclinical Atherosclerosis in Two Independent Cohorts
Cristina Menni et al (including James F. Wilson, Gordan Lauc)
Circulation Research. 2018;122:1555–1564
DOI: 10.1161/CIRCRESAHA.117.312174
- N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells
Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc and Silva Hecimovic
Molecular & Cellular Proteomics April 1, 2018, 17 (4) 631-642
DOI: 10.1074/mcp.RA117.000129
- Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation
Shaza B Zaghlool et al (including Gordan Lauc)
- Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation
Xia Shen et al (including Lucija Klarić, James F. Wilson, Gordan Lauc & Yurii S. Aulchenko)
Nature Communications volume 8: 447 (2017)
DOI: 10.1038/s41467-017-00453-3
Non-open access publications
- Genetic Regulation of Immunoglobulin G Glycosylation
Azra Frkatović ESR4, Olga O. Zaytseva & Lucija Klaric
In: Antibody Glycosylation, pp 259–287, Springer
Part of the Experientia Supplementum book series (EXS,volume 112)
https://doi.org/10.1007/978-3-030-76912-3_8 - Joint Models for Repeatedly Measured Compositional and Normally Distributed Outcomes
Ivonne Martin, Hae-Won Uh, Jeanine Houwing-Duistermaat
In: Datta S., Guha S. (eds) Statistical Analysis of Microbiome Data. Frontiers in Probability and the Statistical Sciences. Springer, Cham., pp 131-173
https://doi.org/10.1007/978-3-030-73351-3_6
(Part of the Frontiers in Probability and the Statistical Sciences book series (FROPROSTAS)) - Investigation of the causal relationships between human IgG N-glycosylation and 12 common diseases associated with changes in the IgG N-glycome
Olga Zaytseva et al (including Arianna Landini, James F Wilson, Gordan Lauc, Yurii S Aulchenko, Lucija Klarić)
Human Molecular Genetics, 2021;, ddab335
https://doi.org/10.1093/hmg/ddab335 - Energy Consumption and Entropy Production in a Stochastic Formulation of BCM Learning
Gastone Castellani, Leon N. Cooper, Luciana Renata De Oliveira, and Brian S. Blais
Journal of Computational Biology, 2021
https://doi.org/10.1089/cmb.2020.0118 - Glycosylation of human plasma lipoproteins reveals a high level of diversity, which directly impacts their functional properties
Vasily Sukhorukov et al (including Gordan Lauc)
Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, May 2019, 1864 (5), 643-654
https://doi.org/10.1016/j.bbalip.2019.01.005 - Glycomics for Type 2 Diabetes Biomarker Discovery: Promise of Immunoglobulin G Subclass-Specific Fragment Crystallizable N-glycosylation in the Uyghur Population
Jiaonan Liu et al (including Gordan Lauc)
OMICS A Journal of Integrative Biology Volume 23, Number 12, 2019
https://doi.org/10.1089/omi.2019.0052 - Why Not Use the Immunoglobulin G N-Glycans as Predictor Variables in Disease Biomarker-Phenotype Association Studies? A Multivariate Analysis
Alyce C Russell et al (including Gordan Lauc)
OMICS: A Journal of Integrative Biology, Dec 2019, 668-670
https://doi.org/10.1089/omi.2019.0155 - The Fine Art of Destruction: A Guide to In‐Depth Glycoproteomic Analyses—Exploiting the Diagnostic Potential of Fragment Ions
Hoffman et al (including Erdmann Rapp)
Proteomics, 2018
https://doi.org/10.1002/pmic.201800282 - glyXtoolMS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data
Pioch et al (including Erdmann Rapp, Marcus Hoffman)
Analytical Chemistry, 2018
https://doi.org/10.1021/acs.analchem.8b02087 - The association between subclass-specific IgG Fc N-glycosylation profiles and hypertension in the Uygur, Kazak, Kirgiz, and Tajik populations
Liu et al (including Gordan Lauc)
Journal of Human Hypertension, 2018
https://doi.org/10.1038/s41371-018-0071-0 - Glycosylation of Immunoglobulin G Associates With Clinical Features of Inflammatory Bowel Diseases
Šimurina et al (including Noortje de Haan, Frano Vučković, Manfred Wuhrer, Gordan Lauc)
Gastroenterology, Volume 154, Issue 5, April 2018, Pages 1320-1333.e10
https://doi.org/10.1053/j.gastro.2018.01.002 - Increased central adiposity is associated with pro-inflammatory immunoglobulin G N-glycans
Russell et al (including Gordan Lauc)
Immunobiology, Volume 224, Issue 1, January 2019, Pages 110-115
https://doi.org/10.1016/j.imbio.2018.10.002 - Improvement of electrospray stability in negative ion mode for nano-PGC-LC-MS glycoanalysis via post-column make-up flow
Nguyen-Khuong et al (including Erdmann Rapp)
Glycoconjugate journal, 2018
https://doi.org/10.1007/s10719-018-9848-1 - Profiling and genetic control of the murine immunoglobulin G glycome
Krištić et al (including Frano Vučković, Gordan Lauc)
Nature Chemical Biology, 2018
https://doi.org/10.1038/s41589-018-0034-3 - The sweet spot for biologics: recent advances in characterization of biotherapeutic glycoproteins
O'Flaherty et al (including Gordan Lauc)
Expert Review of Proteomics, 2017
https://doi.org/10.1080/14789450.2018.1404907