Innovative training in methods for future data

Deliverables

Policy document on training courses for wet and dry lab researchers

IMforFTURUER will contribute to training outside the consortium by producing a vision document on multidisciplinary training in omics research

Integrated workshop

Report on the integrated workshop. This workshop will be interdisciplinary and will be organized by ther ESRs. The ESRs will work together on the same consortium datasets: some of the ESRs will generate and process new data for these studies, others will apply novel statistical and bioinformatics approaches and finally ESRs will be involved in interpretation of the results. All ESRs will present and discuss their work on these datasets in the workshop

Recruitment strategy in place

Strategy for recruitment of excellent ESRs

Dissemination of methods at website

Website with an overview of all developed methods within IMforFUTURE together wiht links to software or code

PhD thesis titles & degrees

List of PhD thesis and degrees

Outreach activities first year of projects

Report on outreach activities in the first year of the projects

Outreach activities second year of projects

Report of lists of outreach activities in the second year of the ESR projects

Outreach activities third year of projects

Report on the outreach activities in the third year of the ESR projects

Open source training modules

Description of all training modules which are open for researchers outside the consortium

Publications

Prediction of vascular aging based on smartphone acquired PPG signals

Author(s): Lorenzo Dall’Olio, Nico Curti, Daniel Remondini, Yosef Safi Harb, Folkert W. Asselbergs, Gastone Castellani, Hae-Won Uh
Published in: Scientific Reports, Issue 10/1, 2020, Page(s) 19756, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-76816-6

Genetic regulation of post-translational modification of two distinct proteins

Author(s): Arianna Landini, Irena Trbojević-Akmačić, Pau Navarro, Yakov A. Tsepilov, Sodbo Z. Sharapov, Frano Vučković, Ozren Polašek, Caroline Hayward, Tea Petrović, Marija Vilaj, Yurii S. Aulchenko, Gordan Lauc, James F. Wilson & Lucija Klarić
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29189-5

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

Author(s): Iva Budimir, Enrico Giampieri, Edoardo Saccenti, Maria Suarez-Diez, Martina Tarozzi, Daniele Dall’Olio, Alessandra Merlotti, Nico Curti, Daniel Remondini, Gastone Castellani & Claudia Sala
Published in: Scientific Reports, Issue 20452322, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-21036-3

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging

Author(s): Claudia Sala, Enrico Giampieri, Silvia Vitali, Paolo Garagnani, Daniel Remondini, Armando Bazzani, Claudio Franceschi, Gastone C. Castellani
Published in: PLOS ONE, Issue 15/10, 2020, Page(s) e0237207, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0237207

A strategy to incorporate prior knowledge into correlation network cutoff selection

Author(s): Elisa Benedetti, Maja Pučić-Baković, Toma Keser, Nathalie Gerstner, Mustafa Büyüközkan, Tamara Štambuk, Maurice H. J. Selman, Igor Rudan, Ozren Polašek, Caroline Hayward, Hassen Al-Amin, Karsten Suhre, Gabi Kastenmüller, Gordan Lauc, Jan Krumsiek
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18675-3

Decreased IgG core fucosylation, a player in antibody-dependent cell-mediated cytotoxicity, is associated with autoimmune thyroid diseases

Author(s): Milena Krnjajic-Tadijanovic; Irena Trbojević-Akmačić; Alicja Hubalewska-Dydejczyk; Marija Vilaj; Gordan Lauc; Tim D. Spector; Scott G. Wilson; Anna Lityńska; John P. Walsh; Marta Ząbczyńska; Martina Martinic Kavur; Ee Mun Lim; Renata Turek-Jabrocka; Ewa Pocheć; Marija Pezer; Malgorzata Trofimiuk-Muldner; Tiphaine Martin; Mirna Šimurina; Andrea Burri; Magdalena Rydlewska; Kamila Kozłowska
Published in: Molecular and Cellular Proteomics, Issue 7, 2020, Page(s) 774-792, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1101/362004

Investigating the impact of Down syndrome on Methylation and Glycomics with two-stage PO2PLS

Author(s): Gu, Zhujie | Uh, Hae-Won | Houwing-Duistermaat, Jeanine | El Bouhaddani, Said
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401004

Immunoglobulin G1 Fc glycosylation as an early hallmark of severe COVID-19

Author(s): Tamas Pongracz Jan Nouta Wenjun Wang Krista E. van Meijgaarden Federica Linty Gestur Vidarsson Simone A. Joosten Tom H.M. Ottenhoff Cornelis H. Hokke Jutte J.C. de Vries Sesmu M. Arbous Anna H.E. Roukens Manfred Wuhrer in collaboration with BEAT-COVID COVID-19 groups
Published in: eBioMedicine, Issue 23523964, 2022, Page(s) 103957, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2022.103957

Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese

Author(s): Xiaoni Meng, Manshu Song, Marija Vilaj, Jerko Štambuk, Mamatyusupu Dolikun, Jie Zhang, Di Liu, Hao Wang, Xiaoyu Zhang, Jinxia Zhang, Weijie Cao, Ana Momčilović, Irena Trbojević-Akmačić, Xingang Li, Deqiang Zheng, Lijuan Wu, Xiuhua Guo, Youxin Wang, Gordan Lauc, Wei Wang
Published in: Journal of Personalized Medicine, Issue 11/7, 2021, Page(s) 614, ISSN 2075-4426
Publisher: MDPI
DOI: 10.3390/jpm11070614

Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference

Author(s): Elisa Benedetti, Nathalie Gerstner, Maja Pučić-Baković, Toma Keser, Karli R. Reiding, L. Renee Ruhaak, Tamara Štambuk, Maurice H.J. Selman, Igor Rudan, Ozren Polašek, Caroline Hayward, Marian Beekman, Eline Slagboom, Manfred Wuhrer, Malcolm G. Dunlop, Gordan Lauc, Jan Krumsiek
Published in: Metabolites, Issue 10/7, 2020, Page(s) 271, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo10070271

Estimage: a webserver hub for the computation of methylation age

Author(s): Pietro Di Lena, Claudia Sala, Christine Nardini
Published in: Nucleic Acids Research, Issue 49/W1, 2021, Page(s) W199-W206, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab426

Effects of Estradiol on Immunoglobulin G Glycosylation: Mapping of the Downstream Signaling Mechanism

Author(s): Anika Mijakovac, Julija Jurić, Wendy M. Kohrt, Jasminka Krištić, Domagoj Kifer, Kathleen M. Gavin, Karlo Miškec, Azra Frkatović, Frano Vučković, Marija Pezer, Aleksandar Vojta, Peter A. Nigrović, Vlatka Zoldoš, Gordan Lauc
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.680227

Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome

Author(s): Yanni Zeng Carmen Amador Chenhao Gao Rosie M. Walker Stewart W. Morris Archie Campbell Azra Frkatović Rebecca A Madden Mark J. Adams Shuai He Andrew D. Bretherick Caroline Hayward David J. Porteous James F. Wilson Kathryn L. Evans Andrew M. McIntosh Pau Navarro Chris S. Haley
Published in: eBioMedicine, Issue 23523964, 2022, Page(s) 103804, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2021.103730

Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain

Author(s): Md Shafiqur Rahman, Bendik S Winsvold, Sergio O Chavez Chavez, Sigrid Børte, Yakov A Tsepilov, Sodbo Zh Sharapov, Yurii S Aulchenko, Knut Hagen, Egil A Fors, Kristian Hveem, John Anker Zwart, Joyce B van Meurs, Maxim B Freidin, Frances MK Williams
Published in: Annals of the Rheumatic Diseases, 2021, Page(s) annrheumdis-2020-219624, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2020-219624

Impact of concurrency on the performance of a whole exome sequencing pipeline

Author(s): Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone Castellani, Enrico Giampieri
Published in: BMC Bioinformatics, Issue 22/1, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03780-3

DNA methylation correlation structure of chromosome 21 in Down syndrome

Author(s): Iva Budimir, Claudia Sala, Gastone Castellani, Paolo Garagnani, Maria Giulia Bacalini
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401008

Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes

Author(s): Matteo Bersanelli, Erica Travaglino, Manja Meggendorfer, Tommaso Matteuzzi, Claudia Sala, Ettore Mosca, Chiara Chiereghin, Noemi Di Nanni, Matteo Gnocchi, Matteo Zampini, Marianna Rossi, Giulia Maggioni, Alberto Termanini, Emanuele Angelucci, Massimo Bernardi, Lorenza Borin, Benedetto Bruno, Francesca Bonifazi, Valeria Santini, Andrea Bacigalupo, Maria Teresa Voso, Esther Oliva, Marta Riva, Marta
Published in: Journal of Clinical Oncology, Issue 39/11, 2021, Page(s) 1223-1233, ISSN 0732-183X
Publisher: American Society of Clinical Oncology
DOI: 10.1200/jco.20.01659

WISDoM: Characterizing Neurological Time Series With the Wishart Distribution

Author(s): Carlo Mengucci, Daniel Remondini, Gastone Castellani, Enrico Giampieri
Published in: Frontiers in Neuroinformatics, Issue 14, 2021, ISSN 1662-5196
Publisher: Frontiers Research Foundation
DOI: 10.3389/fninf.2020.611762

Estimation of the effect of surrogate multi-omic biomarkers

Author(s): Fuady, Angga M. | Houwing-Duistermaat, Jeanine | Uh, Hae-Won | El Bouhaddani, Said
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401006

Statistical integration of two omics datasets using GO2PLS

Author(s): Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat, Hae-Won Uh
Published in: BMC Bioinformatics, Issue 22/1, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-03958-3

Use of shared gamma frailty model in analysis of survival data in twins

Author(s): Annah Mwikali Muli, Jeanine Houwing-Duistermaat, Arief Gusnanto
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401005

Nonparametric clustering for longitudinal functional data with the application to HNMR spectra of Kidney transplant patients : longitudinal functional data clustering

Author(s): Xie, Minzhen | Houwing-Duistermaat, Jeanine | Liu, Haiyan
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401003

Statistical integration of heterogeneous omics data: Probabilistic two-way partial least squares (PO2PLS)

Author(s): Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Jeanine Houwing-Duistermaat
Published in: Journal of the Royal Statistical Society Series C, Issue 09641998, 2022, Page(s) 1451-1470, ISSN 0964-1998
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/rssc.12583

Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease

Author(s): Angga M. Fuady, Willeke M. C. van Roon‐Mom, Szymon M. Kiełbasa, Hae‐Won Uh, Jeanine J. Houwing‐Duistermaat
Published in: Biometrical Journal, Issue 63/4, 2021, Page(s) 745-760, ISSN 0323-3847
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/bimj.201900235

Characterization and comparison of gene-centered human interactomes

Author(s): Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone Castellani, Luciano Milanesi, Daniel Remondini
Published in: Briefings in Bioinformatics, Issue 14675463, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab153

A Transient Expression System with Stably Integrated CRISPR-dCas9 Fusions for Regulation of Genes Involved in Immunoglobulin G Glycosylation

Author(s): Anika Mijakovac, Karlo Miškec, Jasminka Krištić, Vedrana Vičić Bočkor, Vanja Tadić, Maria Bošković, Gordan Lauc, Vlatka Zoldoš, and Aleksandar Vojta
Published in: The CRISPR journal, Issue 25731602, 2022, ISSN 2573-1602
Publisher: Mary Ann Liebert
DOI: 10.1089/crispr.2021.0089

Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation

Author(s): Xia Shen, Lucija Klarić, Sodbo Sharapov, Massimo Mangino, Zheng Ning, Di Wu, Irena Trbojević-Akmačić, Maja Pučić-Baković, Igor Rudan, Ozren Polašek, Caroline Hayward, Timothy D. Spector, James F. Wilson, Gordan Lauc, Yurii S. Aulchenko
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-00453-3

Low galactosylation of IgG associates with higher risk for future diagnosis of rheumatoid arthritis during 10 years of follow-up

Author(s): Ivan Gudelj, Perttu P. Salo, Irena Trbojević-Akmačić, Malena Albers, Dragan Primorac, Markus Perola, Gordan Lauc
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1864/6, 2018, Page(s) 2034-2039, ISSN 0925-4439
Publisher: Elsevier BV
DOI: 10.1016/j.bbadis.2018.03.018

Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation

Author(s): Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana T Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Marija Pezer, Gordan Lauc, Johann
Published in: Human Molecular Genetics, Issue 27/6, 2018, Page(s) 1106-1121, ISSN 0964-6906
Publisher: Oxford University Press
DOI: 10.1093/hmg/ddy006

Glycosylation Profile of Immunoglobulin G Is Cross-Sectionally Associated With Cardiovascular Disease Risk Score and Subclinical Atherosclerosis in Two Independent Cohorts

Author(s): Cristina Menni, Ivan Gudelj, Erin Macdonald-Dunlop, Massimo Mangino, Jonas Zierer, Erim Bešić, Peter K. Joshi, Irena Trbojević-Akmačić, Phil J. Chowienczyk, Tim D. Spector, James F. Wilson, Gordan Lauc, Ana M. Valdes
Published in: Circulation Research, Issue 122/11, 2018, Page(s) 1555-1564, ISSN 0009-7330
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/CIRCRESAHA.117.312174

N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells

Author(s): Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Published in: Molecular & Cellular Proteomics, Issue 17/4, 2018, Page(s) 631-642, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra117.000129

Altered N-glycosylation profiles as potential biomarkers and drug targets in diabetes

Author(s): Najda Rudman, Olga Gornik, Gordan Lauc
Published in: FEBS Letters, 2019, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.13495

Expanding the Reaction Space of Linkage-Specific Sialic Acid Derivatization

Author(s): Tamas Pongracz, Manfred Wuhrer, Noortje de Haan
Published in: Molecules, Issue 24/19, 2019, Page(s) 3617, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24193617

The Role of the Central Limit Theorem in the Heterogeneous Ensemble of Brownian Particles Approach

Author(s): Silvia Vitali, Iva Budimir, Claudio Runfola, Gastone Castellani
Published in: Mathematics, Issue 7/12, 2019, Page(s) 1145, ISSN 2227-7390
Publisher: MDPI AG
DOI: 10.3390/MATH7121145

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform

Author(s): Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini
Published in: PLOS ONE, Issue 15/3, 2020, Page(s) e0229763, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0229763

Small extracellular vesicles deliver miR-21 and miR-217 as pro-senescence effectors to endothelial cells

Author(s): Emanuela Mensà, Michele Guescini, Angelica Giuliani, Maria Giulia Bacalini, Deborah Ramini, Giacomo Corleone, Manuela Ferracin, Gianluca Fulgenzi, Laura Graciotti, Francesco Prattichizzo, Leonardo Sorci, Michela Battistelli, Vladia Monsurrò, Anna Rita Bonfigli, Maurizio Cardelli, Rina Recchioni, Fiorella Marcheselli, Silvia Latini, Serena Maggio, Mirco Fanelli, Stefano Amatori, Gianluca Storci,
Published in: Journal of Extracellular Vesicles, Issue 9/1, 2020, Page(s) 1725285, ISSN 2001-3078
Publisher: Taylor & Francis Group
DOI: 10.1080/20013078.2020.1725285

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods

Author(s): Maria Lorna A. De Leoz, David L. Duewer, Adam Fung, Lily Liu, Hoi Kei Yau, Oscar Potter, Gregory O. Staples, Kenichiro Furuki, Ruth Frenkel, Yunli Hu, Zoran Sosic, Peiqing Zhang, Friedrich Altmann, Clemens Gru«nwald-Grube, Chun Shao, Joseph Zaia, Waltraud Evers, Stuart Pengelley, Detlev Suckau, Anja Wiechmann, Anja Resemann, Wolfgang Jabs, Alain Beck, John W. Froehlich, Chuncui Huang, Yan Li, Yam
Published in: Molecular & Cellular Proteomics, Issue 19/1, 2020, Page(s) 11-30, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra119.001677

Choosing proper normalization is essential for discovery of sparse glycan biomarkers

Author(s): Hae-Won Uh, Lucija Klarić, Ivo Ugrina, Gordan Lauc, Age K. Smilde, Jeanine J. Houwing-Duistermaat
Published in: Molecular Omics, Issue 16/3, 2020, Page(s) 231-242, ISSN 2515-4184
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9mo00174c

Plasma N -Glycans as Emerging Biomarkers of Cardiometabolic Risk: A Prospective Investigation in the EPIC-Potsdam Cohort Study

Author(s): Clemens Wittenbecher, Tamara Štambuk, Olga Kuxhaus, Najda Rudman, Frano Vučković, Jerko Štambuk, Catarina Schiborn, Dario Rahelić, Stefan Dietrich, Olga Gornik, Markus Perola, Heiner Boeing, Matthias B. Schulze, Gordan Lauc
Published in: Diabetes Care, Issue 43/3, 2020, Page(s) 661-668, ISSN 0149-5992
Publisher: American Diabetes Association
DOI: 10.2337/dc19-1507

The structure and role of lactone intermediates in linkage-specific sialic acid derivatization reactions

Author(s): Tamas Pongracz, Aswin Verhoeven, Manfred Wuhrer, Noortje de Haan
Published in: Glycoconjugate Journal, Issue 38/2, 2021, Page(s) 157-166, ISSN 0282-0080
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10719-020-09971-7

Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases

Author(s): M. Tarozzi, A. Bartoletti-Stella, D. Dall’Olio, T. Matteuzzi, S. Baiardi, P. Parchi, G. Castellani & S. Capellari
Published in: BMC Medical Genomics, Issue 17558794, 2022, ISSN 1755-8794
Publisher: BioMed Central
DOI: 10.1186/s12920-022-01173-4

Multivariate functional partial least squares for classification using longitudinal data

Author(s): Dembowska, Sonia | Liu, Haiyan | Houwing-Duistermaat, Jeanine | Frangi, Alex
Published in: Theoretical Biology Forum, Issue 22837175, 2021, ISSN 2283-7175
Publisher: Fabrizio Serra Editore
DOI: 10.19272/202111401007

Node Centrality Measures Identify Relevant Structural MRI Features of Subjects with Autism

Author(s): Marcello Zanghieri, Giulia Menichetti, Alessandra Retico, Sara Calderoni, Gastone Castellani, Daniel Remondini
Published in: Brain Sciences, Issue 11/4, 2021, Page(s) 498, ISSN 2076-3425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/brainsci11040498

Antibody glycomics signatures of SARS-CoV-2 infection and vaccination

Author(s): Tamas Pongracz
Published in: 2022, ISBN 9789464585094
Publisher: Ridderprint

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