Innovative training in methods for future data

Resultado final

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

Publicaciones

Prediction of vascular aging based on smartphone acquired PPG signals

Autores: Lorenzo Dall’Olio, Nico Curti, Daniel Remondini, Yosef Safi Harb, Folkert W. Asselbergs, Gastone Castellani, Hae-Won Uh
Publicado en: Scientific Reports, Edición 10/1, 2020, Página(s) 19756, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-020-76816-6

Genetic regulation of post-translational modification of two distinct proteins

Autores: 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
Publicado en: Nature Communications, Edición 20411723, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-29189-5

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

Autores: Iva Budimir, Enrico Giampieri, Edoardo Saccenti, Maria Suarez-Diez, Martina Tarozzi, Daniele Dall’Olio, Alessandra Merlotti, Nico Curti, Daniel Remondini, Gastone Castellani & Claudia Sala
Publicado en: Scientific Reports, Edición 20452322, 2022, ISSN 2045-2322
Editor: 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

Autores: Claudia Sala, Enrico Giampieri, Silvia Vitali, Paolo Garagnani, Daniel Remondini, Armando Bazzani, Claudio Franceschi, Gastone C. Castellani
Publicado en: PLOS ONE, Edición 15/10, 2020, Página(s) e0237207, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0237207

A strategy to incorporate prior knowledge into correlation network cutoff selection

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Molecular and Cellular Proteomics, Edición 7, 2020, Página(s) 774-792, ISSN 1535-9476
Editor: 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

Autores: Gu, Zhujie | Uh, Hae-Won | Houwing-Duistermaat, Jeanine | El Bouhaddani, Said
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: Fabrizio Serra Editore
DOI: 10.19272/202111401004

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

Autores: 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
Publicado en: eBioMedicine, Edición 23523964, 2022, Página(s) 103957, ISSN 2352-3964
Editor: 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

Autores: 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
Publicado en: Journal of Personalized Medicine, Edición 11/7, 2021, Página(s) 614, ISSN 2075-4426
Editor: MDPI
DOI: 10.3390/jpm11070614

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

Autores: 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
Publicado en: Metabolites, Edición 10/7, 2020, Página(s) 271, ISSN 2218-1989
Editor: MDPI
DOI: 10.3390/metabo10070271

Estimage: a webserver hub for the computation of methylation age

Autores: Pietro Di Lena, Claudia Sala, Christine Nardini
Publicado en: Nucleic Acids Research, Edición 49/W1, 2021, Página(s) W199-W206, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkab426

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

Autores: 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
Publicado en: Frontiers in Immunology, Edición 12, 2021, ISSN 1664-3224
Editor: Frontiers Media SA
DOI: 10.3389/fimmu.2021.680227

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

Autores: 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
Publicado en: eBioMedicine, Edición 23523964, 2022, Página(s) 103804, ISSN 2352-3964
Editor: Elsevier BV
DOI: 10.1016/j.ebiom.2021.103730

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

Autores: 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
Publicado en: Annals of the Rheumatic Diseases, 2021, Página(s) annrheumdis-2020-219624, ISSN 0003-4967
Editor: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2020-219624

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

Autores: Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone Castellani, Enrico Giampieri
Publicado en: BMC Bioinformatics, Edición 22/1, 2021, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-020-03780-3

DNA methylation correlation structure of chromosome 21 in Down syndrome

Autores: Iva Budimir, Claudia Sala, Gastone Castellani, Paolo Garagnani, Maria Giulia Bacalini
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: Fabrizio Serra Editore
DOI: 10.19272/202111401008

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

Autores: 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
Publicado en: Journal of Clinical Oncology, Edición 39/11, 2021, Página(s) 1223-1233, ISSN 0732-183X
Editor: American Society of Clinical Oncology
DOI: 10.1200/jco.20.01659

WISDoM: Characterizing Neurological Time Series With the Wishart Distribution

Autores: Carlo Mengucci, Daniel Remondini, Gastone Castellani, Enrico Giampieri
Publicado en: Frontiers in Neuroinformatics, Edición 14, 2021, ISSN 1662-5196
Editor: Frontiers Research Foundation
DOI: 10.3389/fninf.2020.611762

Estimation of the effect of surrogate multi-omic biomarkers

Autores: Fuady, Angga M. | Houwing-Duistermaat, Jeanine | Uh, Hae-Won | El Bouhaddani, Said
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: Fabrizio Serra Editore
DOI: 10.19272/202111401006

Statistical integration of two omics datasets using GO2PLS

Autores: Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat, Hae-Won Uh
Publicado en: BMC Bioinformatics, Edición 22/1, 2021, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-021-03958-3

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

Autores: Annah Mwikali Muli, Jeanine Houwing-Duistermaat, Arief Gusnanto
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: 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

Autores: Xie, Minzhen | Houwing-Duistermaat, Jeanine | Liu, Haiyan
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: Fabrizio Serra Editore
DOI: 10.19272/202111401003

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

Autores: Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Jeanine Houwing-Duistermaat
Publicado en: Journal of the Royal Statistical Society Series C, Edición 09641998, 2022, Página(s) 1451-1470, ISSN 0964-1998
Editor: 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

Autores: Angga M. Fuady, Willeke M. C. van Roon‐Mom, Szymon M. Kiełbasa, Hae‐Won Uh, Jeanine J. Houwing‐Duistermaat
Publicado en: Biometrical Journal, Edición 63/4, 2021, Página(s) 745-760, ISSN 0323-3847
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/bimj.201900235

Characterization and comparison of gene-centered human interactomes

Autores: Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone Castellani, Luciano Milanesi, Daniel Remondini
Publicado en: Briefings in Bioinformatics, Edición 14675463, 2021, ISSN 1467-5463
Editor: 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

Autores: Anika Mijakovac, Karlo Miškec, Jasminka Krištić, Vedrana Vičić Bočkor, Vanja Tadić, Maria Bošković, Gordan Lauc, Vlatka Zoldoš, and Aleksandar Vojta
Publicado en: The CRISPR journal, Edición 25731602, 2022, ISSN 2573-1602
Editor: Mary Ann Liebert
DOI: 10.1089/crispr.2021.0089

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

Autores: 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
Publicado en: Nature Communications, Edición 8/1, 2017, ISSN 2041-1723
Editor: 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

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

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

Autores: 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
Publicado en: Human Molecular Genetics, Edición 27/6, 2018, Página(s) 1106-1121, ISSN 0964-6906
Editor: 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

Autores: 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
Publicado en: Circulation Research, Edición 122/11, 2018, Página(s) 1555-1564, ISSN 0009-7330
Editor: 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

Autores: Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Publicado en: Molecular & Cellular Proteomics, Edición 17/4, 2018, Página(s) 631-642, ISSN 1535-9476
Editor: 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

Autores: Najda Rudman, Olga Gornik, Gordan Lauc
Publicado en: FEBS Letters, 2019, ISSN 0014-5793
Editor: Elsevier BV
DOI: 10.1002/1873-3468.13495

Expanding the Reaction Space of Linkage-Specific Sialic Acid Derivatization

Autores: Tamas Pongracz, Manfred Wuhrer, Noortje de Haan
Publicado en: Molecules, Edición 24/19, 2019, Página(s) 3617, ISSN 1420-3049
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24193617

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

Autores: Silvia Vitali, Iva Budimir, Claudio Runfola, Gastone Castellani
Publicado en: Mathematics, Edición 7/12, 2019, Página(s) 1145, ISSN 2227-7390
Editor: MDPI AG
DOI: 10.3390/MATH7121145

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

Autores: Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini
Publicado en: PLOS ONE, Edición 15/3, 2020, Página(s) e0229763, ISSN 1932-6203
Editor: 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

Autores: 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,
Publicado en: Journal of Extracellular Vesicles, Edición 9/1, 2020, Página(s) 1725285, ISSN 2001-3078
Editor: 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

Autores: 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
Publicado en: Molecular & Cellular Proteomics, Edición 19/1, 2020, Página(s) 11-30, ISSN 1535-9476
Editor: 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

Autores: Hae-Won Uh, Lucija Klarić, Ivo Ugrina, Gordan Lauc, Age K. Smilde, Jeanine J. Houwing-Duistermaat
Publicado en: Molecular Omics, Edición 16/3, 2020, Página(s) 231-242, ISSN 2515-4184
Editor: 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

Autores: 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
Publicado en: Diabetes Care, Edición 43/3, 2020, Página(s) 661-668, ISSN 0149-5992
Editor: American Diabetes Association
DOI: 10.2337/dc19-1507

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

Autores: Tamas Pongracz, Aswin Verhoeven, Manfred Wuhrer, Noortje de Haan
Publicado en: Glycoconjugate Journal, Edición 38/2, 2021, Página(s) 157-166, ISSN 0282-0080
Editor: 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

Autores: M. Tarozzi, A. Bartoletti-Stella, D. Dall’Olio, T. Matteuzzi, S. Baiardi, P. Parchi, G. Castellani & S. Capellari
Publicado en: BMC Medical Genomics, Edición 17558794, 2022, ISSN 1755-8794
Editor: BioMed Central
DOI: 10.1186/s12920-022-01173-4

Multivariate functional partial least squares for classification using longitudinal data

Autores: Dembowska, Sonia | Liu, Haiyan | Houwing-Duistermaat, Jeanine | Frangi, Alex
Publicado en: Theoretical Biology Forum, Edición 22837175, 2021, ISSN 2283-7175
Editor: Fabrizio Serra Editore
DOI: 10.19272/202111401007

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

Autores: Marcello Zanghieri, Giulia Menichetti, Alessandra Retico, Sara Calderoni, Gastone Castellani, Daniel Remondini
Publicado en: Brain Sciences, Edición 11/4, 2021, Página(s) 498, ISSN 2076-3425
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/brainsci11040498

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

Autores: Tamas Pongracz
Publicado en: 2022, ISBN 9789464585094
Editor: Ridderprint

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