MIMOmics publications

Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules
Matteo Bersanelli, Ettore Mosca, Daniel Remondini1, Gastone Castellani, Luciano Milanesi;  Scientific Reports | 6:34841 | DOI

Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption
Nicola Pirastu, Maarten Kooyman, Antonietta Robino, Ashley van der Spek, Luciano Navarini, Najaf Amin, Lennart C. Karssen, Cornelia M Van Duijn & Paolo Gasparini; Scientific Reports | 6:31590 DOI

Characterization of the metabolic profile associated with serum 25-hydroxyvitamin D: a cross-sectional analysis in population-based data
Susanne Vogt, SimoneWahl, Johannes Kettunen, Susanne Breitner, Gabi Kastenmuller, Christian Gieger,Karsten Suhre, Melanie Waldenberger, Jurgen Kratzsch, Markus Perola, Veikko Salomaa, Stefan Blankenberg, Tanja Zeller, Pasi Soininen, Antti J Kangas, Annette Peters,Harald Grallert, Mika Ala-Korpela and Barbara Thorand; International Journal of Epidemiology, 2016, 1–13 DOI

Metabolites of milk intake: a metabolomic approach in UK twins with findings replicated in two European cohorts
Tess Pallister, Toomas Haller, Barbara Thorand, Elisabeth Altmaier, Aedin Cassidy, Tiphaine Martin, Amy Jennings, Robert P. Mohney, Christian Gieger, Alexander MacGregor, Gabi Kastenmüller, Andres Metspalu, Tim D. Spector and Cristina Menni; Eur J Nutr (2016) DOI

Methods for testing the Markov condition in the illness-death model: a comparative study
M Rodríguez-Girondo and J de Uña-Álvarez (2016); Statistics in Medicine. DOI

Survival analysis with delayed entry in selected families with application to human longevity
M Rodríguez-Girondo, J. Deelen, PE Slagboom, J Houwing-Duistermaat (2016); Statistical Methods in Medical Research. DOI

Making sense of big data in health research: Towards an EU action plan
Charles Auffray, Rudi Balling et.al.; Genome Medicine2016 8:71; DOI

Glycosylation of plasma IgG in colorectal cancer prognosis
Evropi Theodoratou, Kujtim Thaçi, Felix Agakov, Maria N. Timofeeva, Jerko Štambuk, Maja Pučić-Baković, Frano Vučković, Peter Orchard, Anna Agakova, Farhat V. N. Din, Ewan Brown, Pauline M. Rudd, Susan M. Farrington, Malcolm G. Dunlop, Harry Campbell & Gordan Lauc; Scientific Reports 6, Article number: 28098 (2016); DOI

The GenABEL Project for statistical genomics
Lennart C. Karssen, Cornelia M. van Duijn, Yurii A. Aulchenko; F1000Research 2016, 5:914; DOI

The Association Between Low Back Pain and Composition of IgG Glycome
Maxim B. Freidin, Toma Keser, Ivan Gudelj, Jerko Štambuk, Dunja Vučenović, Massimo Allegri, Tamara Pavić, Mirna Šimurina, Stella M. Fabiane, Gordan Lauc & Frances M. K. Williams; Scientific Reports 6:26815 (2016) DOI

DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted glycoproteins
Marija Klasić, Jasminka Krištić, Petra Korać, Tomislav Horvat, Dora Markulin, Aleksandar Vojta, Karli R. Reiding, Manfred Wuhrer, Gordan Lauc & Vlatka Zoldoš; Scientific Reports 6, Article number: 24363 (2016) DOI

CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies
Kaiyin Zhong, Lennart C. Karssen, Manfred Kayser and Fan Liu; BMC Bioinformatics BMC series – open, inclusive and trusted 2016 17:156 DOI

Bayesian non-parametric inference for stochastic epidemic models using Gaussian Processes
X Xu, T Kypraios, PD O’Neill; Biostatistics, 2016 DOI

Overview of Some Interesting Statistical Problems in Biochemical Analysis of Glycans
I. Ugrina – 19th European Young Statisticians Meeting, 2015; ISBN 978-80-7378-301-3

Meningitis Caused by Toscana Virus Is Associated with Strong Antiviral Response in the CNS and Altered Frequency of Blood Antigen-Presenting Cells
S. Varani, F. Gelsomino, M. Bartoletti, P. Viale, A. Mastroianni, E. Briganti, P. Ortolani, F. Albertini, C. Calzetti, F. Prati, P. Cenni, G. Castellani, S. Morini, G. Rossini, M. Paola Landini and V. Sambri; Viruses 2015, 7(11), 5831-5843 DOI

Molecular multiplex network inference using Gaussian mixture hidden Markov models
Petar Velickovic and P. Lio; Journal of complex Networks, DOI

Methods for the integration of multi-omics data: mathematical aspects
M. Bersanelli, E. Mosca, D. Remondini, E. Giampieri, C. Sala, G. Castellani and L. Milanesi; BMC Bioinformatics 2016 17(Suppl 2):15 DOI

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data
C. Sala, S. Vitali, E.Gampirie, I. Faria do Valle, Daniel Remondini, Paolo Garagnani, Matteo Bersanelli, Ettore Mosca, Luciano Milanesi Gastone Castellani; BMC Bioinformatics 2016 17(Suppl 2):16 DOI

Sequential double cross-validation for augmented prediction assessment in high-dimensional omic applications
M. Rodriquez-Girondo, P. Salo, T. Burzykowski, M. Perola, J. Houwing-Duistermaat and B. Mertens; arXiv:1601.08197v1 [stat.ME] 29 Jan 2016

Potential of glycosylation research in graft versus host disease after allogeneichematopoietic stem cell transplantation
Ema Prenc, Drazen Pulanic, Maja Pucic-Bakovic, Marija Pezer, Lana Desnica, Radovan Vrhovac, Damir Nemet, and Steven Z. Pavletic; BBA – General Subjects (2016) DOI

The Detection of Metabolite-Mediated Gene Module Co-Expression Using Multivariate Linear Models
Trishanta Padayachee, Tatsiana Khamiakova, Ziv Shkedy, Markus Perola, Perttu Salo, and Tomasz Burzykowski; PLoS ONE 11(2): e0150257 DOI

A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study
Federica Chiappori, Luca Mattiazzi, Luciano Milanesi and Ivan Merelli; BMC Bioinformatics 2016 17(Suppl 4):57 DOI 

Evaluation of O2PLS in Omics data integration
Said el Bouhaddani, Jeanine Houwing-Duistermaat, Perttu SaloMarkus PerolaGeurt Jongbloed and Hae-Won Uh; BMC Bioinformatics2016, 17(Suppl 2):11DOI

Multiscale characterization of ageing and cancer progression by a novel network entropy measure
G. Menichetti, G. Bianconi, G. Castellani, E. Giampieri and D. Remondini; Mol. BioSyst., 2015, 11. 1824 DOI

Simple multi-trait analysis identifies novel loci associated with growth and obesity measures
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Epigenetic regulation of glycosylation is the quantum mechanics of biology
Gordan Lauc, Aleksandar Vojta, Vlatka Zoldoš; Biochimica et Biophysica Acta – General Subjects, Vol. 1840/Issue 1, 65-70 DOI

The impact of low-frequency and rare variants on lipid levels
Ida Surakka, Momoko Horikoshi, et. al.; Nature Genetics, Vol. 47/Issue 6, 589-597 DOI

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
Kieu Trinh Do, Gabi Kastenmüller, Dennis O. Mook-Kanamori, Noha A. Yousri, Fabian J. Theis, Karsten Suhre, Jan Krumsiek; Journal of Proteome Research, Vol. 14/Issue 2, 1183-1194 DOI

Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses
J. S. Ried, S.-Y. Shin, J. Krumsiek, T. Illig, F. J. Theis, T. D. Spector, J. Adamski, H.- E. Wichmann, K. Strauch, N. Soranzo, K. Suhre, C. Gieger; Human Molecular Genetics, Vol. 23/Issue 21, 5847-5857 DOI

Nonadditive Effects of Genes in Human Metabolomics
Y. A. Tsepilov, S.-Y. Shin, N. Soranzo, T. D. Spector, C. Prehn, J. Adamski, G. Kastenmuller et. al.; Genetics, Vol. 200/Issue 3, 707-718, DOI

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software
Diego Fabregat-Traver, Sodbo Zh. Sharapov, Caroline Hayward, Igor Rudan, Harry Campbell, Yurii Aulchenko, Paolo Bientinesi; F1000Research, 3, 200 DOI

Glycans – the third revolution in evolution
Gordan Lauc, Jasminka KriÅ¡tiÄ , Vlatka ZoldoÅ,; Frontiers in Genetics, Vol. 5, 145 DOI

Inflammatory Bowel Disease Associates with Proinflammatory Potential of the Immunoglobulin G Glycome
Irena Trbojević Akmačić, Nicholas T. Ventham, Evropi Theodoratou et.al.; Inflammatory Bowel Diseases, 21, 1237-47, DOI

The role of glycosylation in IBD
Evropi Theodoratou, Harry Campbell, Nicholas T. Ventham, Daniel Kolarich, Maja Pučić-Baković. et. al.; Nature Reviews Gastroenterology and Hepatology, 11, 588-600 DOI

Comparative Performance of Four Methods for High-throughput Glycosylation Analysis of Immunoglobulin G in Genetic and Epidemiological Research
J. E. Huffman, M. Pu i -Bakovi, L. Klari, R. Hennig, M. H. J. Selman, F. Vu kovi, M. Novokmet et.al.;
Molecular and Cellular Proteomics, Vol. 13/Issue 6, 1598-1610 DOI

Application of high-dimensional feature selection: evaluation for genomic prediction in man
M. L. Bermingham, R. Pong-Wong, A. Spiliopoulou, C. Hayward, I. Rudan, H. Campbell, A. F. Wright. et.al.; Scientific Reports, Vol. 5, 10312 DOI

Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data
Alexia Kakourou, Werner Vach, Bart Mertens; Journal of Computational Biology, Vol. 21/Issue 12, 898-914 DOI

Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus
Ettore Mosca, Roberta Alfieri, Luciano Milanesi; PLoS One, Vol. 9/Issue 12, e113660 DOI

Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems
Daniele D’Agostino, Giulia Pasquale, Andrea Clematis, Carlo Maj, Ettore Mosca, Luciano Milanesi, Ivan Merelli; BioMed Research InternationalVol. 2014DOI

Weighted Multiplex Networks
Giulia Menichetti, Daniel Remondini, Pietro Panzarasa, Raúl J. Mondragón, Ginestra Bianconi; PLoS One, Vol. 9/Issue 6e97857 DOI

Correlations between weights and overlap in ensembles of weighted multiplex networks
Giulia Menichetti, Daniel Remondini, Ginestra Bianconi; Physical Review E – Statistical, Nonlinear, and Soft Matter Physics, Vol. 90/Issue 6, 062817-1- 17 DOI

NETWORK APPROACHES FOR ANALYSIS AND MODELING OF THE HUMAN METABOLISM
GABRIELE FONTANAROSA , GIULIA MENICHETTI. et.al.; Journal of Mechanics in Medicine and Biology, Vol. 15/Issue 02, 1540026 DOI

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis
Lavinia Paternoster, Marie Standl, Johannes Waage, Hansjörg Baurecht, Melanie Hotze, David P Strachan, John A Curtin, et al; Nature Genetics, Epub DOI

Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair
Felix R Day, Katherine S Ruth, et al.; Nature Genetics, Vol. 47/Issue 11, 1294-1303 DOI

Rare coding variants and X-linked loci associated with age at menarche
Kathryn L. Lunetta, Felix R. Day, Patrick Sulem, Katherine S. Ruth, Joyce Y. Tung, David A. Hinds et.al.; Nature Communications, Vol. 6, 7756 DOI

Metabolomics approach reveals effects of antihypertensives and lipid-lowering drugs on the human metabolism
Elisabeth Altmaier, Gisela Fobo, Margit Heier, Barbara Thorand, Christine Meisinger, Et. al.; European Journal of Epidemiology, Vol. 29/Issue 5, 325-336 DOI

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi; PLoS One, Vol. 9/Issue 5, DOI

Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects
Daniele D’Agostino, Andrea Clematis, Alfonso Quarati, Daniele Cesini, et. al.; BioMed Research International, Vol. 2013, 1-19 DOI

Genetics of human metabolism: an update
Gabi Kastenmüller, Johannes Raffler,Christian Gieger and Karsten Suhre; Human Molecular Genetics, 2015, Vol. 24, No R1 R93-101 DOI: 10.1093/hmg/ddv263

Characterization of whole-genome autosomal differences of DNA methylation between men and women
Paula Singmann, Doron Shem-Tov, Simone Wahl, Harald Grallert, Giovanni Fiorito, So-Youn Shin, Katharina Schramm, Petra Wolf, Sonja Kunze, Yael Baran, Simonetta Guarrera, Paolo Vineis, Vittorio Krogh, Salvatore Panico, Rosario Tumino, Anja Kretschmer, Christian Gieger, Annette Peters, Holger Prokisch, Caroline L. Relton, Giuseppe Matullo, Thomas Illig, Melanie Waldenberger and Eran Halperin;  Epigenetics & Chromatin, 2015, 8:43 DOI: 10.1186/s13072-015-0035-3

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
Norihiro Kato, Marie Loh, Fumihiko Takeuchi, Niek Verweij, Xu Wang, Weihua Zhang, Tanika N Kelly, Danish Saleheen, Benjamin Lehne, Irene Mateo Leach, Alexander W Drong, James Abbott, Simone Wahl, Sian-Tsung Tan, William R Scott, Gianluca Campanella, Marc Chadeau-Hyam, Uzma Afzal, Tarunveer S Ahluwalia, Marc Jan Bonder, Peng Chen, Abbas Dehghan, Todd L Edwards, Tõnu Esko, Min Jin Go et al.  Nature Genetics (2015) DOI:10.1038/ng.3405

Glycosylation Profile of IgG in Moderate Kidney Dysfunction
Clara Barrios, Jonas Zierer, Ivan Gudelj, Jerko  Stambuk, Ivo Ugrina, Eva Rodríguez, María José Soler, Tamara Pavic, Mirna  Simurina, Toma Keser, Maja Pucic-Bakovic, Massimo Mangino, Julio Pascual, Tim D Spector, Gordan Lauc and Cristina Menni;  J Am Soc Nephrol 27, 2015. DOI: 10.1681/ASN.2015010109

Systemic lupus erythematosus associates with the decreased immunosuppressive potential of the IgG glycome
Frano Vučković, Jasminka Krištić, Ivan Gudelj, Maria Teruel Artacho, Toma Keser, Marija Pezer, Maja Pučić-Baković, Jerko Štambuk, Irena Trbojević-Akmačić, Clara Barrios, Tamara Pavić, Cristina Menni, Youxin Wang, Yong Zhou, Liufu Cui, Haicheng Song, Qiang Zeng, Xiuhua Guo, Bernardo A. Pons-Estel, Paul McKeigue, Alan Leslie Patrick, Olga Gornik, Tim D. Spector, Miroslav Harjaček, Marta Alarcon-Riquelme, Mariam Molokhia, Wei Wang and Gordan Lauc; Arthritis & Rheumatology, 2015 DOI10.1002/art.39273

Systems medicine of inflammaging
Gastone C. Castellani, Giulia Menichetti, Paolo Garagnani, Maria Giulia Bacalini, Chiara Pirazzini, Claudio Franceschi, Sebastiano Collino, Claudia Sala, Daniel Remondini, Enrico Giampieri, Ettore Mosca.  Brief Bioinform (2015) DOI: 10.1093/bib/bbv062

A simple stochastic model for the feedback circuit between p16INK4a and p53 mediated by p38MAPK: implications for senescence and apoptosis
L. R. de Oliveira,   J. C. M. Mombach and   G. Castellani.  Mol. BioSyst., 2015, 11, 2955-2963 DOI: 10.1039/C5MB00230C

Gender-specific pathway differences in the human serum metabolome
Jan Krumsiek, Kirstin Mittelstrass, Kieu Trinh Do, Ferdinand Stückler, Janina Ried, Jerzy Adamski, Annette Peters, Thomas Illig, Florian Kronenberg et al. Metabolomics December 2015, Volume 11, Issue 6, pp 1815-1833 DOI: 10.1007/s11306-015-0829-0.

Population-specific genotype imputations using minimac or IMPUTE2
Elisabeth M van Leeuwen, Alexandros Kanterakis, Patrick Deelen, Mathijs V Kattenberg, The Genome of the Netherlands Consortium, P Eline Slagboom, Paul I W de Bakker, Cisca Wijmenga, Morris A Swertz, Dorret I Boomsma, Cornelia M van Duijn, Lennart C Karssen & Jouke Jan Hottenga. Nature Protocols 10, 1285–1296 (2015) DOI: 10.1038/nprot.2015.077

Marginal genetic effects estimation in family and twin studies using random-effects models
Roula Tsonaka, Diane van der Woude and Jeanine Houwing-Duistermaat;  Biometrics 2015 July 6 DOI: 10.1111/biom.12350

The Human Blood Metabolome-Transcriptome Interface
Jörg Bartel, Jan Krumsiek, Katharina Schramm, Jerzy Adamski, Christian Gieger, Christian Herder, Maren Carstensen, Annette Peters, Wolfgang Rathmann, Michael Roden, Konstantin Strauch, Karsten Suhre, Gabi Kastenmüller, Holger Prokisch and Fabian J. Theis;
PLOS Genetics 2015 June 18  DOI: 10.1371/journal.pgen.1005274

Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer
Gianluca Ascolani, Annalisa Occhipinti and Pietro Liò; PLOS Computational Biology 2015 May 15. DOI: 10.1371/journal.pcbi.1004199

Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models.
Spiliopoulou A, Nagy R, Bermingham ML, Huffman JE, Hayward C, Vitart V, Rudan I, Campbell H, Wright AF, Wilson JF, Pong-Wong R, Agakov F, Navarro P, Haley CS; Hum Mol Genet. 2015 Apr 26. DOI: 10.1093/hmg/ddv145

Gene co-expression network analysis for family studies based on a meta-analytic approach
Tissier R, Uh HW, van den Akker E, Balliu B, Tsonaka S, Houwing-Duistermaat JJ; To appear in BMC Proc

A Retrospective Likelihood Approach for Efficient Integration of Multiple Omics Factors in Case-Control Association Studies
Balliu B, Tsonaka R, Boehringer S, Houwing-Duistermaat JJ; Genet Epidemiol. 2015 Mar; 39(3): 156-65. DOI: 10.1002/gepi.21884

G-CNV: a GPU-based tool for preparing data to detect CNVs with read-depth methods
Manconi A, Manca E, Moscatelli M, Gnocchi M, Orro A,  Armano G and Milanesi L;
Front. Bioeng. Biotechnol., 2015 March 10. DOI: 10.3389/fbioe.2015.00028

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies
Moni MA and Liò P; BMC Bioinformatics 2014, 15:333. DOI: 10.1186/1471-2105-15-333

Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data.
Shavit Y, Lio’ P; Mol Biosyst. 2014 Jun 6;10(6):1576-85. DOI: 10.1039/C4MB00142G

Changes in IgG and total plasma protein glycomes in acute systemic inflammation
Novokmet M, Lukić E, Vučković F, -Durić Z, Keser T, Rajšl K, Remondini D, Castellani G, Gašparović H, Gornik O, Lauc G; Sci Rep. 2014 Mar 11;4:4347. DOI: 10.1038/srep04347

Modeling TGF-β in early stages of cancer tissue dynamics
Ascolani G, Liò P; PLoS One. 2014 Feb 20;9(2) DOI: 10.1371/journal.pone.0088533

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD
Gertz EM, Hiekkalinna T, Digabel SL, Audet C, Terwilliger JD, Schäffer AA; BMC Bioinformatics. 2014 Feb 17;15(1):47. DOI

Immune parameters identify Italian centenarians with a longer five-year survival independent of their health and functional status.
Bucci L, Ostan R, Giampieri E, Cevenini E, Pini E, Scurti M, Vescovini R, Sansoni P, Caruso C, Mari D, Ronchetti F, Borghi MO, Ogliari G, Grossi C, Capri M, Salvioli S, Castellani G, Franceschi C, Monti D; Exp Gerontol. 2014 Jun;54:14-20. Epub 2014 Jan 31. DOI: 10.1016/j.exger.2014.01.023

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.
Merelli I1, Calabria A, Cozzi P, Viti F, Mosca E, Milanesi L; BMC Bioinformatics. 2013;14 Suppl 1:S9. Epub 2013 Jan 14. DOI: 10.1186/1471-2105-14-S1-S9

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units
Manconi A, Orro A, Manca E, Armano G, Milanesi L; BMC Bioinformatics. 2014;15 Suppl 1:S10. DOI: 10.1186/1471-2105-15-S1-S10

ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis
Shi Y, Nikulenkov F, Zawacka-Pankau J, Li H, Gabdoulline R, Xu J, Eriksson S, Hedström E, Issaeva N, Kel A, Arnér ES, Selivanova G; Cell Death Differ. 2014 Apr;21(4):612-23. DOI: 10.1038/cdd.2013.186

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P;
BMC Bioinformatics. 2014;15 Suppl 1:S2. DOI: 10.1186/1471-2105-15-S1-S2

Development and application of genomic control methods for genome-wide association studies using non-additive models
Tsepilov YA, Ried JS, Strauch K, Grallert H, van Duijn CM, Axenovich TI, Aulchenko YS; PLoS One. 2013 Dec 16;8(12). DOI: 10.1371/journal.pone.0081431

CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks
Shavit Y, Lio’ P; Bioinformatics. 2013 May 1;29(9):1206-7. DOI: 10.1093/bioinformatics/btt120

A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data
Zhou C, Walker MJ, Williamson AJ, Pierce A, Berzuini C, Dive C, Whetton AD; Bioinformatics. 2014 Feb 15;30(4):549-58. Epub 2013 Dec 15. DOI: 10.1093/bioinformatics/btt722

Glycans Are a Novel Biomarker of Chronological and Biological Ages
Krištić J, Vučković F, Menni C, Klarić L, Keser T, Beceheli I, Pučić-Baković M, Novokmet M, Mangino M, Thaqi K, Rudan P, Novokmet N, Šarac J, Missoni S, Kolčić I, Polašek O, Rudan I, Campbell H, Hayward C, Aulchenko Y, Valdes A, Wilson JF, Gornik O, Primorac D, Zoldoš V, Spector T and Lauc G; J Gerontol A Biol Sci Med Sci. 2013 Dec 10. DOI: 10.1093/gerona/glt190

Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds.
Cappelletti M1, Di Gennaro P, D’Ursi P, Orro A, Mezzelani A, Landini M, Fedi S, Frascari D, Presentato A, Zannoni D, Milanesi L; Genome Announc. 2013 Oct 24;1(5) DOI

Glycosylation of Immunoglobulin G: Role of Genetic and Epigenetic Influences.
Menni C, Keser T, Mangino M, Bell JT, Erte I, Akmačić I, Vučković F, Pučić Baković M, Gornik O, McCarthy MI, Zoldoš V, Spector TD, Lauc G, Valdes AM; PLoS One. 2013 Dec 6;8(12):e82558. DOI: 10.1371/journal.pone.0082558

Describing the genes social networks relying on chromosome conformation capture data
Merelli, I, Lio P, Milanesi L; EMBnet.journal 2013 suppl B, 19:73-75, Oct 14. Link

Network-based analysis of omics with multi-objective optimization
Mosca E, Milanesi L; Mol Biosyst. 2013 Dec;9(12):2971-80. DOI: 10.1039/c3mb70327d

A design automation framework for computational bioenergetics in biological networks
Angione C, Costanza J, Carapezza G, Lió P, Nicosia G; Mol Biosyst. 2013 Oct;9(10):2554-64. DOI: 10.1039/c3mb25558a

Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits
Petersen AK, Zeilinger S, Kastenmüller G, Römisch-Margl W, Brugger M, Peters A, Meisinger C, Strauch K, Hengstenberg C, Pagel P, Huber F, Mohney RP, Grallert H, Illig T, Adamski J, Waldenberger M, Gieger C, Suhre K; Hum Mol Genet. Jan 15, 2014; 23(2): 534–545. DOI: 10.1093/hmg/ddt430

Pareto optimality in organelle energy metabolism analysis
Angione C, Carapezza G, Costanza J, Lió P, Nicosia G; IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):1032-44. DOI: 10.1109/TCBB.2013.95

Metabolite profiling reveals new insights into the regulation of serum urate in humans
Albrecht E, Waldenberger M, Krumsiek J, Evans AM, Jeratsch U, Breier M, Adamski J, Koenig W, Zeilinger S, Fuchs C, Klopp N, Theis FJ, Wichmann HE, Suhre K, Illig T, Strauch K, Peters A, Gieger C, Kastenmüller G, Doering A, Meisinger C; Metabolomics. 2014;10:141-151. Epub 2013 Jul 20. DOI: 10.1007/s11306-013-0565-2

Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies
Zoldoš V, Horvat T, Lauc G; Curr Opin Chem Biol. 2013 Feb;17(1):34-40. DOI: 10.1016/j.cbpa.2012.12.007.

Molecular mechanism of allosteric communication in hsp70 revealed by molecular dynamics simulations.
Chiappori F, Merelli I, Colombo G, Milanesi L, Morra G; PLoS Comput Biol. 2012;8(12):e1002844. DOI: 10.1371/journal.pcbi.1002844

CUDA-quicksort: an improved GPU-based implementation of quicksort
Emanuale Manca, Andrea Manconi, Alessandro Orro, Giuliano Armano, Luciano Milanesi; Concurrency and Computation; DOI: 10.1002/cpe.3611

A Genome-Wide Association Study in isolated populations reveals new genes associated to common food likings
Pirastu, N., Kooyman, M., Traglia, M. et al. Rev Endocr Metab Disord (2016) 17: 209. doi:10.1007/s11154-016-9354-3

IgG Glycome in Colorectal Cancer
Frano Vučković, Evropi Theodoratou, Kujtim Thaçi, Maria Timofeeva, Aleksandar Vojta, Jerko Štambuk, Maja Pučić-Baković, Pauline M. Rudd, Lovorka Đerek, Dražen Servis, Annika Wennerström, Susan M. Farrington, Markus Perola, Yurii Aulchenko, Malcolm G. Dunlop, Harry Campbell and Gordan Lauc; Clinical Cancer Research. 2016; 22 vol 12. DOI: 10.1158/1078-0432.CCR-15-1867 

Classification for Longevity Potential: The Use of Novel Biomarkers
Marian Beekman,Hae-Won Uh, Diana van Heemst, Manfred Wuhrer, L. Renee Ruhaak, Vanessa Gonzalez-Covarrubias, Thomas Hankemeier, Jeanine J. Houwing-Duistermaat and P. Eline Slagboom; Front. Public Health, 28 October 2016 | DOI: 10.3389/fpubh.2016.00233

Human Plasma N-glycosylation as Analyzed by Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance-MS Associates with Markers of Inflammation and Metabolic Health
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