This section addresses the Action’s Publications, Proposals / Projects, and Other Outputs:
https://doi.org/10.1093/bib/bbx160
Title: Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine
Authors: Massimiliano Zanin; Ivan Chorbev; Blaz Stres; Egils Stalidzans; Julio Vera; Paolo Tieri; Filippo Castiglione; Derek Groen; Huiru Zheng; Jan Baumbach; Johannes A Schmid; José Basilio; Peter Klimek; Nataša Debeljak; Damjana Rozman; Harald H H W Schmidt
https://doi.org/10.3389/fphys.2017.00250
Title: Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study
Authors: Robert Šket; Nicole Treichel; Tadej Debevec; Ola Eiken; Igor Mekjavic; Michael Schloter; Marius Vital; Jenna Chandler; James M. Tiedje; Boštjan
Murovec; Zala Prevoršek; Blaž Stres
https://doi.org/10.1371/journal.pone.0188556
Title: Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study
Authors: Robert Šket; Nicole Treichel; Susanne Kublik; Tadej Debevec; Ola Eiken; Igor Mekjavić; Michael Schloter; Marius Vital; Jenna Chandler; James M. Tiedje; Boštjan
Murovec; Zala Prevoršek; Matevž Likar; Blaž Stres
https://doi.org/10.3389/fphys.2018.00198
Title: Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis
Authors: Robert Šket; Tadej Debevec; Susanne Kublik; Michael Schloter; Anne
Schoeller; Boštjan Murovec; Katarina Vogel Mikuš; Damjan Makuc; Klemen Pečnik; Janez
Plavec; Igor B. Mekjavić; Ola Eiken; Zala Prevoršek; Blaž Stres
https://doi.org/10.1124/pr.117.014753
Title: Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach
Authors: Antonio Cuadrado; Gina Manda; Ahmed Hassan; María José Alcaraz; Coral
Barbas; Andreas Daiber; Pietro Ghezzi; Rafael León; Manuela G. López; Baldo
Oliva; Marta Pajares; Ana I. Rojo; Natalia Robledinos-Antón; Angela M. Valverde;
Emre Guney; Harald H. H.W. Schmidt
https://doi.org/10.1038/s41540-017-0039-7
Title: A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection
Authors: Friederike Langhauser; Ana I. Casas; Vu-Thao-Vi Dao; Emre Guney; Jörg
Menche; Eva Geuss; Pamela W. M. Kleikers; Manuela G. López; Albert-L. Barabási; Christoph
Kleinschnitz; Harald H. H.W. Schmidt
https://doi.org/10.1089/sysm.2017.28999.jba
Title: The End of Medicine as We Know It: Introduction to the New Journal, Systems Medicine
Authors: Jan Baumbach; Harald H.H.W. Schmidt
https://doi.org/10.1089/sysm.2017.29000.rtd
Title: Expert Panel Discusses the Importance of Systems Medicine
Authors: Harald H.H.W. Schmidt; Jan Baumbach; Joseph Loscalzo; Alvar Agusti; Edwin K. Silverman; Vasco Azevedo
https://doi.org/10.1038/s41596-018-0098-2
Title: Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Authors: S.M. Keating, V. Vlasov, J. Wachowiak, S. Magnusdottir, C. Yu Ng, G. Preciat, A.
Zagare, S.H.J. Chan, M.K. Aurich, C.M. Clancy, J. Modamio, J.T. Sauls, A. Noronha,
- Bordbar, B. Cousins, D.C. El Assal, S. Ghaderi, M. Ahookhosh, M. Ben Guebila, I.
Apaolaza, A. Kostromins, H.M. Le, D. Ma, Y. Sun, L.V. Valcarcel, L. Wang, J.T.
Yurkovich, P.T. Vuong, L.P. El Assal, S. Hinton, W.A. Bryant, F.J. Aragon Artacho,
F.J. Planes, E. Stalidzans, A. Maass, S. Vempala, M. Hucka, M.A. Saunders, C.D.
Maranas, N.E. Lewis, T. Sauter, B.Ø. Palsson, I. Thiele, and R.M.T. Fleming.
https://doi.org/10.1016/j.compbiomed.2017.12.010
Title: Mechanistic modelling of drug release from multi-layer capsules
Authors: Badr Kaoui; Marco Lauricella; Giuseppe Pontrelli
https://doi.org/10.1089/sysm.2019.0008
Title: De novo and supervised endophenotyping using network-guided ensemble learning
Authors: Larsen SJ, Schmidt HHHW, Baumbach J.
https://doi.org/10.1089/nsm.2020.0004
Title: Network and systems medicine: Position paper of the European Collaboration on Science and Technology action on Open Multiscale Systems Medicine
Authors: Comte B, Baumbach J, Benis A, Basílio J, Debeljak N, Flobak A, Franken C, Harel N, He F, Kuiper M, Méndez Pérez JA, Pujos-Guillot E, Režen T, Rozman D, Schmid J.A., Scerri J, Tieri P, Van Steen K, Vasudevan S, Watterson S, Schmidt H.H.H.W.
https://doi.org/10.1002/wsbm.1489
Title: Molecular networks in Network Medicine: Development and applications
Authors: Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J
https://doi.org/10.1093/bioinformatics/btaa245
Title: EpiGEN: an epistasis simulation pipeline
Authors: Blumenthal DB, Viola L, List M, Baumbach J, Tieri P, Kacprowski T
https://doi.org/10.1089/nsm.2020.0002
Title: Mechanistic modeling and multiscale applications for precision medicine: theory and practice
Authors: Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HHHW
https://doi.org/10.1073/pnas.1820799116
Title: From single drug targets to synergistic network pharmacology in ischemic stroke
Authors: Casasa AI, Hassana AA, Larsen SJ, Gomez-Rangel V, Elbatreek M, Kleikers PWM, Guney E, Egeae J, López MG, Baumbach J, Schmidt HHHW
https://doi.org/10.1089/sysm.2018.0013
Title: Time resolved systems medicine reveals viral infection modulating host targets
Authors: Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt H, Pleschka S, Röttger R, Baumbach J
https://doi.org/10.1038/s41540-020-00156-4
Title: Mitochondria-mitochondria interaction networks show altered topological patterns in Parkinson’s disease
Authors: Massimiliano Zanin, Bruno FR Santos, Paul MA Antony, Clara Berenguer-Escuder, Simone B Larsen, Zoe Hanss, Peter Barbuti, Aidos S Baumuratov, Dajana Grossmann, Christophe Capelle, Joseph Weber, Rudi Balling, Markus Ollert, Rejko Krueger, Nico J Diederich, Feng Q He
https://doi.org/10.1038/s41587-020-0446-y
Title: MEMOTE for standardized genome-scale metabolic model testing
Authors: Christian Lieven; Moritz E. Beber; Brett G. Olivier; Frank T. Bergmann; Meric
Ataman; Parizad Babaei; Jennifer A. Bartell; Lars M. Blank; Siddharth Chauhan; Kevin Correia; Christian Diener; Andreas Dräger; Birgitta E. Ebert; Janaka N. Edirisinghe; José P. Faria; Adam M. Feist; Georgios Fengos; Ronan M. T. Fleming; Beatriz García-Jiménez; Vassily Hatzimanikatis; Wout van Helvoirt; Christopher S. Henry; Henning Hermjakob; Markus J. Herrgård; Ali Kaafarani; Hyun Uk Kim; Zachary King; Steffen Klamt; Edda Klipp; Jasper J. Koehorst; Matthias König; Meiyappan Lakshmanan; Dong-Yup Lee; Sang Yup Lee; Sunjae Lee; Nathan E. Lewis; Filipe Liu; Hongwu Ma; Daniel Machado; Radhakrishnan Mahadevan; Paulo Maia; Adil Mardinoglu; Gregory L. Medlock; Jonathan M. Monk; Jens Nielsen; Lars Keld Nielsen; Juan Nogales; Intawat Nookaew; Bernhard O. Palsson; Jason A. Papin; Kiran R. Patil; Mark Poolman; Nathan D. Price; Osbaldo Resendis-Antonio; Anne Richelle; Isabel Rocha; Benjamín J. Sánchez; Peter J. Schaap; Rahuman S. Malik Sheriff; Saeed Shoaie; Nikolaus Sonnenschein; Bas Teusink; Paulo Vilaça; Jon Olav Vik; Judith A. H. Wodke; Joana C. Xavier; Qianqian Yuan; Maksim Zakhartsev; Cheng Zhang
https://doi.org/10.1038/nbt.4072
Title: Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism
Authors: Elizabeth Brunk, Swagatika Sahoo, Daniel C. Zielinski, Ali Altunkaya, Andreas Dräger, Nathan Mih, Francesco Gatto, Avlant Nilsson, German Andres Preciat Gonzalez, Maike Kathrin Aurich, Andreas Prlić, Anand Sastry, Anna D. Danielsdottir, Almut Heinken, Alberto Noronha, Peter W. Rose, Stephen K. Burley, Ronan M.T. Fleming, Jens Nielsen, Ines Thiele, and Bernhard O. Palsson
https://doi.org/10.1109/BIBM.2018.8621361
Title: Multiscale Computing in Systems Medicine: a Brief Reflection
Authors: Huiru Zheng, Jyotsna Talreja Wassan, Mihnea Alexandru Moisescu, Lacramioara Stoicu-Tivadar, João Miranda, Mihaela Crisan-Vida, Ioan Stefan Sacala, Almir Badnjevic, Ivan Chorbev, Boro Jakimovski
https://doi.org/10.1016/j.neuropharm.2020.108118
Title: Opportunities for multiscale computational modelling of serotonergic drug effects in Alzheimer’s disease
Authors: Joshi, A., Wang, D.-H., Watterson, S., McClean, P.L., Behera, C.K., Sharp, T., Wong-Lin, K.
https://doi.org/10.3389/fmolb.2020.00132
Title: Time-Lagged t-Distributed Stochastic Neighbor Embedding (t-SNE) of Molecular Simulation Trajectories
Authors: Spiwok, V., Kříž, P.
https://doi.org/10.1038/s41467-019-10316-8
Title: A neural circuit model of decision uncertainty and change-of-mind
Authors: Atiya, N.A.A., Rañó, I., Prasad, G., Wong-Lin, K.F.
https://doi.org/10.1109/BIBM47256.2019.8983188
Title: SCENARIO: Discovery of Similar Aspects for Gene Similarity Explanation from Gene Information Network
Authors: Zhang, Y., Duan, L., Zheng, H., Li-Ling, J., Hu, B., Qin, R., He, C.
https://doi.org/10.1007/s12021-019-09416-z
Title: Independent Multiple Factor Association Analysis for Multiblock Data in Imaging Genetics
Authors: Vilor-Tejedor, N., Ikram, M.A., Roshchupkin, G.V., Cáceres, A., Alemany, S., Vernooij, M.W., Niessen, W.J., van Duijn, C.M., Sunyer, J., Adams, H.H., González, J.R.
https://doi.org/10.1016/j.eswa.2019.04.022
Title: A practical computerized decision support system for predicting the severity of Alzheimer’s disease of an individual
Authors: Bucholc, M., Ding, X., Wang, H., Glass, D.H., Wang, H., Prasad, G., Maguire, L.P., Bjourson, A.J., McClean, P.L., Todd, S., Finn, D.P., Wong-Lin, K.
https://doi.org/10.1161/CIRCULATIONAHA.119.040423
Title: Red Blood Cell-Derived Nitric Oxide Bioactivity and Hypoxic Vasodilation: To β93 or not to β93?
Authors: Schmidt, H.H.H.W., Feelisch, M.
https://doi.org/10.1109/BIBM.2018.8621436
Title: RADAR: Representation Learning across Disease Information Networks for Similar Disease Detection
Authors: Qin, R., Duan, L., Zheng, H., Li-Ling, J., Song, K., Lan, X.
https://doi.org/10.1109/BIBM.2018.8621343
Title: Correlation Model Analysis of Nitrogen Addition and Tan Sheep Grazing Effects on Soil Bacterial Community in the Loess Plateau, China
Authors: Wang, M., Hou, F., Zheng, H., Wang, H.
https://doi.org/10.1093/nar/gky1176
Title: E. coli gene regulatory networks are inconsistent with gene expression data
Authors: Larsen, S.J., Röttger, R., Schmidt, H.H.H.W., Baumbach, J.
https://doi.org/10.1038/s41598-018-27997-8
Title: A hybrid computational approach for efficient Alzheimer’s disease classification based on heterogeneous data
Authors: Ding, X., Bucholc, M., Wang, H., Glass, D.H., Wang, H., Clarke, D.H., Bjourson, A.J., Dowey, L.R.C., O’Kane, M., Prasad, G., Maguire, L., Wong-Lin, K.
https://doi.org/10.3389/fphys.2018.01659
Title: Gene regulatory network modeling of macrophage differentiation corroborates the continuum hypothesis of polarization states
Authors: Palma, A., Jarrah, A.S., Tieri, P., Cesareni, G., Castiglione, F.
https://doi.org/10.1016/j.neubiorev.2018.06.013
Title: Strategies for integrated analysis in imaging genetics studies
Authors: Vilor-Tejedor, N., Alemany, S., Cáceres, A., Bustamante, M., Pujol, J., Sunyer, J., González, J.R.
https://doi.org/10.1109/FSKD.2018.8687269
Title: Flow simulation on multilayer networks: A new approach to community detection in complex systems
Authors: Wang, H., Zheng, H.
https://doi.org/10.1155/2018/4356767
Title: Parallel Excitatory and Inhibitory Neural Circuit Pathways Underlie Reward-Based Phasic Neural Responses
Authors: Zhou, H., Wong-Lin, K., Wang, D.-H.
https://doi.org/10.1177/0269881117699612
Title: Toward a multiscale modeling framework for understanding serotonergic function
Authors: Wong-Lin, K., Wang, D.-H., Moustafa, A.A., Cohen, J.Y., Nakamura, K.
https://doi.org/10.3389/fnhum.2017.00380
Title: Multi-kernel learning with dartel improves combined MRI-PET classification of Alzheimer’s disease in AIBL data: Group and individual analyses
Authors: Youssofzadeh, V., McGuinness, B., Maguire, L.P., Wong-Lin, K.
https://doi.org/10.1109/BIBM.2016.7822518
Title: Analysis of rumen microbial community in cattle through the integration of metagenomic and network-based approaches
Authors: Wang, H., Zheng, H., Browne, F., Roehe, R., Dewhurst, R.J., Engel, F., Hemmje, M., Walsh, P.
https://doi.org/10.1098/rsif.2016.0902
Title: An integrated modelling framework for neural circuits with multiple neuromodulators
Authors: Joshi, A., Youssofzadeh, V., Vemana, V., McGinnity, T.M., Prasad, G., Wong-Lin, K.F.
https://doi.org/10.3389/fmolb.2019.00025
Title: anncolvar: Approximation of complex collective variables by artificial neural networks for analysis and biasing of molecular simulations.
Authors: Trapl, D., Horvaćanin, I., Mareška, V., Özçelik, F., Unal, G., Spiwok, V.
Doi not yet provided / paper not published yet
Title: An Early Stage Researcher’s Primer on Systems Medicine Terminology.
Authors: Massimiliano Zanin, Nadim A. A. Aitya, José Basilio, Jan Baumbach, Arriel Benis, Chandan K. Behera, Magda Bucholc, Filippo Castiglione, Ioanna Chouvarda, Blandine Comte, Tien-Tuan Dao, Xuemei Ding, Estelle Pujos-Guillot, Nenad Filipovic, David P. Finn, David H. Glass, Nissim Harel, Tomas Iesmantas, Ilinka Ivanoska, Alok Joshi, Karim Zouaoui Boudjeltia, Badr Kaoui, Daman Kaur, Liam P. Maguire, Paula L. McClean, Niamh McCombe, João Luís de Miranda, Mihnea Alexandru Moisescu, Francesco Pappalardo, Annikka Polster, Girijesh Prasad, Damjana Rozman, Ioan Sacala, Jose M. Sanchez-Bornot, Johannes A. Schmid, Trevor Sharp, Jordi Solé-Casals, Vojtěch Spiwok, George M. Spyrou, Egils Stalidzans, Blaž Stres, Tijana Sustersic, Ioannis Symeonidis, Paolo Tieri, Stephen Todd, Kristel Van Steen, Milena Veneva, Da-Hui Wang, Haiying Wang, Hui Wang, Steven Watterson, KongFatt Wong-Lin, Su Yang, Xin Zou, Harald H. H. W. Schmidt.
Doi not yet provided / paper not published yet
Title: A showcase of network applications in systems medicine
Authors: Zanin, Massimiliano; Baumbach, Jan; Bhardwaj , Archana; Sanchez-Bornot, Jose; Ding, Xuemei; Duroux, Diane; Lazareva, Olga; List, Markus; Stalidzans, Egils; Van Steen, Kristel; Wang, Haiying; Watterson, Steven; Wong-Lin, KongFatt; Zheng, Huiru.
Doi not yet provided / paper not published yet
Title: A fast transform for brain connectivity difference evaluation
Authors: Massimiliano Zanin, Ilinka Ivanoska, Bahar Bahar Güntekin, Görsev Yener, Tatjana Loncar-Turukalo, Niksa Jakovljevic, Olivera Sveljo, David Papo
For the Alzheimer’s Disease Neuroimaging Initiativ.
https://doi.org/10.1093/bib/bbaa237
Title: Deep Learning in Systems Medicine: White Paper by the COST Action CA15120 Open Multiscale Systems Medicine
Authors: Haiying Wang, Estelle Pujos-Guillot, Blandine Comte, Joao Luis de Miranda, Vojtech Spiwok, Ivan Chorbev, Filippo Castiglione, Paolo Tieri, Steven Watterson, Roisin McAllister, Tiago de Melo Malaquias, Massimiliano Zanin, Taranjit Singh Rai, Huiru Zheng
Doi not yet provided / paper not published yet
Title: Systems Medicine through COST Action CA15120 – Open Multiscale System (OpenMultiMed)
Author: Marcel Leppée,