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,

  1. 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,