Key publications

A


Agarwal, S. & Moorchung, N. Modifier genes and oligogenic disease

J. Nippon Med. Sch. 72, 326–334 (2005)

Alcaraz, N. et al. De novo pathway-based biomarker identification

Nucleic Acids Res. 45, e151–e151 (2017)

Aguirre-Plans, J. et al. GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets

J. Mol. Biol. 431, 2477–2484 (2019)

Animal Research for Alzheimer Disease: Failures of Science and Ethics

Animal Experimentation: Working Towards a Paradigm Change 480–516 (2019) doi:10.1163/9789004391192_021

Aguirre-Plans, J. et al. Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Pharmaceuticals  11, (2018)

Ansar, S. et al. PocketPipe: A computational pipeline for integrated Pocketome prediction and comparison

Bioinformation vol. 15 295–298 (2019)

Ahrens, I. et al. Measuring oxidative burden and predicting pharmacological response in coronary artery disease patients with a novel direct activator of haem-free/oxidised sGC

Atherosclerosis 218, 431–434 (2011)

B


Barabási, A.-L., Gulbahce, N. & Loscalzo, J. Network medicine: a network-based approach to human disease

Nat. Rev. Genet. 12, 56–68 (2010)

Bhagavat, R., Sankar, S., Srinivasan, N. & Chandra, N. An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

Structure 26, 499–512.e2 (2018)

Bjornstad, G. & Morris, C. Healthy Parent Carers: a research study to test ways to improve the health and wellbeing of parent carers of disabled children and whether the trial design is acceptable to participants

isrctn.com doi:10.1186/isrctn15144652

Byrem, W. C., Armstead, S. C., Kobayashi, S., Eckenhoff, R. G. & Eckmann, D. M. A guest molecule-host cavity fitting algorithm to mine PDB for small molecule targets

Biochim. Biophys. Acta 1764, 1320–1324 (2006)

C


Casas, A. I. et al. From single drug targets to synergistic network pharmacology in ischemic stroke

PROC. NATL. ACAD. SCI. U. S. A. 116, 7129–7136 (2019)

Cirillo, D. et al. Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare

NPJ Digit Med 3, 81 (2020)

Cook, D. et al. Lessons learned from the fate of AstraZeneca’s drug pipeline: a five-dimensional framework

Nat. Rev. Drug Discov. 13, 419–431 (2014)

Chartier, M., Morency, L.-P., Zylber, M. I. & Najmanovich, R. J. Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects

BMC PHARMACOL. TOXICOL. 18, 18 (2017)

Clark, J. et al. A cluster randomised trial of a Needs Assessment Tool for adult Cancer patients and their carers (NAT-C) in primary care: A feasibility study

PLoS One 16, e0245647 (2021)

Cortés, A. et al. Expression of Endothelial NOX5 Alters the Integrity of the Blood-Brain Barrier and Causes Loss of Memory in Aging Mice

Antioxidants (Basel) 10, (2021).

Cheng, F. et al. A genome-wide positioning systems network algorithm for in silico drug repurposing

NAT. COMMUN. 10, 3476 (2019)

Cobb, E. M. et al. Patient Engagement in Neurological Clinical Trials Design: A Conference Summary

Clinical and Translational Science vol. 8 776–778 (2015)

Cheng, F. et al. Network-based approach to prediction and population-based validation of in silico drug repurposing

Nat. Commun. 9, 2691 (2018)

Contopoulos-Ioannidis, D. G., Ntzani, E. E. & Ioannidis, J. P. A. Translation of highly promising basic science research into clinical applications

The American Journal of Medicine vol. 114 477–484 (2003)

D


Dachtler M, Wothe D.  Additive Fertigung in der Pharmaindustrie: Digitale Transformation beeinflusst Geschäftsmodelle und

Supply Chain. 2018; 15-16/2018 CHEManager

E


Elbatreek, M. H. et al. NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

PLoS Biol. 18, e3000885 (2020)

Ellinghaus, D. et al. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

Nat. Genet. 48, 510–518 (2016)

F


Fang, J. et al. Harnessing endophenotypes and network medicine for Alzheimer’s drug repurposing

Med. Res. Rev. 40, 2386–2426 (2020)

Freedman, L. P., Cockburn, I. M. & Simcoe, T. S. The Economics of Reproducibility in Preclinical Research

PLOS Biology vol. 13 e1002165 (2015)

Fanous M. et al. Development of immediate release (IR) 3D-printed oral dosage forms with focus on industrial relevance

Eur. J. Pharm. Sci. 2020; 155: 105558

Farinacci, M. et al. Circulating endothelial cells as biomarker for cardiovascular diseases

Res Pract Thromb Haemost 3, 49–58 (2019)

Fortelny, N. & Bock, C. Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Genome Biol. 21, 190 (2020)

G


Ghiassian, S. D., Menche, J. & Barabási, A.-L. A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

PLoS Comput. Biol. 11, e1004120 (2015)

Goldacre, B. et al. Compliance with requirement to report results on the EU Clinical Trials Register: cohort study and web resource

BMJ k3218 (2018) doi:10.1136/bmj.k3218

Gil, C. & Martinez, A. Is drug repurposing really the future of drug discovery or is new innovation truly the way forward?

Expert Opinion on Drug Discovery 1–3 (2021) doi:10.1080/17460441.2021.1912733

Goyanes A. et al. Fused-filament 3D printing (3DP) for fabrication of tablets

Int. J. Pharm. 2014; 476: 88-92

Gnanasakthy, A. & Basch, E. Assessment of Patient-Reported Outcomes in Industry-Sponsored Clinical Trials

Oncology Clinical Trials (2018) doi:10.1891/9780826168733.0025

Guney, E., Menche, J., Vidal, M. & Barábasi, A.-L. Network-based in silico drug efficacy screening

Nat. Commun. 7, 10331 (2016)

Goh, K.-I. et al. The human disease network

Proceedings of the National Academy of Sciences vol. 104 8685–8690 (2007)

H


Hassan, S. S. et al. The Druggable Pocketome of : A New Approach for Putative Druggable Targets

Front. Genet. 9, 44 (2018)

Himmelstein, D. S. et al. Systematic integration of biomedical knowledge prioritizes drugs for repurposing

Elife 6, (2017)

I


IJzerman, M. J., Koffijberg, H., Fenwick, E. & Krahn, M. Emerging Use of Early Health Technology Assessment in Medical Product Development: A Scoping Review of the Literature

Pharmacoeconomics 35, 727–740 (2017)

J


Januskaite P. et al. I spy with my little eye: a paediatric visual preferences survey of 3D printed tablets

Pharmaceutics. 2020; 12: 1100

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold

Nature (2021) doi:10.1038/s41586-021-03819-2

K


Kiel, C., Lastrucci, C., Luthert, P. J. & Serrano, L. Simple and complex retinal dystrophies are associated with profoundly different disease networks

Sci. Rep. 7, 41835 (2017)

Kvitkina, T., ten Haaf, A., Reken, S., McGauran, N. & Wieseler, B. Patient-relevant outcomes and surrogates in the early benefit assessment of drugs: first experiences

Z. Evid. Fortbild. Qual. Gesundhwes. 108, 528–538 (2014)

Kirchgessner, T. G. et al. Beneficial and Adverse Effects of an LXR Agonist on Human Lipid and Lipoprotein Metabolism and Circulating Neutrophils

Cell Metab. 24, 223–233 (2016)

Kyobula, M. 3D inkjet printing of tablets exploiting bespoke complex geometrics for controlled and tuneable drug release

2017; 261, S. 207 – 215 Journal of Controlled Release

Kleikers, P. W. M. et al. A combined pre-clinical meta-analysis and randomized confirmatory trial approach to improve data validity for therapeutic target validation

Sci. Rep. 5, 13428 (2015)

Kristensen, F. B. et al. Practical tools and methods for health technology assessment in Europe: structures, methodologies, and tools developed by the European Network for Health Technology Assessment, EUnetHTA

Int. J. Technol. Assess. Health Care 25 Suppl 2, 1–8 (2009)

L


Langhauser, F. et al. A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection

NPJ Syst Biol Appl 4, 8 (2018)

List, M. et al. KeyPathwayMinerWeb: online multi-omics network enrichment

Nucleic Acids Res. 44, W98–W104 (2016)

Lazareva, O. et al. BiCoN: Network-constrained biclustering of patients and omics data

Bioinformatics (2020) doi:10.1093/bioinformatics/btaa1076.

López-Rodríguez, I., Reyes-Manzano, C. F., Guzmán-Vargas, A. & Guzmán-Vargas, L. The complex structure of the pharmacological drug–disease network

Entropy  23, 1139 (2021)

Lazareva, O. et al. Multi-Omics Analysis in a Network Context

Reference Module in Biomedical Sciences (Elsevier, 2020)

Louadi, Z. et al. DIGGER: exploring the functional role of alternative splicing in protein interactions

Nucleic Acids Res. (2020) doi:10.1093/nar/gkaa768

Lazareva, O., Baumbach, J., List, M. & Blumenthal, D. B. On the limits of active module identification

Brief. Bioinform. (2021) doi:10.1093/bib/bbab066

M


Ma, J. et al. Using deep learning to model the hierarchical structure and function of a cell

Nat. Methods 15, 290–298 (2018)

Mucke, H. A. M. What patents tell us about drug repurposing for cancer: A landscape analysis

Semin. Cancer Biol. 68, 3–7 (2021)

Madla C.M. et al. Let’s talk about sex: differences in drug therapy in males and females

Adv. Drug Deliv. Rev. 2021; (Published online May 17,21)

Mullard, A. Anti-amyloid failures stack up as Alzheimer antibody flops

Nature Reviews Drug Discovery (2019) doi:10.1038/d41573-019-00064-1

Menche, J. et al. Disease networks. Uncovering disease-disease relationships through the incomplete interactome

Science 347, 1257601 (2015)

Mucke, H. & Mucke, P. Drug repurposing patent documents vs peer review: patent information comes more than 600 days earlier on average

Future Drug Discovery vol. 2 FDD31 (2020)

N


Nelissen, E. et al. Soluble Guanylate Cyclase Stimulator Vericiguat Enhances Long-Term Memory in Rats without Altering Cerebral Blood Volume

Biomedicines 9, (2021)

Neuberger, A., Oraiopoulos, N. & Drakeman, D. L. Renovation as innovation: is repurposing the future of drug discovery research?

Drug Discov. Today 24, 1–3 (2019)

Nunes, A. et al. Prediction of lithium response using clinical data

Acta Psychiatr. Scand. 141, 131–141 (2020)

Cover of the issue of TiPS featuring this Network Pharmacology paper

Nogales et al. (2021) Network Pharmacolog: Curing Causal Mechanisms Instead of Treating Symptoms

Trend in Pharmacological Sciences (2021)

O


O’Rourke, B., Oortwijn, W., Schuller, T. & International Joint Task Group. The new definition of health technology assessment: A milestone in international collaboration

Int. J. Technol. Assess. Health Care 36, 187–190 (2020)

Oprea, T. I. et al. Drug Repurposing from an Academic Perspective

Drug Discov. Today Ther. Strateg. 8, 61–69 (2011)

Otasek, D., Morris, J. H., Bouças, J., Pico, A. R. & Demchak, B. Cytoscape Automation: empowering workflow-based network analysis

Genome Biol. 20, 185 (2019)

P


Pirch, S. et al. The VRNetzer platform enables interactive network analysis in Virtual Reality

Nat. Commun. 12, 2432 (2021)

R


Rantanen J. Khinast J. The future of pharmaceutical manufacturing sciences

J. Pharm. Sci. 2015; 104: 3612-3638

Rintala, T. J., Federico, A., Latonen, L., Greco, D. & Fortino, V. A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery

Brief. Bioinform. (2021) doi:10.1093/bib/bbab314

S


Sadegh, S. et al. Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

Nat. Commun. 11, 3518 (2020)

Seoane-Viaño I.et al. Translating 3D printed pharmaceuticals: from hype to real-world clinical applications

Adv. Drug Deliv. Rev. 2021; 174: 553-575

Song, J.-S., Wang, R.-S., Leopold, J. A. & Loscalzo, J. Network determinants of cardiovascular calcification and repositioned drug treatments

FASEB J. 34, 11087–11100 (2020)

Sanchez-Vega, F. et al. Oncogenic Signaling Pathways in The Cancer Genome Atlas

Cell 173, 321–337.e10 (2018)

Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks

Genome Res. 13, 2498–2504 (2003)

Stewart, K. et al. Patient knowledge, perceptions, and acceptance of generic medicines: a comprehensive review of the current literature

Patient Intelligence 1 (2014) doi:10.2147/pi.s46737

Scannell, J. W., Blanckley, A., Boldon, H. & Warrington, B. Diagnosing the decline in pharmaceutical R&D efficiency

Nat. Rev. Drug Discov. 11, 191–200 (2012)

Silverbush, D. & Sharan, R. A systematic approach to orient the human protein-protein interaction network

Nat. Commun. 10, 3015 (2019)

Schork, N. J. Personalized medicine: Time for one-person trials

Nature 520, 609–611 (2015)

Smith, R. B. Repositioned drugs: integrating intellectual property and regulatory strategies

Drug Discov. Today Ther. Strateg. 8, 131–137 (2011)

T


Tharpe, N. Adverse drug reactions in women’s health care

J. Midwifery Womens. Health 56, 205–213 (2011)

Trenfield S.J. et al. Shaping the future: recent advances of 3D printing in drug delivery and healthcare

Expert Opin. Drug Deliv. 2019; 16: 1081-1094

U


Uveges, M. K. et al. Patient navigation and clinical trial participation: A randomized controlled trial design

Contemporary Clinical Trials Communications vol. 12 98–102 (2018)

V


Vallance, P. An audience with Patrick Vallance

Nat. Rev. Drug Discov. 9, 834 (2010)

Vinayagam, A. et al. Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

Proc. Natl. Acad. Sci. U. S. A. 113, 4976–4981 (2016)

W


Wieseler, B., McGauran, N. & Kaiser, T. New drugs: where did we go wrong and what can we do better?

BMJ 366, l4340 (2019)

Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship

Sci Data 3, 160018 (2016)

Z


Zhang L. Three-dimensional (3D) printed scaffold and material selection for bone repair

2019;  Jan 15;84:16-33. Acta biomaterialia

Zhou, X., Menche, J., Barabási, A.-L. & Sharma, A. Human symptoms-disease network

Nat. Commun. 5, 4212 (2014)

Zhang, M., Zhu, C., Jacomy, A., Lu, L. J. & Jegga, A. G. The orphan disease networks

Am. J. Hum. Genet. 88, 755–766 (2011)

Zolotareva, O. et al. Identification Of Differentially Expressed Gene Modules In Heterogeneous Diseases

Bioinformatics (2020) doi:10.1093/bioinformatics/btaa1038

Zhang, Z., Li, Y., Lin, B., Schroeder, M. & Huang, B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction

Bioinformatics 27, 2083–2088 (2011)

Zhao, S. et al. Systems pharmacology of adverse event mitigation by drug combinations

Sci. Transl. Med. 5, 206ra140 (2013)