Bibliography

A list of papers published by the Pistoia Alliance and articles written about it, or that substantially reference its work, or where it is cited in the authors list. The most recently published articles appear first.

By us

• Norman, R.A. et al., "Computational approaches to therapeutic antibody design: established methods and emerging trends" Briefings in Bioinformatics (2019), DOI: 10.1093/bib/bbz095
• Harrow et al, "Ontology mapping for semantically enabled applications" in Drug Discovery Today 2019 DOI: 10.1016/j.drudis.2019.05.020
• Wise, et al, "Application of bioinformatics in support of precision medicine", Drug Discovery World Summer 2019
• Nitsche, C. Promoting Safety culture: An overview of collaborative chemical safety information initiatives, JCH&S Volume 26, Issue 3, May–June 2019, Pages 27-30 https://doi.org/10.1016/j.jchas.2018.12.004
• Wise et al, "The positive impacts of real world data on the challenges facing the evolution of biopharma" Drug Discovery Today, 2018 https://doi.org/10.1016/j.drudis.2018.01.034
• Wise, et al, "Implementation and relevance of FAIR data principles in biopharmaceutical R&D" Drug Discovery Today 2019 https://doi.org/10.1016/j.drudis.2019.01.008 
• Joint Pistoia Alliance/Clarivate report  "Life Sciences Innovation Report"  https://clarivate.com/g/life-sciences-innovation-report
• Wise, et al, "CDx / NGS & Regulation: 5 perspectives from the Pistoia Alliance" Drug Discovery Today https://doi.org/10.1016/j.drudis.2019.07.002 
• Harrow et al, "Matching disease and phenotype ontologies in the ontology alignment initiative” in J Biomedical Semantics 2016 DOI: 10.1186/s13326-017-0162-9
• Keith Nangle, Mike Furness, "The Use of Next-Generation Sequencing in Drug Development" Drug Discovery World, Winter 2017/2018 
• Cham, JA & Costa K, "UX Design Maximising the Value of Scientific Software in Life Science R&D", Drug Discovery World, Summer 2017
• Nitsche, C. No safety without sharing. ACS Axial, June 2017.
• Wise, J. Real-world data: High on the life science agenda. Pharmafocus, May 2017.

• Wise, J, Real World Data's Importance in the Biopharmaceutical Industry. R&D Magazine, 15th December 2016.
• Holland, R, I, robot. I, the future. Drug Discovery World, October 2016.
• Holland, R, Collaborate or die. The Translational Scientist, January 2016.
• Holland, R, How can HPC help in pharma R&D? Scientific Computing World, 12th November 2015.
• Holland, R, The benefits of not competing. Drug Discovery World, October 2015.
• Holland, R and Nitsche, C, Improving chemical safety in the life sciences industry. Drug Discovery Today 20:1161-1162 (2015). doi:10.1016/j.drudis.2015.07.013
• Holland, R, The future is small: how startups drive innovation. PharmaPhorum, 18th May 2015.
• Holland, R, From Genomic Revolution to Healthcare Revolution. Laboratory News, 1st May 2015.
• Holland, R, New Projects for Pistoia. Bio-IT World, 28th April 2015.
• Holland, R, Think big, not small. Pharmaceutical Market Europe, April 2015, reprinted in PMLive, June 2015.
• Holland, R, Interactive Genome Analysis Challenge. DNAdigest blog, 18th March 2015.
• Taylor, D, et al., The Pistoia Alliance Controlled Substance Compliance Service Project: from start to finish. Drug Discovery Today 20:175-180 (2015). doi:10.1016/j.drudis.2014.09.021
• Holland, R, The challenges of compliance for controlled substances in a global marketplace. Scrip Regulatory Affairs, 9th January 2015.
• Holland, R, Innovation shouldn’t be a dirty secret. Scientific Computing World, 1st December 2014.
  
• Möller, S et al, Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics 15(Suppl 14):S7 (2014). doi:10.1186/1471-2105-15-S14-S7
• Holland, R, Pre-competitive research: Don't compete, collaborate. PharmaPhorum, 6th November 2014.
• Bellamy, C, Why do Pistoia Alliance members contribute to its voluntary projects? Loughborough University MBA Thesis, September 2014.
• Rebholz-Schuhmann, D, et al., A case study: semantic integration of gene–disease associations for type 2 diabetes mellitus from literature and biomedical data resources. Drug Discovery Today 19:7 (2014). doi:10.1016/j.drudis.2013.10.024
• Holland, R and Lynch, N, Sequence squeeze: an open contest for sequence compression. GigaScience 2:5 (2013). doi:10.1186/2047-217X-2-5
• Harrow, I, et al., Towards Virtual Knowledge Broker services for Life Science literature and data resources. Drug Discovery Today 18:9-10 (2013). doi:10.1016/j.drudis.2012.11.012
• Iddo, Squeezing DNA. Byte Size Biology, 25th July 2013.
• Clark, A, The Pistoia App Catalog, and why we need it. Cheminformatics 2.0, 21st Feb 2013.
• Hardy, B, et al., Toxicology Ontology Perspectives. Altex 29(2/2012):139-156.
• Zhang, Tianhong, et al. HELM: A hierarchical notation language for complex biomolecule structure representation. Journal of chemical information and modelling 52.10 (2012): 2796-2806. doi:10.1021/ci3001925
• Harland, L, et al., Empowering industrial research with shared biomedical vocabularies. Drug Discovery Today 16:21-22 (2011). doi:10.1016/j.drudis.2011.09.013
• Wise, J, ELNs - An Essential Productivity Tool – But Which One to Use. European Pharmaceutical Review 4:2011.
• Thornber, S, et al., The Pistoia Alliance - The Sequence Services Project. G.I.T. Laboratory Journal 1-2/2011.
• Waller, C L, et al., Need for Collaborative Technologies in Drug Discovery. Book Chapter in Collaborative Computational Technologies for Biomedical Research, ed. Sean Ekins et al., Wiley (2011).
• The Pistoia Alliance, What are the obstacles to innovation in the Pharmaceutical Industry?. Drug Discovery World, May 2011.

About us

• Buckland, D. What is the true price of good health? The Times / Raconteur, 10th May 2017.

• Come Together: The Pistoia Alliance’s Push For Wearable Device Standards In Clinical Trials. Clinical Informatics News, 3rd May 2017.

• Chemical Safety Library Draws Mixed Reaction. Chemical Processing, 1st May 2017.

• Myshko, D. R&D Partnerships. PharmaVOICE, April 2017.

• Trager, R. New database highlights cumulative chemical dangers. Chemistry World, 20th March 2017.

• Kemsley, J. Database of hazardous reactions launched. C&EN, 14th March 2017.

• Murray, S. Speed need impels diagnostic healthcare advances. Financial Times, 29th November 2016.

• C is for collaboration. Research information, November 2016.

• Startup Stories: Pine Biotech. Life Science Network, 21st November 2016.

• Startup Stories: Medexprim. Life Science Network, 14th November 2016.

• Cookson, C. Alimentary discoveries produce a gut reaction among investors. Financial Times, 6th November 2016.

• Stanganelli, J. Smarter ELNs and Smarter Labs Make for Smarter Science. Bio-IT World, 31st October 2016.

• Moran, T. Establishing Industry Best Practices for Working with Novel Biotherapeutic Entities. Pharmaceutical Processing, 2nd September 2016.

• Tessella elected to board of Life Sciences alliance with mission to lower barriers in innovation in R&D. September 2016.

• Shankar, A. Digitizing The Pharma Research Value Chain For Faster Drug Discovery Through Precompetitive Collaboration. Bio-IT World, 26th August 2016.

• Taylor, N. P. AstraZeneca, Repositive call on Big Pharma to join cancer data sharing consortium. Fierce Biotech, 8th August 2016.

• Pistoia Alliance launches informatics challenge. Scientific Computing World, 28th June 2016.

• On your marks get set...startup!. Laboratory News, 9th June 2016.

• Divakaran, P. Malaysian wins award for mobile app that predicts dengue outbreaks. The Star (Malaysia), 20th April 2016.

• Hodgson, J. Novaseek And Repositive Win Pistoia’s First Start-Up Challenge. Start-Up, March 2016.

• Thomas, U. In Brief This Week. GenomeWeb, 19th February 2016.

• Willighagen, E. Project "Chemical Safety Library", aka redistributable MSDS data. 2nd January 2016.

• Klostermann, S, HAbE: complete registration of novel antibody formats. European Biotechnology, Autumn 2015(14):72.

• Pistoia represents biomolecular data better. Scientific Computing World, 19th October 2015.
• Open Innovation. Roche Diagnostics Deutschland GmbH (via PresseBox), 16th September 2015. (in German, about HELM)
• Martinsrieder Kooperation mit Pharma - Open Innovation im Datenmanagement. Bio-M News, 15th September 2015. (in German, about HELM)
• Klostermann, S, Antikörper-Registrierung leicht gemacht. P&A Magazin, 7th September 2015. (in German, about HELM)
• Pistoia focuses on ontologies, data warehousing and networks of alliances. Scientific Computing World, 14th May 2015.
• Thomas, U G, Pistoia Alliance Launches Project to Develop Ontology Management Standards. GenomeWeb, 30th April 2015.
• MacDonald, G, Pre-competitive groups don't compete; Amgen and Lundbeck join group behind the HELM platform. BioPharma-Reporter.com, 23rd January 2015.
• Krol, A, Universal Language: The Pistoia Alliance Takes on Indescribable Biology. Bio-IT World, 18th July 2014.
• Trigg, J,  Data interchange standards: what, why and when?. Laboratory Informatics Guide 2014:10-12.
• Martin, Y, ChemAxon’s 2013 European User Group Meeting Report. July 2013.
• Wellcome Trust Sanger Institute, Institute researcher is sequence-squeezing champ. 11th May 2012.
• Saxena, V, et al.,  Implementation of a secure genome sequence search platform on public cloud-leveraging open source solutions. Journal of Cloud Computing: Advances, Systems and Applications 2012, 1:14. doi:10.1186/2192-113X-1-14

• Todd, M, A unique alliance from three cultures. Pharmacology Matters, April 2011:7-8. 

• Jensen, J, et al., Bioscience in the Cloud - Next Generation Analysis for Next Generation Sequencing. Proceedings of Science / The International Symposium on Grids and Clouds and the Open Grid Forum, March 2011.

• Kumar, A R, The Pistoia Alliance: A Progress Report. Innovations in Pharmaceutical Technology, March 2011.
• Davies, K, The Italian (Informatics) Job. Bio-IT World, January 2010.
• Barnes, M R, et al., Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. Nature Reviews: Drug Discovery, 2009(8):701-08.