Publications

Fully refereed articles

Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL. "Predicting new molecular targets for known drugs". Nature. 462 175–181.
DOI: 10.1038/nature08506
Gardiner EJ, Gillet VJ, Haranczyk M, Hert J, Holliday JD, Malim N, Patel Y, Willett P. "Turbo similarity searching: Effect of fingerprint and dataset on virtual-screening performance". Statistical Analysis and Data Mining. 2(2) 103–114.
DOI: 10.1002/sam.10037
Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. "Quantifying biogenic bias in screening libraries". Nature Chemical Biology. 5(7) 479–483.
DOI: 10.1038/nchembio.180 [article on PubMed Central]
Press coverage: Chemical & Engineering News–Chemistry World–The curious wavefunction blog

Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. "Quantifying the Relationships among Drug Classes". Journal of Chemical Information and Modeling. 48(4) 755–765.
DOI: 10.1021/ci8000259 [article on PubMed Central]

Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, and Schuffenhauer A. "New Methods for Ligand-Based Virtual Screening: Use of Data-Fusion and Machine-Learning Techniques to Enhance the Effectiveness of Similarity Searching". Journal of Chemical Information and Modeling. 46(2) 462–470.
DOI: 10.1021/ci050348j

Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, and Schuffenhauer A. "Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information". Journal of Medicinal Chemistry 48(22) 7049–7054.
DOI: 10.1021/jm050316n
Beining C, Harrison RF, Hert J, Mpanhanga C, Willett P, and Wilton DJ. "Ligand-based virtual screening using binary kernel discrimination". Molecular Simulation 31(8) 597–604.
DOI: 10.1080/08927020500134177

Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, and Schuffenhauer A. "Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures". Organic and Biomolecular Chemistry 2(22) 3256–3266.
DOI: 10.1039/b409865j [article in pdf]
Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, and Schuffenhauer A. "Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures". Journal of Chemical Information and Computer Sciences 44(3) 1177–1185.
DOI: 10.1021/ci034231b

Keiser MJ, Hert J. "Off-target networks derived from ligand set similarity". In: E. Jacoby (Ed.). Methods in Molecular Biology: Chemogenomics. pp. 195–205. Humana Press.
DOI: 10.1007/978-1-60761-274-2_8

Hert J, Willett P, and Wilton DJ. "New Methods for Similarity-Based Virtual Screening". In: E. Jacoby (Ed.). Chemogenomics, Knowledge-based Approaches to Drug Discovery. pp. 133–156. London: Imperial College Press. [publisher's website]

Hert J, Willett P, and Wilton DJ. "Virtual Screening using Binary Kernal Discrimination". In: Hicks, MG & Kettner, C (Eds.). Proceedings of the International Beilstein Workshop ``The Chemical Theatre of Biological Systems''. pp. 119–131. Frankfurt: Beilstein. [article in pdf]

Hert J, "Can we quantify the relationship between drug targets using their ligands?". Echeminfo – Latest Advances in Drug Discovery & Development, Bryn Mawr, PA, October 15^th–19^th, 2007. [abstract] [slides in pdf]

Hert J, Wilton DJ, & Willett P, "Methods to enhance the perfomance of similarity searching". 232th ACS National Meeting, San Francisco, CA, USA, September 10^th–14^th, 2006. [abstract] [slides in pdf]

Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E & Schuffenhauer A, "Fingerprint-based virtual screening using multiple reference structures". 229th ACS National Meeting, San Diego, CA, USA, March 13^th–17^th, 2005. [abstract] [slides in pdf]

Hert J & Shoichet BK, "Why Does High-Throughput Screening Ever work?". Keystone Symposium on Computer-Aided Drug Design, Steamboat Springs, CO, USA, March 29^th – April 3^rd 2007 [poster in pdf]

Hert J & Shoichet BK, "Pharmacological networks derived from the similarity of ligand-sets". Fourth Joint Sheffield Conference on Chemoinformatics, University of Sheffield, Sheffield, U.K., June 18^th – 20^th 2007. [abstract] [poster in pdf]

Hert J, Willett P, Wilton DJ, Azzaoui K, Jacoby E & Schuffenhauer A, "Turbo similarity searching". Molecular Graphics & Modelling Society, Annual International Meeting, Dublin, Ireland, September 11^th – 14^th 2005. [poster in pdf]
Hert J, Willett P, Wilton DJ, Azzaoui K, Jacoby E & Schuffenhauer A, "Turbo similarity searching". 230th ACS National Meeting, Washington, DC, USA, August 28^th–September 1^st, 2005. [abstract] [poster in pdf]
Poster winner of the CINF-IO Informatics scholarship for scientific excellence.
Hert J, Willett P, Wilton DJ, Azzaoui K, Jacoby E & Schuffenhauer A, "Turbo similarity searching". 7th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands, June 5^th – 9^th, 2005. [abstract] [poster in pdf]

Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E & Schuffenhauer A. "2D-Based Virtual Screening using Multiple Bioactive Reference Structures". Third Joint Sheffield Conference on Chemoinformatics, University of Sheffield, Sheffield, U.K., April 21^st–23^rd, 2004. [abstract] [poster in pdf]