2015 in review

2015 saw the continuation of some research themes from 2014, namely some work on Ebola, rare diseases and Bayesian models for neglected diseases. At the end of the year several papers are in press for next year so more to come. As usual there were some ups and downs in getting some of these to see the light of day.

The following lists many collaborations from the last year or so – several were actually written in 2014 and made it out this year. Some are open access. If you need reprints for any of the others please get in touch.

A big thanks to all collaborators old and new that made this possible.

Shedding Light on Synergistic Chemical Genetic Connections with Machine Learning

Sean Ekins Jair Lage Siqueira-Neto

DOI: http://dx.doi.org/10.1016/j.cels.2015.12.005

Machine learning models identify molecules active against the Ebola virus in vitro [version 1; referees: 2 approved]

Sean Ekins^1-3, Joel S. Freundlich⁴, Alex M. Clark⁵, Manu Anantpadma⁶, Robert A. Davey⁶, Peter Madrid

F1000Research 2015, 4:1091 (doi: 10.12688/f1000research.7217.1)

Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies.

Hanson SM, Ekins S, Chodera JD.

J Comput Aided Mol Des. 2015 Dec;29(12):1073-86. doi: 10.1007/s10822-015-9888-6. Epub 2015 Dec 17.

PMID:: 26678597

Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery.

Ekins S, Madrid PB, Sarker M, Li SG, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M, Freundlich JS.

PLoS One. 2015 Oct 30;10(10):e0141076. doi: 10.1371/journal.pone.0141076. eCollection 2015.

PMID:: 26517557

Free PMC Article

Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy.

Johnson-Kerner BL, Garcia Diaz A, Ekins S, Wichterle H.

PLoS One. 2015 Oct 13;10(10):e0140157. doi: 10.1371/journal.pone.0140157. eCollection 2015.

PMID:: 26460568

Free PMC Article

Predicting Mouse Liver Microsomal Stability with “Pruned” Machine Learning Models and Public Data.

Perryman AL, Stratton TP, Ekins S, Freundlich JS.

Pharm Res. 2015 Sep 28. [Epub ahead of print]

PMID:: 26415647

Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights.

Li SG, Vilchèze C, Chakraborty S, Wang X, Kim H, Anisetti M, Ekins S, Rhee KY, Jacobs WR Jr, Freundlich JS.

Tetrahedron Lett. 2015 Jun 3;56(23):3246-3250.

PMID:: 26257441

Making Transporter Models for Drug-Drug Interaction Prediction Mobile.

Ekins S, Clark AM, Wright SH.

Drug Metab Dispos. 2015 Oct;43(10):1642-5. doi: 10.1124/dmd.115.064956. Epub 2015 Jul 21.

PMID:: 26199424

Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery.

Ekins S, de Siqueira-Neto JL, McCall LI, Sarker M, Yadav M, Ponder EL, Kallel EA, Kellar D, Chen S, Arkin M, Bunin BA, McKerrow JH, Talcott C.

PLoS Negl Trop Dis. 2015 Jun 26;9(6):e0003878. doi: 10.1371/journal.pntd.0003878. eCollection 2015 Jun.

PMID:: 26114876

Free PMC Article

Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.

Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LP, Riccardi G, Cole ST, Pasca MR.

Chem Biol. 2015 Jul 23;22(7):917-27. doi: 10.1016/j.chembiol.2015.05.016. Epub 2015 Jun 18.

PMID:: 26097035

Free PMC Article

Open Source Bayesian Models. 2. Mining a “Big Dataset” To Create and Validate Models with ChEMBL.

Clark AM, Ekins S.

J Chem Inf Model. 2015 Jun 22;55(6):1246-60. doi: 10.1021/acs.jcim.5b00144. Epub 2015 Jun 3.

PMID:: 25995041

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

Clark AM, Dole K, Coulon-Spektor A, McNutt A, Grass G, Freundlich JS, Reynolds RC, Ekins S.

J Chem Inf Model. 2015 Jun 22;55(6):1231-45. doi: 10.1021/acs.jcim.5b00143. Epub 2015 Jun 3.

PMID:: 25994950

Free PMC Article

Finding small molecules for the ‘next Ebola’.

Ekins S, Southan C, Coffee M.

Version 2. F1000Res. 2015 Feb 27 [revised 2015 Jul 7];4:58. doi: 10.12688/f1000research.6181.2. eCollection 2015.

PMID:: 25949804

Free PMC Article

A brief review of recent Charcot-Marie-Tooth research and priorities.

Ekins S, Litterman NK, Arnold RJ, Burgess RW, Freundlich JS, Gray SJ, Higgins JJ, Langley B, Willis DE, Notterpek L, Pleasure D, Sereda MW, Moore A.

F1000Res. 2015 Feb 26;4:53. doi: 10.12688/f1000research.6160.1. eCollection 2015. Review.