Curriculum Vitae

Curriculum Vitae
Sean Ekins M.Sc.,
Ph.D., D.Sc.
ekinssean@yahoo.com

(215) 687-1320 ekinssean@yahoo.com

5616 Hilltop Needmore Road, Fuquay Varina, NC 27526 USA

Summary

 

I am a scientific leader with over 20 years of dense experience in drug discovery at big pharma, start-up companies and rare disease foundations. I have considerable informatics, ADME-Tox and drug discovery expertise, with particular focus in computational and in vitro tools to accelerate research, increase screening efficiency and decrease compound attrition due to predictable liabilities. My research interests include neglected and rare disease drug discovery as well as repurposing approved drugs. I also conduct research on how new computational technologies can be used for scientific research. My collaborative research has enabled >15 successful NIH and EU grant applications since 2005 and I have partnered with collaborators on many more funded grants as a consultant.

 

Leadership Achievements

  • Collaboration and external influencing par excellence with industry, academia, non-profit labs and foundations. I am on advisory boards for companies, academia, 3 rare disease foundations and software companies as well as adjunct professor at 3 US universities.
  • Prolific science communicator with >270 papers and book chapters (most of which have been very well cited, Google Scholar h-index = 60, (Aug 2016), Web of Science h-index = 47 (July 2016)) and given over 200 invited talks at conferences, companies and universities globally. Editor or co-editor of 4 books and Editor of a Pharmaceutical Technology book series for Wiley. Scientific blogger and communicator (Collaborative Chemistry, collabchem.com; Twitter, Collabchem).
  • Commercial orientation: Vast experience from pharma and biotech collaborations at identifying and obtaining opportunities for funding and applying leading edge biological, chemistry and computational technologies. Multiple patents and applications on methods, systems and compounds.
  • Results orientation: An intellectual and scientific risk taker who delivers beyond expectations. Specific focus on applying computational and cheminformatics methods with data in the public domain in order to improve drug discovery research
  • Strategic orientation: Possesses a broad perspective of drug discovery and development having contributed to early drug discovery through to post marketing studies.
  • Flexible: Able to move into new areas and rapidly contribute e.g. neglected disease and analysis of tuberculosis and malaria screening data; helping green chemistry to use mobile applications – Green Solvents, a free Android and iOS app. More recently I have assisted three rare disease foundations, connected with their scientists and contributed to scientific efforts and publications.
  • Obtaining funding: PI on NIH grants and contributor to collaborative European FP7 and Bill and Melinda Gates Foundation grants. Contributor to many other grants as a consultant. Experienced grant writer and ad hoc reviewer (US and International).

 

 

Education

 

D.Sc. Science

 

Thesis title: Computational and in vitro models for predicting drug interactions in humans

University of Aberdeen, Aberdeen, Scotland 2004-2005

Graduated

5th July  2005

Ph.D. Medicine and Therapeutics

(Clinical Pharmacology)

 

Thesis title: Maintenance and cryopreservation of xenobiotic metabolism in precision-cut liver slices. Evaluation of an alternative in vitro model to isolated hepatocytes

University of Aberdeen, Aberdeen, Scotland 1992-1995

Graduated

16th October 1996

M.Sc. Clinical Pharmacology

 

Thesis title: Speculations on the relative roles of cytochrome P450 and flavin containing monooxygenase in the metabolism of S12363

University of Aberdeen, Aberdeen, Scotland 1991-1992

Graduated

9th July 1993

HND Science (Applied Biology)

 

Nottingham Polytechnic (now  Nottingham Trent University), Nottingham. UK 1988-1991

Graduated 1991

 

Industrial Job History

 

Collaborations Pharmaceticals Inc

Fuquay Varina, NC.

 

CEO

-A new company focused on rare and neglected disease drug discovery and collaborations with academic researchers.

– STTR on TB drug discovery pending funding with Dr. Joel Freundlich at Rutgers

 

Nov 2014- present
Collaborations in Chemistry, Fuquay Varina, NC. Senior Consultant

-Computational drug discovery

-Scientific Advisory Group for a consumer products company

-Computational ADME/Tox consulting for consumer products companies and institutes:

– RIFM

Consulting for pharmaceutical companies including:

-Longevica pharmaceuticals

-Ardelyx pharmaceuticals

-Merck

-Resverlogix

-Ipsen

-Hannah’s Hope Foundation

-Hereditary Neuropathy Foundation- Chief Science Officer

-Jonah’s Just Begun

 

Jan 2007- present
Phoenix Nest, Brooklyn, New York CEO

 

 

Chief Scientific Officer

-Responsible for project management and grant writing at this rare disease company working on a cure for Sanfilippo Syndrome.

-Obtained two phase I STTR’s and a phase II STTR with Dr. Patricia Dickson (LA BioMed).

June 2014-present

 

April 2012-present

     
BioGan, Rexford, New York Chief Scientific Officer

-Responsible for project management at this virtual rare disease company working on a cure for Giant Axonal Neuropathy and collaborating with the Hereditary Neuropathy Foundation.

 

Aug 2012-present
Collaborative Drug Discovery Inc, Burlingame, CA Chief Scientific Officer

-I consult for this company 3 days a week. Currently PI on phase II SBIR, phase I STTR, as well as grant writing and new product ideation.

 

Aug 2013- present

 

 

 

  Vice President, Science

-Responsible for a phase II STTR and phase I SBIR. Obtained a further phase II SBIR and phase I STTR. Also responsible for interactions with BMGF, MM4TB projects.

 

Collaborations Director

-Responsible for scientific components of the Bill and Melinda Gates funded CDD Tuberculosis Database project. This project was awarded the Bio-IT 2011 Editors Choice Best Practice Award.

-Responsible for CDD role in More Medicines for TB project funded by EU Framework 7 grant.

-Responsible as PI for STTR with Stanford Research Institute to merge their bioinformatics databases with CDD’s chemistry database.

– data archiving, cheminformatics, mining and collaboration 1:1 support of TB pilot groups representing world class researchers globally.

– NIH SBIR, STTR (Phase I and II) and R01 proposal preparation and submission as PI.

– Marketing via scientific publications, presentations at conferences and at pharmaceutical companies.

 

March 2012- Aug 2013

 

 

 

Nov 2008-March 2012

Snowdon Inc, Piscataway, NJ Director, Discovery Biology

-SBIR/STTR grant writing (as PI) for funding preclinical drug discovery for oncology, CNS and infectious disease candidate molecules

– Project management of computer-aided drug discovery projects funded by SBIRs

 

Nov 2006 – Oct 2008
ACT LLC,

New York, NY.

USA

Senior Vice President, Computational Biology

-Consulting for various companies (ADME/Tox, biomarkers, computational drug discovery, systems biology software and pharmacovigilance) including Pfizer.

– Participated in a pharmacoeconomics study for Novartis, responsible for data interpretation, writing final report and publications.

– Presentations at key conferences and to customers in the industry as well as publications for scientific and marketing purposes.

 

April 2006 – 2010
GeneGo Inc. St. Joseph, MI. USA. (Company bought by Thomson Reuters in 2010) Vice President, Computational Biology

–      Principal Investigator responsible for directing development of a Systems-ADME-Tox software product MetaDrug by a multinational team of > 20 scientists (mostly in Moscow), funded by SBIR. The product was launched in 7 months and had 6 Pharma sales by April 2006 (and won “Best in Show new product” at the 2007 CHI Molecular Medicine Marketplace Meeting).

–      Responsible for the development of new software technologies.

–      Responsible for writing SBIR grants.

–      Responsible for presentations to customers in the industry as well as publications for scientific and marketing purposes.

 

Feb 2004-April 2006
Concurrent Pharmaceuticals Inc., Fort Washington, PA. USA. (now Vitae Pharmaceuticals Inc.) Associate Director, Computational Drug Discovery

–   Worked in a matrix organization of 11 people to develop a number of key computational ADME/Tox computational technologies including GauntletSM and ConTourSM.

–   Set up collaborations with academic groups to in-license custom software.

–   Generated pharmacophore models for rapid ligand-based drug design.

 

Dec 2001-

Feb 2004

Lilly Research Laboratories, Indianapolis, IN. USA Senior Computational Chemist

–   Responsible for development and validation of ADME/Tox computational models using in house data and statistical methods that were made available to all scientists in the company.

–   Managed 3 scientists in the computational, statistics and drug disposition groups.

– Published seminal papers on hERG, PXR, P450 pharmacophores

 

1999-

Dec 2001

Central Research, Pfizer Inc, Groton, CT. USA Research Scientist

–   Responsible for management of 3 scientists that generated CYP interaction data for discovery as well as developed and patented technologies and statistical methods.

–   Generated and patented computational pharmacophore models with in vitro ADME data.

 

1998-1999
Lilly Research Laboratories, Indianapolis, IN. USA Postdoctoral Fellow, Drug Disposition

–   Published 12 papers and book chapters

–   Characterized the human enzyme CYP2B6 in vitro and in silico.

–   Generated computational pharmacophores for CYPs.

 

Apr 1996-1998
Servier Research & Development, Fulmer, UK. Industrial internship, Drug Disposition

–   Prepared and analyzed biological samples from radiolabelled drug disposition studies in various species.

–   Generated drug metabolism in vitro data.

–   Built a strong relationship with the company that went on to fund M.Sc. project and Ph.D. research.

1989-1990, summer 1991

 

 

Academic History

Adjunct Professor, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Sept 2012-present.

Adjunct Professor, Robert Wood Johnson Medical School, University of Medicine and Dentistry New Jersey (Now Rutgers University), July 2007-present.

Adjunct Associate Professor, School of Pharmacy Department of Pharmaceutical Sciences, University of Maryland. MD, Jan 2005-present.

Lecturer for Principals of Drug Discovery (PHAR 600), Department of Pharmaceutical Sciences, University of Maryland, Fall Semester, 2005-2008.

Lecturer for Drug transport and Metabolism (PHAR 707), Department of Pharmaceutical Sciences, University of Maryland, Fall Semester, 2004.

Lecturer for Physiologic Disposition of Drugs (F836), Indiana University Medical Center, Pharmacology Department, IUPUI, Spring semester, 2001.

Adjunct Assistant Professor, Connecticut College, CT. 1998-1999.

 

Students (co-) supervised: Richard Snyder, Butler University, IN (MS, pharmacy project, 2001); Cheng Chang, Ohio State University & The University of Maryland (PhD, 2005; postdoc 2006) now a senior scientist at Pfizer, Akash Khandelwal (postdoc) now at the University of Arizona and Praveen Bahadduri (PhD, 2007) now a senior scientist at Genzyme.

 

PhD committee external member for Praveen Bahadduri, Swan Zheng and Lei Diao (The University of Maryland).

 

Scientific Advisory Board Membership

Emiliem, Inc. http://biospace.com/news_story.aspx?StoryId=30196

http://www.emiliem.com/scientificadboard.html, http://www.emiliem.com (Aug 2006-present)

Indiana University, Chemical Informatics (Jan 2007-present)

ChemSpider http://www.chemspider.com/ (June 2007-May 2011)

Assay Depot http://www.assaydepot.com/ (Aug 2008-2014)

Pistoia Alliance  http://pistoiaalliance.org/ (Oct 2011-Dec 2013)

Bimini Inc (Jan 2012-Jan 2013)

Jonah’s Just Begun http://phoenixnestbiotech.com/ (2012-2014)

Bridge to Cures, Inc. http://www.bridgetocures.com/who-we-are.html (2014 -present)

 

Professional Memberships

ISSX 1995-2011, ASPET since 2002 and ACS since 2005

 

Awards/Honors/Citations

ISSX graduate student in vitro studies presentation, Seattle WA, 2nd place, 1995.

ISSX postdoctoral fellow in vitro studies presentation, Hilton Head, SC, 1st place, 1997.

Int J Clin Pharmacol Ther, In training manuscript competition, honorable mention 1998.

US Catalyst User Group Meeting best presentation, 1999, 2002.

Patents

 

U.S. Patent no 6564152: Ekins S and Smith BJ, Pharmacophore models for, methods of screening for, and identification of the cytochrome P-450 inhibitory potency of neurokinin- 1 receptor antagonists.

U.S. Patent no 6489094: Ekins S,  Kelly KG, Johnson DL, Method and device for drug-drug interaction testing sample preparation.

U.S. Patent no 8211882: Wood RD, Welsh WJ, Ekins S, Ai N, Glutamate Receptor Modulators and Therapeutic Agents. July 3. 2012.

 

Patent Applications

 

European Patent no EP1120723: Ekins S and Smith BJ, Identification of the cytochrome P-450 inhibitory potency of neurokinin-1 receptor antagonists and associated pharmacophore models and screening methods.

Japanese Patent No 2001275697: Ekins S and Smith BJ, Pharmacophore model for neurokinin-1 receptor antagonist, screening method, and identification of cytochrome p-450-inhibiting effectiveness.

U.S. Patent no US2002013372: Ekins S, Pharmacophore models for the identification of the CYP2D6 inhibitory potency of selective serotonin reuptake inhibitors.

European patent No: 1134290: Ekins S, Pharmacophore models for the identification of the CYP2D6 inhibitory potency of selective serotonin reuptake inhibitors.

Japanese Patent No 2001324496: Ekins S, Pharmacophore model for identifying CYP2D6 inhibiting capacity of selective serotonin reintrojection inhibitor.

U.S. Patent no US2002016681: Kelly KG, Meyer, RD, Ekins S, Feng G, Johnson DL. Single point interaction screen to predict IC50.

European patent No: 1139267: Ekins S, Gao F, Johnson DL, Kelly KG, Meyer RD, Single point interaction screen to predict IC50.

Japanese Patent No 2001330600: Ekins S, Gao F, Johnson DL, Kelly KG, Meyer RD. One-point interaction screen for predicting IC50.

International application number No: PCT/US2006/010053: Ekins S, Bugrim A, Nikolskaya T, Nikolsky Y, System and method for prediction of drug metabolism, toxicity, mode of action, and side effects of novel small molecule compounds.

U.S. Patent no 61/067,730 Welsh WJ, Ekins S, Wood R, Modulators of Group 1 Metabotropic Glutamate Receptors and Uses Thereof.

U.S. Patent no 61/068,493 Welsh WJ, Ekins S, Wood R, Metabotropic Glutamate Receptor Modulators and Therapeutic Agents.

U.S. Patent provisional submitted – Ekins S, Kortagere S, Welsh WJ, Compositions and treatments for parasitic disease.

 

U.S. Patent provisional submitted – Wood RD, Welsh WJ, Ekins S, Ai N, Glutamate Receptor Modulators and Therapeutic Agents.

 

U.S. Patent provisional submitted 62/170,518 –McKerrow JH, de Siqueira-Neto J, Ekins S and Bunin BA, Anti-Chagas therapy and compositions.

 

U.S. Patent provisional submitted, Moen DR, Zhang XY, Kan S-H, Wood J, Ekins S, Chou TF and Dickson PI, Enzyme replacement therapy for mucopolysaccharidosis IIID.

 

Publications

Papers

http://www.ncbi.nlm.nih.gov/sites/myncbi/sean.ekins.1/bibliography/45032418/public/?sort=date&direction=descending

 

  1. Martinez-Guerrero LJ, Morales M, Ekins S and Wright SH, Lack of Influence of substrate on ligand interaction with human multidrug and toxin extruder, MATE1, Mol Pharmacol, In press 2016

 

  1. Ekins S, Perryman AL, Clark AM, Reynolds RC and Freundlich JS, Machine learning model analysis and data visualization with small molecules tested in a mouse model of Mycobacterium tuberculosis infection (2014-2015), J Chem Inf Model, 56: 1332-1342, 2016.

 

  1. Djaout K, Singh V, Boum Y, Katawera V, Becker HF, Bush NG, Hearnshaw SJ, Pritchard JE, Bourbon P, Madrid PB, Maxwell A, Mizrahi V, Myllykallio H, Ekins S, Predictive modeling targets thymidylate synthase ThyX in Mycobacterium tuberculosis, Scientific Reports, 6:27792, 2016.

 

  1. Kumar P, Kaushik A, Lloyd EP, Li S, Mattoo R, Perryman AL, Ekins S, Ginell SL, Townsend CA, Freundlich JS, Lamichhane G, Targeting of non-classical transpeptidases results in bacterial growth inhibition, Submitted 2015 In review.

 

  1. Ekins S, Liebler J, Neves BJ, Lewis W, Coffee M, Bienstock R, Southan C and Andrade CH, Illustrating and Homology Modeling the Proteins of the Zika Virus, F1000Res 5: 275, 2016. http://f1000research.com/articles/5-275/v1

 

  1. Ekins S, Mietchen D, Coffee M, Stratton TP,  Freundlich JS, Freitas-Junior LH, Muratov  E, Siqueira-Neto JL,  Williams AJ and Andrade CH, Open drug discovery for the Zika virus, F1000Res 5: 150, 2016. http://f1000research.com/articles/5-150/v1

 

  1. Ekins S and Wood J, Incentives for starting small companies focused on rare and neglected diseases, Pharm Res, 33(4):809-15 2016.

 

  1. Clark AM, Dole K and Ekins S, Open Source Bayesian Models: 3. Composite Models for prediction of binned responses, J Chem Inf Model, 56: 275-85, 2016.

 

  1. Perryman AL, Stratton TP, Ekins S and Freundlich JS, Predicting mouse liver microsomal stability with “pruned’ machine learning models and public data, Pharm Res, 33: 433-49, 2016

 

  1. Ekins S, Litterman NK, Lipinski CA and Bunin BA, Simple proxies of enthalpy and entropy compensate for biases in drug discovery methods, Pharm Res, 33:194-205, 2016

 

  1. Hanson SM, Ekins S and Chodera JD, Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologies, J Comp-Aided Mol Des, 29:1073-86, 2015.

 

  1. Ekins S and Lage de Siqueira-Neto J., Shedding Light on Synergistic Chemical Genetic Connections with Machine Learning, Cell Systems, 1: 377-379, http://www.cell.com/cell-systems/pdf/S2405-4712%2815%2900219-7.pdf

 

  1. Ekins S, Freundlich JS, Clark AM, Anantpadma M, Davey RA and Madrid PB, Machine learning models identify molecules active against Ebola virus in vitro, F1000Research, 4:1091, 2015. http://f1000research.com/articles/4-1091/v2

 

  1. Ekins S*, Madrid PB*, Sarker M, Li S-G, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M and Freundlich JS*. Combining metabolite-based pharmacophores with Bayesian machine learning models for Mycobacterium tuberculosis drug discovery, PLOS ONE, 10: e0141076, 2015.

 

  1. Johnson-Kerner B, Diaz AG, Ekins S and Wichterle H, Kelch domain of gigaxonin interacts with intermediate filament proteins affected in giant axonal neuropathy, PLoS ONE 10(10): e0140157, 2015.

 

  1. Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, Ribiero ALDJL, Marino LB, Centarova I, Svetikova Z, Blasko J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikusova K, Alzari PM, Manganelli R, de Carvalho LPS, Riccardi G and Cole ST, Thiophenecarboxamide derivatives activated by EthA kill Mycobacterium tuberculosis by inhibiting the CTP synthetase PyrG, Chem Biol, 22: 1-11, 2015

 

  1. Ekins S, Clark, AM and Wright SH, Making transporter models for drug-drug interaction prediction mobile, Drug Metab Dispos, 43:1642-5, 2015

 

  1. Ekins S, Lage de Siqueira-Neto J, McCall L-I, Sarker M, Yadav M, Ponder EL, Kallel EA, Kellar D, Chen S, Arkin M, Bunin BA, McKerrow JH and Talcott C, Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery, PLOS Neglected Trop Dis, 9(6):e0003878, 2015.

 

  1. Clark AM, Dole K, Coulon-Spektor A, McNutt A, Grass G, Freundlich JS, Reynolds RC and Ekins S, Open Source Bayesian Models: 1. Application to ADME/Tox and Drug Discovery Datasets, J Chem Inf Model, 55(6):1231-45,

 

  1. Clark AM, and Ekins S Open Source Bayesian Models: 2. Mining a “Big Dataset” to Create and Validate Models with ChEMBL, J Chem Inf Model, 55(6):1246-60,

 

  1. Li S.-G, Vilchèze C, Chakraborty S, Wang X, Kim H, Anisetti M, Ekins S, Rhee KY, Jacobs Jr WR, Freundlich JS, Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights, Tetrahedron Letters 56: 3246-3250, 2015.

 

  1. Ekins S, Southan CD and Coffee M, Finding small molecules for the ‘next Ebola’, F1000Res, 4:58, 2015. http://f1000research.com/articles/4-58/v1

 

  1. Ekins S and Coffee M, FDA Approved Drugs as Potential Ebola Treatments, F1000Res 4: 48, 2015. http://f1000research.com/articles/4-48/v1

 

  1. Litterman NK, Lipinski C and Ekins S, Small molecules with antiviral activity against the Ebola virus, F1000Res 4: 38, 2015. http://f1000research.com/articles/4-38/v1

 

  1. Clark AM, Williams AJ and Ekins S, Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data, J Cheminform 7:9 2015. http://www.jcheminf.com/content/7/1/9

 

  1. Ekins S, Litterman, NK, Arnold RJG, Burgess RW, Freundlich JS, Gray SJ, Higgins JJ, Langley B, Willis DE, Notterpek L, Pleasure D, Sereda MW and Moore A. A brief review of recent Charcot-Marie-Tooth research and priorities, F1000Research 4: 53, 2015 http://f1000research.com/articles/4-53/v1

 

  1. Godbole A, Ahmed W, Bhat RS, Bradley EK, Ekins S, and Nagaraja V, Targeting Mycobacterium tuberculosis topoisomerase I by small molecule inhibitors, Antimicrob Agents Chemother 59:1549-57,

 

  1. Perryman AL, Weixuan Y, Wang X, Ekins S, Forli S, Li S-G, Freundlich JS, Tonge PJ and Olson AJ, GOFight Against Malaria (GO FAM) virtual screen discovers novel inhibitors of Mycobacterium tuberculosis InhA, J Chem Inf Model, 55: 645-659,

 

  1. Ai N, Fan X and Ekins S, In silico methods for predicting Drug-drug interactions with cytochrome P-450s, transporters and beyond, Adv Drug Del Rev, 86:46-60,

 

  1. Litterman N, and Ekins S, Databases and collaboration require standards for human stem cell research, Drug Disc Today, 20, 247-254, 2015.

 

  1. Lipinski CA, Litterman N, Southan C, Williams AJ, Clark AM and Ekins S. Parallel worlds of public and commercial bioactive chemistry data, J Med Chem, 12;58: 2068-76. 2015.

 

  1. Ai N, Ekins S and Fan X, Large scale prediction of the involvement of the organic anion transporter 1 in traditional Chinese medicine-drug interactions, submitted 2014.

 

  1. Ekins S and Freundlich JS and Coffee M, A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus, F1000research, 3: 277, 2014. http://f1000research.com/articles/3-277/v2

 

  1. Ekins S, Collecting rare diseases, F1000research, 3, 260, 2014. http://f1000research.com/articles/3-260/v1

 

  1. Litterman NK, Rhee M, Swinney DC and Ekins S, Collaboration for rare disease drug discovery research, F1000research, 3:261, 2014. http://f1000research.com/articles/3-261/v1

 

  1. Dong Z, Ekins S and Polli JE, A substrate pharmacophore for the human sodium taurocholate co-transporting polypeptide, Int J Pharm. 478(1):88-95, 2014.

 

  1. Litterman N, Lipinski CA, Bunin BA and Ekins S, Computational Prediction and Validation of an Expert’s Evaluation of Chemical Probes, J Chem Inf Model, 54:2996-3004,

 

  1. Ekins S, Freundlich JS and Reynolds RC, Are bigger datasets better for machine learning? Fusing single-point and dual-event dose response data for Mycobacterium tuberculosis, J Chem Inf Model, 54:2157-65,

 

  1. Ekins S, Hacking into the granuloma: could antibody antibiotic conjugates be developed for TB? Tuberculosis, 94(6):715-6, 2014.

 

  1. Ekins S, Clark AM, Swamidass SJ, Litterman N and Williams AJ, Bigger data, collaborative tools and the future of predictive drug discovery, J Comp-Aided Mol Design, 54:2157-65, 2014.

 

  1. Ekins S, Nuermberger EL and Freundlich JS, Minding the gaps in Tuberculosis research, Drug Disc Today, 19:1279-82,

 

  1. Sames L, Moore A, Arnold RJG and Ekins S, Recommendations to enable drug development for inherited neuropathies: Charcot-Marie-Tooth and Giant Axonal Neuropathy, F1000Research, 3:83, 2014. http://f1000research.com/articles/3-83/v1

 

  1. Clark AM, Sarker M and Ekins S, New target predictions and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0, J Cheminform 6: 38, 2014. http://www.jcheminf.com/content/6/1/38

 

  1. Ekins S and Perlstein EO, Ten simple rules of live tweeting at scientific conferences, PLOS Comp Biol, 10(8):e1003789, http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003789

 

  1. Ekins S, Pottorf R, Reynolds RC, Williams AJ, Clark AM, Freundlich JS, Looking back to the future: predicting in vivo efficacy of small molecules versus Mycobacterium tuberculosis, J Chem Inf Model, 54:1070-82, 2014.

 

  1. Dong Z, Ekins S and Polli JE, Quantitative NTCP pharmacophore and lack of association between DILI and NTCP inhibition, Eur J Pharm Sci, 66:1-9, 2014.

 

  1. Krasowski MD and Ekins S, Using cheminformatics to predict cross reactivity of “designer drugs” to their currently available immunoassays. J Cheminform 6:22, http://www.jcheminf.com/content/6/1/22

 

  1. Krasowski MD, Drees D, Morris CS, Maakestad J, Blau JL and Ekins S, Cross-reactivity of Steroid Hormone Immunoassays: Clinical Significance and Two-Dimensional Molecular Similarity Prediction, BMC Clin Pathol, 14:33, 2014. http://www.biomedcentral.com/1472-6890/14/33

 

  1. Godbole AA, Ahmed W, Bhat RS, Bradley EK, Ekins S and Nagaraja V, Inhibition of Mycobacterium tuberculosis I by m-AMSA, a eukaryotic type II topoisomerase poison. Biochem Biophys Res Comm, 446:916-20, 2014.

 

  1. Ekins S and Williams AJ, Curing TB with open science, Tuberculosis, 94:183-5, 2014.

 

  1. Kandel BA, Ekins S, Leuner K, Thasler WE, Harteneck C and Zanger UM, No activation of human PXR by hyperforin-related phloroglucinols, JPET, 348:393-400, 2014.

 

  1. Ekins S, Casey A.C, Roberts D, Parish T. and Bunin BA, Bayesian Models for Screening and TB Mobile for Target Inference with Mycobacterium tuberculosis, Tuberculosis, 94:162-9, 2014.

 

  1. Ekins S, Freundlich JS, Hobrath JV, White EL, Reynolds RC, Combining computational methods for hit to lead optimization in Mycobacterium tuberculosis drug discovery, Pharm Res, 31: 414-35,

 

  1. Ponder EL, Freundlich JS, Sarker M, Ekins S, Computational models for neglected diseases: gaps and opportunities, Pharm Res, 31: 271-277, 2014.

 

  1. Ekins S, Progress in computational toxicology, J Pharmacol Toxicol Methods, 69:115-140 2014.

 

  1. Ekins S, Freundlich JS and Reynolds RC, Fusing dual-event datasets for Mycobacterium Tuberculosis machine learning models and their evaluation, J Chem Inf Model, 53(11):3054-63,

 

  1. Fukuda Y, Takenaka K, Sparreboom A, Cheepala SB, Wu C-P, Ekins S, Ambudkar SV and Schuetz JD, HIV protease inhibitors interact with ABCC4/MRP4: a basis for unanticipated enhanced efficacy and toxicity, Mol Pharmacol, 84:361-71,

 

  1. Wood J, Sames L, Moore A, Ekins S, The multifaceted roles of rare disease parent / patient advocates in drug discovery, Drug Disc Today, 18: 1043–1051, 2013. http://www.drugdiscoverytoday.com/download/1215

 

  1. Ekins S, Goldsmith M-R, Simon A, Zsoldos Z, Ravitz O and Williams AJ, LASSO-ing potential nuclear receptor agonists and antagonists: A New Computational Method For Database Screening, Journal of Computational Medicine, http://dx.doi.org/10.1155/2013/513537, 2013. http://www.hindawi.com/journals/jcm/2013/513537/

 

  1. Li H, Redinbo MR, Venkatesh M, Ekins S, Chaudhary A, Bloch N, Negassa A, Mukherjee P, Kalpana G, Mani S, Novel Yeast-Based Strategy Unveils Antagonist Binding Regions on the Nuclear Xenobiotic Receptor PXR, J Biol Chem, 288:13655-68, 2013

 

  1. Ekins S and Freundlich JS, Computational models for tuberculosis drug discovery, In In silico models in drug discovery, Methods Mol Biol, 993:245-62, 2013.

 

  1. Ekins S and Bunin BA, The collaborative drug discovery (CDD) database, Methods Mol Biol. 993:139-54, 2013

 

  1. Ekins S, Clark AM, Sarker M, TB Mobile: A Mobile App for Anti-tuberculosis Molecules with Known Targets, J Cheminform, 5:13, 2013. http://www.jcheminf.com/content/5/1/13

 

  1. Clark AM, Williams AJ and Ekins S, Cheminformatics workflows using mobile apps, Chem-Bio Informatics Journal, 13: 1-18 http://figshare.com/articles/Cheminformatics_workflows_using_mobile_apps/1290457

 

  1. Anderson JW, Sarantakis D, Terpinski J, Kumar TRS, Tsai H-C, Kuo M, Ager, AL, Jacobs, Jr WR., Schiehser GA, Ekins S, Sacchettini JC, Jacobus DP, Fidock DA, Freundlich JS, Novel diaryl ureas with efficacy in a mouse model of malaria, Bioorg Med Chem Lett, 23: 1022, 2013. PMID: 23313245

 

  1. Ekins S, Clark AM and Williams AJ, Incorporating Green Chemistry Concepts into Mobile Applications and their potential uses, ACS Sustain Chem Eng, 1. 8-13, 2013. http://pubs.acs.org/doi/abs/10.1021/sc3000509

 

  1. Southan C, Williams AJ and Ekins S, Challenges and Recommendations for obtaining chemical structures of industry provided repurposing candidates, Drug Disc Today, 18: 58-70, 2013.

 

  1. Ekins S, Waller CL, Bradley MP, Clark AM and Williams AJ, Four disruptive strategies for removing drug discovery bottlenecks, Drug Discovery Today, 18: 265-271, 2013.

 

  1. Ekins S, Reynolds RC, Franzblau SG, Wan B, Freundlich JS and Bunin BA. Enhancing hit identification in Mycobacterium tuberculosis drug discovery using validated dual-event Bayesian models, PLOS ONE, 8(5): e63240, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063240

 

  1. Ekins S, Reynolds RC, Kim H, Koo M-S, Ekonomidis M, Talaue M, Paget SD, Woolhiser LK Lenaerts AJ, Bunin BA, Connell N and Freundlich JS. Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery, Chem Biol, 20: 370-378, 2013.

 

  1. Ekins S, Olechno J and Williams AJ, Dispensing processes impact apparent biological activity as determined by computational and statistical analyses, PLOSONE, 8: e62325, 2013. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062325

 

  1. Petrie M, Lynch KL, Ekins S, Goetz RJ, Wu AHB, Krasowski MD. Cross reactivity studies and predictive modeling of “bath salts” and other amphetamine-type stimulants with amphetamine screening immunoassays, Clin Toxicol, 51(2):83-91, 2013.

 

  1. Dong Z, Ekins S and Polli JE, Structure activity relationship for FDA approved drugs as inhibitors of the human sodium taurocholate co-transporting polypeptide (NTCP), Mol Pharmaceutics, 10:1008-19, 2013.

 

  1. Yasuda K, Cline C, Vogel P, Onciu M, Fatima S, Sorrentino BP, Thirumaran RK, Ekins S, Urade Y, Fujimori K and Schuetz EG, Drug transporters on arachnoid barrier cells contribute to the blood-cerobrospinal fluid barrier, Drug Metab Dispos, 41(4):923-31, 2013.

 

  1. Zhang L, Fourches D, Sedykh A, Zhu H, Golbraikh A, Ekins S, Clark J, Connelly MC, Sigal M, Hodges D, Guiguemde A, Guy RK, and Tropsha A, The Discovery of Novel Antimalarial Compounds enabled by QSAR-based Virtual Screening, J Chem Inf Model, 25: 475-92.

 

  1. Ekins S, Polli JE, Swaan PW, Wright SH, Computational Modeling to accelerate the identification of transporter substrates and inhibitors that affect drug disposition, Clin Pharm Thera, 92: 661-665, 2012.

 

  1. Williams AJ, Wilbanks J and Ekins S, Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models, PLoS Comput Biol, 8(9):e1002706, 2012. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002706

 

  1. Ekins S, Clark AM and Williams AJ, Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration, Mol Informatics, 31: 585-597, 2012. http://onlinelibrary.wiley.com/doi/10.1002/minf.201200034/abstract

 

  1. Williams AJ, Ekins S, Spjuth O and Willighagen EL, Accessing, using and creating chemical property databases for computational toxicology modeling, Methods in Molecular Biology, 929: 221-241, 2012

 

  1. Kortagere S, Ekins S and Krasowski MD, Ligand and Structure-based Pregnane X receptor models, Methods in Molecular Biology, 929: 359-375, 2012.

 

  1. Beaulieu C, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, Hicks GG, Frey BJ, Boycott KM and MacKenzie, AE., A generalizable pre-clinical research approach for orphan disease therapy. Orphanet, 7(1):39, 2012.

 

  1. Sacan A, Kortagere S and Ekins S, Applications and limitations of in silico methods in drug discovery, Methods Mol Biol, 910:87-124, 2012.

 

  1. Astorga B, Ekins S, Morales M and Wright SH, Molecular Determinants of Ligand Selectivity for the Human Multidrug And Toxin Extrusion Proteins, MATE1 and MATE-2K, J Pharmacol Exp Ther, 341: 743-755, 2012.

 

  1. Ekins S, Waller CL, Bradley MP and Williams AJ, Disruptive strategies for removing drug discovery bottlenecks, Nature Precedings, doi:10.1038/npre.2012.6961.1 http://precedings.nature.com/documents/6961/version/1

 

  1. Ekins S, Shigeta R and Bunin BA, Bottlenecks caused by software gaps in miRNA and RNAi research, Pharm Res, 29: 1717-1721, 2012.

 

  1. Clark, AM, Ekins S and Williams AJ, Redefining cheminformatics with intuitive collaborative mobile apps, Mol Informatics, 31: 569-584, 2012. http://onlinelibrary.wiley.com/doi/10.1002/minf.201200010/abstract

 

  1. Williams AJ, Ekins S and Tkachenko V, Towards a Gold Standard: Regarding Quality in Public Domain Chemistry Databases and Approaches to Improving the Situation, Drug Discovery Today,17 (13-14):685-701, 2012.

 

  1. Sarker M, Talcott C, Madrid P, Chopra S, Bunin BA, Lamichhane G, Freundlich JS and Ekins S, Combining Cheminformatics methods and pathway analysis to identify molecules with whole cell activity against Mycobacterium tuberculosis, Pharm Res, 29: 2115-2127,

 

  1. Ekins S, Diao L and Polli JE, A substrate pharmacophore for the human organic cation/cationic transporter identifies compounds associated with rhabdomyolysis, Mol Pharmaceutics, 9:905-913, 2012.

 

  1. Ekins S and Williams AJ, The future of computational models for predicting human toxicities, ALTEX Proceedings,1/12, Proceedings of WC8, 2012. http://www.altex.ch/resources/549554_EkinsandWilliams2.pdf

 

  1. Fidler AE, Holland PT, Reschly EJ, Ekins S and Krasowski MD, Activation of a tunicate (Ciona intestinalis) xenobiotic receptor orthologue by both natural toxins and synthetic toxicants, Toxicon, 59:365-72,

 

  1. Williams, AJ, Ekins S, Clark AM, Jack JJ and Apodaca RL, Mobile apps for chemistry in the world of drug discovery, Drug Disc Today, 16:928-939, 2011.

 

  1. Ekins S and Williams AJ, Finding promiscuous old drugs for new uses, Pharm Res, 28: 1785-1791, 2011.

 

  1. Ekins S, Williams AJ, Krasowski MD and Freundlich JS, In silico repositioning of approved drugs for rare and neglected diseases, Drug Disc Today, 16: 298-310, 2011.

 

  1. Ekins S and Freundlich JS, Validating new tuberculosis computational models with public whole cell screening aerobic activity datasets, Pharm Res, 28, 1859-1869, 2011.

 

  1. Lamichhane G, Freundlich JS, Ekins S , Wickramaratne N, Nolan, S and Bishai WR, Essential Metabolites of tuberculosis and their small molecule mimics, Mbio, 2: e00301-10, 2011. http://mbio.asm.org/content/2/1/e00301-10.full.pdf+html?sid=c9ad8d09-2237-4b4b-b476-3e486a055663

 

  1. Krasowski MD, Ai N, Hagey LR, Kolliz EM, Kullman SW, Reschly EJ and Ekins S, The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis) and other non-mammalian species, BMC Biochem 12: 5, 2011 http://www.biomedcentral.com/1471-2091/12/5

 

  1. Pan Y, Li L, Kim G, Ekins S, Wang H and Swaan PW, Identification of novel hPXR activators amongst prescribed drugs by integrated structure- and ligand-based virtual screening, Drug Metab Dispos, 39:337-344, 2011.

 

  1. Poulin P, Ekins S and Theil F-P, A hybrid approach to advancing quantitative prediction of tissue distribution of basic drugs in human, Toxicol Appl Pharmacol, 250: 194-212, 2011.

 

  1. Ekins S, Freundlich JS, Choi I, Sarker M and Talcott C, Computational Databases, Pathway and Cheminformatics Tools for Tuberculosis Drug Discovery, Trends In Microbiology, 19: 65-74, 2011.

 

  1. Ekins S, Kaneko T, Lipinski CA, Bradford J, Dole K, Spektor A, Gregory K, Blondeau D, Ernst S, Yang J, Goncharoff N, Hohman M and Bunin BA, Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis, Mol Biosyst, 6: 2316-2324, 2010.

 

  1. Ekins S, Xu JJ and Williams AJ, A predictive ligand-based Bayesian models for human drug induced liver injury, Drug Metab Dispos, 38: 2302-2308, 2010.

 

  1. Gupta RR, Gifford, EM, Liston T, Waller CL, Hohman M, Bunin BA and Ekins S, Using open source computational tools for predicting human metabolic stability and additional ADME/Tox properties, Drug Metab Dispos, 38: 2083-2090, 2010.

 

  1. Ekins S and Williams AJ, When Pharmaceutical Companies Publish Large Datasets: An Abundance of riches or fool’s gold? Drug Disc Today, 15; 812-815, 2010.

 

  • Ekins S, Gupta R, Gifford E, Bunin BA, Waller CL, Chemical Space: missing pieces in cheminformatics, Pharm Res, 27: 2035-2039, 2010.

 

  1. Zheng X, Diao L, Ekins S and Polli JE, Why we should be vigilant: drug cytotoxicity observed with in vitro transporter inhibition studies, Biochem Pharmacol, 80: 1087-1092, 2010.

 

  1. Diao, L, Ekins S and Polli JE, Quantitative structure activity relationship for inhibition of human organic cation/carnitine transporter (OCTN2), Mol Pharm, 7: 2120-2131, 2010.

 

  1. Kortagere S, Krasowski MD, Reschly EJ, Venkatesh M, Mani S and Ekins S, Evaluation of Computational Docking to Identify PXR Agonists in the ToxCastTM Database, Env Health Perspect, 118: 1412-1417, 2010. http://ehp.niehs.nih.gov/1001930/

 

  1. Krasowski MD, Ni A, Hagey LR and Ekins S, Evolution of promiscuous nuclear hormone receptors LXR, FXR, VDR, PXR and CAR, Mol Cell Endocrinol 334: 39-48, 2010.

 

  1. Ekins S, Honeycutt JD and Metz JT, Evolving molecules using multi-objective optimization: applying to ADME/Tox, Drug Disc Today, 15: 451-460, 2010.

 

  1. Arnold RJG and Ekins S, Time for cooperation in health economics among the modeling community, PharmacoEconomics, 28(8):609-613, 2010.

 

  1. Howarth DL, Hagey LR, Law SHW, Ai N, Krasowski MD, Ekins S, Moore JT, Kollitz EM, Hinton DE and Kullman SW.  Two farnesoid X receptor α isoforms in Japanese medaka (Oryzias latipes) are differentially activated in vitro.  Aquat Toxicol 2010; 98: 245-255.

 

  1. Ekins S. and Williams AJ, Reaching out to collaborators: crowdsourcing for pharmaceutical research, Pharm Res, 27: 393-395, 2010.

 

  1. Kortagere S and Ekins S, Troubleshooting computational methods in drug discovery, J Pharm Tox Methods, 61: 67-75, 2010.

 

  1. Ekins S and Williams AJ, Precompetitive Preclinical ADME/Tox Data: Set It Free on The Web to Facilitate Computational Model Building to Assist Drug Development. Lab On A Chip, 10: 13-22, 2010.

 

  1. Zientek M, Stoner C, Ayscue R, Klug-McLeod J, Jiang Y, West M, Collins C and Ekins S, Integrated In Silico- In vitro strategy for addressing Cytochrome P450 3A4 time dependent inhibition, Chem Res Toxicol, 23: 664-676, 2010.

 

  1. Ekins S, Bradford J, Dole K, Spektor A, Gregory K, Blondeau D, Hohman M and Bunin BA, A Collaborative Database and Computational Models for Tuberculosis Drug Discovery, Mol BioSyst, 6: 840-851, 2010.

 

  1. Berg, EL, Yang J, Melrose J, Nguyen D, Privat S, Rosler E, Kunkel EJ and Ekins S., Chemical target and pathway toxicity mechanisms defined in primary human cell systems BioMAP systems for analysis of toxicity pathways and mechanisms. J Pharmacol Toxicol Methods, 61:3-15, 2010.

 

  1. Williams AJ, Tkachenko V, Lipinski C, Tropsha A and Ekins S, Free online resources enabling crowdsourced drug discovery, Drug Discovery World, Winter 2009/10, 33-39.

 

  1. Ekins S, Kortagere S, Iyer M, Reschly EJ, Lill MA, Redinbo MR and Krasowski MD, Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR, PLoS Comput Biol, 5(12): e1000594, 2009. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000594

 

  1. Louise-May S, Bunin B and Ekins S, Towards integrated web-based tools in drug discovery, Touch Briefings – Drug Discovery, 6: 17-21, 2009.

 

  1. Zheng X, Ekins S, Raufman J-P, and Polli J.E., Computational models for drug inhibition of the Human Apical Sodium-dependent Bile Acid Transporter, Mol Pharm, 6: 1591-1603, 2009.

 

  1. Chekmarev D, Kholodovych V, Kortagere S, Welsh WJ and Ekins S, Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors, Pharm Res, 26: 2216-2224, 2009.

 

  1. Ivanenkov, YA, Savchuk NP, Ekins S and Balakin KV, Computational mapping tools for drug discovery, Drug Disc Today, 14: 767-775, 2009.

 

  1. Diao L, Ekins S and Polli JE, Novel Inhibitors of Human Organic Cation/Carnitine Transporter (hOCTN2) via Computational Modeling and In Vitro Testing, Pharm Res, 26:1890-1900, 2009.

 

  1. Biswas A, Mani S, Redinbo MR, Krasowski MD, Li H and Ekins S, Elucidating the ‘Jekyll and Hyde’ nature of PXR: The case for discovering antagonists, Pharm Res, 26:1807-15, 2009.

 

  1. Krasowski MD, Siam MG, Iyer M, Pizon AG, Giannoutsos S and Ekins S, Predicting interference in immunoassays for drug of abuse/toxicology screening using chemoinformatics methods, Clinical Chemistry, 55:1203-13, 2009.

 

  1. Lin YS, Yasuda K, Assem M, Cline C, Barber J, Li C-W, Kholodovych V, Ai N, Chen JD, Welsh WJ, Ekins S and Schuetz EG, The major human PXR splice variant, PXR.2, exhibits significantly diminished ligand-activated transcriptional regulation, Drug Metab Dispos, 37:1295-304, 2009.

 

  1. Krasowski MD, Siam MG, Iyer M and Ekins S, Molecular similarity methods for predicting cross reactivity with therapeutic drug monitoring immunoassays, Thera Drug Monitoring, 31:337-44, 2009.

 

  1. Ai N, Krasowski MD, Welsh WJ and Ekins S, Understanding nuclear receptors using computational methods, Drug Disc Today, 14: 486-494,

 

  1. Krasowski MD, Pizon AF, Siam MG, Giannoutsos S, Iyer M and Ekins S, Using molecular similarity to highlight the challenges of routine immunoassay-based drug of abuse/toxicology screening in emergency medicine.  BMC Emergency Medicine, 9:5, 2009. http://www.biomedcentral.com/1471-227X/9/5

 

  1. Ekins S and Tropsha A, A turning point for blood-brain barrier modeling, Pharm Res, 26: 1283-1284, 2009.

 

  1. Kortagere S, Chekmarev D, Welsh WJ, Ekins S, Hybrid scoring and classification approaches to predict human pregnane X receptor activators, Pharm Res, 26:1001-11, 2009.

 

  1. Kortagere S, Krasowski MD and Ekins S, The importance of discerning shape in molecular pharmacology, Trends Pharmacol Sci, 30:138-47, 2009.

 

  1. Hohman M, Gregory K, Chibale K, Smith PJ, Ekins S and Bunin B, Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery, Drug Disc Today, 14: 261-270,

 

  1. Ekins S, Predicting endogenous or exogenous molecules that interact with P-glycoprotein using pharmacophores, The ChemSpider Journal of Chemistry, http://www.chemmantis.com/Article.aspx?id=846, 2009

 

  1. Marcus P, Arnold RJG, Ekins S, Sacco P, Massanari M, Young SS, Gold H, Kim-Kuan R, Donohue J, Bukstein D, A retrospective randomized analysis of treatment patterns and asthma control in the US: results of the CHARIOT Study, Current Medical Research and Opinion, 24: 3443-3452,

 

  1. Ekins S, Kholodovych V, Ai N, Sinz M, Gal J, Gera L, Welsh WJ, Bachmann K and Mani S, Computational discovery of novel low micromolar human pregnane X receptor antagonists, Mol Pharmacol, 74: 662-672, 2008.

 

  1. Krasowski MD, Reschly EJ and Ekins S, Intrinsic disorder in nuclear hormone receptors, J Proteome Res, 7:4359-4372,

 

  1. Yasuda K, Ranade A, Venkataramanan R, Strom S, Chupka J, Ekins S, Schuetz E and Bachmann K, A comprehensive in vitro and in silico analysis of antibiotics that activate and induce CYP3A4 in liver and intestine, Drug Metab Dispos, 36:1689-97, 2008.

 

  1. Khandelwal A, Krasowski MD, Reschly EJ, Sinz M, Peter W Swaan and Ekins S, Machine learning methods and docking for human Pregnane X Receptor activation, Chem Res Toxicol, 21:1457-67,

 

  1. Swaan PW, Bensman T, Bahadduri PM, Hall MW, Sarker A, Ekins S and Knoell DL, Bacterial dipeptide recognition and immune activation is facilitated by the human peptide transporter PEPT2, Am J Resp Cell Mol Biol, 39: 536-542, 2008.

 

  1. Kortagere S, Ekins S and Welsh WJ, Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships, J Mol Graph Model. 27:170-7, 2008.

 

  1. Kortagere S, Chekmarev DS, Welsh WJ and Ekins S, New predictive models for Blood-Brain Barrier permeability of drug-like molecules, Pharm Res, 25:1836-45,

 

  1. Reschly EJ, Ai N, Ekins S, Welsh WJ, Hagey LR, Hoffman AF, Krasowski MD, Evolution of the bile salt nuclear receptor FXR in vertebrates, J Lipid Res, 49:1577-1587, 2008.

 

  1. Chekmarev DS, Kholodovych V, Balakin KV, Ivanenkov Y, Ekins S and Welsh WJ, Shape Signatures: new descriptors for predicting cardiotoxicity, Chem Res Toxicol, 21:1304-14

 

  1. Ekins S, Reschly EJ, Hagey LR and Krasowski MD, Evolution of pharmacologic specificity in the Pregane X Receptor, BMC Evolutionary Biology, 8:103, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2358886/

 

  1. Reschly EJ, Ai N, Welsh WJ, Ekins S, Hagey LR, Krasowski MD, Ligand specificity and evolution of liver X receptors, J Steroid Biochem Mol Biol, 110:83-94,

 

  1. Ekins S, Iyer M, Krasowski MD and Kharasch ED, Molecular Characterization of CYP2B6 substrates, Curr Drug Metab, 9:363-373, 2008.

 

  1. Zhou H, Wu S, Zhai S, Liu A, Sun Y, Li R, Zhang Y, Ekins S, Swaan PW, Fang B, Zhang B, Yan B, Design, Synthesis, Cytoselective Toxicity, Structure-Activity Relationships and Pharmacophores Of Thiazolidinone Derivatives Targeting Drug-Resistant Lung Cancer Cells, J Med Chem, 51: 1242–1251, 2008

 

  1. Stranz DD, Miao S, Campbell S, Maydwell G and Ekins S, Combined computational metabolite prediction and automated structure based analysis of mass spectrometric data, Toxicology Mechanisms and Methods, 18: 243-250, 2008.

 

  1. Ekins S, Ecker GF, Chiba P and Swaan PW, Future directions for drug transporter modeling, Xenobiotica, 37:1152-1170, 2007.

 

  1. Khandelwal A, Bahadduri PM, Chang C, Polli JE, Swaan PW and Ekins S, Computational models to assign biopharmaceutics drug disposition classification from molecular structure, Pharm Res, 24: 2249-2262, 2007.

 

  1. Hupcey MAZ and Ekins S, Improving the drug selection process for combination medical devices, Drug Disc Today, 12; 844-852, 2007.

 

  1. Ekins S, Chang C, Mani S, Krasowski MD, Reschly EJ, Iyer M, Kholodovych V, Ai N, Welsh WJ, Sinz M, Swaan PW, Patel R and Bachmann K, Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites, Mol Pharmacol, 72: 592-603, 2007.

 

  1. Ekins S, Mestres J and Testa B, In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol, 152: 9-20, 2007.

 

  1. Ekins S, Mestres J and Testa B, In silico pharmacology for drug discovery: applications to targets and beyond. Br J Pharmacol, 152: 21-37, 2007.

 

  1. Jones DR, Ekins S, Li L and Hall SD, Computational approaches that predict metabolic intermediate complex formation with CYP3A4 (+b5). Drug Metab Dispos, 35: 1466-1475, 2007.

 

  1. Embrechts MJ and Ekins S, Classification of metabolites with kernel partial least squares. Drug Metab Dispos, 35: 325-327, 2007.

 

  1. Ekins S, Mankowski DC, Hoover DJ, Lawton MP, Treadway JL and Harwood HJ Jr, Three dimensional-quantitative structure activity relationship (3D-QSAR) analysis of human CYP51 inhibitors, Drug Metab Dispos, 35: 493-500, 2007.

 

  1. Jolivette, LJ and Ekins S, Methods for predicting human drug metabolism, Adv Clin Chem, 43:131-76, 2007.

 

  1. Chang C, Bahadduri P, Swaan, PW and Ekins, S, Application of integrated computational pharmacophore models and in vitro approaches to rapidly identify novel P-glycoprotein ligands. Drug Metab Dispos, 34: 1976-1984, 2006.

 

  1. Chang C, Ekins S, Bahadduri P, Swaan PW, Pharmacophore-based discovery of ligands for drug transporters. Adv Drug Del Rev, 58:1431-50,

 

  1. Ekins S, Shimada J and Chang C, Application of data-mining approaches to drug delivery. Adv Drug Del Rev, 58: 1409-1430, 2006.

 

  1. Ekins S, Bugrim A, Brovold L, Kirillov E, Nikolsky Y, Rakhmatulin E, Sorokina S, Ryabov, A, Serebryiskaya T, Melnikov A, Metz J and Nikolskaya T. Algorithms for Network Analysis in Systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica, 36:877-901, 2006.

 

  1. Ekins S, Balakin K, Savchuk N and Ivanenkov Y. Assessment of Human Ether-a-Go-Go-Related Gene potassium channel inhibition Using Recursive Partitioning and Kohonen and Sammon mapping Techniques. J Med Chem, 49: 5059-5071, 2006.

 

  1. Crumb WJ, Ekins S, Sarazan RD, Wikel JH, Wrighton SA, Carlson C and Beasley CM jr. Effects of Antipsychotic Drugs on Ito, INa, Isus, IKi and hERG: QT Prolongation, Structure Activity Relationship and Network Analysis. Pharm Res, 23: 1133-1143, 2006.

 

  1. Ekins S, Andreyev S, Ryabov A, Kirillov E, Rakhmatulin E, Sorokina S, Bugrim A and Nikolskaya T. A combined approach to drug metabolism and toxicity assessment. Drug Metab Dispos, 34:495-503, 2006.

 

  1. Ekins, S. Systems ADME/Tox: resources and approaches. J Pharm Tox Methods. 53: 38-66, 2006.

 

  1. Swaan PW and Ekins S. Reengineering the pharmaceutical industry by crash-testing molecules. Drug Disc Today, 10: 1191-1200, 2005.

 

  1. Chang C, Pang KS, Swaan PW and Ekins S. Pharmacophore Modeling of Organic Anion Transporting Polypeptides: A Meta-analysis of Rat Oatp1a1 and Human OATP1B1. J Pharmacol Exp Ther 314:533-541 2005.

 

  1. Nikolsky Y, Ekins S, Nikolskaya T and Bugrim A. A Novel Method for Generation of Signature Networks as Biomarkers from Complex High Throughput Data. Tox Lett 158: 20-29, 2005.

 

  1. Ekins S, Andreyev S, Ryabov A, Kirillov E, Rakhmatulin EA, Bugrim A and Nikolskaya T. Computational prediction of human drug metabolism. Expert Opin Drug Metab Toxicol, 1: 303-324, 2005.

 

  1. Balakin KV, Ivanenkov YA, Savchuk NP, Ivashchenko AA and Ekins S, Comprehensive computational assessment of ADME/Tox properties using maps. Curr Drug Disc Tech, 2: 99-113, 2005.

 

  1. Ekins S, Johnston JS, Bahadduri P, D’Souza VM, Ray A, Chang C and Swaan PW, In vitro and pharmacophore based discovery of novel hPepT1 inhibitors. Pharm Res, 22: 512-517, 2005.

 

  1. Ekins S, Nikolsky Y and Nikolskaya T, Techniques: Application of Systems Biology to Absorption, Distribution, Metabolism, Excretion, and Toxicity, Trends Pharmacol Sci, 26: 202-209, 2005.

 

  1. Suhre WM, Ekins S, Chang C, Swaan PW and Wright SH, Molecular determinants of substrate/inhibitor binding to the human and rabbit renal organic cation transporters, hOCT2 and rbOCT2, Mol Pharmacol 67:1067-1077, 2005.

 

  1. Ekins S, Kirillov E, Rakhmatulin EA and Nikolskaya T, A Novel Method For Visualizing Nuclear Hormone Receptor networks Relevant To Drug Metabolism, Drug Metab Dispos 33: 474-481, 2005.

 

  1. Balakin KV, Ekins S, Bugrim A, Ivanenkov YA, Korolev D, Nikolsky YV, Ivashchenko AA, Savchuk NP and Nikolskaya T, Quantitative structure-metabolism relationship of the metabolic N-dealkylation reaction rates, Drug Metab Dispos, 32: 1111-1120, 2004.

 

  1. Balakin KV, Ekins S, Bugrim A, Ivanenkov YA, Korolev D, Nikolsky YV, Skorenko AV, Ivashchenko AA, Savchuk NP and Nikolskaya T, Kohonen maps for prediction of binding to human cytochrome P450 3A4, Drug Metab Dispos, 32: 1183-1189, 2004.

 

  1. Ekins S and Swaan PW, Computational models for enzymes, transporters, channels and receptors relevant to ADME/TOX. Rev Comp Chem. 20: 333-415, 2004.

 

  1. Bachmann K, Patel H, Batayneh Z, Slama J, White D, Posey J, Ekins S, Gold D and Sambucetti L, PXR and the regulation of apoA1 and HDL-cholesterol in rodents. Pharmacol Res. 50: 237-246, 2004.

 

  1. Ekins S, Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Disc Today. 9: 276-285, 2004.

 

  1. Mankowski DC and Ekins S. Prediction of human drug metabolizing enzyme induction. Curr Drug Metab, 4: 381-391, 2003.

 

  1. Ekins S, Berbaum J and Harrison, RK, Generation and validation of rapid computational filters for CYP2D6 and CYP3A4. Drug Metab Dispos, 31: 1077-1080 2003.

 

  1. Ekins S, In silico approaches to predicting metabolism, toxicology and beyond, Biochem Soc Trans, 31(Pt 3):611-4, 2003.

 

  1. Ekins S, Stresser DM and Williams JA, In vitro and pharmacophore insights for CYP3A enzymes, Trends Pharmacol Sci 24: 161-166, 2003.

 

  1. Bednarczyk D, Ekins S, Wikel JH and Wright SH, Influence of molecular structure of substrate binding to the human organic cation transporter, hOCT1. Mol Pharmacol 63: 489-498, 2003.

 

  1. Ekins S, Mirny L and Scheutz EG. A ligand-based approach to understanding selectivity of nuclear receptors PXR, CAR, FXR, LXRa and LXR Pharm Res 19: 1788-1800, 2002.

 

  1. Shimada J, Ekins S, Elkin C, Shaknovich EI and Wery J-P. Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs. Targets 1: 196-205, 2002.

 

  1. Young SS, Ekins S and Lambert G, So many targets, so many compounds, but so few resources. Curr Drug Disc, December: 17-22, 2002.

 

  1. Ekins S, Boulanger B, Swaan PW and Hupcey MAZ. Towards a new age of virtual ADME/TOX and multidimensional drug discovery. J Comp Aided Mol Design, 16: 381-401, 2002.

 

  1. Zhang EY, Knipp GT, Ekins S and Swaan PW, Structural biology and function of solute transporters: implications for identifying and designing substrates, Drug Metab Rev, 34: 709-750, 2002

 

  1. Ekins S and McGowan R, Postgraduate education and the changing interaction with the pharmaceutical industry: a cross-cultural perspective, Foundations of Science, 7: 413-424, 2002.

 

  1. Snyder R, Sangar R, Wang J and Ekins S. Three-dimensional quantitative structure activity relationship for CYP2D6 substrates. Quant Struct Act Relat 21: 357- 368, 2002.

 

  1. Ethell BT, Ekins S, Wang J and Burchell B. Quantitative structure activity relationships for the glucuronidation of simple phenols by expressed human UGT1A6 and UGT1A9. Drug Metab Dispos, 30: 734-738, 2002.

 

  1. Ekins S, Kim RB, Leake BF, Dantzig AH, Schuetz E, Lan LB, Yasuda K, Shepard RL, Winter MA, Wikel JH and Wrighton SA. Application of three dimensional quantitative structure activity relationships of P-glycoprotein inhibitors and substrates. Mol Pharmacol, 61: 974-981, 2002.

 

  1. Ekins S, Kim RB, Leake BF, Dantzig AH, Schuetz E, Lan LB, Yasuda K, Shepard RL, Winter MA, Wikel JH and Wrighton SA. Three dimensional quantitative structure activity relationships of inhibitors of P-glycoprotein. Mol Pharmacol, 61: 964-973 2002.

 

  1. Zhang EY, Phelps MA, Chang C, Ekins S and Swaan PW, Modeling of active transport processes, Adv Drug Del Rev., 54 :329-354 2002.

 

  1. Ekins S, Crumb WJ, Sarazan RD, Wikel JH and Wrighton SA. Three dimensional quantitative structure activity relationship for the inhibition of the hERG (human ether-a-gogo related gene) potassium channel. J Pharmacol Exp Thera, 301: 427-434 2002.

 

  1. Ekins, S and Schuetz EG. The PXR crystal structure: the end of the beginning. Trends Pharmacol Sci, 23: 49-50, 2002.

 

  1. Ekins, S and Erickson, JA. A preliminary pharmacophore for human pregnane-X-receptor ligands. Drug Metab Dispos, 30: 96-99, 2002.

 

  1. Gao F, Johnson DL, Ekins S, Janiszewski J, Kelly KG, Meyer RD and West M, Optimizing higher throughput methods to assess drug-drug interactions for CYP1A2, CYP2C9, CYP2C19, CYP2D6, rCYP2D6 and CYP3A4 in vitro using a single point IC50, J Biomol Screen, 7: 373-382, 2002.

 

  1. de Groot M and Ekins S, Pharmacophore modeling of human cytochrome P450s. Adv Drug Del Rev, 54: 367-383, 2002.

 

  1. Ekins S and Rose JP, In Silico ADME/TOX: The state of the art at the 220th ACS meeting, J Mol Graph, 20: 305-309, 2002.

 

  1. Ekins S, de Groot M and Jones JP, Pharmacophore and three dimensional quantitative Structure activity relationship methods for modeling cytochrome P450 active sites. Drug Metab Dispos, 29: 936-944, 2001.

 

  1. Ekins S and Wrighton SA, Application of in silico approaches to predicting drug-drug interactions: a commentary. J Pharm Tox Methods, 45: 65-69, 2001.

 

  1. Ekins S, Durst GL, Stratford RE, Thorner DA, Lewis R, Loncharich RJ and Wikel JH Three-dimensional quantitative structure activity relationship analysis of caco-2 permeability for a series of inhibitors of rhinovirus replication. J Chem Inf Comput Sci, 41: 1578-1586, 2001.

 

  1. Ekins S and McGowan R, The limits of reductionism: The shifting genomic paradigm’s impact on industry and academia, Philosophy in Science, 9: 179-202, 2001.

 

  1. Ekins S, Ring BJ, Grace J, McRobie-Belle DJ and Wrighton SA, Present and future in vitro approaches for drug metabolism. J Pharm Tox Methods, 44: 313-324, 2000.

 

  1. Ekins S, Waller CL, Swaan PW, Cruciani G, Wrighton SA and Wikel JH, Progress in predicting human ADME parameters in silico. J Pharm Tox Methods, 44; 251-272, 2000.

 

  1. Ekins S and Obach RS, Three dimensional-quantitative structure activity relationship computational approaches for prediction of human in vitro intrinsic clearance. J Pharmacol Exp Ther, 295: 463-473, 2000.

 

  1. Margolis JM, O’Donnell JP, Mankowski DC, Ekins S, Obach RS, R-, S-, and racemic fluoxetine are metabolized by multiple human cytochrome P450 enzymes in vitro. Drug Metab Dispos, 28: 1187-1191, 2000.

 

  1. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH and Wrighton SA, Three and four dimensional-quantitative structure activity relationship (3D / 4D-QSAR) analyses of CYP2C9 inhibitors. Drug Metab Dispos 28: 994-1002, 2000.

 

  1. Mankowski DC, Lawton MP and Ekins S, Characterisation of transgenic mouse strains using six human hepatic cytochrome P450 probe substrates. Xenobiotica, 30; 745-754, 2000.

 

  1. Mankowski DC, Laddison KJ, Christopherson PA, Ekins S, Tweedie DJ and Lawton MP, Molecular cloning, expression, and characterization of CYP2D17 from Cynomolgus monkey liver. Arch Biochem Biophys 372: 189-196, 1999.

 

  1. Ekins S, Bravi G, Ring BJ, Gillespie TA, Gillespie JS, VandenBranden M, Wrighton SA, Wikel JH, Three dimensional-quantitative structure activity relationship (3D-QSAR) analyses of substrates for CYP2B6. J Pharmacol Exp Ther, 288:21-29, 1999.

 

  1. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH, Wrighton SA. Three and four dimensional-quantitative structure activity relationship (3D / 4D-QSAR) analyses of CYP3A4 inhibitors. J Pharmacol Exp Ther, 290:429-438, 1999.

 

  1. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH, Wrighton SA. Three and four dimensional-quantitative structure activity relationship (3D / 4D-QSAR) analyses of CYP2D6 inhibitors. Pharmacogenetics, 9: 477-489, 1999.

 

  1. Ekins S, Wrighton SA, The role of CYP2B6 in human xenobiotic metabolism. Drug Metab Rev, 31: 719-754, 1999.

 

  1. Ekins S, Bravi G, Wikel JH, Wrighton SA. Three dimensional-quantitative structure activity relationship (3D-QSAR) analysis of CYP3A4 substrates. J Pharmacol Exp Ther, 291: 424-433, 1999.

 

  1. Ekins S, Ring BJ, Binkley SN, Hall SD, Wrighton SA, Autoactivation and activation of the cytochrome P450s. Int J Clin Pharmacol Ther 36: 642-651, 1998.

 

  1. Ekins S, VandenBranden M, Ring BJ, Gillespie JS, Yang TJ, Gelboin HV, Wrighton SA, Characterization of the expression in liver and catalytic activity of human CYP2B6. J Pharmacol Exp Ther 286: 1253-1259, 1998.

 

  1. VandenBranden M, Wrighton SA, Ekins S, Gillespie JS, Binkley SN, Ring BJ, Gadberry MG, Mullins DC, Strom SC, Jensen CB, Alterations of the catalytic activities of the drug metabolizing enzymes in cultures of human liver slices. Drug Metab Dispos, 26: 1063-1068, 1998.

 

  1. Ekins S, VandenBranden M, Ring BJ and Wrighton SA, Examination of purported probes of human CYP2B6. Pharmacogenetics 7: 165-179, 1997.

 

  1. Ekins S, Williams JA, Murray GI, Burke MD, Marchant NC, Engeset J and Hawksworth GM, Xenobiotic metabolism in rat, dog, and human precision-cut liver slices, freshly isolated hepatocytes, and vitrified precision-cut liver slices. Drug Metab Dispos 24: 990-995, 1996.

 

  1. Ekins S, Murray GI and Hawksworth GM, Ultrastructural and metabolic effects after vitrification of precision-cut rat liver slices with antifreeze proteins. Cryo-lett 17: 157-164, 1996.

 

  1. Ekins S, Vitrification of precision-cut rat liver slices. Cryo-lett 17: 7-14, 1996.

 

  1. Ekins S, Short term maintenance of phase I and II metabolism in precision-cut liver slices in dynamic organ culture. Drug Metab Dispos 24: 364-366, 1996.

 

  1. Ekins S, Past, present and future applications of precision-cut liver slices for in vitro xenobiotic metabolism Drug Metab Rev 28: 591-623, 1996.

 

  1. Ekins S, Murray GI, Burke MD, Williams JA, Marchant NC and Hawksworth GM, Quantitative differences in phase I and II metabolism between rat precision-cut liver slices and isolated hepatocytes. Drug Metab Dispos 23: 1274-1279, 1995.

 

Edited Books

 

  1. Ekins S, Hupcey MAZ and Williams AJ, Collaborative Computational Technologies for Biomedical Research, Series Editor Ekins S. John Wiley and Sons, July 2011. ISBN 978-0470638033.

 

  1. Ekins S and Xu JJ, Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools, Series Editor Ekins S, John Wiley and Sons. Hoboken, NJ. January 2009. ISBN 978-0-470-22555-4.

 

  1. Ekins S, Computational Toxicology: Risk Assessment For Pharmaceutical and Environmental Chemicals, Series Editor Ekins S. John Wiley and Sons, June 2007. ISBN 978-0-470-04962-4.

 

  1. Ekins S, Computer Applications in Pharmaceutical Research and Development, Series Editor Wang B, John Wiley and Sons, June 2006. ISBN 0-471-73779-8.

 

 

Edited Book Series

 

  1. Sasic S, Pharmaceutical Applications of Raman Spectroscopy, Series Editor Ekins S. John Wiley and Sons, November 2007.

 

  1. Yuryev A, Pathway analysis for drug discovery: computational infrastructure and applications, Series Editor Ekins S. John Wiley and Sons, September 2008

 

  1. Robson B and Baek OK, The Engines of Hippocrates: From the dawn of medicines to medical and pharmaceutical informatics, Series Editor Ekins S. John Wiley and Sons, 2009.

 

  1. Balakin K, Pharmaceutical Data Mining, approaches and applications for drug discovery, Series Editor Ekins S. John Wiley and Sons, December, 2009.

 

  1. Rosenberg MJ, The Agile Approach to Adaptive Research, Series Editor Ekins S. John Wiley and Sons, February, 2010.

 

  1. Babler S, Pharmaceutical and Biomedical Project Management in a Changing Global Environment, Series Editor Ekins S. John Wiley and Sons, September, 2010.

 

  1. Young DL and Michelson S, Systems Biology in Drug Discovery and Development, Series Editor Ekins S. John Wiley and Sons, July, 2011.

 

  1. Williams JA, Lalonde R, Koup JR and Christ DD, Predictive approaches in drug discovery and development: Biomarkers and in vitro/ in vivo correlations, Series Editor Ekins S. John Wiley and Sons, April, 2012.

 

  1. Chaguturu R, Collaborative Innovation in Drug Discovery, Strategies for public and private partnerships, Series Editor Ekins S. John Wiley and Sons, 2014

 

 

Book Chapters

 

 

  1. Ekins S, Clark AM, Dole K, Gregory K, McNutt AM, Coulon Spektor A, Weatherall C, Litterman NK and Bunin BA, Data mining and computational modeling of high throughput screening datasets, Submitted 2016

 

  1. Ekins S, Clark AM, Southan C, Bunin BA and Williams AJ, Small molecule bioactivity databases, Submitted 2016.

 

  1. Clark AM, Williams AJ and Ekins S, Mobile Apps for Green Chemistry, in Sustainable Inorganic Chemistry, ed Atwood, DA, Wiley, 2016.

 

  1. Clark, AM and Ekins S, The need for a green electronic lab notebook, in Green Chemistry Strategies for Drug Discovery, ed Peterson EA and Manley JB, RSC, 2015, pp185-211.

 

  1. Bunin BA and Ekins S, Academic, Commercial and Biodefense Case Studies for Collaborative Drug Discovery: Potential for Disrupting Drug Discovery, in Collaborative Drug Discovery: Strategies for Academic, Industry and Government Partnerships, ed Rathnam Chaturguru, Wiley, pp 303-317, 2014.

 

  1. Grulke CM, Clark AM, Ekins S, Williams AJ, Morris C, Goldsmith MR, Mobile Modeling in the Molecular Sciences. McGraw-Hill Yearbook of Science & Technology 2013 (and accessscience.com), p229-233.

 

  1. Ekins S and Bunin BA, Computational approaches and collaborative drug discovery for trypanosomal diseases.In Trypanosomatid diseases: Molecular routes to Drug discovery, Eds Timo Jäger, Oliver Koch and Leopold Flohė, Wiley-VCH, pp81-102.

 

  1. Bachmann K and Ekins S, The potential of In Silico and In Vitro approaches to predict In Vivo drug-drug interactions and ADME/TOX properties, In Williams JA, Lalonde R, Koup JR and Christ DD, Predictive approaches in drug discovery and development: Biomarkers and in vitro/ in vivo correlations, Editor Ekins S, John Wiley and Sons. Hoboken, NJ. 2012. pp307-330.

 

  1. Ekins S, Kortagere S, Krasowski MD, Williams AJ, Xu JJ and Zientek M, Ligand-based modeling of toxicity, In Davis A.M. and Livingstone D.J., Drug Design Strategies: Quantitative Approaches, Royal Society of Chemistry, Nov 2011, pp310-342.

 

  1. Ekins S, Williams AJ and Pikas CK, Collaborations in Chemistry, In Ekins S, Hupcey MAZ and Williams AJ, Collaborative Computational Technologies for Biomedical Research, Series Editor Ekins S. John Wiley and Sons, July 2011. pp85-98.

 

  1. Ekins S, Williams AJ and Hupcey MAZ, Standards for Collaborative Computational Technologies For Biomedical Research in Chemistry, In Ekins S, Hupcey MAZ and Williams AJ, Collaborative Computational Technologies for Biomedical Research, Series Editor Ekins S. John Wiley and Sons, July 2011. pp201-208.

 

  1. Ekins S, Hohman M and Bunin BA, Pioneering Use of the Cloud for the Development of the Collaborative Drug Discovery (CDD) database., In Ekins S, Hupcey MAZ and Williams AJ, Collaborative Computational Technologies for Biomedical Research, Series Editor Ekins S. John Wiley and Sons, July 2011. pp335-361.

 

  1. Williams AJ, Arnold RJG, Neylon C, Spencer R, Schürer S and Ekins S, Current and Future Challenges for Collaborative Computational Technologies for the Life Sciences., In Ekins S, Hupcey MAZ and Williams AJ, Collaborative Computational Technologies for Biomedical Research, Series Editor Ekins S. John Wiley and Sons, July 2011. pp491-517.

 

  1. Ekins S and Kortagere S, Computational pharmacophores for ADME/Tox Proteins, In Scheiber J and Jenkins J.L., In-silico Methods for Adverse Effect Prediction in Preclinical Drug Discovery, John Wiley and Sons. Hoboken, NJ. submitted, 2009

 

  1. Ekins S, Honeycutt JD and Metz JT, Multiobjective optimization for drug discovery, In Abraham, D.J. and Rotella, D.P., Burger’s Medicinal Chemistry, Drug Discovery and Development, 7th Edition, John Wiley & Sons, Inc. 2010, P259-277.

 

  1. Bahadduri PM, Polli JM, Swaan PW and Ekins S, Targeting drug transporters – combining in silico and in vitro approaches to predict in vivo, In Yan Q, Membrane Transporters in Drug Discovery and Development: Methods and Protocols, The Humana Press/ Springer Press, Totowa, NJ, 2010. Methods Mol Biol. 2010;637:65-103.

 

  1. Ekins S and Arnold RJG, Computer aided decision making from drug discovery to pharmacoeconomics, In, Arnold RJG. Pharmacoeconomics: from theory to practice CRC Press, P209—226, 2009.

 

  1. Krasowski, MD, Siam MG and Ekins S, Immunoassays for tricyclic antidepressants: Unsuitable for therapeutic drug monitoring?, In. Dasgupta A. Recent Advances in Chromatographic Techniques for Therapeutic Drug
    Monitoring; Edited by Amitava Dasgupta Recent Advances in Chromatographic Techniques for Therapeutic Drug Monitoring, CRC Press, P179-190, 2009.

 

  1. Ekins S and Scheiber J, Toxicity Pathways and Models: Mining for Potential Side Effects, in Ekins S and Xu JJ, Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools, Series Editor Ekins S, John Wiley and Sons. Hoboken, NJ. P135-153, 2009.

 

  1. Xu JJ, Ekins S, McGlashen M and Lauffenburger D, Future Perspectives of Biological Engineering in Pharmaceutical Research: The Paradigm of Modeling, Mining, Manipulation and Measurements in Ekins S and Xu JJ, Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools, Series Editor Ekins S, Wiley and Sons, P351-379, 2009.

 

  1. Ekins S, Drug transporter pharmacophores, in Ecker G and Chiba P, Transporters as drug carriers, Vol 33 of series Methods and Principles in Medicinal Chemistry John Wiley and Sons. Hoboken, NJ. P215-227, 2009.

 

  1. Ekins S and Abramovitz DL, A systems-biology view of drug transporters, in Ecker G and Chiba P, Transporters as drug carriers, Vol 33 of series Methods and Principles in Medicinal Chemistry, John Wiley and Sons. Hoboken, NJ. P365-385, 2009.

 

  1. Ekins S and Giroux C, Mammalian proteome and toxicant network analysis, in Yuryev A, Pathway analysis for drug discovery: computational infrastructure and applications, Series Editor Ekins S, John Wiley and Sons. Hoboken, NJ. P165-194, 2008.

 

  1. Ekins S, Application of QSAR to enzymes involved in toxicology, in Ekins S, Computational toxicology: Risk assessment for pharmaceutical and environmental chemicals, Series Editor Ekins S, John Wiley and Sons, Hoboken, NJ. p277-294, 2007.

 

  1. Aronov AM, Balakin KV, Kiselyov A, Varma-O’Brien S and Ekins S, Applications of computational methods to ion channels, in Ekins S, Computational toxicology: Risk assessment for pharmaceutical and environmental chemicals, Series Editor Ekins S, John Wiley and Sons, Hoboken, NJ. p353-390, 2007.

 

  1. Ekins S, Embrechts MJ, Breneman CM, Jim K and Wery J-P. Novel applications of kernel-partial least squares to modeling a comprehensive array of properties for drug discovery, in Ekins S, Computational toxicology: Risk assessment for pharmaceutical and environmental chemicals, Series Editor Ekins S, John Wiley and Sons, Hoboken, NJ. p403-432, 2007.

 

  1. Ekins S and Giroux C, Computers and systems biology for Pharmaceutical Research and Development, in Ekins S, Computer Applications in Pharmaceutical Research and Development, Series Editor Wang B, John Wiley and Sons, Hoboken, NJ. p139-165, 2006.

 

  1. Ekins S Computer methods for predicting drug metabolism, in Ekins S, Computer Applications in Pharmaceutical Research and Development, Series Editor Wang B, John Wiley and Sons, Hoboken, NJ. p445-468, 2006.

 

  1. Ekins S, Nikolsky Y, Bugrim A, Kirillov E and Nikolskaya T, Pathway Mapping Tools For Analysis of High Content Data, in Taylor DL, Haskins JA and Giuliano KA, High Content Screening: A Powerful Approach to Systems Cell Biology and Drug Discovery, (Methods Mol Biol:356), The Humana Press, Totowa, NJ p319-350, 2006.

 

  1. Chang C and Ekins S. Pharmacophores for human ADME/Tox related proteins, in Hoffman RD and Langer T, Pharmacophores and Pharmacophore Searches. Wiley-VCH, p299-324, 2006.

 

  1. Ekins S, Bugrim A, Nikolsky Y and Nikolskaya T, Systems biology: applications in drug discovery. In: Gad, S.C., Drug Discovery Handbook, John Wiley & Sons, Hoboken, NJ. p123-183, 2005.

 

  1. Ekins S, Berbaum J, Harrison RK, Zecher M, Yuan J, Ischchenko AV, Berezin K, Chubukov, V, Lawson D and Hupcey MAZ. Applying Computational and In Vitro Approaches To Lead Selection. In: Borchardt RT, Kerns EH, Lipinski CA, Thakker DR, Wang B, Pharmaceutical Profiling in Drug Discovery for Lead Selection. AAPS Press p361-389, 2004.

 

  1. Ekins S, Ring BJ, Bravi G, Wikel JH and Wrighton SA, Predicting drug-drug interactions in silico using pharmacophores: a paradigm for the next millennium. In: Guner OF, Pharmacophore perception, development, and use in drug design. IUL, San Diego, pp 269-299, 2000.

 

  1. Ekins S, Mäenpää J and Wrighton SA, In vitro metabolism: Subcellular fractions. In: Woolf TF, Handbook of drug metabolism. Marcel Dekker Inc, New York, pp 363-399, 1999.

 

Editorials

  1. Ekins S. Disrupting Drug Discovery with alternative business models, Drug Discovery Today, Editors Choice February 2013. http://www.drugdiscoverytoday.com/view/30121/disrupting-drug-discovery-with-alternative-business-models/

 

  1. Ekins, S. In: Annual Review 2011, Royal Society of Chemistry, p22 http://www.rsc.org/images/AnnualReview2011_tcm18-219895.pdf

 

  1. Williams AJ and Ekins S, The long term cost of inferior database quality. Drug Discovery Today, Editors Choice January 2012. http://www.drugdiscoverytoday.com/view/22579/the-long-term-cost-of-inferior-database-quality/

 

  1. Williams AJ and Ekins S. A Quality Alert and Call for Improved Curation of Public Chemistry Databases, Drug Disc Today, 16: 747-750, 2011.

 

  1. Bunin BA and Ekins S, Alternative business models for drug discovery, Drug Disc Today, 16: 643-645, 2011.

 

  1. Williams AJ and Ekins S, Invited editorial for Drug Discovery Today, Editors Choice – Drug Metabolism, Jan 2010 http://csemails.elsevier.com/DDT/jan2010/

 

  1. Bingham A and Ekins S, Competitive Collaboration in the Pharmaceutical and Biotechnology Industry, Drug Disc Today, 14, 1079-1081, 2009.

 

  1. Ekins S, ChemSpider, Chemistry World, October 70, 2009.

9.    Ekins S, J Pharm Tox Methods, 53:30, 2006.

10. Ekins S, Invited editorial for Drug Discovery Today, Editors Choice – Drug Metabolism, July 2006. http://www.drugdiscoverytoday.com/echoice/jul2006/

Responses to Articles

1.    Ekins S and Williams AJ, Reengineering Translational Science: Is the NIH the right place for this? http://stm.sciencemag.org/content/3/90/90cm17.full/reply#scitransmed_el_423

 

Abstracts

 

 

 

 

  1. Ekins S, Using machine learning models based on phenotypic data to discover new molecules for neglected diseases, ACS San Diego 2016

 

  1. Ekins S and Bunin BA, From CDD Vault, CDD Vision to CDD Models: software for biologists and chemists doing drug discovery, ACS San Diego 2016

 

  1. Wood J, Moen D.R. Ekins S, Virtual Collaborations for Developing Sanfilippo Syndrome Treatments on a Shoestring, ACS San Diego 2016

 

  1. Handelin B, Basile RA, Ekins S et al., How rare peripheral neuropathy disease patient organizations can bridge from academic research to a drug candidate, J Peripheral Nerve System 20: 154-155, 2015

 

  1. Sames L, Moore A and Ekins S, Global Registry for inherited neuropathies (GRIN), J Peripheral Nerve System 20: 225, 2015

 

  1. Ekins S*, Madrid PB*, Sarker M, Li S-G, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M and Freundlich JS*. Combining metabolite-based pharmacophores with Bayesian machine learning models for Mycobacterium tuberculosis drug discovery, SERMACS, Memphis Nov 2015.

 

  1. Ekins S, Coulon-Spektor A, Gregory K, Weatherall C, Dole K, McNutt A, Nyberg P, Gilligan T, Ba X, Holtz B, Ernst S, Cole F, Navre M, Clark AM and Bunin BA, CDD: Vault, CDD: Vision and CDD: Models for Drug Discovery Collaborations, SERMACS, Memphis Nov 2015.

 

  1. McNutt AM, Ekins S, Gregory K, CDD Vision: A New Reactive Web Platform for Multidimensional Drug Discovery Data Mining and Visualization, SERMACS, Memphis Nov 2015.

 

  1. Ekins S, De Siqueira JL, McCall L-I, Sarker M, Yadav M, Ponder EL, Kallel A, Bunin BA, McKerrow J and Talcott C. Applying cheminformatics and bioinformatics approaches to neglected tropical disease big data, ACS August 2015.

 

  1. Clark AM, Dole K, Coulon-Spector A, McNutt A, Grass G, Freundlich JS, Reynolds RC and Ekins S, Development and sharing of ADME/Tox and Drug Discovery machine learning models, ACS August 2015.

 

  1. Ekins S, Making it Open – Putting cheminformatics to use against the Ebola virus, ACS August 2015.

 

  1. Clark AM and Ekins S, Mining Big Datasets to Create and Validate Machine Learning Models, ACS August 2015.

 

  1. Ekins S and Wood J, Starting Small Companies Focused on Rare Diseases, ACS August 2015.

 

  1. Ekins S, Clark AM, Polli JE and Wright SH, Mobile Apps for Transporter Drug-Drug Interaction Prediction – A Tool of the Future, now, ACS August 2015.

 

  1. Ekins S, Clark AM, Reynolds RC and Freundlich JS, Using Bayesian machine learning for bioactivity and target prediction for Mycobacterium Tuberculosis. Gordon Research Conference on Tuberculosis, July 2015

 

  1. Perryman AL, Wang X, Li S-G, Paget SD, Stratton TP, Olson AJ, Ekins S and Freundlich JS, A novel approach to biological target-guided chemical tools and its application to Mycobacterium tuberculosis. Gordon Research Conference on Biorganic Chemistry, June 2015.

 

  1. Ekins S and Wood J, Phoenix Nest: Starting a small company focused on Sanfilippo syndrome, Molecular Genetics and Metabolism, 114: S40-S41, 2015.

 

  1. Wood J, Siedman S, Siedman J, Levy P, Brown K, McBride K, Flanigan K, Marques R, Feldman A, Plecha R and Ekins S, Sanfilippo syndrome registry project and natural history studies: an example of patients, parents and researchers collaborating for a cure. Orphanet J Rare Dis 9: (Suppl 1), p7, 2014

 

  1. Ekins S, Clark AM and Freundlich JS, Collaborative sharing of molecules and data in the mobile age, ACS – San Francisco 2014.

 

  1. Ekins S, Freundlich JS, Sarker M, Talcott C, Madrid P, Bunin BA and Lamichhane G, Expanding the metabolite mimic approach to identify hits for Mycobacterium tuberculosis, ACS – San Francisco 2014.

 

  1. Ekins S, Clark AM, Wood J, Sames L and Moore A. Why there needs to be open data for ultrarare and rare disease drug discovery, ACS – San Francisco 2014.

 

  1. Ekins S, Progress in computational toxicology, ACS – San Francisco 2014.

 

  1. Ekins S, and Clark AM, Examples of how to inspire the next generation to pursue computational chemistry/cheminformatics, ACS – San Francisco 2014.

 

  1. Ekins S, Applying computational models for transporters to predict toxicity, ACS – San Francisco 2014.

 

  1. Ekins S, Clark AM, Sarker M, New target prediction and visualization tools incorporating open source molecular fingerprints for TB mobile version 2, ACS – San Francisco 2014.

 

  1. Ekins S, Pottorf R, Reynolds RC, Williams AJ, Clark AM, Freundlich JS, Looking back at Mycobacterium tuberculosis mouse efficacy testing to move new drugs forward, ACS – Dallas 2014

 

  1. Ekins S, Wood J, Sames L, Moore A and Clark AM, Creating champions for open source rare disease drug discovery with an App, Mol Genetics and Metabolism 111: S40, 2014

 

  1. Clark AM, Williams AJ and Ekins S, Cheminformatics workflows using mobile apps for drug discovery, SLAS – San Diego 2014.

 

  1. Ekins S, Freundlich JS and Reynolds RC, Dual response and dataset fusion for machine learning models for hit to lead optimization in Mycobacterium tuberculosis Drug discovery. SLAS – San Diego 2014

 

  1. Ekins S, Reynolds RC, Wan B, Franzblau SG, Freundlich JS and Bunin BA, Enhancing High Throughput Screening For Mycobacterium tuberculosis Drug Discovery Using Bayesian Models, ACS – New Orleans 2013

 

  1. Ekins S, Clark AM, Sarker M, Talcott C and Bunin BA,TB Mobile: Appifying Data on Anti-tuberculosis Molecule Targets, ACS – New Orleans 2013

 

  1. Ekins S, Reynolds RC, Kim H, Koo M-S, Ekonomidis M, Talaue M, Paget SD, Woolhiser LK, Lenaerts AJ, Bunin BA, Connell N and Freundlich JS, Dual-event Machine Learning Models to Accelerate Drug Discovery, ACS – New Orleans 2013

 

  1. Southan C, Williams AJ and Ekins S, Challenges and Recommendations for Obtaining Chemical Structures of Industry-Provided Repurposing Candidates, ACS – New Orleans 2013

 

  1. Ekins S, Olechno J, Williams AJ, Dispensing Processes Profoundly Impact Biological Assays and Computational and Statistical Analyses, ACS – New Orleans 2013

 

  1. Ekins S, Clark A and Wood J, Raising awareness of the rare disease Sanfilippo syndrome type C using the Open Drug Discovery teams (ODDT) mobile app. Mol Genetics and Metabolism 108: S36-S40, 2013.

 

  1. Ekins S and Williams AJ, Collaborative Computational Technologies for Biomedical Research: An Enabler Of More Open Drug Discovery, ACS –[107] San Diego, 2012.

 

  1. Ekins S and Williams AJ, Finding Promiscuous Old Drugs for new uses, ACS –[23] San Diego, 2012.

 

  1. Williams AJ, Ekins S, Clark AM, Mobile Apps for drug discovery, ACS –[70] San Diego, 2012.

 

  1. Williams AJ and Ekins S, Towards a Gold standard: Improving the quality of public domain chemistry databases, ACS –[129] San Diego, 2012.

 

  1. Sarker M, Talcott C, Madrid P, Chopra S, Bunin BA, Lamichhane G, Freundlich JS and Ekins S, Combining Cheminformatics Methods and Pathway Analysis To Identify Molecules With Whole-Cell Activity Against Mycobacterium tuberculosis ACS –[524] San Diego, 2012

 

  1. Ekins S, Dole K, Spektor A, Gregory K, Blondeau D, Ernst S, Hohman MM, and Bunin BA, Collaborative Drug Discovery: A platform for transforming Tuberculosis R&D and beyond. Keystone Symposia Tuberculosis: Immunology, cell biology and novel vaccination strategies. Jan 15-20, Fairmont Hotel Vancouver, Vancouver, British Columbia, Canada. 2011.

 

  1. Lamichhane G, Freundlich, JS, Ekins S, Wickramaratne N, Nolan S, Bishai WR, Essential Metabolites of M. tuberculosis and their Molecular Mimics. Keystone Symposia Tuberculosis: Immunology, cell biology and novel vaccination strategies. Jan 15-20, Fairmont Hotel Vancouver, Vancouver, British Columbia, Canada. 2011.

 

  1. Dehal, SS, Gangl E, Perloff ES, Mason AK, Blanchard AP, Ekins S and Stresser DM. The alcohol withdrawal agent clomethiazole is a time-dependent inhibitor of CYP2E1, ISSX 2010

 

  1. Pan Y, Li L, Ekins S, Wang H and Swaan P, Rational Identification of hPXR Activators by Integrated Structure and ligand Based Strategies, AAPS 2010.

 

  1. Krasowski MD, Ekins S, Kortagere S.  Prediction of Immunoassay Cross-Reactivity Using Chemoinformatic Methods.  Academy of Clinical Laboratory Physicians and Scientists Annual Meeting, Nashville, TN, June 2010.  Published in Am J Clin Pathol 2010;134:502.

 

  1. Gupta RR, Gifford EM, Liston T, Waller C, Bunin BA and Ekins S, Using open source descriptors and algorithms for modeling ADME properties, ACS Boston 2010.

 

  1. Ekins, S, Bradford J, Dole, K, Spektor A, Gregory K, Blondeau D, Ernst S, Hohman M and Bunin BA, Collaborative Drug Discovery: A platform for transforming neglected disease R&D and beyond, ACS Boston 2010.

 

  1. Ekins, S, Bradford J, Dole, K, Spektor A, Gregory K, Blondeau D, Hohman M and Bunin BA, Collaborative database and computational models for tuberculosis drug discovery decision making, ACS Boston 2010.

 

  1. Lamichane G, Freundlich JS, Ekins S, Wickramaratne N and Bishai WR, Essential metabolites of M. Tuberculosis and their molecular mimics as therapeutic agents, ACS Boston 2010.

 

  1. Simon A, Zsoldos Z, Ravitz O, Williams AJ and Ekins S, LASSO-ing potential pregnane X receptor agonists, ACS Boston 2010.

 

  1. Zheng X, Ekins S, Polli JE. In Vitro and Pharmacophore Based Discovery of FDA Approved Drugs Includes Calcium Channel Blockers and HMG CoA-Reductase Inhibitors that Inhibit human Apical Sodium-dependent Bile Acid Transporter (hASBT). AAPS Annual Meeting, Nov 2009, Los Angeles, CA.

 

  1. Zheng X, Ekins S, and Polli JE. Discovery of FDA Approved Drugs that are hASBT Inhibitors. AAPS Workshop on Evolving Science and Technology in Physical Pharmacy and Biopharmaceutics. May, 2009. Baltimore, MD; AAPS Workshop on Drug Transporters in ADME: From the Bench to the Bedside. Apr, 2009. Baltimore, MD.
  2. Ekins S, Reschly, Hagey LR and Krasowski MD, Evolution of pharmacologic specificity and species differences in the Pregnane X Receptor, Drug Metab Rev 41 Supplement 1: Abstract 30, 2009.

 

  1. Ekins S, Hohman M, Ernst S, Gregory K and Bunin B, Global launch of the collaborative drug discovery TB researcher network, Keystone Symposia, Tuberculosis: biology, pathology and therapy, Abstract 149, 2009.

 

  1. Ekins S, Hohman M and Bunin B, A new collaborative web-based database for the tuberculosis research community, Keystone Symposia, Tuberculosis: biology, pathology and therapy, Abstract 204, 2009.

 

  1. Welsh WJ, Ekins S, Chekmarev D, Kortagere S and Kholodvych V, Shape Signatures: an integrated computational platform useful for defense applications, CBDPST 2008.

 

  1. Diao L, Ekins S and Polli JE, Inhibition Requirements of Human Organic Cation/Carnitine Transporter (OCTN2). AAPS 2008.

 

  1. Krasowski MD and Ekins S, Increasing Limitations of Drug Screens in an Era of Expanding Molecular Diversity. Academy of Clinical Laboratory Physicians and Scientists. 2008.

 

  1. Marcus P, Arnold RJG, Ekins S, Sacco P, Massanari M, Donohue J and Bukstein D. Treatment patterns and asthma control among US allergy and pulmonary community practices: Results of the CHARIOT study. American Academy of Allergy Asthma and Immunology, 2008.

 

  1. Balakin K, Ekins S, Savchuk NP and Ivanenkov YA, New insights for hERG inhibition using mapping techniques. CMPTI, Russia, 2007.

 

  1. Olinga P, Ekins S, Elferink M.G.L., Bauerschmidt S, Polman J, Schoonen WGEJ, Draaisma AL, Merema MT and Groothuis G.M.M. Gene network analysis of acetaminophen and carbon tetrachloride treated rat liver slices identifies hepatotoxicity mechanisms observed in vivo. Drug Metab Rev: 39, S1, 1-388, 2007.

 

  1. Bahadduri PM, Chang C, Ekins S and Swaan PW; Integrated Approach to Identify novel P-glycoprotein Substrates and Inhibitors. Experimental Biology Meeting, Washington, DC, 2007.

 

  1. Bahadduri PM, Chang C, Swaan PW and Ekins S Application of integrated computational pharmacophore models and in vitro approaches to rapidly identify P-glycoprotein ligands. AAPS 2006.

 

  1. Chang C, Bahadduri PM, Swaan PW and Ekins S; Application of Integrated Pharmacophore Models and In Vitro Approaches to Rapidly Identify Novel P-glycoprotein Ligands; 231st ACS Atlanta, GA, 2006.

 

  1. Chang C, Bahadduri P, Polli JE, Swaan PW and Ekins S, Application of pharmacophore models to rapidly identify novel P-glycoprotein ligands. ISSX 2006.

 

  1. Ekins S, Fisher MB, Jolivette L, Mahmood I, Testa B, Tucker GT, & Obach RS. (2006, January). Debate: In vivo versus in vitro versus in silico: What is the best way to predict the human pharmacokinetics for new compounds?. In DRUG METABOLISM REVIEWS (Vol. 38, pp. 25-26).

 

  1. Ekins S, Jones DR, Li L and Hall SD, Computational approaches that predict metabolic intermediate complex formation with CYP3A4. ACS San Francisco 2006.

 

  1. Ekins S, Computational Prediction of Human Drug Metabolism. Drugs Fut 31 (suppl A) L65, 2006.

 

  1. Ekins S, Andreyev S, Ryabov A, Kirillov E, Rakhmatulin EA, Sorokina S, Bugrim A, Nikolskaya T. A combined quantitative structure activity relationship and systems biology approach to drug metabolism and toxicity assessment. SOT 2006.

 

  1. Bahadduri PM, Johnston J, D’Souza VM, Ray A, Swaan PW and Ekins S; Identification of novel hPEPT1 inhibitors by in vitro and pharmacophore based approaches. AAPS Workshop on Drug Transporters in ADME: From the Bench to the Bedside, Parsippany, NJ, USA. 2005

 

  1. Bahadduri P, Chang C, Swaan P and Ekins S. Rapid identification of molecules with affinity for P-glycoprotein by pharmacophore modeling and in vitro screening. AAPS 2005.

 

  1. Ekins S. In silico toxicity prediction, Drug Metab Reviews, 37 Suppl 1, 30. 2005.

 

  1. Ekins S, Giroux C, Nikolsky Y, Bugrim A and Nikolsyaka T. A signature gene network approach to toxicity. SOT 2005.

 

  1. Giroux C, Ekins S, Fan J, Abdullah I, Nikolsky Y, Bugrim A and Nikolskaya T. A genetic network approach to comparative toxicogenomics and risk assessment: the oxidative stress response. SOT 2005.

 

  1. Ekins S, Progress in computational modeling of P-glycoprotein. ACS, San Diego 2005.

 

  1. Chang C, Pang KS, Ekins S and Swaan P. Comparative pharmacophore modeling of organic anion transporting polypeptides: a meta-analysis of rat Oatp1a1, human OATP1A2 and OATP1B1. ACS, San Diego 2005.

 

  1. Chang C, Ekins S and Swaan P. Application of P-gp Pharmacophore Models in Database Screening ACS, San Diego 2005.

 

  1. Ekins S, Bugrim A, Nikolsky YV and Nikolskaya, T. “Network signatures” as predictors of cell response to chemical treatments. IBC 9th Annual World Congress, Drug Discovery technology 2004.

 

  1. Balakin KV, Ekins S, Bugrim A, Ivanenkov YA, Korolev D, Nikolsky YV, Skorenko AV, Ivashchenko AA, Savchuk NP and Nikolskaya Kohonen self organizing maps and neural networks for predicting human CYP affinity and rate of metabolism Drug Metab Rev 36:67, 2004.

 

  1. Jones DR, Ekins S and Hall SD. Computational approaches that predict metabolic intermediate complex formation with CYP3A4. Drug Metab Rev 36:284, 2004.

 

  1. D’Souza VM, Johnston J, Bahadurri P, Ray A, Swaan PW and Ekins S. In vitro and pharmacophore based discovery of novel hpept1 inhibitors. Drug Metab Rev 36:258, 2004.

 

  1. Ekins S, Williams JA and Stresser DM. Pharmacophore insights into the active sites of the CYP3A enzymes. The Pharmacologist 44: (suppl) 114.4, 2002.

 

  1. Ekins S, Snyder R, Sanger R, Jones DR, Hall SD, Lewis RA, Wikel JH and Wrighton SA. QSAR and pharmacophore models for the prediction of cytochrome P450 substrate and inhibitor specificity. Drug Metab Revs 33: 22, 2001.

 

84. Ekins S, Kim RB, Dantzig AH, Schuetz EG, Leake BF, Lan L-B, Yasuda K, Shepard RL, Winter MA, Wikel JH and Wrighton SA. Multiple P-glycoprotein pharmacophore models for inhibition of binding and transport. Drug Metab Revs 33: 178, 2001.

 

85. Ekins S and McGowan RJ. Investigating the feminist standpoint in modern science. ILS 12th Interdisciplinary conference on Science and Culture, Kentucky State University, 2001.

 

86. Ekins S, Durst GL, Stratford RE, Thorner DA, Lewis R, Loncharich RJ and Wikel JH Multiple 3D-QSAR approaches for prediction of Caco-2 permeability for rhinovirus replication inhibitors. Drug Metab Revs 33: 301, 2000.

 

  1. Ekins S, Molecular modeling – shifting the drug metabolism paradigm. ISSX training course, Indianapolis 2000.

 

  1. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH and Wrighton SA.

Present and future applications of pharmacophores for prediction of CYP drug-drug interactions. Drug Metab Revs 33: 140, 2000.

 

  1. Margolis JM, O’Donnell JP, Mankowski DC, Ekins S, Obach RS, R-, S-, and racemic fluoxetine are metabolized by multiple human cytochrome P450 enzymes in vitro. Drug Metab Revs 33: 250, 2000

 

  1. Johnson DL, Kelly KG, Gao F, Meyer RD, Morris JC, Ekins S and West M, Single point screening for high throughput methods to predict drug-drug interaction potential. Drug Metab Revs 33: 185, 2000.

 

  1. Ekins S and Obach RS, Computational approaches for prediction of human in vitro intrinsic clearance, ACS August 2000

 

  1. Mankowski DC and Ekins S, Characterization of hepatic cytochrome P450 activities in transgenic mouse strains, ISSX Proceedings 15: 322, 1999.

 

  1. Ekins, S and McGowan, R, Postgraduate education and the changing interaction with the pharmaceutical Industry: a cross-cultural perspective. ILS 10th Interdisciplinary conference on Science and Culture, Kentucky State University, 1999.

 

  1. Ekins S, Bravi G, Wikel JH and Wrighton SA, Three dimensional quantitative structure activity relationship (3D-QSAR) analysis of CYP3A4 substrates. 28th Annual Gordon Research Conference on Drug Metabolism A40, 1998.

 

  1. Ekins S, The limits of reductionism: The shifting genomic paradigm’s impact on industry and academia, ILS 9th Interdisciplinary conference on Science and Culture, Kentucky State University, 1998.

 

  1. Wrighton SA, Maenpaa, J, Ekins S. The CYP3A family. Pharmacological and toxicological implications. Microsomes and Drug Oxidations, Montpellier, France, 1998.

 

  1. Ekins S, Binkley S, Gillespie JS, VandenBranden M, Ring BJ, Wikel JH and Wrighton SA, Preliminary inhibitor pharmacophores for human CYP’s, ISSX Proceedings 12: 314,

 

  1. Ekins S, VandenBranden M, Gillespie JS, Ring BJ, Wrighton SA and Wikel JH, A preliminary substrate pharmacophore for CYP2B6, ISSX Proceedings 12: 125, 1997.

 

  1. Wrighton SA, Ekins S. The examination of in vitro probes reported to be selective for human CYP2B6, ISSX Proceedings 12; 22, 1997.

 

  1. Jensen CB, Gadberry MG, Mullins DC, Gillespie JS, VandenBranden MR, Ekins S, Horn JW, Meador VP and Wrighton SW, Alterations in the catalytic activities of drug metabolizing enzymes in long-term cultures of precision-cut liver slices, ISSX Proceedings 12: 328,

 

  1. VandenBranden MR, Wrighton SA, Gillespie JS, Binkley SN, Ekins S, Ring BJ, Gadberry MG, Mullins DC, Strom SC and Jensen CB, Alteration of the drug metabolizing enzymes in human liver slice culture over 96 hours, ISSX Proceedings 12; 331,

 

  1. Ekins S, VandenBranden M, Ring BJ and Wrighton SA, Kinetic and inhibition characteristics of CYP2B6. ISSX Proceedings 10: 232,1996.

 

  1. Ekins S, Murray GI, Watson RD, Merle O, Hawksworth GM and Burke MD, A new substrate for the fluorescence detection of cytochrome P450 activity in individual cells. Hum Exp Toxicol 15: 147, 1996.

 

  1. Ekins S, Murray GI, Burke MD, Marchant NC and Hawksworth GM, Quantitative differences in xenobiotic metabolism by precision-cut liver slices and isolated hepatocytes. ISSX Proceedings 8: 419, 1995.

 

  1. Ekins S, Murray GI, Burke MD, Marchant NC and Hawksworth GM, Epoxidation, diol formation and glutathione conjugation in rat hepatocytes and precision-cut liver slices. Br J Clin Pharmacol 40: 180P, 1995.

 

  1. Ekins S, Murray GI, Marchant NC, Burke MD and Hawksworth GM, Qualitative and quantitative comparison of testosterone hydroxylation and 7-ethoxycoumarin O-deethylation in Sprague Dawley rat hepatocytes and precision-cut liver slices. Br J Clin Pharmacol 38: 164-165P, 1994.

 

  1. Ekins S, Collins GC, Newlands AJ, Williams JA, Marchant NC, Lucas C and Hawksworth GM, The role of cytochrome P4503A in the metabolism of the vinca alkaloid a-aminophosphonate derivative S12363 by human liver microsomes. Br J Clin Pharmacol 36: 165-166P, 1993.

 

 

Interviews

 

  1. Cressey D, Data Sharing aids in the fight against malaria, Nature 14 Feb 2012 doi:10.1038/nature.2012.10018
  2. Jarvis LM, Orphans find a home, C&E News, May 13 2013, 10-23
  3. Marx V, Pouring Over liquid handling, Nature Methods, 11, 33-38, 2014 http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2785.html
  4. Extance A, Robot scientist discovers potential malaria drug, Scientific American, 5th Feb 2015, http://www.scientificamerican.com/article/robot-scientist-discovers-potential-malaria-drug/
  5. Steinmark IE, Expert wiki to expose low-quality chemical probes, ChemistryWorld, 21 July 2015  http://www.rsc.org/chemistryworld/2015/07/expert-wiki-expose-low-quality-chemical-probes
  6. Willyard C, Foretelling toxicity: FDA researchers work to predict risk of liver injury from drugs, Nature Medicine, 22: 450-451, 2016

 

Other publication roles

Organized a special issue for the Journal of Pharmacological and Toxicological Methods “OMICs and beyond: new technologies applied to toxicology” published in Jan 2006.

 

Editing a multivolume series for John Wiley and Sons “Technologies for the Pharmaceutical Industry.

 

Oral Presentations

April 1995                  British Pharmacological Society, Canterbury University.

May 1995                   Scottish and Newcastle Drug Metabolism Group, Strathclyde                                               University, Glasgow.

August 1995             4th International ISSX Meeting, Seattle.

September 1995       British Toxicological Society, New College, Oxford University.

Hepatocyte User Group, Glasgow University.

Drug Metabolism Discussion Group, Loughborough University.

September 1997       Midwest Cytochromes P450 Symposium, Purdue University.

October 1997            8th North American ISSX Meeting, Hilton Head.

April 1998                  ILS 9th Interdisciplinary conference on Science and Culture,

Kentucky State University

April 1999                  ILS 10th Interdisciplinary conference on Science and Culture, Kentucky State University

Sept 2001                  Midwest Cytochromes P450 Symposium, Purdue University.

Invited Seminars

December 1995        The University of Groningen, The Netherlands.

March 1999               US Catalyst User Group, San Diego.

April 1999                  MSI Seminar Series, Boston

July 1999                   QSAR Gordon Conference, Tilton School, New Hampshire.

August 1999             Screen 99- High Throughput Screening Technologies, San Diego.

August 1999             Glaxo Wellcome, Ware, UK.

October 1999            UK Catalyst User Group Meeting, Cambridge, UK.

July 2000                   Drug Metabolism Gordon Conference, New Hampshire.

August 2000             ACS meeting, Washington DC.

September 2000       New technologies to increase drug candidate survivability, Philadelphia

October 2000            Ohio State University, Dept of Pharmaceutics (Dr Peter Swaan)

October 2000            10th North American ISSX Meeting, Indianapolis (2 presentations)

November 2000        EUFEPS Meeting Basle, Switzerland.

November 2000        University of Connecticut, Department of Pharmacology, Farmington.(Prof Schenkman)

November 2000        North Jersey ACS Drug Metabolism Discussion Group Fall Symposium, Somerset, NJ

February 2001          Computational early ADME, Tokyo

June 2001                 EUFEPS World Conference on drug absorption and drug delivery, Copenhagen

October 2001            European ISSX, Munich, Germany

November 2001        Ohio State University, Dept of Pharmaceutics (Dr Peter Swaan)

November 2001        Predictive and Emerging technologies for lead selection and optimization, IBC conference, San Diego (2 presentations)

February 2002          University of California at Davis, Biotechnology seminar (Prof Bruce Hammock)

March 2002               University of Iowa, Medicinal Chemistry Seminar (Prof Michael Duffel)

May 2002                   US Catalyst User Group, Princeton

June 2002                 Predictive Toxicology, CBI Conference, Philadelphia

July 2002                   IUPHAR World congress of Pharmacology, San Francisco

November 2002        Ohio State University, Dept of Pharmaceutics (Dr Peter Swaan)

November 2002        Japanese Catalyst User Group, Tokyo.

December 2002        Predictive Toxicology, IBC conference, Philadelphia

February 2003          Biochemistry Society, Loughborough, UK.

February 2003          Accelrys World, San Diego, USA

April 2003                  University of Pennsylvania (lecture to graduate organic chemists on ADME/Tox)

May 2003                   ADMET in the 21st Century, ACS Prospectives, St. Petersburg, Tampa

May 2003                   AAPS Workshop on pharmaceutical profiling in drug discovery for lead selection, Whippany, NJ.

June 2003                 Beyond Genome 2003, CHI Conference, San Diego

June 2003                 North Jersey ACS Drug Metabolism Discussion Group, Somerset, NJ.

Sept 2003                  Maximize Phase I trials, CBI Conference, Washington, DC.

Oct 2003                    US Catalyst User Group, Johnson & Johnson, PA.

January 2004           Temple University, School of Pharmacy, PA.

March 2004               Rensselaer Polytechnic Institute, Department of Chemistry Seminar series (Prof Alan Cutler)

March 2004               ADME, Vision in Business, London.

March 2004               Pfizer, Sandwich, UK.

April 2004                  University of Toledo (Prof  Paul W. Erhardt)

May 2004                   Accelrys Life Science seminar, Boston, MA.

May 2004                   Rib-X, New Haven, CT.

May 2004                   University of Maryland, Baltimore, MD (Dr. Peter Swaan)

June 2004                 ACS meeting, Indianapolis, IN.

June 2004                 University of Toronto (Prof. K. Sandy Pang)

June 2004                 IBC Conference, London

October 2004            University of Utah (Prof. David Moody)

November 2004        IUPUI School of Bioinformatics (Dr. David Wild)

November 2004        AAPS National Meeting, Baltimore, MD

November 2004        CHI, Idiosyncratic Toxicity: Understanding, Prediction and Prevention, Philadelphia

December 2004        3rd Annual Drug Discovery and Development Summit, Institute for Scientific Exchange, San Diego, CA.

December 2004        New Jersey Drug Metabolism Discussion Group, Langhorne, PA

December 2004        CHI Metabolic Profiling: pathways in discovery, Lake Buena Vista, FL.

March 2005               ACS, San Diego, CA.

March 2005               SOT, New Orleans.

March 2005               Cyprotex Drug Discovery Workshop, Cambridge, MA.

June 2005                 The University of Groningen, The Netherlands (Dr. Peter Olinga).

June 2005                 European ISSX, Nice, France

June 2005                 North Jersey ACS Drug Metabolism Discussion Group, Somerset, NJ

August 2005             IBC DDT 2005, Boston MA

November 2005        AAPS, Nashville, TN. (2 presentations)

November 2005        IUPUI School of Bioinformatics (Dr. David Wild)

Feb 2006                   ECVAM Workshop on Molecular Modeling Approaches for Human Hazard Assessment of Chemicals, Ispra, Italy

March 2006               BioFocus meeting, San Francisco

May 2006                   New York Academy of Sciences, Predictive Toxicology Discussion Group, NY. http://www.nyas.org/ebriefreps/main.asp?intEBriefID=585

May 2006                   Great Lakes Regional ACS, Milwaukee, WI.

June 2006                 CHI Structure based drug design, Boston, MA. (Roundtable) http://www.pharmadd.com/archives/Nov_2006/TT_Structure_Based_Drug_Design.asp

July 2006                   Chem-Bio Informatics (CBI) society, Tokyo, Japan

August 2006             The XIXth International Symposium on Medicinal Chemistry ISMC-2006, Istanbul, Turkey.

September 2006       ACS meeting, San Francisco, CA

October 2006            North American ISSX, Puerto Rico (Debate speaker)

November 2006        PKUK meeting, Sheffield, UK

December 2006        IUPUI School of Bioinformatics (Dr. David Wild)

February 2007          Mt Sinai School of Medicine, New York, NY

April 2007                  SIMCYP Seminar, Baltimore, MD

April 2007                  Pharmaceutical Sciences World Congress, Amsterdam, The Netherlands.

May 2007                   International Science Forum on Computational Toxicology, RTP, NC. (session co-chair)

Oct 2007                    North Jersey ACS Drug Metabolism Discussion Group Fall Symposium, Somerset, NJ

Toxicology Seminar series UNC (Dr’s Ivan Rusyn and Alex Tropsha)

Accelrys Science Forum, Boston & Princeton.

Dec 2007                   IUPUI School of Bioinformatics (Dr. David Wild)

April 2008                  EbCTC Systems Toxicology Symposia, Piscataway, NJ

May 2008                   AAPS meeting San Mateo, CA

July 2008                   Microsomes and Drug Oxidations, Saratoga, NY.

Aug 2008                   Chemaxon User Group, Boston

Sept 2008                  BMS, NJ

Oct 2008                    CDD User Group, San Francisco

Chem-Bio Informatics (CBI) society, Tokyo, Japan (session co-chair)

CHI, Bridging Pharma and IT, Providence, RI.

Nov 2008                   AAPS Atlanta

Feb 2009                   Accelrys User Group Meeting, San Diego, CA.

March 2009               Rutgers University, Piscataway, NJ. (Prof. Antony Kong)

UMDNJ Medical School, Newark, NJ.

May 2009                   11th European regional ISSX meeting, Lisbon, Portugal.

June 2009                 Drug Discovery: Easing Chemistry Bottleneck, Philadelphia.

Sept 2009                  Drexel University, Philadelphia (Dr. Sandhya Kortagere)

October 2009            CDD User Group, San Francisco (Panel chair)

FIGON Dutch Medicines Days, Lunteren, The Netherlands.

Opal Drug Discovery Partnership, filling the pipeline, Boston, MA (panelist)

March 2010               CRIMALDDI, EU funded initiative, Liverpool, UK

April 2010                  EurasiaBio-2010, Moscow, Russia.

May 2010                   Accelrys Global User groups meeting, Boston, MA.

QSAR 2010 – Montreal, Canada – Keynote presentation

June 2010                 Systems biology of mammalian cells, Freiberg, Germany

Second Annual Collaborative Innovation in Biomedicine: Strategies and Best Practices, Philadelphia.

August 2010             ACS, Boston (3 oral presentations)

February 2011          Seminar at University of Arizona (Dr. Steve Wright)

March 2011               AAPS Workshop on Drug Transporters, Bethesda, MD.

April 2011                  CHI’s Third Annual Collaborative Innovation in Biomedicine: Open Innovation, Consortia and Crowd-Sourcing, Philadelphia, PA.

April 2011                  Pistoia meeting, Boston

BioIT, Boston, MA.

Seminar at FDA (Darrell Abernathy)

Seminar at Yale (Green Chemistry)

May 2011                   Accelrys North American User Group Meeting, Jersey City, NJ.

June 2011                 15th Annual Green Chemistry & Engineering Conference (Washington DC)

Aug 2011                   World congress on Alternatives and Animal Use in the Life Sciences (Montreal Canada)

Sept 2011                  XX Helsinki Drug Research Congress (Helsinki, Finland)

Oct 2011                    PRISME meeting, Boston, MA

Nov 2011                   Partnering for cures, New York, http://www.bing.com/videos/search?q=partnering+for+cures+2011&view=detail&mid=9BAB80EBC42EEC11EC4E9BAB80EBC42EEC11EC4E&first=0&qpvt=partnering+for+cures+2011

Seminar at University of Iowa, (Dr. Matthew Krasowski),

Seminar at St Judes (Dr. Erin Schuetz)

Seminar in Toronto (Dr. Alex McKenzie)

Feb 2012                   Tri-Conference (SF)

Mar 2012                   SOT Short course (SF)

CHI Indications Discovery and Drug Repurposing Conference (Philadelphia)

ACS (chair of session, and 5 oral presentations plus one flash talk SD)

April 2012                  Pistoia Alliance meeting (Boston)

Nov 2012                   SERMACS, Raleigh, NC, co-chairing session

Partnering for Cures, New York http://partneringforcures.org/2012/p4cprogram.taf?function=detail&EvID=3918&eventid=p4c11

Jan 2013                   SLAS, Florida

April 2013                  ACS, New Orleans – 6 talks and co-chairing 2 CINF sessions

Sept 2013                  NIH/NIAID Workshop: Systems Biology Approaches for Tuberculosis, Bethesda

Jan 2014                   SLAS, San Diego

April 2014                  ACS, Texas –talk and co-chairing, CINF session

June 2014                 BIO 2014 – panel discussion invited by the European Commission

Aug 2014                   ACS, SF – 6 talks

Dec 2014                   In silico Drug Discovery conference, RTP

Jan 2015                   LABioMed – (Dr. Patti Dickson)

Feb 2015                   SLAS – Washington DC

April 2015                  The Neurotech Investing and Partnering Conference 2015, San Francisco

May 2015                   Contrasts in Pharmacology 2.0 – Turin, Italy

Aug 2015                   ACS, Boston 5 talks and chairing CINF session

Sept 2015                  C&EN virtual symposium

EPA, invited talk (Antony Williams)

Oct 2015                    Rutgers-Camden (Hao Zao)

Nov 2015                   SERMACS (2 talks)

Dec 2015                   Life Sciences Summit, NY

Jan 2016                   SLAS –San Diego, invited speaker

Feb 2016                   BIO-CEO – NY

March 2016               ACS – San Diego, invited speaker (3 talks)

April 2016                  LA BIOMED’S innovation showcase

May 2016                   Biovia- Boston

June 2016                 BIO – San Francisco

Nov 2016                   AAPS – Denver

 

Invited Chairperson

October 2000            Short course on molecular modeling and human CYPs, 10th North American ISSX Meeting, Indianapolis.

October 2000            Computational approaches in drug metabolism, 10th North American ISSX Meeting, Indianapolis.

 

Editorial Positions

Guest Editor: SpringerPlus (for the Journal Collection Pharmaceutical Sciences), April 2015-

Associate Editor: Journal of Pharmacological and Toxicological Methods, Jan 2001- Feb 2015

Editorial Board: Drug Metabolism and Disposition, 2003-2011, Drug Discovery Today, since 2005, The Open Drug Delivery Journal 2007-2009, Current Drug Metabolism 2007-2009, Drug Metabolism Letters since 2007-2009. Pharmaceutical Research (Editor of Reviews) since 2009, Mutation Research-Reviews 2009-2014, The ChemSpider Journal of Chemistry 2009-2010, Chem-bio informatics since 2011 http://cbi-society.org/cbi/journal/cbi_journal/index_e.html

Editorial Advisory Board: Pharmaceutical Research, 2006-2008

Grant reviewer

Agence Nationale De La Recherche (France), Wellcome Trust (UK), EPA (USA) Computational Toxicology Centers, NSF (USA), Vienna Science and Technology Fund (WWTF, Vienna), FWF – Austrian Science Fund, Translational Research Fund (Vienna), Biotechnology and Biological Sciences Research Council (BBSRC, UK), ZonMw (The Netherlands), NHMRC (Australia). NIH NIGMS special emphasis panel 2008/10 ZGM1 MDRS-X CH. PHS 2010-1 SBIR PHASE I TOPIC 108., SBIR 2012 Biological Chemistry, Biophysics, and Drug Discovery IMST10.  2013 R15 Bioengineering Sciences and Technologies (BST) Special Emphasis Panel (ZRG1 BST-T [90]), Wellcome Trust Technology Transfer Expert Review (UK). NIH R15 panel (7/19/16), NIH R21 Zika panel (July 2016).

 

NIH Grants

2R44GM069124-02  In Silico Assessment of Drug Metabolism and Toxicity, SBIR phase II (Ekins, principal investigator) Funded (~$750,000 total cost) from 08/01/05 to 08/01/07.

1R43NS061376-01 Targeted Aggregation Inhibitors for the Treatment of Amyloid Diseases, SBIR phase I (Ekins, principal investigator) Funded ($124,425 total cost) from 10/01/07 to 03/31/2008

 

1R43CA130183-01A1 Computer-Aided Design, Synthesis, And Testing Of A Novel Family Of Triazole-Based Anticancer Therapeutics, SBIR phase I (Ekins, principal investigator) Funded (Total cost $114,818) From 05/01/08- 10/31/08

 

1R43AI078763-01A1 Development of an Inhibitor of Toxoplasma gondii, NIAID Advanced Technology SBIR (Ekins, principal investigator on proposal submitted then replaced upon leaving company) Funded (Total cost $638,000)

 

1R41AI088893-01 Identification of novel therapeutics for tuberculosis combining cheminformatics, diverse databases and logic based pathway analysis, STTR phase I (Ekins, Principal Investigator) Funded (Total cost $149,382) 07/10/10 – 06/30/11

 

1 R43 LM011152-01 Biocomputation across distributed private datasets to enhance drug discovery SBIR phase I (Ekins, Co-Investigator, Bunin PI) Funded (Total cost $149,999) 07/01/11-03/31/12

 

2R42 AI088893-02 Identification of novel therapeutics for tuberculosis combining cheminformatics, diverse databases and logic based pathway analysis, STTR phase II (Ekins, Principal Investigator) Funded (Total cost $999,999), 07/01/2012-10/30/2014

 

9R44TR000942-02 Biocomputation across distributed private datasets to enhance drug discovery, SBIR phase II (Ekins, Principal Investigator) Funded (Total cost $1,404,278) 08/16/2013 – 07/31/2016

 

1R41AI108003-01 Identification and Validation of Targets of Phenotypic High Throughput Screening, STTR Phase I (Ekins, Principal Investigator) Funded (Total cost $255,221) 08/20/2013 – 07/31/2014

 

1DP2OD008459  (Lamichhane) New Drug for Treatment of Chronic Bacterial Infection, Supplement (Consultant) Funded $114,824    09/01/2013 – 08/31/2014   

5R01DK058251-14 (Wright, Steve PI)  Molecular organization of renal and hepatic organic cation transporters, (Consultant)  Funded (Total cost $532,109)  08/01/2014 -07/31/2017

 

1R21AI111739-01 (Lamichhane)   Development of Oral Carbapenem Drugs for treatment of Drug Resistant TB. (Consultant) Funded $236,056  3/1/2014 – 02/29/2016

 

1R21AI111647-01 (Alland)              Discovery and validation of drug targets in vulnerable pathways of Mtb. (Consultant)  Funded $218,623 3/1/2014 – 02/29/2016

 

1U19 AI109713-01 (Perlin – PD; Freundlich – PI) Center to develop therapeutic countermeasures to high-threat bacterial agents. Funded $25M (Consultant) 03/01/2014 – 02/28/2019         

 

1R41NS89061-01 Development and in vitro validation of therapy for mucopolysaccharidosis III, STTR Phase I (Ekins, PI and Dickson Co-PI) Funded $222,296.50  04/01/2014- 03/31/2015

 

R43 DK105694  (Wrobel) Pregnane X Receptor (PXR) Antagonists for Non-Alcoholic Fatty Liver Disease (Consultant)

 

2R42NS089061-02 Development and in vitro validation of therapy for mucopolysaccharidosis III  STTR phase II (Ekins / Dickson)        Funded $1,495,008.00  06/01/2015 – 03/31/2018                

 

1R41NS092221-01A1 Engineering stem cells to make mucopolysaccharidosis IIIB (Ekins / Dickson)     STTR phase I  $224,889.39  Funded 12/05/2015 – 12/04/2016
   

1R41AI122434-01 (Ekins/ Freundlich)    09/01/2015- 08/31/2016      1.2 month/calendar year

NIAID                                                                         $150,000

Optimization of small molecule triazine antituberculars for in vivo efficacy

Starting from a series of triazines active compounds we will optimize ADME properties and test in an in vivo mouse model of infection.

 

European Grants

Part of the consortia for the framework grant More Medicines for Tuberculosis (MM4TB)

Specific Programme “Cooperation” – Theme “Health”

Call identifier: FP7-HEALTH-2010-single-stage

Proposal No: 260872

Acronym: MM4TB

Funded approx 250,000 Euro over 5 years from Feb 2011-July 2016 with 6 month no cost extension. PI for the CDD component.

 

Other

2008-2010 I participated in a Bill and Melinda Gates grant to CDD, performing computational modeling with various groups. Several publications resulted from this effort.

 

Journal cover art

Ekins S, Perryman AL, Clark AM, Reynolds RC and Freundlich JS, Machine learning model analysis and data visualization with small molecules tested in a mouse model of Mycobacterium tuberculosis infection (2014-2015), J Chem Inf Model, 56: 1332-1342, 2016.

 

Ai N, Fan X and Ekins S, In silico methods for predicting Drug-drug interactions with cytochrome P-450s, transporters and beyond, Adv Drug Del Rev, 86:46-60, 2015.

 

Ekins S, Clark AM and Williams AJ, Incorporating Green Chemistry Concepts into Mobile Applications and their potential uses, ACS Sustain Chem Eng, 1. 8-13, 2013.

 

Gupta RR, Gifford, EM, Liston T, Waller CL, Hohman M, Bunin BA and Ekins S, Using open source computational tools for predicting human metabolic stability and additional ADME/Tox properties, Drug Metab Dispos, 38: 2083-2090, 2010.

 

Ekins S and Williams AJ, Meta-analysis of molecular property patterns and filtering of public datasets of antimalarial “hits” and drugs, MedChemComm, 1: 325-330, 2010.

 

Ekins S, Mankowski DC, Hoover DJ, Lawton MP, Treadway JL and Harwood HJ Jr, Three dimensional-quantitative structure activity relationship (3D-QSAR) analysis of human CYP51 inhibitors, Drug Metab Dispos, 35: 493-500, 2007.

 

Balakin KV, Ekins S, Bugrim A, Ivanenkov YA, Korolev D, Nikolsky YV, Skorenko AV, Ivashchenko AA, Savchuk NP and Nikolskaya T, Kohonen maps for prediction of binding to human cytochrome P450 3A4, Drug Metab Dispos, 32: 1183-1189, 2004.

 

Ekins S, Mirny L and Scheutz EG. A ligand-based approach to understanding selectivity of nuclear receptors PXR, CAR, FXR, LXRa and LXRb. Pharm Res 19: 1788-1800, 2002.

 

Ekins S, Bravi G, Ring BJ, Gillespie TA, Gillespie JS, VandenBranden M, Wrighton SA, Wikel JH, Three dimensional-quantitative structure activity relationship (3D-QSAR) analyses of substrates for CYP2B6. J Pharmacol Exp Ther, 288:21-29, 1999.

 

Software Experience

Computational chemistry: Catalyst, Cerius2, Discovery Studio, MOE, Dragon

Systems biology: MetaDrug, MetaCore, Ingenuity Pathways Analysis

Statistical: JMP, SPSS

Databases: ISIS, CambridgeSoft, CDD

 

I am on the web here:

Own website: http://www.collaborations.com/CHEMISTRY.HTM

ScientistsDB: http://www.scientistsdb.com/index.php?title=Ekins,_Sean

Wikipedia: http://en.wikipedia.org/wiki/Sean_Ekins

Blog: http://www.collabchem.com

Twitter: http://twitter.com/collabchem

Slideshare: http://www.slideshare.net/ekinssean/presentations

Linkedin: http://www.linkedin.com/profile/view?id=559027&authType=name&authToken=JJfV&pvs=pp&trk=ppro_viewmore

Google Scholar: http://scholar.google.com/citations?user=fX40O84AAAAJ&hl=en

ResearcherID: http://www.researcherid.com/rid/F-7630-2010

Community of Science: http://myprofile.cos.com/ekinssean

Mendeley: http://www.mendeley.com/profiles/sean-ekins/

ResearchGate: http://www.researchgate.net/profile/Sean_Ekins?ev=hdr_xprf

About.me: http://about.me/Sean_Ekins

Skype: sean.ekins

Kudos: https://www.growkudos.com/

ORCID: 0000-0002-5691-5790 http://orcid.org/0000-0002-5691-5790

 

Interests

Jazz, vinyl record collecting, modern architecture, collecting modern design and acrylic and watercolor painting. Cycling.

British and US Citizen

 

No comment yet

1 ping

  1. Collaboration is about contribution » Collaborative Chemistry says:

    […] Curriculum Vitae […]

Leave a Reply

Your email address will not be published.

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>