Publications

With almost 20 years of combined research experience, In Siliflo has a strong basis in science and academic achievement. It is through this experience that we are able to deliver the right solution at the right price every time.

Craig Knox

Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, Young N, Xia J, Knox C, et al. The Human Serum Metabolome. The Human Serum Metabolome. PLoS ONE 6(2): e16957. doi:10.1371/journal.pone.0016957

Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41

Frolkis A, Knox C, Lim E, Jewison T, Law V, Hau DD, Liu P, Gautam B, Ly S, Guo AC, Xia J, Liang Y, Shrivastava S, Wishart DS. SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 2010 Jan;38(Database issue):D480-7

Lim E, Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo AC, Neveu V, Wishart DS. T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res. 2010 Jan;38(Database issue):D781-6

Neveu V, Perez-Jiménez J, Vos F, Crespy V, du Chaffaut L, Mennen L, Knox C, Eisner R, Cruz J, Wishart D, Scalbert A. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database (Oxford). 2010;2010:bap024

Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10

Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6

Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405

Wishart D, Tzur D, Knox C, Eisner R, et al. HMDB: the Human Metabolome Database. Nucleic Acids Research (NAR), 35, pp D521 -- D526, January 2007

Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS. BioSpider: a web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145-156, 2007

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72

Joseph Cruz

Berjanskii M, Liang Y, Zhou J, Tang P, Stothard P, Zhou Y, Cruz J, MacDonell C, Lin G, Lu P, Wishart DS. PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W633-40. Epub 2010 May 11

Berjanskii M, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS. GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W670-7. Epub 2009 Apr 30

Montgomerie S, Cruz JA, Shrivastava S, Arndt D, Berjanskii M, Wishart DS. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W202-9

Mueller TF, Reeve J, Jhangri GS, Mengel M, Jacaj Z, Cairo L, Obeidat M, Todd G, Moore R, Famulski KS, Cruz J, Wishart D, Meng C, Sis B, Solez K, Kaplan B, Halloran PF. The transcriptome of the implant biopsy identifies donor kidneys at increased risk of delayed graft function. Am J Transplant. 2008 Jan;8(1):78-85

Mueller TF, Einecke G, Reeve J, Sis B, Mengel M, Jhangri GS, Bunnag S, Cruz J, Wishart D, Meng C, Broderick G, Kaplan B, Halloran PF. Microarray analysis of rejection in human kidney transplants using pathogenesis-based transcript sets. Am J Transplant. 2007 Dec;7(12):2712-22

Sis B, Campbell PM, Mueller T, Cockfield SM, Cruz J, Meng C, Wishart D, Solez K, Halloran PF. Transplant glomerulopathy, late antibody-mediated rejection and the ABCD tetrad in kidney allograft biopsies for cause. Am J Transplant. 2007 Jul;7(7):1743-52

Cruz JA, Wishart DS. Applications of machine learning in cancer prediction and prognosis. Cancer Informatics. 2006:2 59-78

Van Domselaar GH, Stothard P, Shrivastava,S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9

Wishart, DS, Yang R, Arndt D, Tang P, Cruz J. Dynamic cellular automata: an alternative approach to cellular simulation. In Silico Biol. 2005;5(2):139-61

Stothard P, Van Domselaar G, Shrivistava S, Guo A, O’Neill B, Cruz J, Ellison M, Wishart DS. BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D317-20

Roman Eisner

Eisner R, Stretch C, Eastman T, Xia J, Hau D, Damaraju S, Greiner R, Wishart DS, Baracos VE. Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites. Metabolomics, August 2010

Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong Y, Cheng D, Eisner R, et al. The human cerebrospinal fluid metabolome. J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):164-73

Wishart D, Tzur D, Knox C, Eisner R, et al. HMDB: the Human Metabolome Database. Nucleic Acids Research (NAR), 35, pp D521 -- D526, January 2007

Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS. BioSpider: a web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145-156, 2007

Poulin B, Eisner R, Szafron D, Lu P, Greiner R, Wishart DS, Fyshe A, Pearcy B, MacDonell C, Anvik J. Visual Explanation of Evidence in Additive Classifiers. 18th Conference on Innovative Applications of Artificial Intelligence (IAAI), July 2006

Eisner R, Poulin B, Szafron D, Lu P, Greiner R. Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005, 10 ms

Lu P, Szafron D, Greiner R, Wishart DS, Fyshe A, Pearcy B, Poulin B, Eisner R, Ngo D, Lamb N. PA-GOSUB: A Searchable Database of Model Organism Protein Sequences With Their Predicted GO Molecular Function and Subcellular Localization. Nucleic Acids Research, Volume 33, January 2005, ms. 6

Szafron D, Lu P, Greiner R, Wishart DS, Poulin B, Eisner R, Lu Z, Anvik J, Macdonell C, Fyshe A, Meeuwis D. Proteome Analyst: Custom Predictions with Explanations in a Web-based Tool for High-throughput Proteome Annotations. Nucleic Acids Research, Volume 32, July 2004, pp. W365-W371

Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R. Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers. Bioinformatics, Volume 20, Issue 4, March 2004, pp. 547 - 556

Szafron D, Lu P, Greiner R, Wishart DS, Lu Z, Poulin B, Eisner R, Anvik J, Macdonell C. Proteome Analyst, Transparent High-throughput Protein Annotation: Function, Localization and Custom Predictors. ICML Workshop - Bioinformatics, August 2003, Washington, U.S.A., pp. 2-10

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Publications

Craig Knox

Joseph Cruz

Roman Eisner