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Items: 1 to 20 of 47


Scalable and cost-effective NGS genotyping in the cloud.

Souilmi Y, Lancaster AK, Jung JY, Rizzo E, Hawkins JB, Powles R, Amzazi S, Ghazal H, Tonellato PJ, Wall DP.

BMC Med Genomics. 2015 Oct 15;8:64. doi: 10.1186/s12920-015-0134-9.


Histopathologic alterations associated with global gene expression due to chronic dietary TCDD exposure in juvenile zebrafish.

Liu Q, Spitsbergen JM, Cariou R, Huang CY, Jiang N, Goetz G, Hutz RJ, Tonellato PJ, Carvan MJ 3rd.

PLoS One. 2014 Jul 2;9(7):e100910. doi: 10.1371/journal.pone.0100910. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e106605.


COSMOS: Python library for massively parallel workflows.

Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung JY, Souilmi Y, Wall DP, Tonellato PJ.

Bioinformatics. 2014 Oct 15;30(20):2956-8. doi: 10.1093/bioinformatics/btu385. Epub 2014 Jun 30.


Analysis of sequence-based copy number variation detection tools for cancer studies.

Nabavi S, Cai Z, Tonellato PJ.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:124. eCollection 2013. No abstract available.


Streaming support for data intensive cloud-based sequence analysis.

Issa SA, Kienzler R, El-Kalioby M, Tonellato PJ, Wall D, Bruggmann R, Abouelhoda M.

Biomed Res Int. 2013;2013:791051. doi: 10.1155/2013/791051. Epub 2013 Apr 24.


Differential gene expression associated with dietary methylmercury (MeHg) exposure in rainbow trout (Oncorhynchus mykiss) and zebrafish (Danio rerio).

Liu Q, Basu N, Goetz G, Jiang N, Hutz RJ, Tonellato PJ, Carvan MJ 3rd.

Ecotoxicology. 2013 May;22(4):740-51. doi: 10.1007/s10646-013-1066-9. Epub 2013 Mar 26.


Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome.

Przybytkowski E, Aguilar-Mahecha A, Nabavi S, Tonellato PJ, Basik M.

Methods Mol Biol. 2013;973:15-38. doi: 10.1007/978-1-62703-281-0_2.


A systems approach to designing effective clinical trials using simulations.

Fusaro VA, Patil P, Chi CL, Contant CF, Tonellato PJ.

Circulation. 2013 Jan 29;127(4):517-26. doi: 10.1161/CIRCULATIONAHA.112.123034. Epub 2012 Dec 21.


The future of genomics in pathology.

Wall DP, Tonellato PJ.

F1000 Med Rep. 2012;4:14. doi: 10.3410/M4-14. Epub 2012 Jul 2.


A simulation platform to examine heterogeneity influence on treatment.

Chi CL, Fusaro VA, Patil P, Crawford MA, Content CF, Tonellato PJ.

AMIA Jt Summits Transl Sci Proc. 2012;2012:19-24. Epub 2012 Mar 19.


Systems analysis of inflammatory bowel disease based on comprehensive gene information.

Suzuki S, Takai-Igarashi T, Fukuoka Y, Wall DP, Tanaka H, Tonellato PJ.

BMC Med Genet. 2012 Apr 5;13:25. doi: 10.1186/1471-2350-13-25.


Biomedical cloud computing with Amazon Web Services.

Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ.

PLoS Comput Biol. 2011 Aug;7(8):e1002147. doi: 10.1371/journal.pcbi.1002147. Epub 2011 Aug 25.


The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.

J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.


Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

Kudtarkar P, Deluca TF, Fusaro VA, Tonellato PJ, Wall DP.

Evol Bioinform Online. 2010 Dec 22;6:197-203. doi: 10.4137/EBO.S6259.


Genotator: a disease-agnostic tool for genetic annotation of disease.

Wall DP, Pivovarov R, Tong M, Jung JY, Fusaro VA, DeLuca TF, Tonellato PJ.

BMC Med Genomics. 2010 Oct 29;3:50. doi: 10.1186/1755-8794-3-50.


Cloud computing for comparative genomics.

Wall DP, Kudtarkar P, Fusaro VA, Pivovarov R, Patil P, Tonellato PJ.

BMC Bioinformatics. 2010 May 18;11:259. doi: 10.1186/1471-2105-11-259.


BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat.

Kwitek AE, Jacob HJ, Baker JE, Dwinell MR, Forster HV, Greene AS, Kunert MP, Lombard JH, Mattson DL, Pritchard KA Jr, Roman RJ, Tonellato PJ, Cowley AW Jr.

Physiol Genomics. 2006 Apr 13;25(2):303-13. Epub 2006 Feb 14.


Tools and strategies for physiological genomics: the Rat Genome Database.

Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ.

Physiol Genomics. 2005 Oct 17;23(2):246-56. Epub 2005 Aug 16.


Automated analysis of conserved syntenies for the zebrafish genome.

Postlethwait J, Ruotti V, Carvan MJ, Tonellato PJ.

Methods Cell Biol. 2004;77:255-71. No abstract available.

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