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Items: 15

1.

Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory.

Hartman P, Beckman K, Silverstein K, Yohe S, Schomaker M, Henzler C, Onsongo G, Lam HC, Munro S, Daniel J, Billstein B, Deshpande A, Hauge A, Mroz P, Lee W, Holle J, Wiens K, Karnuth K, Kemmer T, Leary M, Michel S, Pohlman L, Thayanithy V, Nelson A, Bower M, Thyagarajan B.

Mol Genet Metab Rep. 2019 Mar 1;19:100464. doi: 10.1016/j.ymgmr.2019.100464. eCollection 2019 Jun.

2.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, GrĂ¼ning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ.

Cancer Res. 2017 Nov 1;77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331.

3.

CNV-RF Is a Random Forest-Based Copy Number Variation Detection Method Using Next-Generation Sequencing.

Onsongo G, Baughn LB, Bower M, Henzler C, Schomaker M, Silverstein KA, Thyagarajan B.

J Mol Diagn. 2016 Nov;18(6):872-881. doi: 10.1016/j.jmoldx.2016.07.001. Epub 2016 Sep 3.

PMID:
27597741
4.

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

Vishwanathan N, Bandyopadhyay AA, Fu HY, Sharma M, Johnson KC, Mudge J, Ramaraj T, Onsongo G, Silverstein KA, Jacob NM, Le H, Karypis G, Hu WS.

Biotechnol J. 2016 Sep;11(9):1151-7. doi: 10.1002/biot.201500455. Epub 2016 Jul 19.

PMID:
27374913
5.

Clinical validation of targeted next-generation sequencing for inherited disorders.

Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A, Spears MD, Beckman K, Silverstein KA, Thyagarajan B.

Arch Pathol Lab Med. 2015 Feb;139(2):204-10. doi: 10.5858/arpa.2013-0625-OA.

PMID:
25611102
6.

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ.

J Proteome Res. 2014 Dec 5;13(12):5898-908. doi: 10.1021/pr500812t. Epub 2014 Oct 23.

7.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM.

BMC Genomics. 2014 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.

8.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KA, Thyagarajan B.

BMC Res Notes. 2014 May 23;7:314. doi: 10.1186/1756-0500-7-314.

9.

Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential.

Stone MD, Odland RM, McGowan T, Onsongo G, Tang C, Rhodus NL, Jagtap P, Bandhakavi S, Griffin TJ.

Clin Proteomics. 2010 Sep;6(3):75-82. Epub 2010 Jul 25.

10.

LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.

Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ.

Proteomics. 2010 Oct;10(19):3533-8. doi: 10.1002/pmic.201000189.

11.

Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions.

de Jong EP, Xie H, Onsongo G, Stone MD, Chen XB, Kooren JA, Refsland EW, Griffin RJ, Ondrey FG, Wu B, Le CT, Rhodus NL, Carlis JV, Griffin TJ.

PLoS One. 2010 Jun 17;5(6):e11148. doi: 10.1371/journal.pone.0011148.

12.

Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response.

Bandhakavi S, Kim YM, Ro SH, Xie H, Onsongo G, Jun CB, Kim DH, Griffin TJ.

Mol Cell Proteomics. 2010 Feb;9(2):403-14. doi: 10.1074/mcp.M900326-MCP200. Epub 2009 Nov 23.

13.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

Bandhakavi S, Stone MD, Onsongo G, Van Riper SK, Griffin TJ.

J Proteome Res. 2009 Dec;8(12):5590-600. doi: 10.1021/pr900675w.

14.

Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry.

Xie H, Onsongo G, Popko J, de Jong EP, Cao J, Carlis JV, Griffin RJ, Rhodus NL, Griffin TJ.

Mol Cell Proteomics. 2008 Mar;7(3):486-98. Epub 2007 Nov 28.

15.

Data exploration tools for the Gene Ontology database.

Shoop E, Casaes P, Onsongo G, Lesnett L, Petursdottir EO, Donkor EK, Tkach D, Cosimini M.

Bioinformatics. 2004 Dec 12;20(18):3442-54. Epub 2004 Jul 22.

PMID:
15271779

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