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Items: 11

1.

An open resource for accurately benchmarking small variant and reference calls.

Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY, De La Vega FM, Xiao C, Sherry S, Salit M.

Nat Biotechnol. 2019 May;37(5):561-566. doi: 10.1038/s41587-019-0074-6. Epub 2019 Apr 1.

PMID:
30936564
2.

Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):567. doi: 10.1038/s41587-019-0108-0.

PMID:
30899106
3.

Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):555-560. doi: 10.1038/s41587-019-0054-x. Epub 2019 Mar 11. Erratum in: Nat Biotechnol. 2019 Mar 21;:.

PMID:
30858580
4.

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing.

Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS.

J Mol Diagn. 2019 Mar;21(2):318-329. doi: 10.1016/j.jmoldx.2018.10.009. Epub 2019 Jan 3.

5.

Prevalence and properties of intragenic copy-number variation in Mendelian disease genes.

Truty R, Paul J, Kennemer M, Lincoln SE, Olivares E, Nussbaum RL, Aradhya S.

Genet Med. 2019 Jan;21(1):114-123. doi: 10.1038/s41436-018-0033-5. Epub 2018 Jun 12.

PMID:
29895855
6.

Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM.

J Mol Diagn. 2017 May;19(3):417-426. doi: 10.1016/j.jmoldx.2016.12.001. Epub 2017 Mar 18.

7.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

8.

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Whalen S, Truty RM, Pollard KS.

Nat Genet. 2016 May;48(5):488-96. doi: 10.1038/ng.3539. Epub 2016 Apr 4.

9.

Integrating diverse datasets improves developmental enhancer prediction.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677. eCollection 2014 Jun.

10.

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG.

Cell. 2012 Sep 28;151(1):206-20. doi: 10.1016/j.cell.2012.07.035. Epub 2012 Sep 12.

11.

Novel bacterial taxa in the human microbiome.

Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS.

PLoS One. 2012;7(6):e35294. doi: 10.1371/journal.pone.0035294. Epub 2012 Jun 13.

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