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Items: 50

1.

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 Jan 3. pii: S1525-1578(18)30291-5. doi: 10.1016/j.jmoldx.2018.10.009. [Epub ahead of print]

2.

Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials.

Cleveland MH, Zook JM, Salit M, Vallone PM.

J Mol Diagn. 2018 Sep;20(5):583-590. doi: 10.1016/j.jmoldx.2018.04.005. Epub 2018 Jun 26.

PMID:
29959024
3.

Tools for annotation and comparison of structural variation.

Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM.

F1000Res. 2017 Oct 3;6:1795. doi: 10.12688/f1000research.12516.1. eCollection 2017.

4.

Challenging a bioinformatic tool's ability to detect microbial contaminants using in silico whole genome sequencing data.

Olson ND, Zook JM, Morrow JB, Lin NJ.

PeerJ. 2017 Sep 12;5:e3729. doi: 10.7717/peerj.3729. eCollection 2017.

5.

Genome-wide reconstruction of complex structural variants using read clouds.

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.

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.

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships.

Kalman LV, Datta V, Williams M, Zook JM, Salit ML, Han JY.

Ann Lab Med. 2016 Nov;36(6):513-20. doi: 10.3343/alm.2016.36.6.513. Review.

8.

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.

9.

Advancing Benchmarks for Genome Sequencing.

Zook JM, Salit M.

Cell Syst. 2015 Sep 23;1(3):176-7. doi: 10.1016/j.cels.2015.09.004. Epub 2015 Sep 23.

10.

A research roadmap for next-generation sequencing informatics.

Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T.

Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Review.

11.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.

Olson ND, Lund SP, Zook JM, Rojas-Cornejo F, Beck B, Foy C, Huggett J, Whale AS, Sui Z, Baoutina A, Dobeson M, Partis L, Morrow JB.

Biomol Detect Quantif. 2015 Mar 5;3:17-24. doi: 10.1016/j.bdq.2015.01.004. eCollection 2015 Mar.

12.

PEPR: pipelines for evaluating prokaryotic references.

Olson ND, Zook JM, Samarov DV, Jackson SA, Salit ML.

Anal Bioanal Chem. 2016 Apr;408(11):2975-83. doi: 10.1007/s00216-015-9299-5. Epub 2016 Mar 2.

13.

Medical implications of technical accuracy in genome sequencing.

Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA.

Genome Med. 2016 Mar 2;8(1):24. doi: 10.1186/s13073-016-0269-0.

14.

svclassify: a method to establish benchmark structural variant calls.

Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M.

BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2.

15.

svviz: a read viewer for validating structural variants.

Spies N, Zook JM, Salit M, Sidow A.

Bioinformatics. 2015 Dec 15;31(24):3994-6. doi: 10.1093/bioinformatics/btv478. Epub 2015 Aug 18.

PMID:
26286809
16.

Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, Schupp JM, Keim P, Morrow JB, Salit ML, Zook JM.

Front Genet. 2015 Jul 7;6:235. doi: 10.3389/fgene.2015.00235. eCollection 2015. Review.

17.

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available.

PMID:
26154004
18.

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M.

Nat Biotechnol. 2014 Mar;32(3):246-51. doi: 10.1038/nbt.2835. Epub 2014 Feb 16.

PMID:
24531798
19.

Assuring the quality of next-generation sequencing in clinical laboratory practice.

Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM.

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403. No abstract available.

20.

Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.

Zook JM, Samarov D, McDaniel J, Sen SK, Salit M.

PLoS One. 2012;7(7):e41356. doi: 10.1371/journal.pone.0041356. Epub 2012 Jul 31.

21.

Measuring agglomerate size distribution and dependence of localized surface plasmon resonance absorbance on gold nanoparticle agglomerate size using analytical ultracentrifugation.

Zook JM, Rastogi V, Maccuspie RI, Keene AM, Fagan J.

ACS Nano. 2011 Oct 25;5(10):8070-9. doi: 10.1021/nn202645b. Epub 2011 Sep 29.

PMID:
21888410
22.

Measuring silver nanoparticle dissolution in complex biological and environmental matrices using UV-visible absorbance.

Zook JM, Long SE, Cleveland D, Geronimo CL, MacCuspie RI.

Anal Bioanal Chem. 2011 Oct;401(6):1993-2002. doi: 10.1007/s00216-011-5266-y. Epub 2011 Aug 2.

PMID:
21808990
23.

Bat wing sensors support flight control.

Sterbing-D'Angelo S, Chadha M, Chiu C, Falk B, Xian W, Barcelo J, Zook JM, Moss CF.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11291-6. doi: 10.1073/pnas.1018740108. Epub 2011 Jun 20.

24.

Stable nanoparticle aggregates/agglomerates of different sizes and the effect of their size on hemolytic cytotoxicity.

Zook JM, Maccuspie RI, Locascio LE, Halter MD, Elliott JT.

Nanotoxicology. 2011 Dec;5(4):517-30. doi: 10.3109/17435390.2010.536615. Epub 2010 Dec 13.

PMID:
21142841
25.

Interpretation of chronopotentiometric transients of ion-selective membranes with two transition times.

Zook JM, Bodor S, Gyurcsányi RE, Lindner E.

J Electroanal Chem (Lausanne). 2010 Jan 15;638(2):254-261.

27.

Magnetic connectors for microfluidic applications.

Atencia J, Cooksey GA, Jahn A, Zook JM, Vreeland WN, Locascio LE.

Lab Chip. 2010 Jan 21;10(2):246-9. doi: 10.1039/b913331c. Epub 2009 Nov 16.

PMID:
20066254
29.
30.

Electrochemical methods for the determination of the diffusion coefficient of ionophores and ionophore-ion complexes in plasticized PVC membranes.

Bodor S, Zook JM, Lindner E, Tóth K, Gyurcsányi RE.

Analyst. 2008 May;133(5):635-42. doi: 10.1039/b718110h. Epub 2008 Feb 27.

PMID:
18427685
31.

Mathematical model of current-polarized ionophore-based ion-selective membranes.

Zook JM, Buck RP, Langmaier J, Lindner E.

J Phys Chem B. 2008 Feb 21;112(7):2008-15. doi: 10.1021/jp074612i. Epub 2008 Jan 25.

PMID:
18217742
32.

Statistical analysis of fractal-based brain tumor detection algorithms.

Zook JM, Iftekharuddin KM.

Magn Reson Imaging. 2005 Jun;23(5):671-8.

PMID:
16051042
33.

Geniculo-collicular descending projections in the gerbil.

Kuwabara N, Zook JM.

Brain Res. 2000 Sep 29;878(1-2):79-87.

PMID:
10996138
34.
35.
36.

Classification of the principal cells of the medial nucleus of the trapezoid body.

Kuwabara N, Zook JM.

J Comp Neurol. 1991 Dec 22;314(4):707-20.

PMID:
1816272
37.

Afferents to the medial nucleus of the trapezoid body and their collateral projections.

Kuwabara N, DiCaprio RA, Zook JM.

J Comp Neurol. 1991 Dec 22;314(4):684-706.

PMID:
1816271
38.
39.
40.

Origin of ascending projections to an isofrequency region of the mustache bat's inferior colliculus.

Ross LS, Pollak GD, Zook JM.

J Comp Neurol. 1988 Apr 22;270(4):488-505.

PMID:
2836478
41.
42.

Variability in hand surface representations in areas 3b and 1 in adult owl and squirrel monkeys.

Merzenich MM, Nelson RJ, Kaas JH, Stryker MP, Jenkins WM, Zook JM, Cynader MS, Schoppmann A.

J Comp Neurol. 1987 Apr 8;258(2):281-96.

PMID:
3584541
43.

Projections from the cochlear nuclei in the mustache bat, Pteronotus parnellii.

Zook JM, Casseday JH.

J Comp Neurol. 1985 Jul 15;237(3):307-24.

PMID:
2995459
44.
45.

Somatosensory cortical map changes following digit amputation in adult monkeys.

Merzenich MM, Nelson RJ, Stryker MP, Cynader MS, Schoppmann A, Zook JM.

J Comp Neurol. 1984 Apr 20;224(4):591-605.

PMID:
6725633
47.
48.
49.
50.

Competitive fighting in the rat.

Zook JM, Adams DB.

J Comp Physiol Psychol. 1975 Jan;88(1):418-23.

PMID:
1168210

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