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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.

Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW.

Nat Biotechnol. 2019 Aug 12. doi: 10.1038/s41587-019-0217-9. [Epub ahead of print]


High-coverage, long-read sequencing of Han Chinese trio reference samples.

Wang YC, Olson ND, Deikus G, Shah H, Wenger AM, Trow J, Xiao C, Sherry S, Salit ML, Zook JM, Smith M, Sebra R.

Sci Data. 2019 Jun 14;6(1):91. doi: 10.1038/s41597-019-0098-2.


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.


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.


CrowdVariant: a crowdsourcing approach to classify copy number variants.

Greenside P, Zook J, Salit M, Cule M, Poplin R, DePristo M.

Pac Symp Biocomput. 2019;24:224-235.


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;:.


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.


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.


Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.

Olmos JL Jr, Pandey S, Martin-Garcia JM, Calvey G, Katz A, Knoska J, Kupitz C, Hunter MS, Liang M, Oberthuer D, Yefanov O, Wiedorn M, Heyman M, Holl M, Pande K, Barty A, Miller MD, Stern S, Roy-Chowdhury S, Coe J, Nagaratnam N, Zook J, Verburgt J, Norwood T, Poudyal I, Xu D, Koglin J, Seaberg MH, Zhao Y, Bajt S, Grant T, Mariani V, Nelson G, Subramanian G, Bae E, Fromme R, Fung R, Schwander P, Frank M, White TA, Weierstall U, Zatsepin N, Spence J, Fromme P, Chapman HN, Pollack L, Tremblay L, Ourmazd A, Phillips GN Jr, Schmidt M.

BMC Biol. 2018 May 31;16(1):59. doi: 10.1186/s12915-018-0524-5.


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.


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.


Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.

Martin-Garcia JM, Conrad CE, Nelson G, Stander N, Zatsepin NA, Zook J, Zhu L, Geiger J, Chun E, Kissick D, Hilgart MC, Ogata C, Ishchenko A, Nagaratnam N, Roy-Chowdhury S, Coe J, Subramanian G, Schaffer A, James D, Ketwala G, Venugopalan N, Xu S, Corcoran S, Ferguson D, Weierstall U, Spence JCH, Cherezov V, Fromme P, Fischetti RF, Liu W.

IUCrJ. 2017 May 24;4(Pt 4):439-454. doi: 10.1107/S205225251700570X. eCollection 2017 Jul 1.


Agriculture erases climate-driven β-diversity in Neotropical bird communities.

Karp DS, Frishkoff LO, Echeverri A, Zook J, Juárez P, Chan KMA.

Glob Chang Biol. 2018 Jan;24(1):338-349. doi: 10.1111/gcb.13821. Epub 2017 Aug 18.


Size and mineral composition of airborne particles generated by an ultrasonic humidifier.

Sain AE, Zook J, Davy BM, Marr LC, Dietrich AM.

Indoor Air. 2018 Jan;28(1):80-88. doi: 10.1111/ina.12414. Epub 2017 Sep 18.


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.


Role of Stereotactic Body Radiation Therapy Before Orthotopic Liver Transplantation: Retrospective Evaluation of Pathologic Response and Outcomes.

Mannina EM, Cardenes HR, Lasley FD, Goodman B, Zook J, Althouse S, Cox JA, Saxena R, Tector J, Maluccio M.

Int J Radiat Oncol Biol Phys. 2017 Apr 1;97(5):931-938. doi: 10.1016/j.ijrobp.2016.12.036. Epub 2017 Jan 4.


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.


Structural enzymology using X-ray free electron lasers.

Kupitz C, Olmos JL Jr, Holl M, Tremblay L, Pande K, Pandey S, Oberthür D, Hunter M, Liang M, Aquila A, Tenboer J, Calvey G, Katz A, Chen Y, Wiedorn MO, Knoska J, Meents A, Majriani V, Norwood T, Poudyal I, Grant T, Miller MD, Xu W, Tolstikova A, Morgan A, Metz M, Martin-Garcia JM, Zook JD, Roy-Chowdhury S, Coe J, Nagaratnam N, Meza D, Fromme R, Basu S, Frank M, White T, Barty A, Bajt S, Yefanov O, Chapman HN, Zatsepin N, Nelson G, Weierstall U, Spence J, Schwander P, Pollack L, Fromme P, Ourmazd A, Phillips GN Jr, Schmidt M.

Struct Dyn. 2016 Dec 15;4(4):044003. doi: 10.1063/1.4972069. eCollection 2017 Jul.


The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.

Edlund P, Takala H, Claesson E, Henry L, Dods R, Lehtivuori H, Panman M, Pande K, White T, Nakane T, Berntsson O, Gustavsson E, Båth P, Modi V, Roy-Chowdhury S, Zook J, Berntsen P, Pandey S, Poudyal I, Tenboer J, Kupitz C, Barty A, Fromme P, Koralek JD, Tanaka T, Spence J, Liang M, Hunter MS, Boutet S, Nango E, Moffat K, Groenhof G, Ihalainen J, Stojković EA, Schmidt M, Westenhoff S.

Sci Rep. 2016 Oct 19;6:35279. doi: 10.1038/srep35279.


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.


Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.

Munke A, Andreasson J, Aquila A, Awel S, Ayyer K, Barty A, Bean RJ, Berntsen P, Bielecki J, Boutet S, Bucher M, Chapman HN, Daurer BJ, DeMirci H, Elser V, Fromme P, Hajdu J, Hantke MF, Higashiura A, Hogue BG, Hosseinizadeh A, Kim Y, Kirian RA, Reddy HK, Lan TY, Larsson DS, Liu H, Loh ND, Maia FR, Mancuso AP, Mühlig K, Nakagawa A, Nam D, Nelson G, Nettelblad C, Okamoto K, Ourmazd A, Rose M, van der Schot G, Schwander P, Seibert MM, Sellberg JA, Sierra RG, Song C, Svenda M, Timneanu N, Vartanyants IA, Westphal D, Wiedorn MO, Williams GJ, Xavier PL, Yoon CH, Zook J.

Sci Data. 2016 Aug 1;3:160064. doi: 10.1038/sdata.2016.64.


Full inactivation of alphaviruses in single particle and crystallized forms.

Lawrence RM, Zook JD, Hogue BG.

J Virol Methods. 2016 Oct;236:237-244. doi: 10.1016/j.jviromet.2016.07.020. Epub 2016 Jul 25.


Climate change and habitat conversion favour the same species.

Frishkoff LO, Karp DS, Flanders JR, Zook J, Hadly EA, Daily GC, M'Gonigle LK.

Ecol Lett. 2016 Sep;19(9):1081-90. doi: 10.1111/ele.12645. Epub 2016 Jul 11.


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.


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.


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.


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.


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.


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.


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.


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.


Achieving high-sensitivity for clinical applications using augmented exome sequencing.

Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R.

Genome Med. 2015 Jul 16;7:71. doi: 10.1186/s13073-015-0197-4. eCollection 2015.


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.


A novel inert crystal delivery medium for serial femtosecond crystallography.

Conrad CE, Basu S, James D, Wang D, Schaffer A, Roy-Chowdhury S, Zatsepin NA, Aquila A, Coe J, Gati C, Hunter MS, Koglin JE, Kupitz C, Nelson G, Subramanian G, White TA, Zhao Y, Zook J, Boutet S, Cherezov V, Spence JC, Fromme R, Weierstall U, Fromme P.

IUCrJ. 2015 Jun 30;2(Pt 4):421-30. doi: 10.1107/S2052252515009811. eCollection 2015 Jul 1.


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.


ACR Appropriateness Criteria® Ductal Carcinoma in Situ.

Kaufman SA, Harris EE, Bailey L, Chadha M, Dutton SC, Freedman GM, Goyal S, Halyard MY, Horst KC, Novick KL, Park CC, Suh WW, Toppmeyer D, Zook J, Haffty BG.

Oncology (Williston Park). 2015 Jun;29(6):446-58, 460-1. Review.


Cicadas impact bird communication in a noisy tropical rainforest.

Hart PJ, Hall R, Ray W, Beck A, Zook J.

Behav Ecol. 2015 May-Jun;26(3):839-842.


NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

Zook J, Mo G, Sisco NJ, Craciunescu FM, Hansen DT, Baravati B, Cherry BR, Sykes K, Wachter R, Van Horn WD, Fromme P.

Structure. 2015 Jun 2;23(6):1116-22. doi: 10.1016/j.str.2015.03.025. Epub 2015 May 21.


An analytical framework for optimizing variant discovery from personal genomes.

Highnam G, Wang JJ, Kusler D, Zook J, Vijayan V, Leibovich N, Mittelman D.

Nat Commun. 2015 Feb 25;6:6275. doi: 10.1038/ncomms7275.


Loss of avian phylogenetic diversity in neotropical agricultural systems.

Frishkoff LO, Karp DS, M'Gonigle LK, Mendenhall CD, Zook J, Kremen C, Hadly EA, Daily GC.

Science. 2014 Sep 12;345(6202):1343-6. doi: 10.1126/science.1254610.


Low temperature assembly of functional 3D DNA-PNA-protein complexes.

Flory JD, Simmons CR, Lin S, Johnson T, Andreoni A, Zook J, Ghirlanda G, Liu Y, Yan H, Fromme P.

J Am Chem Soc. 2014 Jun 11;136(23):8283-95. doi: 10.1021/ja501228c. Epub 2014 May 28.


Purification and biophysical characterization of the CapA membrane protein FTT0807 from Francisella tularensis.

Martin-Garcia JM, Hansen DT, Zook J, Loskutov AV, Robida MD, Craciunescu FM, Sykes KF, Wachter RM, Fromme P, Allen JP.

Biochemistry. 2014 Apr 1;53(12):1958-70. doi: 10.1021/bi401644s. Epub 2014 Mar 18.


ACR Appropriateness Criteria®-Anal Cancer.

Expert Panel on Radiation Oncology–Rectal/Anal Cancer, Hong TS, Pretz JL, Herman JM, Abdel-Wahab M, Azad N, Blackstock AW, Das P, Goodman KA, Jabbour SK, Jones WE 3rd, Konski AA, Koong AC, Rodriguez-Bigas M, Small W Jr, Thomas CR Jr, Zook J, Suh WW.

Gastrointest Cancer Res. 2014 Jan;7(1):4-14.


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.


High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane.

Zook JD, Molugu TR, Jacobsen NE, Lin G, Soll J, Cherry BR, Brown MF, Fromme P.

PLoS One. 2013 Oct 29;8(10):e78116. doi: 10.1371/journal.pone.0078116. eCollection 2013.


Evaluation of superficial dosimetry between treatment planning system and measurement for several breast cancer treatment techniques.

Akino Y, Das IJ, Bartlett GK, Zhang H, Thompson E, Zook JE.

Med Phys. 2013 Jan;40(1):011714. doi: 10.1118/1.4770285.


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.


Spinal metastasis from acinic cell carcinoma of the parotid gland: a case report.

Zook JD, Djurasovic M, Dimar JR 2nd, Carreon LY.

Spine J. 2012 Aug;12(8):e7-10. doi: 10.1016/j.spinee.2012.08.021.


ACR appropriateness criteria®  resectable rectal cancer.

Jones WE 3rd, Thomas CR Jr, Herman JM, Abdel-Wahab M, Azad N, Blackstock W, Das P, Goodman KA, Hong TS, Jabbour SK, Konski AA, Koong AC, Rodriguez-Bigas M, Small W Jr, Zook J, Suh WW.

Radiat Oncol. 2012 Sep 24;7:161. doi: 10.1186/1748-717X-7-161.


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.

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