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Items: 1 to 50 of 157

1.

Next-Generation Sequencing Technologies.

McCombie WR, McPherson JD, Mardis ER.

Cold Spring Harb Perspect Med. 2018 Nov 26. pii: a036798. doi: 10.1101/cshperspect.a036798. [Epub ahead of print]

PMID:
30478097
2.

Future Promises and Concerns of Ubiquitous Next-Generation Sequencing.

McCombie WR, McPherson JD.

Cold Spring Harb Perspect Med. 2018 Nov 26. pii: a025783. doi: 10.1101/cshperspect.a025783. [Epub ahead of print]

PMID:
30478095
3.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.

Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

4.

DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders.

Ryan NM, Lihm J, Kramer M, McCarthy S, Morris SW, Arnau-Soler A, Davies G, Duff B, Ghiban E, Hayward C, Deary IJ, Blackwood DHR, Lawrie SM, McIntosh AM, Evans KL, Porteous DJ, McCombie WR, Thomson PA.

Mol Psychiatry. 2018 Dec;23(12):2254-2265. doi: 10.1038/s41380-018-0087-4. Epub 2018 Jun 7.

5.

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.

Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499. doi: 10.1073/pnas.1721487115. Epub 2018 May 16.

6.

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing.

Wang B, Regulski M, Tseng E, Olson A, Goodwin S, McCombie WR, Ware D.

Genome Res. 2018 Jun;28(6):921-932. doi: 10.1101/gr.227462.117. Epub 2018 Apr 30.

7.

Altered DNA methylation associated with a translocation linked to major mental illness.

McCartney DL, Walker RM, Morris SW, Anderson SM, Duff BJ, Marioni RE, Millar JK, McCarthy SE, Ryan NM, Lawrie SM, Watson AR, Blackwood DHR, Thomson PA, McIntosh AM, McCombie WR, Porteous DJ, Evans KL.

NPJ Schizophr. 2018 Mar 19;4(1):5. doi: 10.1038/s41537-018-0047-7.

8.

Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.

Monson ET, Pirooznia M, Parla J, Kramer M, Goes FS, Gaine ME, Gaynor SC, de Klerk K, Jancic D, Karchin R, McCombie WR, Zandi PP, Potash JB, Willour VL.

Mol Neuropsychiatry. 2017 Jul;3(1):1-11. doi: 10.1159/000454773. Epub 2017 Jan 18.

9.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

10.

1D Genome Sequencing on the Oxford Nanopore MinION.

Goodwin S, Wappel R, McCombie WR.

Curr Protoc Hum Genet. 2017 Jul 11;94:18.11.1-18.11.14. doi: 10.1002/cphg.39.

PMID:
28696556
11.

Rare disruptive variants in the DISC1 Interactome and Regulome: association with cognitive ability and schizophrenia.

Teng S, Thomson PA, McCarthy S, Kramer M, Muller S, Lihm J, Morris S, Soares DC, Hennah W, Harris S, Camargo LM, Malkov V, McIntosh AM, Millar JK, Blackwood DH, Evans KL, Deary IJ, Porteous DJ, McCombie WR.

Mol Psychiatry. 2018 May;23(5):1270-1277. doi: 10.1038/mp.2017.115. Epub 2017 Jun 20.

12.

Improved maize reference genome with single-molecule technologies.

Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D.

Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.

PMID:
28605751
13.

The pangenome of an agronomically important crop plant Brassica oleracea.

Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D.

Nat Commun. 2016 Nov 11;7:13390. doi: 10.1038/ncomms13390.

14.

Preparing Polymerase Chain Reaction (PCR) Products for Capillary Sequencing.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot094599. doi: 10.1101/pdb.prot094599.

PMID:
27803282
15.

Agarose Gel Size Selection for DNA Sequencing Libraries.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot094698. doi: 10.1101/pdb.prot094698.

PMID:
27803281
16.

Whole-Genome Sequencing: Manual Library Preparation.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jan 3;2017(1). doi: 10.1101/pdb.prot094615.

PMID:
27803280
17.

Whole-Genome Sequencing: Automated, Nonindexed Library Preparation.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Mar 1;2017(3). doi: 10.1101/pdb.prot094623.

PMID:
27803279
18.

Preparing Plasmid Subclones for Capillary Sequencing.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot094581. doi: 10.1101/pdb.prot094581.

PMID:
27803278
19.

Library Quantification Using PicoGreen Fluorometry.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 May 1;2017(5). doi: 10.1101/pdb.prot094722.

PMID:
27803277
20.

Automated Library Preparation for DNA Sequencing.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Mar 1;2017(3). doi: 10.1101/pdb.prot094631.

PMID:
27803276
21.

RNA-Seq: RNA Conversion to cDNA and Amplification.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot094672. doi: 10.1101/pdb.prot094672.

PMID:
27803275
22.

Solution-Phase Exome Capture.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot094680. doi: 10.1101/pdb.prot094680.

PMID:
27803274
23.

Preparation of an 8-kb Mate-Pair Library for Illumina Sequencing.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Apr 3;2017(4):pdb.prot094664. doi: 10.1101/pdb.prot094664.

PMID:
27803273
24.

Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Apr 3;2017(4):pdb.prot094656. doi: 10.1101/pdb.prot094656.

PMID:
27803272
25.

Library Quantification: Fluorometric Quantitation of Double-Stranded or Single-Stranded DNA Samples Using the Qubit System.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jun 1;2017(6):pdb.prot094730. doi: 10.1101/pdb.prot094730.

PMID:
27803271
26.

Whole-Genome Sequencing: Automated, Indexed Library Preparation.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Mar 1;2017(3). doi: 10.1101/pdb.prot094649.

PMID:
27803270
27.

Cycle-Sequencing Reactions.

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jul 5;2017(7):pdb.prot094607. doi: 10.1101/pdb.prot094607.

PMID:
27803269
28.

Library Quantification Using SYBR Green-Quantitative Polymerase Chain Reaction (qPCR).

Mardis E, McCombie WR.

Cold Spring Harb Protoc. 2017 Jun 1;2017(6):pdb.prot094714. doi: 10.1101/pdb.prot094714.

PMID:
27803268
29.

DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling.

Martin PM, Stanley RE, Ross AP, Freitas AE, Moyer CE, Brumback AC, Iafrati J, Stapornwongkul KS, Dominguez S, Kivimäe S, Mulligan KA, Pirooznia M, McCombie WR, Potash JB, Zandi PP, Purcell SM, Sanders SJ, Zuo Y, Sohal VS, Cheyette BNR.

Mol Psychiatry. 2018 Feb;23(2):467-475. doi: 10.1038/mp.2016.184. Epub 2016 Oct 18.

30.

Coming of age: ten years of next-generation sequencing technologies.

Goodwin S, McPherson JD, McCombie WR.

Nat Rev Genet. 2016 May 17;17(6):333-51. doi: 10.1038/nrg.2016.49. Review.

PMID:
27184599
31.

Exome Sequencing of Familial Bipolar Disorder.

Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, Stahl E, Moran JL, Hultman CM, Landén M, Purcell SM, Sklar P, Zandi PP, McCombie WR, Potash JB.

JAMA Psychiatry. 2016 Jun 1;73(6):590-7. doi: 10.1001/jamapsychiatry.2016.0251.

32.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR.

Genome Res. 2015 Nov;25(11):1750-6. doi: 10.1101/gr.191395.115. Epub 2015 Oct 7.

33.

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.

Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12462-7. doi: 10.1073/pnas.1516718112. Epub 2015 Sep 21.

34.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.

35.

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.

Li Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, Edwards MB, McCombie WR, Martienssen RA, Coruzzi GM.

Genome Biol. 2015 Apr 19;16:79. doi: 10.1186/s13059-015-0640-2.

36.

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.

Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.

Bioinformatics. 2015 Jun 15;31(12):2040-2. doi: 10.1093/bioinformatics/btv089. Epub 2015 Feb 13.

37.

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR.

Genome Biol. 2014;15(11):506.

38.

The contribution of de novo coding mutations to autism spectrum disorder.

Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M.

Nature. 2014 Nov 13;515(7526):216-21. doi: 10.1038/nature13908. Epub 2014 Oct 29.

39.

Validation and assessment of variant calling pipelines for next-generation sequencing.

Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, Zandi PP.

Hum Genomics. 2014 Jul 30;8:14. doi: 10.1186/1479-7364-8-14.

40.

Two waves of de novo methylation during mouse germ cell development.

Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ.

Genes Dev. 2014 Jul 15;28(14):1544-9. doi: 10.1101/gad.244350.114.

41.

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.

Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10371-6. doi: 10.1073/pnas.1404657111. Epub 2014 Jun 23.

42.

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability.

McCarthy SE, Gillis J, Kramer M, Lihm J, Yoon S, Berstein Y, Mistry M, Pavlidis P, Solomon R, Ghiban E, Antoniou E, Kelleher E, O'Brien C, Donohoe G, Gill M, Morris DW, McCombie WR, Corvin A.

Mol Psychiatry. 2014 Jun;19(6):652-8. doi: 10.1038/mp.2014.29. Epub 2014 Apr 29.

43.

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

Grativol C, Regulski M, Bertalan M, McCombie WR, da Silva FR, Zerlotini Neto A, Vicentini R, Farinelli L, Hemerly AS, Martienssen RA, Ferreira PC.

Plant J. 2014 Jul;79(1):162-72. doi: 10.1111/tpj.12539. Epub 2014 Jun 17.

44.

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.

Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR.

Bioinformatics. 2014 Apr 15;30(8):1175-1176. Epub 2014 Jan 5.

PMID:
24395755
45.

Unlocking the treasure trove: from genes to schizophrenia biology.

McCarthy SE, McCombie WR, Corvin A.

Schizophr Bull. 2014 May;40(3):492-6. doi: 10.1093/schbul/sbu042. Epub 2014 Mar 27. Review.

46.

DISC1 as a genetic risk factor for schizophrenia and related major mental illness: response to Sullivan.

Porteous DJ, Thomson PA, Millar JK, Evans KL, Hennah W, Soares DC, McCarthy S, McCombie WR, Clapcote SJ, Korth C, Brandon NJ, Sawa A, Kamiya A, Roder JC, Lawrie SM, McIntosh AM, St Clair D, Blackwood DH.

Mol Psychiatry. 2014 Feb;19(2):141-3. doi: 10.1038/mp.2013.160. No abstract available.

47.

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T.

Rice (N Y). 2013 Feb 6;6(1):4. doi: 10.1186/1939-8433-6-4.

48.

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.

Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA.

BMC Genomics. 2013 Oct 11;14:701. doi: 10.1186/1471-2164-14-701.

49.

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.

Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S, Zhu W, Davidson NO, Denoya P, Li E.

BMC Bioinformatics. 2013;14 Suppl 9:S1. doi: 10.1186/1471-2105-14-S9-S1. Epub 2013 Jun 28.

50.

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA.

Nat Commun. 2013;4:2145. doi: 10.1038/ncomms3145.

PMID:
23900278

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