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Items: 22

1.

Author Correction: Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG.

Nat Commun. 2018 Dec 19;9(1):5398. doi: 10.1038/s41467-018-07917-0.

2.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis.

Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ.

Genome Res. 2018 May;28(5):639-653. doi: 10.1101/gr.226993.117. Epub 2018 Apr 11.

3.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo.

Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH Jr, Ewing AD, Faulkner GJ.

Genome Res. 2017 Aug;27(8):1395-1405. doi: 10.1101/gr.219022.116. Epub 2017 May 8.

4.

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

Carreira PE, Ewing AD, Li G, Schauer SN, Upton KR, Fagg AC, Morell S, Kindlova M, Gerdes P, Richardson SR, Li B, Gerhardt DJ, Wang J, Brennan PM, Faulkner GJ.

Mob DNA. 2016 Nov 11;7:21. doi: 10.1186/s13100-016-0076-6. eCollection 2016.

5.

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG.

Nat Commun. 2016 Jan 8;7:10286. doi: 10.1038/ncomms10286. Erratum in: Nat Commun. 2018 Dec 19;9(1):5398.

6.

Ubiquitous L1 mosaicism in hippocampal neurons.

Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, van der Knaap MS, Brennan PM, Vanderver A, Faulkner GJ.

Cell. 2015 Apr 9;161(2):228-39. doi: 10.1016/j.cell.2015.03.026.

7.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

8.

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Nat Protoc. 2014 May;9(5):989-1009. doi: 10.1038/nprot.2014.058. Epub 2014 Apr 3.

PMID:
24705597
9.

Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L.

Clarke WE, Parkin IA, Gajardo HA, Gerhardt DJ, Higgins E, Sidebottom C, Sharpe AG, Snowdon RJ, Federico ML, Iniguez-Luy FL.

PLoS One. 2013 Dec 3;8(12):e81992. doi: 10.1371/journal.pone.0081992. eCollection 2013.

10.

An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse.

Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E.

Genome Biol. 2013;14(9):R96.

11.

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N.

Plant J. 2013 Nov;76(3):494-505. doi: 10.1111/tpj.12294. Epub 2013 Aug 24.

12.

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.

Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, Samuel D, Natoli G, Carninci P, Ciccarelli FD, Garcia-Perez JL, Faivre J, Faulkner GJ.

Cell. 2013 Mar 28;153(1):101-11. doi: 10.1016/j.cell.2013.02.032.

13.

Changes in genome content generated via segregation of non-allelic homologs.

Liu S, Ying K, Yeh CT, Yang J, Swanson-Wagner R, Wu W, Richmond T, Gerhardt DJ, Lai J, Springer N, Nettleton D, Jeddeloh JA, Schnable PS.

Plant J. 2012 Nov;72(3):390-9. doi: 10.1111/j.1365-313X.2012.05087.x. Epub 2012 Aug 30.

14.

Targeted re-sequencing of the allohexaploid wheat exome.

Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D'Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ.

Plant Biotechnol J. 2012 Aug;10(6):733-42. doi: 10.1111/j.1467-7652.2012.00713.x. Epub 2012 Jun 18.

15.

Structural variants in the soybean genome localize to clusters of biotic stress-response genes.

McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM.

Plant Physiol. 2012 Aug;159(4):1295-308. doi: 10.1104/pp.112.194605. Epub 2012 Jun 13.

16.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

17.

Somatic retrotransposition alters the genetic landscape of the human brain.

Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ.

Nature. 2011 Oct 30;479(7374):534-7. doi: 10.1038/nature10531.

18.

Mutation discovery in mice by whole exome sequencing.

Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst FJ, Bergstrom DE, Murray SA, Bult C, Richardson J, Kile BT, Gut I, Hager J, Sigurdsson S, Mauceli E, Di Palma F, Lindblad-Toh K, Cunningham ML, Cox TC, Justice MJ, Spector MS, Lowe SW, Albert T, Donahue LR, Jeddeloh J, Shendure J, Reinholdt LG.

Genome Biol. 2011 Sep 14;12(9):R86. doi: 10.1186/gb-2011-12-9-r86.

19.

Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean.

Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP.

Plant Physiol. 2011 May;156(1):240-53. doi: 10.1104/pp.110.170811. Epub 2011 Feb 14.

20.

The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82.

Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM.

Plant Physiol. 2011 Feb;155(2):645-55. doi: 10.1104/pp.110.166736. Epub 2010 Nov 29.

21.

Repeat subtraction-mediated sequence capture from a complex genome.

Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS.

Plant J. 2010 Jun 1;62(5):898-909. doi: 10.1111/j.1365-313X.2010.04196.x. Epub 2010 Mar 4.

22.

First Report of Cactodera milleri in Wisconsin.

Schroeder NE, Gerhardt DJ, Phibbs A, MacGuidwin AE.

Plant Dis. 2008 Apr;92(4):656. doi: 10.1094/PDIS-92-4-0656B.

PMID:
30769664

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