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Items: 20

1.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

2.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

3.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

4.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

5.

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.

PMID:
23698360
6.

The genome of Chelonid herpesvirus 5 harbors atypical genes.

Ackermann M, Koriabine M, Hartmann-Fritsch F, de Jong PJ, Lewis TD, Schetle N, Work TM, Dagenais J, Balazs GH, Leong JA.

PLoS One. 2012;7(10):e46623. doi: 10.1371/journal.pone.0046623. Epub 2012 Oct 2.

7.

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.

Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A.

Cancer Genet. 2011 Aug;204(8):447-57. doi: 10.1016/j.cancergen.2011.07.009. Erratum in: Cancer Genet. 2011 Dec;204(12):694. Coarfa, Cristian [added];Schoenherr, Caroline [added].

8.

The genome of the green anole lizard and a comparative analysis with birds and mammals.

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K.

Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390.

9.

Evolution of a bitter taste receptor gene cluster in a New World sparrow.

Davis JK, Lowman JJ, Thomas PJ, ten Hallers BF, Koriabine M, Huynh LY, Maney DL, de Jong PJ, Martin CL; NISC Comparative Sequencing Program, Thomas JW.

Genome Biol Evol. 2010 Jul 12;2:358-70. doi: 10.1093/gbe/evq027.

10.

Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map.

McGraw LA, Davis JK, Lowman JJ, ten Hallers BF, Koriabine M, Young LJ, de Jong PJ, Rudd MK, Thomas JW.

BMC Genomics. 2010 Jan 28;11:70. doi: 10.1186/1471-2164-11-70.

11.

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster.

Venken KJ, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, Wan KH, Koriabine M, de Jong PJ, White KP, Bellen HJ, Hoskins RA.

Nat Methods. 2009 Jun;6(6):431-4. doi: 10.1038/nmeth.1331.

12.

Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy.

Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, Sabol SL, Cui C, Bai Y, Koriabine M, Yoshinaga Y, Cheng JF, Chen F, Martin J, Schackwitz W, Gunn TM, Kramer KL, De Jong PJ, Pennacchio LA, Lo CW.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3219-24. doi: 10.1073/pnas.0813400106. Epub 2009 Feb 13.

13.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

14.

Construction of a California condor BAC library and first-generation chicken-condor comparative physical map as an endangered species conservation genomics resource.

Romanov MN, Koriabine M, Nefedov M, de Jong PJ, Ryder OA.

Genomics. 2006 Dec;88(6):711-718. doi: 10.1016/j.ygeno.2006.06.005. Epub 2006 Aug 1.

15.

Exploring transformation-associated recombination cloning for selective isolation of genomic regions.

Kouprina N, Noskov VN, Koriabine M, Leem SH, Larionov V.

Methods Mol Biol. 2004;255:69-89. No abstract available.

PMID:
15020816
16.

Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast.

Kouprina N, Leem SH, Solomon G, Ly A, Koriabine M, Otstot J, Pak E, Dutra A, Zhao S, Barrett JC, Larionov V.

EMBO Rep. 2003 Mar;4(3):257-62.

17.

Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes.

Kouprina N, Ebersole T, Koriabine M, Pak E, Rogozin IB, Katoh M, Oshimura M, Ogi K, Peredelchuk M, Solomon G, Brown W, Barrett JC, Larionov V.

Nucleic Acids Res. 2003 Feb 1;31(3):922-34.

18.

A genetic system for direct selection of gene-positive clones during recombinational cloning in yeast.

Noskov V, Kouprina N, Leem SH, Koriabine M, Barrett JC, Larionov V.

Nucleic Acids Res. 2002 Jan 15;30(2):E8.

19.

Defining the minimal length of sequence homology required for selective gene isolation by TAR cloning.

Noskov VN, Koriabine M, Solomon G, Randolph M, Barrett JC, Leem SH, Stubbs L, Kouprina N, Larionov V.

Nucleic Acids Res. 2001 Mar 15;29(6):E32.

20.

Integrity of human YACs during propagation in recombination-deficient yeast strains.

Kouprina N, Nikolaishvili N, Graves J, Koriabine M, Resnick MA, Larionov V.

Genomics. 1999 Mar 15;56(3):262-73.

PMID:
10087193

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