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Items: 1 to 50 of 86

1.

New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing.

Martinez-Viaud KA, Lawley CT, Vergara MM, Ben-Zvi G, Biniashvili T, Baruch K, St Leger J, Le J, Natarajan A, Rivera M, Guillergan M, Jaeger E, Steffy B, Zimin A.

Gigascience. 2019 Jan 29. doi: 10.1093/gigascience/giy168. [Epub ahead of print]

PMID:
30698692
2.

A Russian validation study of the Coma Recovery Scale-Revised (CRS-R).

Iazeva EG, Legostaeva LA, Zimin AA, Sergeev DV, Domashenko MA, Samorukov VY, Yusupova DG, Ryabinkina JV, Suponeva NA, Piradov MA, Bodien YG, Giacino JT.

Brain Inj. 2018 Nov 2:1-8. doi: 10.1080/02699052.2018.1539248. [Epub ahead of print]

PMID:
30388893
3.

[The Russian version of Coma Recovery Scale-revised - a standardized method for assessment of patients with disorders of consciousness].

Mochalova EG, Legostaeva LA, Zimin AA, Yusupova DG, Sergeev DV, Ryabinkina YV, Bodien Y, Suponeva NA, Piradov MA.

Zh Nevrol Psikhiatr Im S S Korsakova. 2018;118(3. Vyp. 2):25-31. doi: 10.17116/jnevro20181183225-31. Russian.

PMID:
29798977
4.

Mineral Grains, Dimples, and Hot Volcanic Organic Streams: Dynamic Geological Backstage of Macromolecular Evolution.

Skoblikow NE, Zimin AA.

J Mol Evol. 2018 Apr;86(3-4):172-183. doi: 10.1007/s00239-018-9839-7. Epub 2018 Mar 28.

PMID:
29594426
5.

[The first episode of spontaneous pneumothorax (errors, hazards, complications)].

Polyantsev AA, Bykov AV, Polyantsev AA, Kotrunov VV, Zimin AG, Dyachkova YA.

Khirurgiia (Mosk). 2018;(3):64-69. doi: 10.17116/hirurgia2018364-69. Russian.

PMID:
29560962
6.

Two novel thermally resistant endolysins encoded by pseudo T-even bacteriophages RB43 and RB49.

Mikoulinskaia GV, Chernyshov SV, Shavrina MS, Molochkov NV, Lysanskaya VY, Zimin AA.

J Gen Virol. 2018 Feb 1. doi: 10.1099/jgv.0.001014. [Epub ahead of print]

PMID:
29458521
7.

MUMmer4: A fast and versatile genome alignment system.

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A.

PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. doi: 10.1371/journal.pcbi.1005944. eCollection 2018 Jan.

8.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.

PMID:
29143815
9.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL.

Gigascience. 2017 Nov 1;6(11):1-7. doi: 10.1093/gigascience/gix097.

10.

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

Williams JL, Iamartino D, Pruitt KD, Sonstegard T, Smith TPL, Low WY, Biagini T, Bomba L, Capomaccio S, Castiglioni B, Coletta A, Corrado F, Ferré F, Iannuzzi L, Lawley C, Macciotta N, McClure M, Mancini G, Matassino D, Mazza R, Milanesi M, Moioli B, Morandi N, Ramunno L, Peretti V, Pilla F, Ramelli P, Schroeder S, Strozzi F, Thibaud-Nissen F, Zicarelli L, Ajmone-Marsan P, Valentini A, Chillemi G, Zimin A.

Gigascience. 2017 Oct 1;6(10):1-6. doi: 10.1093/gigascience/gix088.

11.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

12.

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans).

Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL.

G3 (Bethesda). 2017 Nov 6;7(11):3831-3836. doi: 10.1534/g3.117.300107.

13.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

14.

Far-Zone Resonant Energy Transfer in X-ray Photoemission as a Structure Determination Tool.

Céolin D, Rueff JP, Zimin A, Morin P, Kimberg V, Polyutov S, Ågren H, Gel'mukhanov F.

J Phys Chem Lett. 2017 Jun 15;8(12):2730-2734. doi: 10.1021/acs.jpclett.7b00835. Epub 2017 Jun 7.

PMID:
28562043
15.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

16.

Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering.

Ignatova N, Cruz VV, Couto RC, Ertan E, Zimin A, Guimarães FF, Polyutov S, Ågren H, Kimberg V, Odelius M, Gel'mukhanov F.

Sci Rep. 2017 Mar 7;7:43891. doi: 10.1038/srep43891.

17.

Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species.

Muñoz A, Santos Muñoz D, Zimin A, Yorke JA.

BMC Genomics. 2016 Nov 11;17(Suppl 10):826. doi: 10.1186/s12864-016-3102-7.

18.

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL.

Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27.

19.

Polychromatic light (480-3400nm) similar to the terrestrial solar spectrum without its UV component in post-surgical immunorehabilitation of breast cancer patients.

Zhevago NA, Zimin AA, Glazanova TV, Davydova NI, Bychkova NV, Chubukina ZV, Buinyakova AI, Ballyuzek MF, Samoilova KA.

J Photochem Photobiol B. 2017 Jan;166:44-51. doi: 10.1016/j.jphotobiol.2016.10.040. Epub 2016 Nov 5.

PMID:
27865134
20.

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.

Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH.

G3 (Bethesda). 2017 Jan 5;7(1):109-117. doi: 10.1534/g3.116.035923.

21.

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.

22.

In vitro study of the antibacterial effect of the bacteriophage T5 thermostable endolysin on Escherichia coli cells.

Shavrina MS, Zimin AA, Molochkov NV, Chernyshov SV, Machulin AV, Mikoulinskaia GV.

J Appl Microbiol. 2016 Nov;121(5):1282-1290. doi: 10.1111/jam.13251. Epub 2016 Sep 19.

PMID:
27501055
23.

Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions.

Schmitz J, Noll A, Raabe CA, Churakov G, Voss R, Kiefmann M, Rozhdestvensky T, Brosius J, Baertsch R, Clawson H, Roos C, Zimin A, Minx P, Montague MJ, Wilson RK, Warren WC.

Nat Commun. 2016 Oct 6;7:12997. doi: 10.1038/ncomms12997.

24.

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.

Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC.

Nat Commun. 2016 Jun 2;7:11757. doi: 10.1038/ncomms11757.

25.

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ.

G3 (Bethesda). 2016 Jun 1;6(6):1607-16. doi: 10.1534/g3.116.028746.

26.

The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.

PMID:
27088604
27.
28.

Regulatory systemic effect of postsurgical polychromatic light (480-3400 nm) irradiation of breast cancer patients on the proliferation of tumor and normal cells in vitro.

Samoilova KA, Zimin AA, Buinyakova AI, Makela AM, Zhevago NA.

Photomed Laser Surg. 2015 Nov;33(11):555-63. doi: 10.1089/pho.2014.3878. Epub 2015 Oct 5.

PMID:
26436466
29.

QuorUM: An Error Corrector for Illumina Reads.

Marçais G, Yorke JA, Zimin A.

PLoS One. 2015 Jun 17;10(6):e0130821. doi: 10.1371/journal.pone.0130821. eCollection 2015.

30.

Transposable element islands facilitate adaptation to novel environments in an invasive species.

Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, Oettler J.

Nat Commun. 2014 Dec 16;5:5495. doi: 10.1038/ncomms6495.

31.

A new rhesus macaque assembly and annotation for next-generation sequencing analyses.

Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, Treangen T, Salzberg SL, Yorke JA, Norgren RB Jr.

Biol Direct. 2014 Oct 14;9(1):20. doi: 10.1186/1745-6150-9-20.

32.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

33.

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.

34.

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.

35.

Next-generation sequencing strategies for characterizing the turkey genome.

Dalloul RA, Zimin AV, Settlage RE, Kim S, Reed KM.

Poult Sci. 2014 Feb;93(2):479-84. doi: 10.3382/ps.2013-03560.

PMID:
24570472
36.

The MaSuRCA genome assembler.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.

Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476. Epub 2013 Aug 29.

37.

[The efficacy of polychromatic visible and infrared radiation used for the postoperative immunological rehabilitation of patients with breast cancer].

zhevago NA, Samoĭlova KA, Davydova NI, Bychkova NV, Glazanova TV, Chubukina ZhV, Buĭniakova AI, Zimin AA.

Vopr Kurortol Fizioter Lech Fiz Kult. 2012 Jul-Aug;(4):23-32. Russian.

PMID:
22994061
38.

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA.

PLoS One. 2012;7(8):e42680. doi: 10.1371/journal.pone.0042680. Epub 2012 Aug 3.

39.
40.

[Survival among patients with prostate cancer after distant radiotherapy and low-intensity near-infrared phototherapy].

Zharinov GM, Zimin AA, Samoĭlova KA, Neklasova NIu.

Vopr Onkol. 2011;57(4):457-61. Russian.

PMID:
22191234
41.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

42.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5667-72. doi: 10.1073/pnas.1007901108. Epub 2011 Jan 31.

43.

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile).

Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5673-8. doi: 10.1073/pnas.1008617108. Epub 2011 Jan 31.

44.
45.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

PLoS Biol. 2010 Sep 7;8(9). pii: e1000475. doi: 10.1371/journal.pbio.1000475.

46.

[Application of low-power visible and near infrared radiation in clinical oncology].

Zimin AA, Zhevago NA, Buĭniakova AI, Samoĭlova KA.

Vopr Kurortol Fizioter Lech Fiz Kult. 2009 Nov-Dec;(6):49-52. Review. Russian.

PMID:
20017385
47.

Identification and characterization of the metal ion-dependent L-alanoyl-D-glutamate peptidase encoded by bacteriophage T5.

Mikoulinskaia GV, Odinokova IV, Zimin AA, Lysanskaya VY, Feofanov SA, Stepnaya OA.

FEBS J. 2009 Dec;276(24):7329-42. doi: 10.1111/j.1742-4658.2009.07443.x.

48.

A whole-genome assembly of the domestic cow, Bos taurus.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL.

Genome Biol. 2009;10(4):R42. doi: 10.1186/gb-2009-10-4-r42. Epub 2009 Apr 24.

49.

Role of nitric oxide in the visible light-induced rapid increase of human skin microcirculation at the local and systemic levels: II. healthy volunteers.

Samoilova KA, Zhevago NA, Petrishchev NN, Zimin AA.

Photomed Laser Surg. 2008 Oct;26(5):443-9. doi: 10.1089/pho.2007.2205.

PMID:
18922087
50.

Improving Phrap-based assembly of the rat using "reliable" overlaps.

Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J.

PLoS One. 2008 Mar 19;3(3):e1836. doi: 10.1371/journal.pone.0001836.

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