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Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.
Published in:
PLoS Genetics, 2020, v. 16, n. 1, p. 1, doi. 10.1371/journal.pgen.1008571
By:
- Read, Andrew C.;
- Moscou, Matthew J.;
- Zimin, Aleksey V.;
- Pertea, Geo;
- Meyer, Rachel S.;
- Purugganan, Michael D.;
- Leach, Jan E.;
- Triplett, Lindsay R.;
- Salzberg, Steven L.;
- Bogdanove, Adam J.
Publication type:
Article
Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation.
Published in:
Genetics, 2014, v. 196, n. 3, p. 891, doi. 10.1534/genetics.113.159996
By:
- Wegrzyn, Jill L.;
- Liechty, John D.;
- Stevens, Kristian A.;
- Le-Shin Wu;
- Loopstra, Carol A.;
- Vasquez-Gross, Hans A.;
- Dougherty, William M.;
- Lin, Brian Y.;
- Zieve, Jacob J.;
- Martínez-García, Pedro J.;
- Holt, Carson;
- Yandell, Mark;
- Zimin, Aleksey V.;
- Yorke, James A.;
- Crepeau, Marc W.;
- Puiu, Daniela;
- Salzberg, Steven L.;
- de Jong, Pieter J.;
- Mockaitis, Keithanne;
- Main, Doreen
Publication type:
Article
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29584-y
By:
- Sork, Victoria L.;
- Cokus, Shawn J.;
- Fitz-Gibbon, Sorel T.;
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Garcia, Jesse A.;
- Gugger, Paul F.;
- Henriquez, Claudia L.;
- Zhen, Ying;
- Lohmueller, Kirk E.;
- Pellegrini, Matteo;
- Salzberg, Steven L.
Publication type:
Article
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus.
Published in:
GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad002
By:
- Miller, Jeremiah;
- Zimin, Aleksey V;
- Gordus, Andrew
Publication type:
Article
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.
Published in:
GigaScience, 2020, v. 9, n. 5, p. N.PAG, doi. 10.1093/gigascience/giaa050
By:
- Marrano, Annarita;
- Britton, Monica;
- Zaini, Paulo A;
- Zimin, Aleksey V;
- Workman, Rachael E;
- Puiu, Daniela;
- Bianco, Luca;
- Pierro, Erica Adele Di;
- Allen, Brian J;
- Chakraborty, Sandeep;
- Troggio, Michela;
- Leslie, Charles A;
- Timp, Winston;
- Dandekar, Abhaya;
- Salzberg, Steven L;
- Neale, David B
Publication type:
Article
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.
Published in:
GigaScience, 2017, v. 6, n. 11, p. 1, doi. 10.1093/gigascience/gix097
By:
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Hall, Richard;
- Kingan, Sarah;
- Clavijo, Bernardo J.;
- Salzberg, Steven L.
Publication type:
Article
An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.
Published in:
GigaScience, 2017, v. 6, n. 1, p. 1, doi. 10.1093/gigascience/giw016
By:
- Zimin, Aleksey V.;
- Stevens, Kristian A.;
- Crepeau, Marc W.;
- Puiu, Daniela;
- Wegrzyn, Jill L.;
- Yorke, James A.;
- Langley, Charles H.;
- Neale, David B.;
- Salzberg, Steven L.
Publication type:
Article
Mis-Assembled "Segmental Duplications" in Two Versions of the Bos taurus Genome.
Published in:
PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0042680
By:
- Zimin, Aleksey V.;
- Kelley, David R.;
- Roberts, Michael;
- Marçais, Guillaume;
- Salzberg, Steven L.;
- Yorke, James A.;
- Jordan, I. King
Publication type:
Article
Improving Phrap-Based Assembly of the Rat Using "Reliable" Overlaps.
Published in:
PLoS ONE, 2008, v. 3, n. 3, p. 1, doi. 10.1371/journal.pone.0001836
By:
- Roberts, Michael;
- Zimin, Aleksey V.;
- Hayes, Wayne;
- Hunt, Brian R.;
- Ustun, Cevat;
- White, James R.;
- Havlak, Paul;
- Yorke, James
Publication type:
Article
The SAMBA tool uses long reads to improve the contiguity of genome assemblies.
Published in:
PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009860
By:
- Zimin, Aleksey V.;
- Salzberg, Steven L.
Publication type:
Article
A genome sequence for the threatened whitebark pine.
Published in:
G3: Genes | Genomes | Genetics, 2024, v. 14, n. 5, p. 1, doi. 10.1093/g3journal/jkae061
By:
- Neale, David B;
- Zimin, Aleksey V;
- Meltzer, Amy;
- Bhattarai, Akriti;
- Amee, Maurice;
- Corona, Laura Figueroa;
- Allen, Brian J;
- Puiu, Daniela;
- Wright, Jessica;
- Torre, Amanda R De La;
- McGuire, Patrick E;
- Timp, Winston;
- Salzberg, Steven L;
- Wegrzyn, Jill L
Publication type:
Article
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual.
Published in:
G3: Genes | Genomes | Genetics, 2023, v. 13, n. 3, p. 1, doi. 10.1093/g3journal/jkac321
By:
- Kuan-Hao Chao;
- Zimin, Aleksey V.;
- Pertea, Mihaela;
- Salzberg, Steven L.
Publication type:
Article
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.
Published in:
G3: Genes | Genomes | Genetics, 2022, v. 12, n. 1, p. 1, doi. 10.1093/g3journal/jkab380
By:
- Neale, David B.;
- Zimin, Aleksey V.;
- Zaman, Sumaira;
- Scott, Alison D.;
- Shrestha, Bikash;
- Workman, Rachael E.;
- Puiu, Daniela;
- Allen, Brian J.;
- Moore, Zane J.;
- Sekhwal, Manoj K.;
- De La Torre, Amanda R.;
- McGuire, Patrick E.;
- Burns, Emily;
- Timp, Winston;
- Wegrzyn, Jill L.;
- Salzberg, Steven L.
Publication type:
Article
A Reference Genome Sequence for Giant Sequoia.
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 11, p. 3907, doi. 10.1534/g3.120.401612
By:
- Scott, Alison D.;
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Workman, Rachael;
- Britton, Monica;
- Zaman, Sumaira;
- Caballero, Madison;
- Read, Andrew C.;
- Bogdanove, Adam J.;
- Burns, Emily;
- Wegrzyn, Jill;
- Timp, Winston;
- Salzberg, Steven L.;
- Neale, David B.
Publication type:
Article
The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.
Published in:
G3: Genes | Genomes | Genetics, 2017, v. 7, n. 9, p. 3157, doi. 10.1534/g3.117.300078
By:
- Neale, David B.;
- McGuire, Patrick E.;
- Wheeler, Nicholas C.;
- Stevens, Kristian A.;
- Crepeau, Marc W.;
- Cardeno, Charis;
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Pertea, Geo M.;
- Sezen, U. Uzay;
- Casola, Claudio;
- Koralewski, Tomasz E.;
- Paul, Robin;
- Gonzalez-Ibeas, Daniel;
- Zaman, Sumaira;
- Cronn, Richard;
- Yandell, Mark;
- Holt, Carson;
- Langley, Charles H.;
- Yorke, James A.
Publication type:
Article
A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.
Published in:
G3: Genes | Genomes | Genetics, 2016, v. 6, n. 6, p. 1607, doi. 10.1534/g3.116.028746
By:
- Gang Li;
- Hillier, LaDeana W.;
- Grahn, Robert A.;
- Zimin, Aleksey V.;
- David, Victor A.;
- Menotti-Raymond, Marilyn;
- Middleton, Rondo;
- Hannah, Steven;
- Hendrickson, Sher;
- Makunin, Alex;
- O' Brien, Stephen J.;
- Minx, Pat;
- Wilson, Richard K.;
- Lyons, Leslie A.;
- Warren, Wesley C.;
- Murphy, William J.
Publication type:
Article
Extracting Envelopes of Nonzonally Propagating Rossby Wave Packets.
Published in:
Monthly Weather Review, 2006, v. 134, n. 4, p. 1329, doi. 10.1175/MWR3122.1
By:
- Zimin, Aleksey V.;
- Szunyogh, Istvan;
- Hunt, Brian R.;
- Ott, Edward
Publication type:
Article
Extracting Envelopes of Rossby Wave Packets.
Published in:
Monthly Weather Review, 2003, v. 131, n. 5, p. 1011, doi. 10.1175/1520-0493(2003)131<1011:EEORWP>2.0.CO;2
By:
- Zimin, Aleksey V.;
- Szunyogh, Istvan;
- Patil, D. J.;
- Hunt, Brian R.;
- Ott, Edward
Publication type:
Article
Propagation of the Effect of Targeted Observations: The 2000 Winter Storm Reconnaissance Program.
Published in:
Monthly Weather Review, 2002, v. 130, n. 5, p. 1144, doi. 10.1175/1520-0493(2002)130<1144:POTEOT>2.0.CO;2
By:
- Szunyogh, Istvan;
- Toth, Zoltan;
- Zimin, Aleksey V.;
- Majumdar, Sharanya J.;
- Persson, Anders
Publication type:
Article
Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly.
Published in:
Genome Biology & Evolution, 2023, v. 15, n. 7, p. 1, doi. 10.1093/gbe/evad118
By:
- Reinhardt, Josephine A;
- Baker, Richard H;
- Zimin, Aleksey V;
- Ladias, Chloe;
- Paczolt, Kimberly A;
- Werren, John H;
- Hayashi, Cheryl Y;
- Wilkinson, Gerald S
Publication type:
Article
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.
Published in:
Genome Biology, 2014, v. 15, n. 2, p. R59, doi. 10.1186/gb-2014-15-3-r59
By:
- Neale, David B.;
- Wegrzyn, Jill L.;
- Stevens, Kristian A.;
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Crepeau, Marc W.;
- Cardeno, Charis;
- Koriabine, Maxim;
- Holtz-Morris, Ann E.;
- Liechty, John D.;
- Martínez-García, Pedro J.;
- Vasquez-Gross, Hans A.;
- Lin, Brian Y.;
- Zieve, Jacob J.;
- Dougherty, William M.;
- Fuentes-Soriano, Sara;
- Le-Shin Wu;
- Gilbert, Don;
- Marçais, Guillaume;
- Roberts, Michael
Publication type:
Article
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
Published in:
PLoS Computational Biology, 2020, v. 16, n. 6, p. 1, doi. 10.1371/journal.pcbi.1007981
By:
- Zimin, Aleksey V.;
- Salzberg, Steven L.
Publication type:
Article
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
Published in:
PLoS Computational Biology, 2023, v. 19, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011032
By:
- Guo, Alina;
- Salzberg, Steven L.;
- Zimin, Aleksey V.
Publication type:
Article
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis.
Published in:
PLoS Biology, 2010, v. 8, n. 9, p. 1, doi. 10.1371/journal.pbio.1000475
By:
- Dalloul, Rami A.;
- Long, Julie A.;
- Zimin, Aleksey V.;
- Aslam, Luqman;
- Beal, Kathryn;
- Blomberg, Le Ann;
- Bouffard, Pascal;
- Burt, David W.;
- Crasta, Oswald;
- Crooijmans, Richard P. M. A.;
- Cooper, Kristal;
- Coulombe, Roger A.;
- De, Supriyo;
- Delany, Mary E.;
- Dodgson, Jerry B.;
- Dong, Jennifer J.;
- Evans, Clive;
- Frederickson, Karin M.;
- Flicek, Paul;
- Florea, Liliana
Publication type:
Article
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Published in:
Nature, 2012, v. 487, n. 7405, p. 94, doi. 10.1038/nature11041
By:
- Dasmahapatra, Kanchon K.;
- Walters, James R.;
- Briscoe, Adriana D.;
- Davey, John W.;
- Whibley, Annabel;
- Nadeau, Nicola J.;
- Zimin, Aleksey V.;
- Hughes, Daniel S. T.;
- Ferguson, Laura C.;
- Martin, Simon H.;
- Salazar, Camilo;
- Lewis, James J.;
- Adler, Sebastian;
- Ahn, Seung-Joon;
- Baker, Dean A.;
- Baxter, Simon W.;
- Chamberlain, Nicola L.;
- Chauhan, Ritika;
- Counterman, Brian A.;
- Dalmay, Tamas
Publication type:
Article
Assembly reconciliation.
Published in:
Bioinformatics, 2008, v. 24, n. 1, p. 42, doi. 10.1093/bioinformatics/btm542
By:
- Aleksey V. Zimin;
- Douglas R. Smith;
- Granger Sutton;
- James A. Yorke
Publication type:
Article
A reference-quality, fully annotated genome from a Puerto Rican individual.
Published in:
Genetics, 2022, v. 220, n. 2, p. 1, doi. 10.1093/genetics/iyab227
By:
- Zimin, Aleksey V.;
- Shumate, Alaina;
- Shinder, Ida;
- Heinz, Jakob;
- Puiu, Daniela;
- Pertea, Mihaela;
- Salzberg, Steven L.
Publication type:
Article
Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies.
Published in:
Genetics, 2020, v. 216, n. 2, p. 599, doi. 10.1534/genetics.120.303501
By:
- Alonge, Michael;
- Shumate, Alaina;
- Puiu, Daniela;
- Zimin, Aleksey V.;
- Salzberg, Steven L.
Publication type:
Article
A new rhesus macaque assembly and annotation for next-generation sequencing analyses.
Published in:
Biology Direct, 2014, v. 9, n. 1, p. 20, doi. 10.1186/1745-6150-9-20
By:
- Zimin, Aleksey V.;
- Cornish, Adam S.;
- Maudhoo, Mnirnal D.;
- Gibbs, Robert M.;
- Xiongfei Zhang;
- Pandey, Sanjit;
- Meehan, Daniel T.;
- Wipfler, Kristin;
- Bosinger, Steven E.;
- Johnson, Zachary P.;
- Tharp, Gregory K.;
- Marçais, Guillaume;
- Roberts, Michael;
- Ferguson, Betsy;
- Fox, Howard S.;
- Treangen, Todd;
- Salzberg, Steven L.;
- Yorke, James A.;
- Norgren Jr, Robert B.
Publication type:
Article
Assembly and annotation of an Ashkenazi human reference genome.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02047-7
By:
- Shumate, Alaina;
- Zimin, Aleksey V.;
- Sherman, Rachel M.;
- Puiu, Daniela;
- Wagner, Justin M.;
- Olson, Nathan D.;
- Pertea, Mihaela;
- Salit, Marc L.;
- Zook, Justin M.;
- Salzberg, Steven L.
Publication type:
Article
Transcriptome assembly from long-read RNA-seq alignments with StringTie2.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1910-1
By:
- Kovaka, Sam;
- Zimin, Aleksey V.;
- Pertea, Geo M.;
- Razaghi, Roham;
- Salzberg, Steven L.;
- Pertea, Mihaela
Publication type:
Article
The MaSuRCA genome assembler.
Published in:
Bioinformatics, 2013, v. 29, n. 21, p. 2669, doi. 10.1093/bioinformatics/btt476
By:
- Zimin, Aleksey V.;
- Marçais, Guillaume;
- Puiu, Daniela;
- Roberts, Michael;
- Salzberg, Steven L.;
- Yorke, James A.
Publication type:
Article

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