Aleksey V. Zimin, Ph.D. - Publications

Institution:
University of Maryland, College Park, College Park, MD

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nature Communications. 13: 2047. PMID 35440538 DOI: 10.1038/s41467-022-29584-y  0.348
2022 Zimin AV, Salzberg SL. The SAMBA tool uses long reads to improve the contiguity of genome assemblies. Plos Computational Biology. 18: e1009860. PMID 35120119 DOI: 10.1371/journal.pcbi.1009860  0.419
2022 Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, et al. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (Bethesda, Md.). 12. PMID 35100403 DOI: 10.1093/g3journal/jkab380  0.442
2021 Zimin AV, Shumate A, Shinder I, Heinz J, Puiu D, Pertea M, Salzberg SL. A reference-quality, fully annotated genome from a Puerto Rican individual. Genetics. PMID 34897437 DOI: 10.1093/genetics/iyab227  0.447
2021 Masonbrink RE, Alt D, Bayles DO, Boggiatto P, Edwards W, Tatum F, Williams J, Wilson-Welder J, Zimin A, Severin A, Olsen S. A pseudomolecule assembly of the Rocky Mountain elk genome. Plos One. 16: e0249899. PMID 33909645 DOI: 10.1371/journal.pone.0249899  0.389
2020 Alonge M, Shumate A, Puiu D, Zimin AV, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics. 216: 599-608. PMID 33954615 DOI: 10.1534/genetics.120.303501  0.423
2020 Puiu D, Zimin A, Shumate A, Ge Y, Qiu J, Bhaskaran M, Salzberg SL. The genome of the American groundhog, . F1000research. 9: 1137. PMID 33274050 DOI: 10.12688/F1000Research.25970.1  0.546
2020 Scott AD, Zimin AV, Puiu D, Workman R, Britton M, Zaman S, Caballero M, Read AC, Bogdanove AJ, Burns E, Wegrzyn J, Timp W, Salzberg SL, Neale DB. A Reference Genome Sequence for Giant Sequoia. G3 (Bethesda, Md.). PMID 32948606 DOI: 10.1534/G3.120.401612  0.536
2020 Alonge M, Shumate A, Puiu D, Zimin A, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics. PMID 32796007 DOI: 10.1534/Genetics.120.303501  0.507
2020 Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. Plos Computational Biology. 16: e1007981. PMID 32589667 DOI: 10.1371/Journal.Pcbi.1007981  0.497
2020 Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Salit ML, Zook JM, Salzberg SL. Assembly and annotation of an Ashkenazi human reference genome. Genome Biology. 21: 129. PMID 32487205 DOI: 10.1186/S13059-020-02047-7  0.447
2020 Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, et al. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience. 9. PMID 32432329 DOI: 10.1093/Gigascience/Giaa050  0.409
2020 Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, et al. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 9. PMID 32191811 DOI: 10.1093/Gigascience/Giaa021  0.498
2020 Giordano R, Donthu RK, Zimin A, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger J, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, et al. Soybean Aphid Biotype 1 Genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology. 103334. PMID 32109587 DOI: 10.1016/J.Ibmb.2020.103334  0.354
2020 Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. Plos Genetics. 16: e1008571. PMID 31986137 DOI: 10.1371/Journal.Pgen.1008571  0.461
2019 Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology. 20: 278. PMID 31842956 DOI: 10.1186/S13059-019-1910-1  0.367
2019 Breitwieser FP, Pertea M, Zimin A, Salzberg SL. Human contamination in bacterial genomes has created thousands of spurious proteins. Genome Research. PMID 31064768 DOI: 10.1101/Gr.245373.118  0.522
2019 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. New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing. Gigascience. PMID 30698692 DOI: 10.1093/Gigascience/Giy168  0.506
2018 Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. Plos Computational Biology. 14: e1005944. PMID 29373581 DOI: 10.1371/Journal.Pcbi.1005944  0.538
2017 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, ... ... Zimin AV, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. PMID 29143815 DOI: 10.1038/Nature24486  0.53
2017 Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience. PMID 29069494 DOI: 10.1093/Gigascience/Gix097  0.529
2017 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, ... ... Zimin A, et al. Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50). Gigascience. PMID 29048578 DOI: 10.1093/Gigascience/Gix088  0.51
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1. PMID 29020755 DOI: 10.1093/Gigascience/Gix072  0.462
2017 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. First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans). G3 (Bethesda, Md.). PMID 28963165 DOI: 10.1534/G3.117.300107  0.493
2017 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, et al. The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 (Bethesda, Md.). PMID 28751502 DOI: 10.1534/G3.117.300078  0.531
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1-4. PMID 28369353 DOI: 10.1093/Gigascience/Giw016  0.462
2017 Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. PMID 28130360 DOI: 10.1101/Gr.213405.116  0.514
2016 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, et al. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (Bethesda, Md.). PMID 27852011 DOI: 10.1534/G3.116.035923  0.533
2016 Stevens KA, Wegrzyn J, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeaz D, Koriabine M, Holtz-Morris A, Martinez-Garcia P, Sezen U, Marcais G, Jermstad K, McGuire P, et al. Sequence of the Sugar Pine Megagenome. Genetics. PMID 27794028 DOI: 10.1534/Genetics.116.193227  0.513
2016 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, et al. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nature Communications. 7: 12997. PMID 27708261 DOI: 10.1038/Ncomms12997  0.504
2016 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, ... ... Zimin A, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7: 11757. PMID 27249958 DOI: 10.1038/Ncomms11757  0.492
2016 Li G, Hillier LW, Grahn R, 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, et al. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda, Md.). PMID 27172201 DOI: 10.1534/G3.116.028746  0.412
2016 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, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. PMID 27088604 DOI: 10.1038/Nature17164  0.515
2015 Marçais G, Yorke JA, Zimin A. QuorUM: An Error Corrector for Illumina Reads. Plos One. 10: e0130821. PMID 26083032 DOI: 10.1371/Journal.Pone.0130821  0.414
2014 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, et al. Transposable element islands facilitate adaptation to novel environments in an invasive species. Nature Communications. 5: 5495. PMID 25510865 DOI: 10.1038/Ncomms6495  0.411
2014 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, et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct. 9: 20. PMID 25319552 DOI: 10.1186/1745-6150-9-20  0.5
2014 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, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 196: 891-909. PMID 24653211 DOI: 10.1534/Genetics.113.159996  0.488
2014 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. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 196: 875-90. PMID 24653210 DOI: 10.1534/Genetics.113.159715  0.535
2014 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, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 15: R59. PMID 24647006 DOI: 10.1186/Gb-2014-15-3-R59  0.553
2014 Dalloul RA, Zimin AV, Settlage RE, Kim S, Reed KM. Next-generation sequencing strategies for characterizing the turkey genome. Poultry Science. 93: 479-84. PMID 24570472 DOI: 10.3382/Ps.2013-03560  0.529
2013 Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics (Oxford, England). 29: 2669-77. PMID 23990416 DOI: 10.1093/Bioinformatics/Btt476  0.502
2012 Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. Plos One. 7: e42680. PMID 22880081 DOI: 10.1371/Journal.Pone.0042680  0.523
2012 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. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111  0.534
2011 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, et al. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proceedings of the National Academy of Sciences of the United States of America. 108: 5667-72. PMID 21282651 DOI: 10.1073/Pnas.1007901108  0.504
2011 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, et al. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America. 108: 5673-8. PMID 21282631 DOI: 10.1073/Pnas.1008617108  0.491
2010 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, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  0.543
2009 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. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42  0.531
2008 Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J. Improving Phrap-based assembly of the rat using "reliable" overlaps. Plos One. 3: e1836. PMID 18350171 DOI: 10.1371/Journal.Pone.0001836  0.501
2008 Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics (Oxford, England). 24: 42-5. PMID 18057021 DOI: 10.1093/Bioinformatics/Btm542  0.437
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Zimin AV, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.493
2006 Zimin AV, Szunyogh I, Hunt BR, Ott E. Extracting envelopes of nonzonally propagating Rossby wave packets Monthly Weather Review. 134: 1329-1333. DOI: 10.1175/Mwr3122.1  0.395
2004 Baek SJ, Hunt BR, Szunyogh I, Zimin A, Ott E. Localized error bursts in estimating the state of spatiotemporal chaos. Chaos (Woodbury, N.Y.). 14: 1042-9. PMID 15568918 DOI: 10.1063/1.1788091  0.575
2004 Ott E, Hunt BR, Szunyogh I, Zimin AV, Kostelich EJ, Corazza M, Kalnay E, Patil DJ, Yorke JA. A local ensemble Kalman filter for atmospheric data assimilation Tellus, Series a: Dynamic Meteorology and Oceanography. 56: 415-428. DOI: 10.3402/Tellusa.V56I5.14462  0.441
2004 Hunt BR, Kalnay E, Kostelich EJ, Ott E, Patil DJ, Sauer T, Szunyogh I, Yorke JA, Zimin AV. Four-dimensional ensemble Kalman filtering Tellus, Series a: Dynamic Meteorology and Oceanography. 56: 273-277. DOI: 10.3402/Tellusa.V56I4.14424  0.43
2004 Ott E, Hunt BR, Szunyogh I, Zimin AV, Kostelich EJ, Corazza M, Kalnay E, Patil DJ, Yorke JA. Estimating the state of large spatio-temporally chaotic systems Physics Letters, Section a: General, Atomic and Solid State Physics. 330: 365-370. DOI: 10.1016/J.Physleta.2004.08.004  0.443
2003 Zimin AV, Hunt BR, Ott E. Bifurcation scenarios for bubbling transition. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 67: 016204. PMID 12636582 DOI: 10.1103/Physreve.67.016204  0.405
2003 Zimin AV, Szunyogh I, Patil DJ, Hunt BR, Ott E. Extracting envelopes of Rossby wave packets Monthly Weather Review. 131: 1011-1017. DOI: 10.1175/1520-0493(2003)131<1011:Eeorwp>2.0.Co;2  0.421
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