Aleksey photo

Aleksey V. Zimin

Associate Research Scientist

Center for Computational Biology
Department of Biomedical Engineering

Johns Hopkins University

Contact:
Wyman Park Building,
3100 Wyman Park Drive, Room S237
Baltimore, MD 21211
E-mail: alekseyz jhu edu

Publications

 

73 total, 21 first or senior author; Google Scholar citations: 18,714, h-index:43


1.      Badger JH, Giordano R, Zimin A, Wappel R, Eskipehlivan SM, Muller S, Donthu R, Soto-Adames F, Vieira P, Zasada I, Goodwin S. Direct sequencing of insect symbionts via nanopore adaptive sampling. Current Opinion in Insect Science. 2023 Nov 4:101135.

2.      Lee H, Greer SU, Pavlichin DS, Zhou B, Urban AE, Weissman T, Liao WW, .. [92 authors]…, Zimin AV,..[15 authors]…, Paten, B. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell Reports Methods. 2023 Aug 28;3(8).

3.      Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, …[112 authors]…, Zimin AV, Zook JM. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research. 2023 Apr 1;33(4):496-510.

4.      Guo A, Salzberg SL, Zimin AV. JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. PLoS Computational Biology. 2023 Mar 31;19(3):e1011032.

5.      Liao WW, …,[102 authors]…, Zimin AV, …[14 authors]…, Paten B. A draft human pangenome reference. Nature. 2023 May 11;617(7960):312-24.

6.      Reinhardt JA, Baker RH, Zimin AV, Ladias C, Paczolt KA, Werren JH, Hayashi CY, Wilkinson GS. Impacts of sex ratio meiotic drive on genome structure and function in a stalk-eyed fly. Genome Biology and Evolution. 2023 Jul;15(7):evad118.

7.      Pockrandt C, Zimin AV, Salzberg SL, (2022). Metagenomic classification with KrakenUniq on low-memory computers. Journal of Open Source Software, 7(80), 4908,  2022.

8.      Chao KH, Zimin AV, Pertea M, Salzberg SL. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual. G3: Genes, Genomes, Genetics. 2023 Mar;13(3):jkac321.

9.      Miller J, Zimin AV, Gordus A. Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus. GigaScience. 2023;12:giad002.

10.  Orvis J, Albertin CB, Shrestha P, Chen S, Zheng M, Rodriguez CJ, Tallon LJ, Mahurkar A, Zimin AV, Kim M, Liu K. The evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences. 2022 Jul 12;119(28):e2122301119.

11.  Jarvis ED, …[69 authors]…, Zimin AV,…,[11 authors]…,Miga KH and Human Pangenome Reference Consortium. Semi-automated assembly of high-quality diploid human reference genomes. Nature. 2022 Nov;611(7936):519-31.

12.  Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nature Communications. 2022 Apr 19;13(1):1-5.

13.  Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3: Genes, Genomes, Genetics. 2022 Jan;12(1):jkab380.

14.  Zimin AV, Salzberg SL. The SAMBA tool uses long reads to improve the contiguity of genome assemblies. PLoS Computational Biology. 2022 Feb 4;18(2):e1009860.

15.  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. 2022 Feb;220(2):iyab227.

16.  Polinski JM, Zimin AV, Clark KF, Kohn AB, Sadowski N, Timp W, Ptitsyn A, Khanna P, Romanova DY, Williams P, Greenwood SJ. The American lobster genome reveals insights on longevity, neural, and immune adaptations. Science Advances. 2021 Jun 1;7(26):eabe8290.

17.  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. 2021 Apr 28;16(4):e0249899.

18.  Dobson LK, Zimin A, Bayles D, Fritz‐Waters E, Alt D, Olsen S, Blanchong J, Reecy J, Smith TP, Derr JN. De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Animal Genetics. 2021 Mar 29.

19.  Puiu D, Zimin A, Shumate A, Ge Y, Qiu J, Bhaskaran M, Salzberg SL. The genome of the American groundhog, Marmota monax. F1000 Research. 2020 Sep 16;9(1137):1137.

20.  Scott AD, Zimin AV, Puiu D, Workman R, Britton M, Zaman S, Caballero M, Read AC, Bogdanove AJ, Burns E, Wegrzyn J. A reference genome sequence for giant sequoia. G3: Genes, Genomes, Genetics. 2020 Nov 1;10(11):3907-19.

21.  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. 2020 Dec;21(1):1-8. (Shumate and Zimin are co-first authors)

22.  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. 2020 Oct 1;216(2):599-608.

23.  Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Computational Biology. 2020 Jun 26;16(6):e1007981.

24.  Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EA, Allen BJ, Chakraborty S, Troggio M. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. GigaScience. 2020 May;9(5):giaa050.

25.  Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 2020 Mar;9(3):giaa021.

26.  Giordano R, Donthu RK, Zimin A, Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger J, Nguyen M, Flores A. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology. 2020 Feb 25:103334.

27.  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. 2020 Jan 27;16(1):e1008571.

28.  Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology. 2019 Dec;20(1):1-3.

29.  Breitwieser FP, Pertea M, Zimin AV, Salzberg SL. Human contamination in bacterial genomes has created thousands of spurious proteins. Genome Research. 2019 Jun 1;29(6):954-60.

30.  Martinez-Viaud KA, Lawley CT, …[11 authors]…., Zimin AV. New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing. GigaScience. 2019 Jan 29;8(3):giy168.

31.  Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLoS Computational Biology. 2018 Jan 26;14(1):e1005944.

32.  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. 2017 Nov;6(11):gix097.

33.  Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang S, and Slazberg SL. First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans). G3: Genes, Genomes, Genetics. 2017 Jan 1:g3-300107.

34.  Williams JL, …[33 authors]…, Zimin AV. Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2 n= 50). GigaScience. 2017 Oct;6(10):gix088.

35.  Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C. The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3: Genes, Genomes, Genetics. 2017 Jan 1:g3-300078.

36.  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. 2017 Jan 1;6(1):1-4.

37.  Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Yorke JA, Dvorak J, Salzberg S. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. 2017 Jan 1:066100.

38.  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. Sequence of the sugar pine megagenome. Genetics. 2016 Dec 1;204(4):1613-26.

39.  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 and Warren W. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nature Communications. 2016;7.

40.  Muñoz A, Muñoz DS, Zimin A, Yorke JA. Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species. BMC Genomics. 2016 Nov 11;17(10):145.

41.  Liu Z, …[16 authors]…, Zimin AV, …[33 authors]…, Waldbeiser, G. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 2016 Jun 2;7.

42.  Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016 Apr 18.

43.  Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O’Brien SJ. A high-resolution SNP array-based linkage map anchors a new domestic cat draft genome assembly and provides detailed patterns of recombination. G3: Genes Genomes Genetics. 2016 Jun 1;6(6):1607-16.

44.  Marçais G, Yorke JA, Zimin A. QuorUM: an error corrector for Illumina reads. PloS One. 2015 Jun 17;10(6):e0130821.

45.  Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y. Transposable element islands facilitate adaptation to novel environments in an invasive species. Nature Communications. 2014 Dec 16;5.

46.  Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 2014 Oct 14;9(1):20.

47.  Williams JL, Iamartino D, Sonstegard T, Reecy J, Van Tassell C, Zimin A. The buffalo genome: structure and function. Chromosome Research 2014 Sep 1 (Vol. 22, No. 3, pp. 406-406).

48.  Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 2014 Mar 4;15(3):R59.

49.  Wegrzyn JL, … [11 authors]…, Zimin AV, …[8 authors]…, Neale DB. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 2014 Mar 1;196(3):891-909.

50.  Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB. Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics. 2014 Mar 1;196(3):875-90.

51.  Dalloul RA, Zimin AV, Settlage RE, Kim S, Reed KM. Next-generation sequencing strategies for characterizing the turkey genome. Poultry science. 2014 Feb 1;93(2):479-84.

52.  Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013 Nov 1;29(21):2669-77.

53.  Schmitt KR, Zimin AV, Marcaçs G, Yorke JA, Girvan M. A hierarchical network heuristic for solving the orientation problem in genome assembly. arXiv:1307.0541. 2013 Jul 1.

NOTE: The first author is a student co-advised by Zimin

54.  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. 2012 Aug 3;7(8):e42680.

55.  Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 2012 Mar 1;22(3):557-67.

56.  Heliconius Genome Consortium [Zimin is a member]. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 2012 Jul 5;487(7405):94-8.

57.  Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences. 2011 Apr 5;108(14):5673-8.

58.  Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proceedings of the National Academy of Sciences. 2011 Apr 5;108(14):5667-72.

59.  Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology. 2010 Sep 7;8(9):e1000475. (Dalloul, Long and Zimin are co-first authors)

60.  Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 2009 Apr 24;10(4):R42.

61.  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. 2008 Mar 19;3(3):e1836.

62.  Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5.

63.  Drosophila 12 genomes Consortium [Zimin is a member]. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18.

64.  Zimin AV, Szunyogh I, Hunt BR, Ott E. Extracting envelopes of nonzonally propagating Rossby wave packets. Monthly Weather Review. 2006 Apr;134(4):1329-33.

65.  Baek SJ, Hunt BR, Szunyogh I, Zimin A, Ott E. Localized error bursts in estimating the state of spatiotemporal chaos. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2004 Dec;14(4):1042-9.

66.  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 A. 2004 Oct 1;56(5):415-28.

67.  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 A. 2004 Sep 27;330(5):365-70.

68.  Hunt BR, Kalnay E, Kostelich EJ, Ott E, Patil DJ, Sauer T, Szunyogh I, Yorke JA, Zimin AV. Four‐dimensional ensemble Kalman filtering. Tellus A. 2004 Aug 1;56(4):273-7.

69.  Patil DJ, Szunyogh I, Zimin AV, Hunt BR, Ott E, Kalnay E, Yorke JA. Local low dimensionality and relation to effects of targeted weather observations. V, Kocarev L, Boccaletti S, Gluckman BJ, editors. AIP Conference Proceedings. 2003 Aug 19 (Vol. 676, No. 1, pp. 139-153). AIP.

70.  Zimin AV, Szunyogh I, Patil DJ, Hunt BR, Ott E. Extracting envelopes of Rossby wave packets. Monthly Weather Review. 2003 May;131(5):1011-7.

71.  Zimin AV, Hunt BR, Ott E. Bifurcation scenarios for bubbling transition. Physical Review E. 2003 Jan 8;67(1):016204.

72.  Szunyogh I, Toth Z, Zimin AV, Majumdar SJ, Persson A. Propagation of the effect of targeted observations: The 2000 Winter Storm Reconnaissance Program. Monthly Weather Review. 2002 May;130(5):1144-65.

73.  Szunyogh I, Zimin AV, Patil DJ, Hunt BR, Kalnay E, Ott E, Yorke JA. On the dynamical basis of targeting weather observations. EGS General Assembly Conference Abstracts. 2002 (Vol. 27, p. 2034).