Tandem repeats finder: a program to analyze DNA sequences

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

An introduction to probability theory and its applications

(1958) · Journal of the Franklin Institute · doi:10.1016/0016-0032(58)90688-4 · Cited by 29,621

Improved tools for biological sequence comparison.

Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes

MACDONALD, M. (1993) · Cell · doi:10.1016/0092-8674(93)90585-e · Cited by 8,366

The American Journal of Human Genetics

S., J. (1950) · Population · doi:10.2307/1523704 · Cited by 5,124

Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome

Verkerk, A. J. M. H., Pieretti, M., Sutcliffe, J. S., Fu, Y.-H., Kuhl, D. P. A., Pizzuti, A., Reiner, O., Richards, S., Victoria, M. F., Zhang, F., et al. (1991) · Cell · doi:10.1016/0092-8674(91)90397-h · Cited by 3,481

Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction.

Weber, J. L., & May, P. E. (1989) · Europe PMC (PubMed Central) · Cited by 3,399

Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy

Spada, A. L., Wilson, E. M., Lubahn, D. B., Harding, A., & Fischbeck, K. (1991) · Nature · doi:10.1038/352077a0 · Cited by 2,801

Friedreich's Ataxia: Autosomal Recessive Disease Caused by an Intronic GAA Triplet Repeat Expansion

Campuzano, V., Montermini, L., Moltò, M. D., Pianese, L., Cossée, M., Cavalcanti, F., Monros, E., Rodius, F., Duclos, F., Monticelli, A., et al. (1996) · Science · doi:10.1126/science.271.5254.1423 · Cited by 2,786

An Unstable Triplet Repeat in a Gene Related to Myotonic Muscular Dystrophy

Fu, Y., Pizzuti, A., Fenwick, R. G., King, J., Rajnarayan, S., Dunne, P. W., Dubel, J., Nasser, G. A., Ashizawa, T., de Jong, P., et al. (1992) · Science · doi:10.1126/science.1546326 · Cited by 1,453

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400

Genome sequence of the human malaria parasite Plasmodium falciparum

Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) · Nature · doi:10.1038/nature01097 · Cited by 4,407

Molecular and genetic properties of tumors associated with local immune cytolytic activity

Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825

Repbase Update, a database of eukaryotic repetitive elements

Jurka, J., Kapitonov, V. V., Pavlíček, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084979 · Cited by 3,413

MISA-web: a web server for microsatellite prediction

Beier, S., Thiel, T., Münch, T., Scholz, U., & Mascher, M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx198 · Cited by 2,644

REPuter: the manifold applications of repeat analysis on a genomic scale

Kurtz, S. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.22.4633 · Cited by 2,637

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S. E., Scott, G., Steffen, D. L., Worley, K. C., Burch, P. E., et al. (2004) · Nature · doi:10.1038/nature02426 · Cited by 2,170

De novo identification of repeat families in large genomes

Price, A. L., Jones, N. C., & Pevzner, P. A. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1018 · Cited by 2,138

Prescribing Personalized Nutrition for Cardiovascular Health: Are We Ready?

Juma, S., Imrhan, V., Vijayagopal, P., & Prasad, C. (2014) · Lifestyle Genomics · doi:10.1159/000370213 · Cited by 1,908

The UCSC Genome Browser Database

Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,890

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

Grissa, I., Vergnaud, G., & Pourcel, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm360 · Cited by 1,877

Genic microsatellite markers in plants: features and applications

Varshney, R. K., Graner, A., & Sorrells, M. E. (2004) · Trends in biotechnology · doi:10.1016/j.tibtech.2004.11.005 · Cited by 1,862

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S. J., Chan, S. W.-L., Chen, H., Henderson, I. R., Shinn, P., Pellegrini, M. A., Jacobsen, S. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.08.003 · Cited by 1,850

The Diploid Genome Sequence of an Individual Human

Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., & Borodovsky, M. Y. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa108 · Cited by 1,667

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

Ou, S., & Jiang, N. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01310 · Cited by 1,514

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454

Multiple Alignment of DNA Sequences with MAFFT

Katoh, K., Asimenos, G., & Toh, H. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-251-9_3 · Cited by 1,436

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Ou, S., Su, W., Liao, Y., Chougule, K. M., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1905-y · Cited by 1,522

Conservation and divergence of methylation patterning in plants and animals

Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002720107 · Cited by 1,285

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

The International Aphid Genomics Consortium (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000313 · Cited by 1,333

Adaptive seeds tame genomic sequence comparisonPreprint

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,287

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Varshney, R. K., Song, C., Saxena, R. K., Azam, S., Sheng, Y., Sharpe, A., Cannon, S. B., Baek, J., Rosen, B. D., Tar’an, B., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2491 · Cited by 1,302

CPGAVAS2, an integrated plastome sequence annotator and analyzer

Shi, L., Chen, H., Jiang, M., Wang, L., Wu, X., Huang, L., & Liu, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz345 · Cited by 1,279

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129

Integrated molecular analysis of clear-cell renal cell carcinoma

Sato, Y., Yoshizato, T., Shiraishi, Y., Maekawa, S., Okuno, Y., Kamura, T., Shimamura, T., Sato‐Otsubo, A., Nagae, G., Suzuki, H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2699 · Cited by 1,257

The Ensembl gene annotation system

Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., García Girón, C., Hourlier, T., et al. (2016) · Database · doi:10.1093/database/baw093 · Cited by 1,086

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

Li, F., Fan, G., Lu, C., Xiao, G., Zou, C., Kohel, R. J., Ma, Z., Shāng, H., Ma, X., Wu, J., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3208 · Cited by 1,119

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

de Koning, A. P. J., Gu, W., Castoe, T. A., Batzer, M. A., & Pollock, D. D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002384 · Cited by 1,149

The genome of the pear ( Pyrus bretschneideri Rehd.)Preprint

Wu, J., Wang, Z., Shi, Z., Zhang, S., Ming, R., Zhu, S., Khan, M. A., Tao, S., Korban, S. S., Wang, H., et al. (2012) · Genome Research · doi:10.1101/gr.144311.112 · Cited by 1,059

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Grissa, I., Vergnaud, G., & Pourcel, C. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-172 · Cited by 888

SSAHA: A Fast Search Method for Large DNA Databases

Ning, Z., Cox, A. J., & Mullikin, J. C. (2001) · Genome Research · doi:10.1101/gr.194201 · Cited by 965

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Silva, C. D., Labadie, K., Alberti, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4657 · Cited by 993

Multiple wheat genomes reveal global variation in modern breeding

Walkowiak, S., Gao, L., Monat, C., Haberer, G., Kassa, M. T., Brinton, J., Ramirez-Gonzalez, R. H., Kolodziej, M. C., Delorean, E., Thambugala, D., et al. (2020) · Nature · doi:10.1038/s41586-020-2961-x · Cited by 963

Alignment of whole genomes

Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., & Salzberg, S. L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.11.2369 · Cited by 893

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Varshney, R. K., Chen, W., Li, Y., Bharti, A. K., Saxena, R. K., Schlueter, J. A., Donoghue, M. T. A., Azam, S., Fan, G., Whaley, A. M., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2022 · Cited by 890

Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1932072100 · Cited by 850

The UCSC Genome Browser database: 2015 update

Rosenbloom, K. R., Armstrong, J. C., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1177 · Cited by 883

Genome sequence of the cultivated cotton Gossypium arboreum

Li, F., Fan, G., Wang, K., Sun, F., Yuán, Y., Song, G., Qin, L., Ma, Z., Lu, C., Zou, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.2987 · Cited by 870

Microsatellite markers: what they mean and why they are so useful

Vieira, M. L. C., Santini, L., Diniz, A. L., & Munhoz, C. D. F. (2016) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2016-0027 · Cited by 842

A high-coverage Neandertal genome from Vindija Cave in Croatia

Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Zhang, G., Liu, X., Quan, Z., Cheng, S., Xu, X., Pan, S., Xie, M., Zeng, P., Yue, Z., Wang, W., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2195 · Cited by 794

Large-scale whole-genome sequencing of the Icelandic population

Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3247 · Cited by 791

The Dfam database of repetitive DNA families

Hubley, R. M., Finn, R. D., Clements, J., Eddy, S. R., Jones, T. A., Bao, W., Smit, A. F. A., & Wheeler, T. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1272 · Cited by 768

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

Eisen, J. A., Coyne, R. S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J. R., Badger, J. H., Ren, Q., Amedeo, P., Jones, K. M., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040286 · Cited by 771

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

Sloan, D. B., Alverson, A. J., Chuckalovcak, J. P., Wu, M., McCauley, D. E., Palmer, J. D., & TAYLOR, D. R. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001241 · Cited by 769

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Kubicek, C. P., Herrera‐Estrella, A., Seidl‐Seiboth, V., Martinez, D. A., Druzhinina, I. S., Thon, M. R., Zeilinger, S., Casas‐Flores, S., Horwitz, B. A., Mukherjee, P. K., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-4-r40 · Cited by 752

The Dfam community resource of transposable element families, sequence models, and genome annotations

Storer, J. M., Hubley, R. M., Rosen, J. R., Wheeler, T. J., & Smit, A. F. A. (2021) · Mobile DNA · doi:10.1186/s13100-020-00230-y · Cited by 757

Personalized copy number and segmental duplication maps using next-generation sequencing

Alkan, C., Kidd, J. M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J. O., Baker, C., Malig, M., Mutlu, O., et al. (2009) · Nature Genetics · doi:10.1038/ng.437 · Cited by 748

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia

Smith, C. C., Wang, Q., Chin, C.-S., Salerno, S. N., Damon, L. E., Levis, M. J., Perl, A. E., Travers, K. J., Wang, S., Hunt, J. P., et al. (2012) · Nature · doi:10.1038/nature11016 · Cited by 738

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

Carlton, J. M., Angiuoli, S. V., Suh, B. B., Kooij, T. W. A., Pertea, M., da Silva, J. C. F., Ermolaeva, M. D., Allen, J., Selengut, J., Koo, H. L., et al. (2002) · Nature · doi:10.1038/nature01099 · Cited by 734

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang, J.-S., Zhang, X.-T., Tang, H.-B., Zhang, Q., Hua, X.-T., Ma, X.-K., Zhu, F., Jones, T. C., Zhu, X.-G., Bowers, J., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0237-2 · Cited by 596

Genome analysis of the platypus reveals unique signatures of evolution

paper, A. L. O. A. A. T. A. A. A. T. E. O. T. (2008) · Nature · doi:10.1038/nature06936 · Cited by 719

PILER: identification and classification of genomic repeats

Edgar, R. C., & Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1003 · Cited by 725

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., et al. (2021) · Science · doi:10.1126/science.abg5289 · Cited by 747

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm, J. C., Minoche, A. E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., Sörensen, T. R., Stracke, R., Reinhardt, R., et al. (2013) · Nature · doi:10.1038/nature12817 · Cited by 675

Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum

Gao, Q., Jin, K., Ying, S., Zhang, Y., Xiao, G., Shang, Y., Duan, Z., Hu, X., Xie, X., Zhou, G., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001264 · Cited by 674

The Schistosoma japonicum genome reveals features of host–parasite interplay

Zhou, Y., Zheng, H., Chen, Y., Zhang, L., Wang, K., Guo, J., Huang, Z., Zhang, B., Huang, W., Liu, F., et al. (2009) · Nature · doi:10.1038/nature08140 · Cited by 658

GENCODE: producing a reference annotation for ENCODE

Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s4 · Cited by 648

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Denœud, F., Carretero‐Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., et al. (2014) · Science · doi:10.1126/science.1255274 · Cited by 666

DNA sequence and analysis of human chromosome 9

Humphray, S., Oliver, K., Hunt, A. R., Plumb, R. W., Loveland, J. E., Howe, K., Andrews, T. D., Searle, S., Hunt, S. E., Scott, C., et al. (2004) · Nature · doi:10.1038/nature02465 · Cited by 640

The tobacco genome sequence and its comparison with those of tomato and potato

Sierro, N., Battey, J. N. D., Ouadi, S., Bakaher, N., Bovet, L., Willig, A., Goepfert, S., Peitsch, M. C., & Ivanov, N. V. (2014) · Nature Communications · doi:10.1038/ncomms4833 · Cited by 641

A C9orf72 promoter repeat expansion in a Flanders-Belgian cohort with disorders of the frontotemporal lobar degeneration-amyotrophic lateral sclerosis spectrum: a gene identification study

Gijselinck, I., Langenhove, T. V., van der Zee, J., Sleegers, K., Philtjens, S., Kleinberger, G., Janssens, J., Bettens, K., Cauwenberghe, C. V., Pereson, S., et al. (2011) · The Lancet Neurology · doi:10.1016/s1474-4422(11)70261-7 · Cited by 655

CPGView : A package for visualizing detailed chloroplast genome structures

Liu, S., Ni, Y., Li, J., Zhang, X., Yang, H., Chen, H., & Liu, C. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13729 · Cited by 632

QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects

Meglécz, E., Costedoat, C., Dubut, V., André Gilles, A., Malausa, T., Pech, N., & Martin, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp670 · Cited by 613

Improved reference genome of Aedes aegypti informs arbovirus vector control

Matthews, B. J., Dudchenko, O., Kingan, S. B., Koren, S., Antoshechkin, I. A., Crawford, J. E., Glassford, W. J., Herre, M., Redmond, S. N., Rose, N. H., et al. (2018) · Nature · doi:10.1038/s41586-018-0692-z · Cited by 594

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

Zhang, G., Cowled, C. J., Shi, Z., Huang, Z., Bishop‐Lilly, K. A., Fang, X., Wynne, J. W., Xiong, Z., Baker, M. L., Zhao, W., et al. (2012) · Science · doi:10.1126/science.1230835 · Cited by 630

Characterizing the Major Structural Variant Alleles of the Human Genome

Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492

Genetic evidence for complex speciation of humans and chimpanzees

Patterson, N. J., Richter, D. J., Gnerre, S., Lander, E. S., & Reich, D. (2006) · Nature · doi:10.1038/nature04789 · Cited by 582

The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair

Fineran, P. C., Blower, T. R., Foulds, I. J., Humphreys, D. P., Lilley, K. S., & Salmond, G. P. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808832106 · Cited by 574

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments

Wen, M., Shen, Y., Shi, S., & Tang, T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-140 · Cited by 574

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

Richard, G., Kerrest, A., & Dujon, B. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00011-08 · Cited by 590

A heterozygous moth genome provides insights into herbivory and detoxification

You, M., Yue, Z., He, W., Yang, X., Yang, G., Xie, M., Zhan, D., Baxter, S. W., Vasseur, L., Gurr, G. M., et al. (2013) · Nature Genetics · doi:10.1038/ng.2524 · Cited by 556

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Iorizzo, M., Ellison, S. L., Senalik, D. A., Zeng, P., Satapoomin, P., Huang, J., Bowman, M. J., Iovene, M., Sanseverino, W., Cavagnaro, P. F., et al. (2016) · Nature Genetics · doi:10.1038/ng.3565 · Cited by 545

The Rosa genome provides new insights into the domestication of modern roses

Raymond, O., Gouzy, J., Just, J., Badouin, H., Verdenaud, M., Lemainque, A., Vergne, P., Moja, S., Choisne, N., Pont, C., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0110-3 · Cited by 463

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Melters, D. P., Bradnam, K. R., Young, H. A., Telis, N., May, M. R., Ruby, J. G., Sebra, R., Peluso, P. S., Eid, J. S., Rank, D. R., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r10 · Cited by 528

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Nishiyama, T., Sakayama, H., de Vries, J., Buschmann, H., Saint‐Marcoux, D., Ullrich, K. K., Haas, F. B., Vanderstraeten, L., Becker, D., Lang, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.033 · Cited by 522

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser‐Klopp, G., Wang, J., Yang, S., Liang, J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2478 · Cited by 531

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J. G., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3943 · Cited by 528

The sheep genome illuminates biology of the rumen and lipid metabolism

Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., et al. (2014) · Science · doi:10.1126/science.1252806 · Cited by 514

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., Paten, B., Salama, S. R., & Haussler, D. (2014) · Nature · doi:10.1038/nature13760 · Cited by 506

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

Neale, D. B., Wegrzyn, J., Stevens, K., Zimin, A. V., Puiu, D., Crepeau, M., Cardeno, C., Koriabine, M., Holtz-Morris, A. E., Liechty, J. D., et al. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r59 · Cited by 517

The genome sequence of the orchid Phalaenopsis equestris

Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W., Liu, K., Chen, L., He, Y., Xu, Q., Bian, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.3149 · Cited by 507

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Li, F., Brouwer, P., Carretero‐Paulet, L., Cheng, S., de Vries, J., Delaux, P., Eily, A. N., Koppers, N., Kuo, L., Li, Z., et al. (2018) · Nature Plants · doi:10.1038/s41477-018-0188-8 · Cited by 492

Considering Transposable Element Diversification in De Novo Annotation Approaches

Flutre, T., Duprat, É., Feuillet, C., & Quesneville, H. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016526 · Cited by 514

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

Morgulis, A. O., Gertz, E. M., Schäffer, A. A., & Agarwala, R. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.1028 · Cited by 498

The genome of Prunus mume

Zhang, Q., Chen, W., Sun, L., Zhao, F., Huang, B., Yang, W., Tao, Y., Wang, J., Yuan, Z., Fan, G., et al. (2012) · Nature Communications · doi:10.1038/ncomms2290 · Cited by 493

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471

Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy

Hart, T. C., Gorry, M. C., Hart, P., Woodard, A. S., Shihabi, Z. K., Sandhu, J. S., Shirts, B. H., Xu, L. B., Zhu, H., Barmada, M. M., et al. (2002) · Journal of Medical Genetics · doi:10.1136/jmg.39.12.882 · Cited by 478

Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q

Xie, W., Chen, C., Yang, Z., Guo, L., Yang, X., Wang, D., Chen, M., Huang, J., Wen, Y., Zeng, Y., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix018 · Cited by 473

Dense sampling of bird diversity increases power of comparative genomics

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., et al. (2020) · Nature · doi:10.1038/s41586-020-2873-9 · Cited by 459

Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa

Chen, H., Zeng, Y., Yang, Y. P., Huang, L., Tang, B., Zhang, H., Hao, F., Liu, W., Li, Y., Liu, Y., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16338-x · Cited by 481

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

McVicker, G., Gordon, D., Davis, C., & Green, P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000471 · Cited by 456

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

Wiemann, P., Sieber, C. M. K., von Bargen, K. W., Studt, L., Niehaus, E., Espino, J. J., Huß, K., Michielse, C. B., Albermann, S., Wagner, D., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003475 · Cited by 457

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

Zhang, L.-Y., Hu, J. Y., Han, X., Li, J., Gao, Y., Richards, C. M., Zhang, C., Tian, Y., Liu, G., Gul, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09518-x · Cited by 472

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Ling, H., Ma, B., Shi, X., Liu, H., Dong, L., Sun, H., Cao, Y., Gao, Q., Zheng, S., Li, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0108-0 · Cited by 455

Towards the Development of Tandem Repeat Analyzer for Genome Sequence Data

Ingle, E., & Bhise, A. (2010) · doi:10.1109/iccea.2010.285

An algorithm for finding tandem repeats of unspecified pattern size

Benson, G. (1998) · Annual International Conference on Research in Computational Molecular Biology · doi:10.1145/279069.279079 · Cited by 26

A Fast Method for Determining the Repeat Pattern Size in DNA Sequences

Zhou, H., & Yan, H. (2007) · International Conference on Machine Learning and Cybernetics · doi:10.1109/icmlc.2007.4370720

Filtering Tandem Repeats in DNA Sequences.

Sokol, D., & Tojeira, J. (2006)

Tandem repeats over the edit distance

Sokol, D., Benson, G., & Tojeira, J. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl309 · Cited by 86