Tablet-next generation sequence assembly visualization.

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Genome sequencing in microfabricated high-density picolitre reactors

Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · see citing works

Consed: a graphical tool for sequence finishing.Preprint

Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,706 · see citing works

EagleView: A genome assembly viewer for next-generation sequencing technologiesPreprint

Huang, W., & Marth, G. (2008) · Genome Research · doi:10.1101/gr.076067.108 · Cited by 125 · see citing works

Hawkeye: an interactive visual analytics tool for genome assemblies

Schatz, M. C., Phillippy, A. M., Shneiderman, B., & Salzberg, S. L. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r34 · Cited by 91 · see citing works

MapView: visualization of short reads alignment on a desktop computer

Bao, H., Guo, H., Wang, J., Zhou, R., Lu, X., & Shi, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp255 · Cited by 79 · see citing works

Integrative genomics viewer

Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

Chin, C., Alexander, D., Marks, P., Klammer, A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,008 · see citing works

Unipro UGENE: a unified bioinformatics toolkit

Okonechnikov, K., Golosova, O., Fursov, M., & the UGENE team (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts091 · Cited by 3,181 · see citing works

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Hahn, C., Bachmann, L., & Chevreux, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt371 · Cited by 1,854 · see citing works

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461 · see citing works

A chromosome conformation capture ordered sequence of the barley genome

Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450 · see citing works

Performance comparison of benchtop high-throughput sequencing platforms

Loman, N. J., Misra, R., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. R., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,334 · see citing works

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

Carver, T. J., Harris, S. R., Berriman, M., Parkhill, J., & Keane, J. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr703 · Cited by 1,191 · see citing works

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2017.066 · Cited by 1,190 · see citing works

Uncovering the roles of rare variants in common disease through whole-genome sequencing

Cirulli, E. T., & Goldstein, D. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2779 · Cited by 1,136 · see citing works

Using Tablet for visual exploration of second-generation sequencing data

Milne, I., Stephen, G., Bayer, M., Cock, P., Pritchard, L., Cardle, L., Shaw, P. D., & Marshall, D. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs012 · Cited by 949 · see citing works

A survey of sequence alignment algorithms for next-generation sequencing

Li, H., & Homer, N. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq015 · Cited by 875 · see citing works

Navigating the tip of the genomic iceberg: Next‐generation sequencing for plant systematics

Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R., & Liston, A. (2011) · American Journal of Botany · doi:10.3732/ajb.1100335 · Cited by 693 · see citing works

Applications of next-generation sequencing to phylogeography and phylogenetics

McCormack, J. E., Hird, S. M., Zellmer, A. J., Carstens, B. C., & Brumfield, R. T. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.12.007 · Cited by 642 · see citing works

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

Minoche, A. E., Dohm, J. C., & Himmelbauer, H. (2011) · Genome biology · doi:10.1186/gb-2011-12-11-r112 · Cited by 620 · see citing works

Sequence-specific error profile of Illumina sequencers

Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A. M., Takahashi, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr344 · Cited by 593 · see citing works

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573 · see citing works

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

Comadran, J., Kilian, B., Russell, J., Ramsay, L., Stein, N., Ganal, M. W., Shaw, P. D., Bayer, M., Thomas, W. T. B., Marshall, D., et al. (2012) · Nature Genetics · doi:10.1038/ng.2447 · Cited by 485 · see citing works

Antagonists to the Wnt Cascade Exhibit Sex-Specific Expression in Gonads of Sexually Mature Shovelnose Sturgeon

Amberg, J. J., Goforth, R. R., & Sepúlveda, M. S. (2013) · Sexual Development · doi:10.1159/000354280 · Cited by 477 · see citing works

Chromatin accessibility: a window into the genome

Tsompana, M., & Buck, M. J. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-33 · Cited by 437 · see citing works

Uncovering the Complexity of Transcriptomes with RNA-Seq

Costa, V., Angelini, C., Feis, I. D., & Ciccodicola, A. (2010) · BioMed Research International · doi:10.1155/2010/853916 · Cited by 439 · see citing works

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

Loman, N. J., Constantinidou, C., Chan, J. Z.-M., Halachev, M. R., Sergeant, M. J., Penn, C. W., Robinson, E., & Pallen, M. J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2850 · Cited by 426 · see citing works

Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of ‘Lito’ Chromosome 1 and Analysis of Candidate Genes

Mori, G. D., Falchi, R., Testolin, R., Bassi, D., Savazzini, F., Dondini, L., Tartarini, S., Palmisano, F., Minafra, A., Spadotto, A., et al. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01576 · Cited by 376 · see citing works

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Clooney, A. G., Ryan, F. J., Sutton, T., Draper, L. A., González-Tortuero, E., Ross, R. P., & Hill, C. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.10.002 · Cited by 297 · see citing works

SNP Discovery through Next-Generation Sequencing and Its Applications

Kumar, S. D., Banks, T. W., & Cloutier, S. (2012) · International Journal of Plant Genomics · doi:10.1155/2012/831460 · Cited by 312 · see citing works

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

Shen, Y., Zhou, Z., Wang, Z., Li, W., Fang, C. Q., Wu, M., Ma, Y., Liu, T., Kong, L., Peng, D., et al. (2014) · The Plant Cell · doi:10.1105/tpc.114.122739 · Cited by 280 · see citing works

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

Pomerantz, A. F., Peñafiel, N., Arteaga, A., Bustamante, L., Pichardo, F., Coloma, L. A., Barrio-Amorós, C. L., Salazar‐Valenzuela, D., & Prost, S. (2018) · GigaScience · doi:10.1093/gigascience/giy033 · Cited by 256 · see citing works

Comparing de novo assemblers for 454 transcriptome data

Kumar, S., & Blaxter, M. L. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-571 · Cited by 255 · see citing works

A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris

Giampetruzzi, A., Roumi, V., Roberto, R., Malossini, U., Yoshikawa, N., Notte, P. L., Terlizzi, F., Credi, R., & Saldarelli, P. (2011) · Virus Research · doi:10.1016/j.virusres.2011.10.010 · Cited by 242 · see citing works

High-resolution human cytomegalovirus transcriptome

Gatherer, D., Seirafian, S., Cunningham, C., Holton, M., Dargan, D. J., Baluchova, K., Hector, R. D., Galbraith, J., Herzyk, P., Wilkinson, G. W. G., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1115861108 · Cited by 229 · see citing works

Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

Strickler, S. R., Bombarely, A., & Mueller, L. A. (2012) · American Journal of Botany · doi:10.3732/ajb.1100292 · Cited by 222 · see citing works

Gap5—editing the billion fragment sequence assembly

Bonfield, J., & Whitwham, A. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq268 · Cited by 223 · see citing works

Evolution and Diversity in Human Herpes Simplex Virus Genomes

SZPARA, M. L., Gatherer, D., Ochoa, A., Greenbaum, B. D., Dolan, A., Bowden, R. J., Enquist, L. W., Legendre, M., & Davison, A. J. (2013) · Journal of Virology · doi:10.1128/jvi.01987-13 · Cited by 222 · see citing works

Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial

Wolf, J. B. W. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12109 · Cited by 219 · see citing works

De novo assembly of short sequence reads

Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204 · see citing works

Discovery of a novel methanogen prevalent in thawing permafrost

Mondav, R., Woodcroft, B. J., Kim, E., Mccalley, C. K., Hodgkins, S. B., Crill, P., Chanton, J. P., Hurst, G. B., VerBerkmoes, N. C., SALESKA, S. R., et al. (2014) · Nature Communications · doi:10.1038/ncomms4212 · Cited by 203 · see citing works

Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Abdullah, A., Mehmood, F., Shahzadi, I., Waseem, S., Mirza, B., Ahmed, I., & Waheed, M. T. (2019) · Genomics · doi:10.1016/j.ygeno.2019.04.010 · Cited by 198 · see citing works

Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids

Sloan, D. B., & Moran, N. A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss180 · Cited by 194 · see citing works

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

Timmermans, M. J. T. N., Dodsworth, S., Culverwell, C. L., Bocák, L., AHRENS, D. C., Littlewood, D. T. J., Pons, J., & Vogler, A. P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq807 · Cited by 185 · see citing works

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Bratcher, H. B., Corton, C. H., Jolley, K. A., Parkhill, J., & Maiden, M. C. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1138 · Cited by 184 · see citing works

Mutational Dynamics of Aroid Chloroplast Genomes

Ahmed, I., Biggs, P. J., Matthews, P. J., Collins, L. J., Hendy, M. D., & Lockhart, P. J. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs110 · Cited by 178 · see citing works

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

Tao, X., Gu, Y.-H., Wang, H.-Y., Zheng, W., Li, X., Zhao, C.-W., & Zhang, Y.-Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036234 · Cited by 168 · see citing works

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

Barrett, C. F., & Davis, J. I. (2012) · American Journal of Botany · doi:10.3732/ajb.1200256 · Cited by 171 · see citing works

GenomeView: a next-generation genome browser

Abeel, T., Parys, T. V., Saeys, Y., Galagan, J. E., & de Peer, Y. V. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr995 · Cited by 165 · see citing works

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)

Sloan, D. B., Triant, D. A., Forrester, N. J., Bergner, L. M., Wu, M., & TAYLOR, D. R. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.12.004 · Cited by 163 · see citing works

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

Jerlström-Hultqvist, J., Franzén, O., Ankarklev, J., Xu, F., Nohýnková, E., Andersson, J. O., Svärd, S. G., & Andersson, B. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-543 · Cited by 157 · see citing works

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

Bock, D. G., Kane, N. C., Ebert, D., & Rieseberg, L. H. (2013) · New Phytologist · doi:10.1111/nph.12560 · Cited by 154 · see citing works

Comparative Genomics of Carp Herpesviruses

Davison, A. J., Kurobe, T., Gatherer, D., Cunningham, C., Korf, I. F., Fukuda, H., Hedrick, R. P., & Waltzek, T. B. (2012) · Journal of Virology · doi:10.1128/jvi.03206-12 · Cited by 153 · see citing works

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

Noyes, N. R., Yang, X., Linke, L., Magnuson, R. J., Cook, S. R., Zaheer, R., Yang, H., Woerner, D. R., Geornaras, I., McArt, J. A. A., et al. (2016) · Scientific Reports · doi:10.1038/srep24645 · Cited by 149 · see citing works

Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae

Shahzadi, I., Abdullah, A., Mehmood, F., Ali, Z., Ahmed, I., & Mirza, B. (2019) · Genomics · doi:10.1016/j.ygeno.2019.08.016 · Cited by 148 · see citing works

Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae

Mehmood, F., Abdullah, A., Shahzadi, I., Ahmed, I., Waheed, M. T., & Mirza, B. (2019) · Genomics · doi:10.1016/j.ygeno.2019.08.024 · Cited by 141 · see citing works

Within-Host Evolution of Burkholderia pseudomallei over a Twelve-Year Chronic Carriage Infection

Price, E. P., Sarovich, D. S., Mayo, M. J., Tuanyok, A., Drees, K. P., Kaestli, M., Beckstrom‐Sternberg, S. M., Babic-Sternberg, J. S., Kidd, T. J., Bell, S. C., et al. (2013) · mBio · doi:10.1128/mbio.00388-13 · Cited by 135 · see citing works

Next-generation sequencing technologies: breaking the sound barrier of human genetics

Bahassi, E. M., & Stambrook, P. J. (2014) · Mutagenesis · doi:10.1093/mutage/geu031 · Cited by 133 · see citing works

Use of next‐generation sequencing for the identification and characterization of M aize chlorotic mottle virus and S ugarcane mosaic virus causing maize lethal necrosis in K enya

Adams, I. P., Miano, D. W., Kinyua, Z. M., Wangai, A. W., Kimani, E. N., Phiri, N. A., Reeder, R., Harju, V., Glover, R. H., Hany, U., et al. (2012) · Plant Pathology · doi:10.1111/j.1365-3059.2012.02690.x · Cited by 131 · see citing works

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex

Debortoli, N., Li, X., Eyres, I., Fontaneto, D., Hespeels, B., Tang, C. Q., Flot, J., & Doninck, K. V. (2016) · Current Biology · doi:10.1016/j.cub.2016.01.031 · Cited by 131 · see citing works

CancerDR: Cancer Drug Resistance Database

Kumar, R., Chaudhary, K., Gupta, S., Singh, H., Kumar, S., Gautam, A., Kapoor, P., & Raghava, G. P. S. (2013) · Scientific Reports · doi:10.1038/srep01445 · Cited by 129 · see citing works

Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia

Wiersma, A. T., Gaines, T. A., Preston, C. D., Hamilton, J. P., Giacomini, D. A., Buell, C. R., Leach, J. E., & Westra, P. H. (2014) · Planta · doi:10.1007/s00425-014-2197-9 · Cited by 128 · see citing works

Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa

Gómez‐Lozano, M., Marvig, R. L., Molin, S., & Long, K. S. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02759.x · Cited by 124 · see citing works

From next-generation resequencing reads to a high-quality variant data set

Pfeifer, S. P. (2016) · Heredity · doi:10.1038/hdy.2016.102 · Cited by 122 · see citing works

Next Generation Sequencing in Predicting Gene Function in Podophyllotoxin Biosynthesis

Marques, J. V., Kim, K., Lee, C., Costa, M. A., May, G. D., Crow, J., Davin, L. B., & Lewis, N. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.400689 · Cited by 123 · see citing works

Plastid genomes and deep relationships among the commelinid monocot angiosperms

Barrett, C. F., Davis, J. I., Leebens‐Mack, J., Conran, J. G., & Stevenson, D. W. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00418.x · Cited by 120 · see citing works

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Straub, S. C. K., Fishbein, M., Livshultz, T., Foster, Z., Parks, M., Weitemier, K., Cronn, R., & Liston, A. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-211 · Cited by 121 · see citing works

Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing

Messenger, L. A., Llewellyn, M. S., Bhattacharyya, T., Franzén, O., Lewis, M. D., Ramírez, J. D., Carrasco, H. J., Andersson, B., & Miles, M. A. (2012) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0001584 · Cited by 121 · see citing works

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

Zhang, R., Marshall, D., Bryan, G. J., & Hornyik, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057233 · Cited by 119 · see citing works

iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

Zheng, Y., Zhao, L.-J., Gao, J.-P., & Fei, Z. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-453 · Cited by 127 · see citing works

Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

Thorpe, P., Cock, P., & Bos, J. I. B. (2016) · BMC Genomics · doi:10.1186/s12864-016-2496-6 · Cited by 119 · see citing works

A spliced latency-associated VZV transcript maps antisense to the viral transactivator gene 61

Depledge, D. P., Ouwendijk, W. J. D., Sadaoka, T., Braspenning, S. E., Mori, Y., Cohrs, R. J., Verjans, G. M. G. M., & Breuer, J. (2018) · Nature Communications · doi:10.1038/s41467-018-03569-2 · Cited by 119 · see citing works

From Omics to Multi-Omics: A Review of Advantages and Tradeoffs

Hayes, C. N., Nakahara, H., Ono, A., Tsuge, M., & Oka, S. (2024) · Genes · doi:10.3390/genes15121551 · Cited by 119 · see citing works

Origin and domestication of papaya Y h chromosomePreprint

VanBuren, R., Zeng, F., Chen, C., Zhang, J., Wai, C. M., Han, J. O., Aryal, R., Gschwend, A. R., Wang, J., Na, J.-K., et al. (2015) · Genome Research · doi:10.1101/gr.183905.114 · Cited by 118 · see citing works

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

Melo‐Ferreira, J., Vilela, J. E. R., Fonseca, M. M., da Fonseca, R. R., Boursot, P., & Alves, P. C. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu059 · Cited by 115 · see citing works

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Pavlopoulos, G. A., Malliarakis, D., Papanikolaou, N., Θεοδοσίου, Θ., Enright, A. J., & Iliopoulos, I. (2015) · GigaScience · doi:10.1186/s13742-015-0077-2 · Cited by 113 · see citing works

The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Chang, S., Wang, Y., Lu, J., Gai, J., Li, J., Chu, P., Guan, R., & Zhao, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056502 · Cited by 114 · see citing works

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Galardini, M., Pini, F., Bazzicalupo, M., Biondi, E. G., & Mengoni, A. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt027 · Cited by 112 · see citing works

Savant: genome browser for high-throughput sequencing data

Fiume, M., Williams, V. R., Brook, A. L., & Brudno, M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq332 · Cited by 112 · see citing works

MinION nanopore sequencing of an influenza genome

Wang, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00766 · Cited by 111 · see citing works

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

Barrett, C. F., Specht, C. D., Leebens‐Mack, J., Stevenson, D. W., Zomlefer, W. B., & Davis, J. I. (2013) · Annals of Botany · doi:10.1093/aob/mct264 · Cited by 109 · see citing works

Chemical and transcriptional responses of Norway spruce genotypes with different susceptibility to Heterobasidion spp. infection

Danielsson, M., Lundén, K., Elfstrand, M., Hu, J., Zhao, T., Arnerup, J., Ihrmark, K., Swedjemark, G., Borg‐Karlson, A., & Stenlid, J. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-154 · Cited by 108 · see citing works

Asexual genome evolution in the apomictic R anunculus auricomus complex: examining the effects of hybridization and mutation accumulation

Pellino, M., Hojsgaard, D., Schmutzer, T., Scholz, U., Hörandl, E., Vogel, H., & Sharbel, T. F. (2013) · Molecular Ecology · doi:10.1111/mec.12533 · Cited by 107 · see citing works

Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1

Bonfiglio, S., Ginja, C., De Gaetano, A., Achilli, A., Olivieri, A., Colli, L., Tesfaye, K., Agha, S. H., Gama, L. T., Cattonaro, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038601 · Cited by 106 · see citing works

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

Emerson, J., Thomas, B. C., Andrade, K., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.01212-12 · Cited by 105 · see citing works

Novel Bacterial Taxa in the Human Microbiome

Wylie, K. M., Truty, R., Sharpton, T. J., Mihindukulasuriya, K. A., Zhou, Y., Gao, H., Sodergren, E. J., Weinstock, G. M., & Pollard, K. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035294 · Cited by 100 · see citing works

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance

Urayama, S., Takaki, Y., & Nunoura, T. (2016) · Microbes and Environments · doi:10.1264/jsme2.me15171 · Cited by 98 · see citing works

Identification of putative candidate genes involved in cuticle formation in Prunus avium (sweet cherry) fruit

Alkio, M., Jonas, U., Sprink, T., van Nocker, S., & Knoche, M. (2012) · Annals of Botany · doi:10.1093/aob/mcs087 · Cited by 95 · see citing works

Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes

Huotari, T., & Korpelainen, H. (2012) · Gene · doi:10.1016/j.gene.2012.07.020 · Cited by 93 · see citing works

Bioinformatics for Next Generation Sequencing Data

Magi, A., Benelli, M., Gozzini, A., Girolami, F., Torricelli, F., & Brandi, M. L. (2010) · Genes · doi:10.3390/genes1020294 · Cited by 93 · see citing works

Phylogenomic Analysis Reveals an Asian Origin for African Burkholderia pseudomallei and Further Supports Melioidosis Endemicity in Africa

Sarovich, D. S., Garin, B., Smet, B. D., Kaestli, M., Mayo, M. J., Vandamme, P. A. R., Jacobs, J. A., Lompo, P., Tahita, M. C., Tinto, H., et al. (2016) · mSphere · doi:10.1128/msphere.00089-15 · Cited by 92 · see citing works

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26

Reid, C. J., Wyrsch, E. R., Chowdhury, P. R., Zingali, T., Liu, M., Darling, A., Chapman, T., & Djordjevic, S. (2017) · bioRxiv · doi:10.1099/mgen.0.000143 · Cited by 87 · see citing works

Widespread Genome Reorganization of an Obligate Virus Mutualist

Burke, G. R., Walden, K. K. O., Whitfield, J. B., Robertson, H. M., & Strand, M. R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004660 · Cited by 89 · see citing works

Multidrug resistant Mannheimia haemolytica isolated from high-risk beef stocker cattle after antimicrobial metaphylaxis and treatment for bovine respiratory disease

Woolums, A. R., Karisch, B. B., Frye, J. G., Epperson, W. B., Smith, D. R., Blanton, J. R., Austin, F. W., Kaplan, R. M., Hiott, L. M., Woodley, T. A., et al. (2018) · Veterinary Microbiology · doi:10.1016/j.vetmic.2018.06.005 · Cited by 89 · see citing works

Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

Zanini, S. F., Bayer, P. E., Wells, R., Snowdon, R. J., Batley, J., Varshney, R. K., Nguyen, H. T., Edwards, D., & Golicz, A. A. (2021) · The Plant Genome · doi:10.1002/tpg2.20177 · Cited by 92 · see citing works

The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

Li, J., Li, J., Ma, Y., Kou, L., Wei, J., & Wang, W. (2022) · BMC Genomics · doi:10.1186/s12864-022-08706-2 · Cited by 86 · see citing works

Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

Xiong, J., Alexander, D. C., Ma, J. H., Déraspe, M., Low, D. E., Jamieson, F., & Roy, P. H. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00423-13 · Cited by 85 · see citing works

Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

Kupczok, A., Neve, H., Huang, K. D., Hoeppner, M. P., Heller, K. J., Franz, C. M. A. P., & Dagan, T. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy027 · Cited by 85 · see citing works

Bioinformatics tools and databases for analysis of next-generation sequence data

Lee, H. C., Lai, K., Lorenc, M. T., Imelfort, M., Duran, C., & Edwards, D. (2011) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr037 · Cited by 84 · see citing works

Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer

Zhang, D., Qi, J., Yue, J., Huang, J., Sun, T., Li, S., Wen, J., Hettenhausen, C., Wu, J., Wang, L., et al. (2014) · BMC Plant Biology · doi:10.1186/1471-2229-14-19 · Cited by 83 · see citing works

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

Kazakoff, S. H., Imelfort, M., Edwards, D., Koehorst, J. J., Biswas, B., Batley, J., Scott, P. T., & Gresshoff, P. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051687 · Cited by 82 · see citing works

Augmented Reality in K–12 Education: A Systematic Review and Meta-Analysis of the Literature from 2000 to 2020

Zhang, J., Li, G., Huang, Q., Feng, Q., & Luo, H. (2022) · Sustainability · doi:10.3390/su14159725 · Cited by 81 · see citing works

Correlations among oligonucleotide repeats, nucleotide substitutions, and insertion–deletion mutations in chloroplast genomes of plant family Malvaceae

Abdullah, A., Mehmood, F., Shahzadi, I., Ali, Z., Islam, M., Naeem, M., Mirza, B., Lockhart, P. J., Ahmed, I., & Waheed, M. T. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12585 · Cited by 79 · see citing works

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

Guida, A., Lindstädt, C., Maguire, S. L., Ding, C., Higgins, D. G., Corton, N. J., Berriman, M., & Butler, G. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-628 · Cited by 78 · see citing works

1 Sequence Analysis Tablet – Next Generation Sequence Assembly Visualization

Milne, I., Bayer, M., Cardle, L., Shaw, P. D., Stephen, G., Wright, F., & Marshall, D. (2014)

Using Tablet for visual exploration of second-generation sequencing data

Milne, I., Stephen, G., Bayer, M., Cock, P., Pritchard, L., Cardle, L., Shaw, P. D., & Marshall, D. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs012 · Cited by 949 · see citing works

Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings

Milne, I., Bayer, M., Stephen, G., Cardle, L., & Marshall, D. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3167-5_14 · Cited by 49 · see citing works

GenomeView: a next-generation genome browser

Abeel, T., Parys, T. V., Saeys, Y., Galagan, J. E., & de Peer, Y. V. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr995 · Cited by 165 · see citing works

Sequence analysis MapView: visualization of short reads alignment on a desktop computer

Bao, H., Guo, H., Wang, J., Zhou, R., Lu, X., Shi, S., & Dopazo, J. (2009)