| 1 | Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes | 3.2 | 13 | Citations (PDF) |
| 2 | Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding | 4.6 | 30 | Citations (PDF) |
| 3 | High-quality metagenome assembly from long accurate reads with metaMDBG | 29.8 | 157 | Citations (PDF) |
| 4 | Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy | 29.8 | 59 | Citations (PDF) |
| 5 | The variation and evolution of complete human centromeres | 37.9 | 175 | Citations (PDF) |
| 6 | Parsnp 2.0: scalable core-genome alignment for massive microbial datasets | 4.7 | 74 | Citations (PDF) |
| 7 | The complete sequence and comparative analysis of ape sex chromosomes | 37.9 | 109 | Citations (PDF) |
| 8 | ModDotPlot—rapid and interactive visualization of tandem repeats | 4.7 | 53 | Citations (PDF) |
| 9 | Telomere-to-telomere assembly of diploid chromosomes with Verkko | 29.8 | 378 | Citations (PDF) |
| 10 | A draft human pangenome reference | 37.9 | 1,066 | Citations (PDF) |
| 11 | Recombination between heterologous human acrocentric chromosomes | 37.9 | 133 | Citations (PDF) |
| 12 | Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation | 24.6 | 125 | Citations (PDF) |
| 13 | Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation | 4.7 | 38 | Citations (PDF) |
| 14 | The complete sequence of a human Y chromosome | 37.9 | 418 | Citations (PDF) |
| 15 | Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks | 13.7 | 44 | Citations (PDF) |
| 16 | Improved sequence mapping using a complete reference genome and lift-over | 24.6 | 19 | Citations (PDF) |
| 17 | StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps | 4.7 | 161 | Citations (PDF) |
| 18 | Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation | 24.6 | 70 | Citations (PDF) |
| 19 | Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies | 24.6 | 115 | Citations (PDF) |
| 20 | Epigenetic patterns in a complete human genome | 36.3 | 273 | Citations (PDF) |
| 21 | Complete genomic and epigenetic maps of human centromeres | 36.3 | 563 | Citations (PDF) |
| 22 | From telomere to telomere: The transcriptional and epigenetic state of human repeat elements | 36.3 | 392 | Citations (PDF) |
| 23 | A complete reference genome improves analysis of human genetic variation | 36.3 | 364 | Citations (PDF) |
| 24 | The complete sequence of a human genome | 36.3 | 2,922 | Citations (PDF) |
| 25 | Segmental duplications and their variation in a complete human genome | 36.3 | 326 | Citations (PDF) |
| 26 | Long-read mapping to repetitive reference sequences using Winnowmap2 | 24.6 | 246 | Citations (PDF) |
| 27 | A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex | 7.5 | 25 | Citations (PDF) |
| 28 | Semi-automated assembly of high-quality diploid human reference genomes | 37.9 | 186 | Citations (PDF) |
| 29 | The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning | 3.4 | 20 | Citations (PDF) |
| 30 | The structure, function and evolution of a complete human chromosome 8 | 37.9 | 343 | Citations (PDF) |
| 31 | Evolutionary and biomedical insights from a marmoset diploid genome assembly | 37.9 | 65 | Citations (PDF) |
| 32 | Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C | 13.7 | 114 | Citations (PDF) |
| 33 | Complete vertebrate mitogenomes reveal widespread repeats and gene duplications | 8.1 | 115 | Citations (PDF) |
| 34 | Towards complete and error-free genome assemblies of all vertebrate species | 37.9 | 2,847 | Citations (PDF) |
| 35 | Population genomics of the critically endangered kākāpō | 6.8 | 226 | Citations (PDF) |
| 36 | Platypus and echidna genomes reveal mammalian biology and evolution | 37.9 | 161 | Citations (PDF) |
| 37 | Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential | 9.6 | 87 | Citations (PDF) |
| 38 | Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies | 3.9 | 197 | Citations (PDF) |
| 39 | Weighted minimizer sampling improves long read mapping | 4.7 | 204 | Citations (PDF) |
| 40 | Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs | 4.4 | 41 | Citations (PDF) |
| 41 | Telomere-to-telomere assembly of a complete human X chromosome | 37.9 | 716 | Citations (PDF) |
| 42 | Improved reference genome of the arboviral vector Aedes albopictus | 8.1 | 109 | Citations (PDF) |
| 43 | Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies | 8.1 | 3,382 | Citations (PDF) |
| 44 | HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads | 4.6 | 718 | Citations (PDF) |
| 45 | Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes | 29.8 | 526 | Citations (PDF) |
| 46 | Effect of sequence depth and length in long-read assembly of the maize inbred NC358 | 13.7 | 49 | Citations (PDF) |
| 47 | A robust benchmark for detection of germline large deletions and insertions | 29.8 | 403 | Citations (PDF) |
| 48 | An improved pig reference genome sequence to enable pig genetics and genomics research | 3.2 | 343 | Citations (PDF) |
| 49 | Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle | 13.7 | 122 | Citations (PDF) |
| 50 | Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle | 3.2 | 68 | Citations (PDF) |
| 51 | De novo assembly of the cattle reference genome with single-molecule sequencing | 3.2 | 632 | Citations (PDF) |
| 52 | Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome | 29.8 | 1,680 | Citations (PDF) |
| 53 | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation | 8.1 | 99 | Citations (PDF) |
| 54 | Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps | 13.7 | 157 | Citations (PDF) |
| 55 | De novo assembly of the goldfish (
Carassius auratus
) genome and the evolution of genes after whole-genome duplication | 10.9 | 247 | Citations (PDF) |
| 56 | Mash Screen: high-throughput sequence containment estimation for genome discovery | 8.1 | 286 | Citations (PDF) |
| 57 | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | 3.1 | 709 | Citations (PDF) |
| 58 | Reply to ‘Errors in long-read assemblies can critically affect protein prediction’ | 29.8 | 34 | Citations (PDF) |
| 59 | A chromosome-scale assembly of the major African malaria vector
Anopheles funestus | 3.2 | 69 | Citations (PDF) |
| 60 | HLA*LA—HLA typing from linearly projected graph alignments | 4.7 | 151 | Citations (PDF) |
| 61 | New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes | 3.3 | 34 | Citations (PDF) |
| 62 | Nanopore sequencing and assembly of a human genome with ultra-long reads | 29.8 | 1,868 | Citations (PDF) |
| 63 | Analysis of the
Aedes albopictus
C6/36 genome provides insight into cell line utility for viral propagation | 3.2 | 65 | Citations (PDF) |
| 64 | A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases | 1.5 | 67 | Citations (PDF) |
| 65 | Improved reference genome of Aedes aegypti informs arbovirus vector control | 37.9 | 596 | Citations (PDF) |
| 66 | High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries | 13.7 | 5,350 | Citations (PDF) |
| 67 | A fast adaptive algorithm for computing whole-genome homology maps | 4.7 | 160 | Citations (PDF) |
| 68 | RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification | 8.1 | 174 | Citations (PDF) |
| 69 | De novo assembly of haplotype-resolved genomes with trio binning | 29.8 | 514 | Citations (PDF) |
| 70 | Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing | 15.5 | 93 | Citations (PDF) |
| 71 | MUMmer4: A fast and versatile genome alignment system | 3.1 | 2,531 | Citations (PDF) |
| 72 | The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation | 2.8 | 46 | Citations (PDF) |
| 73 | Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly | 4.6 | 1,173 | Citations (PDF) |
| 74 | New advances in sequence assembly | 4.6 | 71 | Citations (PDF) |
| 75 | Canu: scalable and accurate long-read assembly via adaptive
k
-mer weighting and repeat separation | 4.6 | 7,539 | Citations (PDF) |
| 76 | Draft Genome Sequences from a Novel Clade of Bacillus cereus
Sensu Lato
Strains, Isolated from the International Space Station | 0.7 | 15 | Citations (PDF) |
| 77 | Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes | 7.5 | 104 | Citations (PDF) |
| 78 | The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts | 13.7 | 271 | Citations (PDF) |
| 79 | Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru | 3.0 | 12 | Citations (PDF) |
| 80 | Assembling large genomes with single-molecule sequencing and locality-sensitive hashing | 29.8 | 962 | Citations (PDF) |
| 81 | One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly | 7.0 | 453 | Citations (PDF) |
| 82 | Long-read, whole-genome shotgun sequence data for five model organisms | 5.7 | 163 | Citations (PDF) |
| 83 | Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp.
aureus
ATCC 25923 | 0.7 | 73 | Citations (PDF) |
| 84 | High-coverage sequencing and annotated assemblies of the budgerigar genome | 3.2 | 79 | Citations (PDF) |
| 85 | Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever | 0.7 | 9 | Citations (PDF) |
| 86 | Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever | 0.7 | 8 | Citations (PDF) |
| 87 | Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies | 6.6 | 56 | Citations (PDF) |
| 88 | Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species | 3.2 | 644 | Citations (PDF) |
| 89 | Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis | 0.7 | 5 | Citations (PDF) |
| 90 | Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle | 0.7 | 22 | Citations (PDF) |
| 91 | Reducing assembly complexity of microbial genomes with single-molecule sequencing | 8.1 | 397 | Citations (PDF) |
| 92 | The rise of a digital immune system | 3.2 | 32 | Citations (PDF) |
| 93 | Molecular Epidemiologic Investigation of an Anthrax Outbreak among Heroin Users, Europe | 3.8 | 87 | Citations (PDF) |
| 94 | GAGE: A critical evaluation of genome assemblies and assembly algorithms | 4.6 | 638 | Citations (PDF) |
| 95 | Hybrid error correction and de novo assembly of single-molecule sequencing reads | 29.8 | 1,005 | Citations (PDF) |
| 96 | Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp | 2.9 | 202 | Citations (PDF) |
| 97 | Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity | 3.3 | 84 | Citations (PDF) |
| 98 | Assemblathon 1: A competitive assessment of de novo short read assembly methods | 4.6 | 465 | Citations (PDF) |
| 99 | Complex microbiome underlying secondary and primary metabolism in the tunicate-
Prochloron
symbiosis | 7.5 | 162 | Citations (PDF) |
| 100 | Bacillus anthracis
comparative genome analysis in support of the Amerithrax investigation | 7.5 | 166 | Citations (PDF) |
| 101 | Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification | 3.3 | 83 | Citations (PDF) |
| 102 | Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray | 3.6 | 26 | Citations (PDF) |
| 103 | Transcriptomic Responses ofSalmonella entericaSerovars Enteritidis and Typhimurium to Chlorine-Based Oxidative Stress | 3.6 | 93 | Citations (PDF) |
| 104 | Insignia: a DNA signature search web server for diagnostic assay development | 15.5 | 41 | Citations (PDF) |
| 105 | Efficient oligonucleotide probe selection for pan-genomic tiling arrays | 3.0 | 25 | Citations (PDF) |
| 106 | Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A | 3.3 | 346 | Citations (PDF) |
| 107 | Comprehensive DNA Signature Discovery and Validation | 3.1 | 65 | Citations (PDF) |
| 108 | Evolution of genes and genomes on the Drosophila phylogeny | 37.9 | 2,006 | Citations (PDF) |
| 109 | Comparative genome assembly | 6.6 | 200 | Citations (PDF) |
| 110 | Using
MUMmer
to Identify Similar Regions in Large Sequence Sets | 3.3 | 566 | Citations (PDF) |
| 111 | Fast algorithms for large-scale genome alignment and comparison | 15.5 | 1,002 | Citations (PDF) |
| 112 | The whale shark genome reveals patterns of vertebrate gene family evolution | 0.7 | 38 | Citations (PDF) |
| 113 | The genome of the colonial hydroid
Hydractinia
reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals | 4.6 | 14 | Citations (PDF) |
| 114 | Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes | 6.8 | 9 | Citations (PDF) |
| 115 | Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA | 1.7 | 1 | Citations (PDF) |
| 116 | Germline sequence variation within the ribosomal DNA is associated with human complex traits | 6.8 | 0 | Citations (PDF) |
