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Computational Pan-Genomics: Status, Promises and Challenges
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1001/jama.2013.3231openalex-snapshot
A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
inferredcites →https://doi.org/10.1007/978-3-319-05269-4_2openalex-snapshot
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
inferredcites →https://doi.org/10.1007/978-3-319-05269-4_4openalex-snapshot
On the Representation of de Bruijn Graphs
inferredcites →https://doi.org/10.1007/978-3-319-19929-0_4openalex-snapshot
Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis
inferredcites →https://doi.org/10.1007/978-3-642-02008-7_9openalex-snapshot
Storage and Retrieval of Individual Genomes
inferredcites →https://doi.org/10.1007/978-3-642-23038-7_23openalex-snapshot
Indexing Finite Language Representation of Population Genotypes
inferredcites →https://doi.org/10.1007/978-3-642-40453-5_17openalex-snapshot
Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes
inferredcites →https://doi.org/10.1007/978-3-662-48221-6_16openalex-snapshot
Bloom Filter Trie – A Data Structure for Pan-Genome Storage
inferredcites →https://doi.org/10.1007/s12033-011-9443-1openalex-snapshot
Emerging Knowledge from Genome Sequencing of Crop Species
inferredcites →https://doi.org/10.1016/j.bdq.2015.02.001openalex-snapshot
Assessing the performance of the Oxford Nanopore Technologies MinION
inferredcites →https://doi.org/10.1016/j.ccell.2014.12.001openalex-snapshot
Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution
inferredcites →https://doi.org/10.1016/j.cell.2008.10.049openalex-snapshot
Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors
inferredcites →https://doi.org/10.1016/j.coviro.2011.12.004openalex-snapshot
Metagenomics and future perspectives in virus discovery
inferredcites →https://doi.org/10.1016/j.gpb.2015.01.007openalex-snapshot
A Brief Review of Software Tools for Pangenomics
inferredcites →https://doi.org/10.1016/j.mib.2014.11.016openalex-snapshot
Ten years of pan-genome analyses
inferredcites →https://doi.org/10.1016/j.pbi.2007.02.001openalex-snapshot
Transposable elements and the plant pan-genomes
inferredcites →https://doi.org/10.1016/j.sbi.2006.04.004openalex-snapshot
Multiple sequence alignment
inferredcites →https://doi.org/10.1016/j.ygeno.2010.03.001openalex-snapshot
Assembly algorithms for next-generation sequencing data
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/523149aopenalex-snapshot
Data analysis: Create a cloud commons
inferredcites →https://doi.org/10.1038/nature04226openalex-snapshot
A haplotype map of the human genome
inferredcites →https://doi.org/10.1038/nature07743openalex-snapshot
Population genomics of domestic and wild yeasts
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nature11450openalex-snapshot
A metagenome-wide association study of gut microbiota in type 2 diabetes
inferredcites →https://doi.org/10.1038/nature11532openalex-snapshot
A map of rice genome variation reveals the origin of cultivated rice
inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot
An integrated map of genetic variation from 1,092 human genomes
inferredcites →https://doi.org/10.1038/nature12213openalex-snapshot
Mutational heterogeneity in cancer and the search for new cancer-associated genes
inferredcites →https://doi.org/10.1038/nature12634openalex-snapshot
Mutational landscape and significance across 12 major cancer types
inferredcites →https://doi.org/10.1038/nature12779openalex-snapshot
An archaeal origin of eukaryotes supports only two primary domains of life
inferredcites →https://doi.org/10.1038/nature13127openalex-snapshot
Guidelines for investigating causality of sequence variants in human disease
inferredcites →https://doi.org/10.1038/nature13394openalex-snapshot
Genome sequencing identifies major causes of severe intellectual disability
inferredcites →https://doi.org/10.1038/nature13400openalex-snapshot
The ctenophore genome and the evolutionary origins of neural systems
inferredcites →https://doi.org/10.1038/nature13907openalex-snapshot
Resolving the complexity of the human genome using single-molecule sequencing
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nbt.2727openalex-snapshot
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
inferredcites →https://doi.org/10.1038/nbt.2833openalex-snapshot
Whole-genome haplotyping using long reads and statistical methods
inferredcites →https://doi.org/10.1038/nbt.2942openalex-snapshot
An integrated catalog of reference genes in the human gut microbiome
inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
inferredcites →https://doi.org/10.1038/nbt.3432openalex-snapshot
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
inferredcites →https://doi.org/10.1038/ncomms10001openalex-snapshot
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
inferredcites →https://doi.org/10.1038/ncomms3320openalex-snapshot
Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum
inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/ng.2312openalex-snapshot
Genome-wide genetic changes during modern breeding of maize
inferredcites →https://doi.org/10.1038/ng.3021openalex-snapshot
Whole-genome sequence variation, population structure and demographic history of the Dutch population
inferredcites →https://doi.org/10.1038/ng.3036openalex-snapshot
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1038/ng.3062openalex-snapshot
Data use under the NIH GWAS Data Sharing Policy and future directions
inferredcites →https://doi.org/10.1038/ng.3121openalex-snapshot
Comprehensive variation discovery in single human genomes
inferredcites →https://doi.org/10.1038/ng.3221openalex-snapshot
Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
inferredcites →https://doi.org/10.1038/ng.3257openalex-snapshot
Improved genome inference in the MHC using a population reference graph
inferredcites →https://doi.org/10.1038/ng.3622openalex-snapshot
Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis
inferredcites →https://doi.org/10.1038/nmeth.1422openalex-snapshot
Visualizing genomes: techniques and challenges
inferredcites →https://doi.org/10.1038/nmeth.2206openalex-snapshot
DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nmeth.3654openalex-snapshot
Efficient genotype compression and analysis of large genetic-variation data sets
inferredcites →https://doi.org/10.1038/nprot.2016.095openalex-snapshot
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
inferredcites →https://doi.org/10.1038/nrc3261openalex-snapshot
Intra-tumour heterogeneity: a looking glass for cancer?
inferredcites →https://doi.org/10.1038/nrg2796openalex-snapshot
Genotype imputation for genome-wide association studies
inferredcites →https://doi.org/10.1038/nrg2950openalex-snapshot
The importance of phase information for human genomics
inferredcites →https://doi.org/10.1038/nrg2958openalex-snapshot
Genome structural variation discovery and genotyping
inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot
Genotype and SNP calling from next-generation sequencing data
inferredcites →https://doi.org/10.1038/nrg3031openalex-snapshot
Exome sequencing as a tool for Mendelian disease gene discovery
inferredcites →https://doi.org/10.1038/nrg3054openalex-snapshot
Haplotype phasing: existing methods and new developments
inferredcites →https://doi.org/10.1038/nrg3484openalex-snapshot
Eukaryotic transcriptional dynamics: from single molecules to cell populations
inferredcites →https://doi.org/10.1038/nrg3707openalex-snapshot
Comparative primate genomics: emerging patterns of genome content and dynamics
inferredcites →https://doi.org/10.1038/nrg3903openalex-snapshot
Haplotype-resolved genome sequencing: experimental methods and applications
inferredcites →https://doi.org/10.1038/nrmicro1477openalex-snapshot
Bioinformatics-assisted anti-HIV therapy
inferredcites →https://doi.org/10.1073/pnas.0506758102openalex-snapshot
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”
inferredcites →https://doi.org/10.1073/pnas.0914638107openalex-snapshot
High-resolution human genome structure by single-molecule analysis
inferredcites →https://doi.org/10.1073/pnas.1402564111openalex-snapshot
Tackling soil diversity with the assembly of large, complex metagenomes
inferredcites →https://doi.org/10.1089/cmb.2009.0169openalex-snapshot
Storage and Retrieval of Highly Repetitive Sequence Collections
inferredcites →https://doi.org/10.1089/cmb.2010.0252openalex-snapshot
Cactus Graphs for Genome Comparisons
inferredcites →https://doi.org/10.1089/cmb.2014.0146openalex-snapshot
Building a Pan-Genome Reference for a Population
inferredcites →https://doi.org/10.1089/cmb.2014.0157openalex-snapshot
W hats H ap : Weighted Haplotype Assembly for Future-Generation Sequencing Reads
inferredcites →https://doi.org/10.1093/bfgp/elt008openalex-snapshot
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
inferredcites →https://doi.org/10.1093/bib/bbq015openalex-snapshot
A survey of sequence alignment algorithms for next-generation sequencing
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s181openalex-snapshot
Splicing graphs and EST assembly problem
inferredcites →https://doi.org/10.1093/bioinformatics/btm015openalex-snapshot
Assessment of phylogenomic and orthology approaches for phylogenetic inference
inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btp377openalex-snapshot
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
inferredcites →https://doi.org/10.1093/bioinformatics/bts217openalex-snapshot
GenomeRing: alignment visualization based on SuperGenome coordinates
inferredcites →https://doi.org/10.1093/bioinformatics/btt020openalex-snapshot
DSK: k -mer counting with very low memory usage
inferredcites →https://doi.org/10.1093/bioinformatics/btt213openalex-snapshot
Haplotype assembly in polyploid genomes and identical by descent shared tracts
inferredcites →https://doi.org/10.1093/bioinformatics/btt215openalex-snapshot
Short read alignment with populations of genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btu014openalex-snapshot
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
inferredcites →https://doi.org/10.1093/bioinformatics/btu406openalex-snapshot
GATB: Genome Assembly & Analysis Tool Box
inferredcites →https://doi.org/10.1093/bioinformatics/btu438openalex-snapshot
Journaled string tree—a scalable data structure for analyzing thousands of similar genomes on your laptop
inferredcites →https://doi.org/10.1093/bioinformatics/btu484openalex-snapshot
Probabilistic single-individual haplotyping
inferredcites →https://doi.org/10.1093/bioinformatics/btu534openalex-snapshot
Comparative assembly hubs: Web-accessible browsers for comparative genomics
inferredcites →https://doi.org/10.1093/bioinformatics/btu756openalex-snapshot
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
inferredcites →https://doi.org/10.1093/bioinformatics/btv022openalex-snapshot
KMC 2: fast and resource-frugal k -mer counting
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btv495openalex-snapshot
H ap C ol : accurate and memory-efficient haplotype assembly from long reads
inferredcites →https://doi.org/10.1093/bioinformatics/btv603openalex-snapshot
Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/gbe/evq077openalex-snapshot
A Survey of Combinatorial Methods for Phylogenetic Networks
inferredcites →https://doi.org/10.1093/gbe/evv121openalex-snapshot
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream
inferredcites →https://doi.org/10.1093/genetics/165.4.2213openalex-snapshot
Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gks794openalex-snapshot
Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
inferredcites →https://doi.org/10.1093/nar/gkv1209openalex-snapshot
Ensembl Genomes 2016: more genomes, more complexity
inferredcites →https://doi.org/10.1101/018259openalex-snapshot
Efficient genotype compression and analysis of large genetic variation datasets
inferredcites →https://doi.org/10.1101/gr.076554.108openalex-snapshot
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot
Mapping short DNA sequencing reads and calling variants using mapping quality scores
inferredcites →https://doi.org/10.1101/gr.118414.110openalex-snapshot
Estimation of rearrangement phylogeny for cancer genomes
inferredcites →https://doi.org/10.1101/gr.123356.111openalex-snapshot
Cactus: Algorithms for genome multiple sequence alignment
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.147710.112openalex-snapshot
A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
inferredcites →https://doi.org/10.1101/gr.2289704openalex-snapshot
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
inferredcites →https://doi.org/10.1101/gr.2395204openalex-snapshot
De Novo Repeat Classification and Fragment Assembly
inferredcites →https://doi.org/10.1109/tcbb.2013.2297101openalex-snapshot
Indexing Graphs for Path Queries with Applications in Genome Research
inferredcites →https://doi.org/10.1111/tpj.12616openalex-snapshot
Exploring genetic variation in the tomato ( Solanum section Lycopersicon ) clade by whole‐genome sequencing
inferredcites →https://doi.org/10.1126/science.1058040openalex-snapshot
The Sequence of the Human Genome
inferredcites →https://doi.org/10.1126/science.1123061openalex-snapshot
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
inferredcites →https://doi.org/10.1126/science.1261498openalex-snapshot
Patterns and ecological drivers of ocean viral communities
inferredcites →https://doi.org/10.1126/science.284.5423.2124openalex-snapshot
Phylogenetic Classification and the Universal Tree
inferredcites →https://doi.org/10.1126/science.7542800openalex-snapshot
Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd
inferredcites →https://doi.org/10.1128/jvi.01998-12openalex-snapshot
Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
inferredcites →https://doi.org/10.1128/jvi.76.1.463-465.2002openalex-snapshot
Quasispecies Theory in Virology
inferredcites →https://doi.org/10.1128/mbio.01721-14openalex-snapshot
Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155522openalex-snapshot
Rules of Engagement: Molecular Insights from Host-Virus Arms Races
inferredcites →https://doi.org/10.1146/annurev-med-100708-204735openalex-snapshot
Structural Variation in the Human Genome and its Role in Disease
inferredcites →https://doi.org/10.1146/annurev.micro.59.030804.121233openalex-snapshot
GENOME TREES AND THE NATURE OF GENOME EVOLUTION
inferredcites →https://doi.org/10.1186/1471-2105-12-119openalex-snapshot
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
inferredcites →https://doi.org/10.1186/1471-2105-12-333openalex-snapshot
Efficient counting of k-mers in DNA sequences using a bloom filter
inferredcites →https://doi.org/10.1186/1471-2105-14-102openalex-snapshot
Mobilomics in Saccharomyces cerevisiaestrains
inferredcites →https://doi.org/10.1186/1471-2105-14-s5-s1openalex-snapshot
Discovering motifs that induce sequencing errors
inferredcites →https://doi.org/10.1186/1471-2105-15-99openalex-snapshot
Genome alignment with graph data structures: a comparison
inferredcites →https://doi.org/10.1186/1471-2105-16-s11-s3openalex-snapshot
Pan-Tetris: an interactive visualisation for Pan-genomes
inferredcites →https://doi.org/10.1186/1471-2105-8-s7-s21openalex-snapshot
A survey of DNA motif finding algorithms
inferredcites →https://doi.org/10.1186/1471-2164-15-654openalex-snapshot
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
inferredcites →https://doi.org/10.1186/1745-6150-1-11openalex-snapshot
A survey of motif discovery methods in an integrated framework.
inferredcites →https://doi.org/10.1186/gb-2009-10-5-107openalex-snapshot
The 1001 Genomes Project for Arabidopsis thaliana
inferredcites →https://doi.org/10.1186/gb-2009-10-9-r98openalex-snapshot
Simultaneous alignment of short reads against multiple genomes
inferredcites →https://doi.org/10.1186/gb-2013-14-5-r51openalex-snapshot
Characterizing and measuring bias in sequence data
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12859-016-1103-9openalex-snapshot
Read mapping on de Bruijn graphs
inferredcites →https://doi.org/10.1186/s12864-015-1519-zopenalex-snapshot
Genome assembly using Nanopore-guided long and error-free DNA reads
inferredcites →https://doi.org/10.1186/s13059-015-0607-3openalex-snapshot
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes
inferredcites →https://doi.org/10.1186/s13073-014-0073-7openalex-snapshot
Whole-genome haplotyping approaches and genomic medicine
inferredcites →https://doi.org/10.1186/s13073-014-0109-zopenalex-snapshot
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
inferredcites →https://doi.org/10.1371/journal.pcbi.0030123openalex-snapshot
Recent Evolutions of Multiple Sequence Alignment Algorithms
inferredcites →https://doi.org/10.1371/journal.pcbi.1003515openalex-snapshot
Viral Quasispecies Assembly via Maximal Clique Enumeration
inferredcites →https://doi.org/10.1371/journal.pgen.1004776openalex-snapshot
Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages
inferredcites →https://doi.org/10.1371/journal.pone.0001456openalex-snapshot
The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples
inferredcites →https://doi.org/10.1371/journal.pone.0017722openalex-snapshot
Single Virus Genomics: A New Tool for Virus Discovery
inferredcites →https://doi.org/10.1371/journal.pone.0055864openalex-snapshot
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome
inferredcites →https://doi.org/10.1371/journal.pone.0109384openalex-snapshot
Indexes of Large Genome Collections on a PC
inferredcites →https://doi.org/10.1371/journal.pone.0138259openalex-snapshot
Robustness of Massively Parallel Sequencing Platforms
inferredcites →https://doi.org/10.1534/genetics.115.183483openalex-snapshot
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
inferredcites →https://doi.org/10.3389/fbioe.2015.00012openalex-snapshot
Searching and Indexing Genomic Databases via Kernelization
inferredcites →https://doi.org/10.3389/fbioe.2015.00092openalex-snapshot
Detection of Genomic Structural Variants from Next-Generation Sequencing Data
inferredcites →https://doi.org/10.3389/fmicb.2012.00329openalex-snapshot
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
inferredcites →https://doi.org/10.3389/fmicb.2015.00224openalex-snapshot
Beyond research: a primer for considerations on using viral metagenomics in the field and clinic
inferredcites →https://doi.org/10.3389/fmicb.2015.00766openalex-snapshot
MinION nanopore sequencing of an influenza genome
inferredcites →https://doi.org/10.4137/ebo.s29089openalex-snapshot
The Origin of Land Plants: A Phylogenomic Perspective
inferredcites →https://doi.org/10.4230/oasics.gcb.2013.35openalex-snapshot
PanCake: A Data Structure for Pangenomes
inferredcites →https://doi.org/10.5220/0005098402510257openalex-snapshot
Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research
inferredcites →https://doi.org/10.7554/elife.01123openalex-snapshot
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/leg3.16openalex-snapshot
The future of legume genetic data resources: Challenges, opportunities, and priorities
inferred← citeshttps://doi.org/10.1007/978-1-4939-7463-4_3openalex-snapshot
Comparative Genomics for Prokaryotes
inferred← citeshttps://doi.org/10.1007/978-3-319-78723-7_41openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00425-023-04242-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00453-022-01007-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10482-022-01806-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10791-017-9297-7openalex-snapshot
Document retrieval on repetitive string collections
inferred← citeshttps://doi.org/10.1007/s40484-019-0181-xopenalex-snapshot
Overlap graphs and de Bruijn graphs: data structures for de novogenome assembly in the big data era
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00001-9openalex-snapshot
Pan-omics focused to Crick's central dogma
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00002-0openalex-snapshot
Bioinformatics approaches applied in pan-genomics and their challenges
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00003-2openalex-snapshot
Evolutionary pan-genomics and applications
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00005-6openalex-snapshot
Pan-genomics of veterinary pathogens and its applications
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00006-8openalex-snapshot
Pan-genomics of plant pathogens and its applications
inferred← citeshttps://doi.org/10.1016/b978-0-12-817076-2.00014-7openalex-snapshot
Pan-genomics of plants and its applications
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00184-6openalex-snapshot
Variations and Polymorphisms: The Human Pangenome Project
inferred← citeshttps://doi.org/10.1016/b978-0-443-26791-8.00016-9openalex-snapshot
Pangenomics for developing fungal disease-resistant plants
inferred← citeshttps://doi.org/10.1016/bs.aivir.2017.08.004openalex-snapshot
Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2024.11.007openalex-snapshot
Mapping the pathogenic nexus: Gene overlap and protein interaction networks in Alzheimer’s and breast cancer as a precursor to protein structure prediction and analysis
inferred← citeshttps://doi.org/10.1016/j.ajhg.2023.09.011openalex-snapshot
Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes
inferred← citeshttps://doi.org/10.1016/j.ajhg.2024.05.012openalex-snapshot
From complete genomes to pangenomes
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.04.035openalex-snapshot
Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains
inferred← citeshttps://doi.org/10.1016/j.ic.2021.104748openalex-snapshot
On the complexity of approximately matching a string to a directed graph
inferred← citeshttps://doi.org/10.1016/j.ic.2025.105296openalex-snapshot
Elastic-degenerate string comparison
inferred← citeshttps://doi.org/10.1016/j.isci.2019.07.011openalex-snapshot
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
inferred← citeshttps://doi.org/10.1016/j.isci.2021.102755openalex-snapshot
Linearization of genome sequence graphs revisited
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2017.07.017openalex-snapshot
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers
inferred← citeshttps://doi.org/10.1016/j.jgg.2025.03.015openalex-snapshot
Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat
inferred← citeshttps://doi.org/10.1016/j.patrec.2021.03.018openalex-snapshot
Two parallel versions of VF3: Performance analysis on a wide database of graphs
inferred← citeshttps://doi.org/10.1016/j.pbi.2017.03.001openalex-snapshot
Network approaches for plant phylogenomic synteny analysis
inferred← citeshttps://doi.org/10.1016/j.pbi.2018.11.001openalex-snapshot
Plant genome sequences: past, present, future
inferred← citeshttps://doi.org/10.1016/j.pbi.2020.04.009openalex-snapshot
The rise and fall of genes: origins and functions of plant pathogen pangenomes
inferred← citeshttps://doi.org/10.1016/j.tcs.2019.08.012openalex-snapshot
Approximate pattern matching on elastic-degenerate text
inferred← citeshttps://doi.org/10.1016/j.tcs.2023.114269openalex-snapshot
Elastic founder graphs improved and enhanced
inferred← citeshttps://doi.org/10.1016/j.tig.2019.11.006openalex-snapshot
Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications
inferred← citeshttps://doi.org/10.1016/j.tig.2020.12.002openalex-snapshot
The genome atlas: navigating a new era of reference genomes
inferred← citeshttps://doi.org/10.1016/j.xplc.2024.101137openalex-snapshot
Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees
inferred← citeshttps://doi.org/10.1038/s41586-025-09290-7openalex-snapshot
Structural variation in 1,019 diverse humans based on long-read sequencing
inferred← citeshttps://doi.org/10.1038/s41587-020-0719-5openalex-snapshot
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
inferred← citeshttps://doi.org/10.1038/s41598-025-29683-yopenalex-snapshot
Conserved accessory genes link a phylogenetically distinct Bacillus subtilis strain from Indian bekang to the Japanese natto clade
inferred← citeshttps://doi.org/10.1038/s42003-021-02556-6openalex-snapshot
Building a Chinese pan-genome of 486 individuals
inferred← citeshttps://doi.org/10.1039/9781837674916-00109openalex-snapshot
Epigenomic Sequencing Technologies
inferred← citeshttps://doi.org/10.1039/9781837674916-part2openalex-snapshot
Emerging Technologies for Epigenetic Drug Discovery
inferred← citeshttps://doi.org/10.1093/bib/bbad297openalex-snapshot
Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches
inferred← citeshttps://doi.org/10.1093/bib/bbae266openalex-snapshot
NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach
inferred← citeshttps://doi.org/10.1093/bioadv/vbad149openalex-snapshot
Allele detection using k -mer-based sequencing error profiles
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf018openalex-snapshot
Assessing genome conservation on pangenome graphs with PanSel
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa640openalex-snapshot
Efficient dynamic variation graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab077openalex-snapshot
Detecting high-scoring local alignments in pangenome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab281openalex-snapshot
Constructing small genome graphs via string compression
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab302openalex-snapshot
A variant selection framework for genome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab516openalex-snapshot
Founder reconstruction enables scalable and seamless pangenomic analysis
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab688openalex-snapshot
Panache: a web browser-based viewer for linearized pangenomes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac308openalex-snapshot
ODGI: understanding pangenome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac448openalex-snapshot
BubbleGun: enumerating bubbles and superbubbles in genome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac506openalex-snapshot
PanTools v3: functional annotation, classification and phylogenomics
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac743openalex-snapshot
Unbiased pangenome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad320openalex-snapshot
Efficient short read mapping to a pangenome that is represented by a graph of ED strings
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad460openalex-snapshot
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae292openalex-snapshot
RecGraph: recombination-aware alignment of sequences to variation graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae363openalex-snapshot
Pangenome graph layout by Path-Guided Stochastic Gradient Descent
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae609openalex-snapshot
Cluster-efficient pangenome graph construction with nf-core/pangenome
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf225openalex-snapshot
Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw426openalex-snapshot
Snowball: strain aware gene assembly of metagenomes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx254openalex-snapshot
Discovery and genotyping of novel sequence insertions in many sequenced individuals
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty506openalex-snapshot
SOPanG: online text searching over a pan-genome
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty567openalex-snapshot
DREAM-Yara: an exact read mapper for very large databases with short update time
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty614openalex-snapshot
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty812openalex-snapshot
PRESM: personalized reference editor for somatic mutation discovery in cancer genomics
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz162openalex-snapshot
Bit-parallel sequence-to-graph alignment
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz341openalex-snapshot
Fully-sensitive seed finding in sequence graphs using a hybrid index
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz575openalex-snapshot
Haplotype-aware graph indexes
inferred← citeshttps://doi.org/10.1093/dnares/dsaa030openalex-snapshot
Building pan-genome infrastructures for crop plants and their use in association genetics
inferred← citeshttps://doi.org/10.1093/gbe/evaa059openalex-snapshot
Single-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates
inferred← citeshttps://doi.org/10.1093/gbe/evad121openalex-snapshot
The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes
inferred← citeshttps://doi.org/10.1093/jxb/erac412openalex-snapshot
Graph-based pan-genomes: increased opportunities in plant genomics
inferred← citeshttps://doi.org/10.1093/nar/gkac832openalex-snapshot
ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics
inferred← citeshttps://doi.org/10.1093/nar/gkad989openalex-snapshot
CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions
inferred← citeshttps://doi.org/10.1093/nargab/lqaa047openalex-snapshot
MinYS: mine your symbiont by targeted genome assembly in symbiotic communities
inferred← citeshttps://doi.org/10.1093/nargab/lqaf034openalex-snapshot
Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen
inferred← citeshttps://doi.org/10.1093/plcell/koaa002openalex-snapshot
Plant NLR diversity: the known unknowns of pan-NLRomes
inferred← citeshttps://doi.org/10.1099/mgen.0.000690openalex-snapshot
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids
inferred← citeshttps://doi.org/10.1101/2020.04.23.056317openalex-snapshot
Succinct dynamic variation graphs
inferred← citeshttps://doi.org/10.1101/2023.06.02.542089openalex-snapshot
Construction and representation of human pangenome graphs
inferred← citeshttps://doi.org/10.1101/858142openalex-snapshot
The Collaborative Cross Graphical Genome
inferred← citeshttps://doi.org/10.1109/bibm.2017.8217903openalex-snapshot
A crowdsourcing method for correcting sequencing errors for the third-generation sequencing data
inferred← citeshttps://doi.org/10.1109/bibm.2018.8621093openalex-snapshot
Fast and Accurate Genome-Scale Identification of DNA-Binding Sites
inferred← citeshttps://doi.org/10.1109/ccgrid.2017.116openalex-snapshot
Representing Variant Calling Format as Directed Acyclic Graphs to Enable the Use of Cloud Computing for Efficient and Cost Effective Genome Analysis
inferred← citeshttps://doi.org/10.1109/ipdps.2019.00055openalex-snapshot
Accelerating Sequence Alignment to Graphs
inferred← citeshttps://doi.org/10.1109/tcbb.2018.2831691openalex-snapshot
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics
inferred← citeshttps://doi.org/10.1109/tcbb.2018.2864564openalex-snapshot
Exploring Frequented Regions in Pan-Genomic Graphs
inferred← citeshttps://doi.org/10.1109/tcbbio.2024.3515469openalex-snapshot
A Novel Methodology for a Comprehensive Analysis of Genomic Sequence-to-Graph Alignment Tools
inferred← citeshttps://doi.org/10.1109/tvcg.2023.3282364openalex-snapshot
PanVA: Pangenomic Variant Analysis
inferred← citeshttps://doi.org/10.1111/mec.14264openalex-snapshot
Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
inferred← citeshttps://doi.org/10.1126/science.abf7117openalex-snapshot
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
inferred← citeshttps://doi.org/10.1145/3301312openalex-snapshot
Sparse Dynamic Programming on DAGs with Small Width
inferred← citeshttps://doi.org/10.1146/annurev-arplant-090823-015358openalex-snapshot
What Are We Learning from Plant Pangenomes?
inferred← citeshttps://doi.org/10.1146/annurev-genom-021623-081639openalex-snapshot
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
inferred← citeshttps://doi.org/10.1155/2024/9377016openalex-snapshot
Exploring Lead-Like Molecules of Traditional Chinese Medicine for Treatment Quest against Aliarcobacter butzleri: In Silico Toxicity Assessment, Dynamics Simulation, and Pharmacokinetic Profiling
inferred← citeshttps://doi.org/10.1186/s12859-017-1678-9openalex-snapshot
Coordinates and intervals in graph-based reference genomes
inferred← citeshttps://doi.org/10.1186/s12859-018-2362-4openalex-snapshot
Efficient inference of homologs in large eukaryotic pan-proteomes
inferred← citeshttps://doi.org/10.1186/s12859-021-03983-2openalex-snapshot
IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences
inferred← citeshttps://doi.org/10.1186/s12864-019-6263-3openalex-snapshot
Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization
inferred← citeshttps://doi.org/10.1186/s12864-020-6685-yopenalex-snapshot
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
inferred← citeshttps://doi.org/10.1186/s12915-020-0744-3openalex-snapshot
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
inferred← citeshttps://doi.org/10.1186/s13015-016-0083-7openalex-snapshot
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
inferred← citeshttps://doi.org/10.1186/s13059-018-1595-xopenalex-snapshot
FORGe: prioritizing variants for graph genomes
inferred← citeshttps://doi.org/10.1186/s13059-021-02297-zopenalex-snapshot
Simplitigs as an efficient and scalable representation of de Bruijn graphs
inferred← citeshttps://doi.org/10.1186/s13073-022-01026-wopenalex-snapshot
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007732openalex-snapshot
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008678openalex-snapshot
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007758openalex-snapshot
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
inferred← citeshttps://doi.org/10.1371/journal.pone.0195924openalex-snapshot
Correction: DNA Sequence Variants in the Five Prime Untranslated Region of the Cyclooxygenase-2 Gene Are Commonly Found in Healthy Dogs and Gray Wolves
inferred← citeshttps://doi.org/10.1371/journal.pone.0255260openalex-snapshot
Distributed hybrid-indexing of compressed pan-genomes for scalable and fast sequence alignment
inferred← citeshttps://doi.org/10.18174/499180openalex-snapshot
Application of high performance compute technology in bioinformatics
inferred← citeshttps://doi.org/10.18174/571907openalex-snapshot
Genomics underlying a canine hereditary thyroid follicular cell carcinoma
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1415605/v1openalex-snapshot
Plant pan-genomes are highly vulnerable to methodological considerations
inferred← citeshttps://doi.org/10.24072/pcjournal.415openalex-snapshot
Revisiting pangenome openness with k-mers
inferred← citeshttps://doi.org/10.2478/amns-2024-1891openalex-snapshot
Construction of personalized genomics model and clinical application in precision medicine
inferred← citeshttps://doi.org/10.3168/jds.2019-17693openalex-snapshot
Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection
inferred← citeshttps://doi.org/10.3389/fmicb.2021.665858openalex-snapshot
Multi-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni
inferred← citeshttps://doi.org/10.3390/a14010014openalex-snapshot
Subpath Queries on Compressed Graphs: A Survey
inferred← citeshttps://doi.org/10.3390/biom13091403openalex-snapshot
Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes
inferred← citeshttps://doi.org/10.3390/genes12010048openalex-snapshot
Probably Correct: Rescuing Repeats with Short and Long Reads
inferred← citeshttps://doi.org/10.3390/ijms20205062openalex-snapshot
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data
inferred← citeshttps://doi.org/10.3390/ijms23052671openalex-snapshot
Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species
inferred← citeshttps://doi.org/10.3390/life11060502openalex-snapshot
Advances in Cereal Crop Genomics for Resilience under Climate Change
inferred← citeshttps://doi.org/10.33915/etd.12835openalex-snapshot
Phylogenomics and Biogeography of Zinniinae (Asteraceae: Heliantheae) using plastome and nuclear datasets
inferred← citeshttps://doi.org/10.3410/f.734326805.793570658openalex-snapshot
Faculty Opinions recommendation of Whole-Genome Alignment and Comparative Annotation.
inferred← citeshttps://doi.org/10.3892/ijmm.2024.5479openalex-snapshot
Advancements in omics technologies: Molecular mechanisms of acute lung injury and acute respiratory distress syndrome (Review)
inferred← citeshttps://doi.org/10.5220/0011666900003414openalex-snapshot
Fast Exact String to D-Texts Alignments
inferred← citeshttps://doi.org/10.5772/intechopen.71374openalex-snapshot
Uropathogenic Escherichia coli and Fimbrial Adhesins Virulome
inferred← citeshttps://doi.org/10.5935/2526-5393.20210039openalex-snapshot
Papel do genoma e do microbioma na patogenia e abordagem terapêutica da asma
inferred← citeshttps://doi.org/10.7150/ijbs.58220openalex-snapshot
Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity
inferred← citeshttps://doi.org/10.7249/rra2520-1openalex-snapshot
Plagues, Cyborgs, and Supersoldiers: The Human Domain of War
inferred← citeshttps://doi.org/10.7287/peerj.5963v0.1/reviews/1openalex-snapshot
Peer Review #1 of "First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5963v0.1/reviews/2openalex-snapshot
Peer Review #2 of "First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5963v0.1/reviews/3openalex-snapshot
Peer Review #3 of "First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes (v0.1)"
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.