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Repetitive DNA and next-generation sequencing: computational challenges and solutions

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

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Sequence organization of the human genome

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Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

inferredcites →https://doi.org/10.1016/j.tig.2007.12.006openalex-snapshot

Bioinformatics challenges of new sequencing technology

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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot

A map of human genome variation from population-scale sequencing

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Genome sequence and analysis of the tuber crop potato

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An Archaeopteryx-like theropod from China and the origin of Avialae

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot

Integrative genomics viewer

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/ng.437openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot

A framework for variation discovery and genotyping using next-generation DNA sequencing data

inferredcites →https://doi.org/10.1038/nmeth.1223openalex-snapshot

Stem cell transcriptome profiling via massive-scale mRNA sequencing

inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot

Mapping and quantifying mammalian transcriptomes by RNA-Seq

inferredcites →https://doi.org/10.1038/nmeth.1374openalex-snapshot

Computational methods for discovering structural variation with next-generation sequencing

inferredcites →https://doi.org/10.1038/nmeth.1517openalex-snapshot

De novo assembly and analysis of RNA-seq data

inferredcites →https://doi.org/10.1038/nmeth.1527openalex-snapshot

Limitations of next-generation genome sequence assembly

inferredcites →https://doi.org/10.1038/nmeth.1613openalex-snapshot

Computational methods for transcriptome annotation and quantification using RNA-seq

inferredcites →https://doi.org/10.1038/nrg2641openalex-snapshot

ChIP–seq: advantages and challenges of a maturing technology

inferredcites →https://doi.org/10.1038/nrg2841openalex-snapshot

Advances in understanding cancer genomes through second-generation sequencing

inferredcites →https://doi.org/10.1038/nrg2958openalex-snapshot

Genome structural variation discovery and genotyping

inferredcites →https://doi.org/10.1038/nrg798openalex-snapshot

Alu repeats and human genomic diversity

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The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes

inferredcites →https://doi.org/10.1073/pnas.1014330107openalex-snapshot

Transposable element insertions have strongly affected human evolution

inferredcites →https://doi.org/10.1073/pnas.1016657108openalex-snapshot

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

inferredcites →https://doi.org/10.1073/pnas.1019276108openalex-snapshot

Demographic history and rare allele sharing among human populations

inferredcites →https://doi.org/10.1073/pnas.1108918108openalex-snapshot

Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase ( MAK ) as a cause of retinitis pigmentosa

inferredcites →https://doi.org/10.1073/pnas.171285098openalex-snapshot

An Eulerian path approach to DNA fragment assembly

inferredcites →https://doi.org/10.1093/bioinformatics/btn548openalex-snapshot

Aggressive assembly of pyrosequencing reads with mates

inferredcites →https://doi.org/10.1093/bioinformatics/btp113openalex-snapshot

Statistical inferences for isoform expression in RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp336openalex-snapshot

SOAP2: an improved ultrafast tool for short read alignment

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btp373openalex-snapshot

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

inferredcites →https://doi.org/10.1093/bioinformatics/btp692openalex-snapshot

RNA-Seq gene expression estimation with read mapping uncertainty

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btq216openalex-snapshot

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

inferredcites →https://doi.org/10.1093/bioinformatics/btr085openalex-snapshot

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

inferredcites →https://doi.org/10.1093/bioinformatics/btr169openalex-snapshot

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions

inferredcites →https://doi.org/10.1093/bioinformatics/btr355openalex-snapshot

Identification of novel transcripts in annotated genomes using RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btr427openalex-snapshot

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

inferredcites →https://doi.org/10.1093/dnares/dsq028openalex-snapshot

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

inferredcites →https://doi.org/10.1093/jhered/esp086openalex-snapshot

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

inferredcites →https://doi.org/10.1093/molbev/msh262openalex-snapshot

Patterns of Segmental Duplication in the Human Genome

inferredcites →https://doi.org/10.1093/nar/gkq211openalex-snapshot

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

inferredcites →https://doi.org/10.1093/nar/gkq622openalex-snapshot

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

inferredcites →https://doi.org/10.1093/nar/gkr342openalex-snapshot

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

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.081422.108openalex-snapshot

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

inferredcites →https://doi.org/10.1101/gr.088013.108openalex-snapshot

SNP detection for massively parallel whole-genome resequencing

inferredcites →https://doi.org/10.1101/gr.088773.108openalex-snapshot

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

inferredcites →https://doi.org/10.1101/gr.096388.109openalex-snapshot

A SNP discovery method to assess variant allele probability from next-generation resequencing data

inferredcites →https://doi.org/10.1101/gr.101360.109openalex-snapshot

Assembly of large genomes using second-generation sequencing

inferredcites →https://doi.org/10.1101/gr.111120.110openalex-snapshot

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

inferredcites →https://doi.org/10.1126/science.1071837openalex-snapshot

Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis

inferredcites →https://doi.org/10.1126/science.1141319openalex-snapshot

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

inferredcites →https://doi.org/10.1126/science.1158441openalex-snapshot

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot

The B73 Maize Genome: Complexity, Diversity, and Dynamics

inferredcites →https://doi.org/10.1126/science.1186176openalex-snapshot

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

inferredcites →https://doi.org/10.1146/annurev.genom.8.080706.092416openalex-snapshot

Repetitive Sequences in Complex Genomes: Structure and Evolution

inferredcites →https://doi.org/10.1186/1471-2105-12-200openalex-snapshot

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration

inferredcites →https://doi.org/10.1186/1471-2105-12-95openalex-snapshot

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

inferredcites →https://doi.org/10.1186/1479-7364-4-4-271openalex-snapshot

State of the art de novo assembly of human genomes from massively parallel sequencing data

inferredcites →https://doi.org/10.1186/1745-6150-6-19openalex-snapshot

The struggle for life of the genome's selfish architects

inferredcites →https://doi.org/10.1186/gb-2008-9-3-r55openalex-snapshot

Genome assembly forensics: finding the elusive mis-assembly

inferredcites →https://doi.org/10.1186/gb-2009-10-2-r16openalex-snapshot

High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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-2010-11-10-r104openalex-snapshot

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

inferredcites →https://doi.org/10.1186/gb-2011-12-3-r31openalex-snapshot

A vertebrate case study of the quality of assemblies derived from next-generation sequences

inferredcites →https://doi.org/10.1186/gb-2011-12-6-r55openalex-snapshot

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

inferredcites →https://doi.org/10.1186/gb-2011-12-8-r72openalex-snapshot

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

inferredcites →https://doi.org/10.1371/journal.pcbi.1002111openalex-snapshot

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

inferredcites →https://doi.org/10.1371/journal.pone.0007767openalex-snapshot

BFAST: An Alignment Tool for Large Scale Genome Resequencing

inferredcites →https://doi.org/10.1371/journal.pone.0008407openalex-snapshot

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Clickable Nucleic Acids: Sequence‐Controlled Periodic Copolymer/Oligomer Synthesis by Orthogonal Thiol‐X Reactions

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inferred← citeshttps://doi.org/10.1007/978-3-319-10265-8_1openalex-snapshot

BINOS4DNA: Bitmap Indexes and NoSQL for Identifying Species with DNA Signatures through Metagenomics Samples

inferred← citeshttps://doi.org/10.1007/978-3-319-17157-9_13openalex-snapshot

CNV and Structural Variation in Plants: Prospects of NGS Approaches

inferred← citeshttps://doi.org/10.1007/978-3-319-17157-9_4openalex-snapshot

Variant Calling Using NGS Data in European Aspen (Populus tremula)

inferred← citeshttps://doi.org/10.1007/978-3-319-22521-0_20openalex-snapshot

Next-Generation Sequencing (NGS) Tools and Impact in Plant Breeding

inferred← citeshttps://doi.org/10.1007/978-3-319-29279-3_7openalex-snapshot

Genetics of Antarctic Krill

inferred← citeshttps://doi.org/10.1007/978-3-319-41324-2_19openalex-snapshot

From Compositional Chemical Ecologies to Self-replicating Ribosomes and on to Functional Trait Ecological Networks

inferred← citeshttps://doi.org/10.1007/978-3-319-43694-4_6openalex-snapshot

Quantity, Distribution, and Evolution of Major Repeats in Brassica napus

inferred← citeshttps://doi.org/10.1007/978-3-319-44203-7_1openalex-snapshot

Introduction to Molecular Genetics

inferred← citeshttps://doi.org/10.1007/978-3-319-55520-1_22openalex-snapshot

Epigenetic Characterization of Satellite DNA in Sugar Beet (Beta vulgaris)

inferred← citeshttps://doi.org/10.1007/978-3-319-55729-8_12openalex-snapshot

Physiological and Molecular Mechanisms and Adaptation Strategies in Soybean (Glycine max) Under Phosphate Deficiency

inferred← citeshttps://doi.org/10.1007/978-3-319-59826-0_14openalex-snapshot

Assembly-Free Techniques for NGS Data

inferred← citeshttps://doi.org/10.1007/978-3-319-61510-3_7openalex-snapshot

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach

inferred← citeshttps://doi.org/10.1007/978-3-319-66135-3_9openalex-snapshot

Repetitive Sequences in the Potato and Related Genomes

inferred← citeshttps://doi.org/10.1007/978-3-319-71147-8_38openalex-snapshot

On the Linearization of Scaffolds Sharing Repeated Contigs

inferred← citeshttps://doi.org/10.1007/978-3-319-71997-9_2openalex-snapshot

Informatics of Wild Relatives of Rice

inferred← citeshttps://doi.org/10.1007/978-3-319-78890-6_15openalex-snapshot

ReneGENE-GI: Empowering Precision Genomics with FPGAs on HPCs

inferred← citeshttps://doi.org/10.1007/978-3-319-89689-2_5openalex-snapshot

RNA Degradation in Neurodegenerative Disease

inferred← citeshttps://doi.org/10.1007/978-3-319-93997-1_25openalex-snapshot

Correction to: Molecular Biodiversity Convergence with Biogeography and Ethnobotany of Rare and Endangered Medicinal Plants from Northern Vietnam

inferred← citeshttps://doi.org/10.1007/978-3-319-96830-8_17openalex-snapshot

Implementation of Exome Sequencing Assay

inferred← citeshttps://doi.org/10.1007/978-3-642-29627-7_7openalex-snapshot

lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

inferred← citeshttps://doi.org/10.1007/978-3-642-37925-3_147openalex-snapshot

Elongation of Trinucleotide Repeats by DNA Polymerase

inferred← citeshttps://doi.org/10.1007/978-3-642-40193-0_2openalex-snapshot

The Sequence Reconstruction Problem

inferred← citeshttps://doi.org/10.1007/978-4-431-55576-6_1openalex-snapshot

Complexity of Mammalian Transcriptome Analyzed by RNA Deep Sequencing

inferred← citeshttps://doi.org/10.1007/978-81-322-2172-2_27openalex-snapshot

Applications of Bioinformatics in Plant and Agriculture

inferred← citeshttps://doi.org/10.1007/978-94-007-7572-5_13openalex-snapshot

FISHIS: A New Way in Chromosome Flow Sorting Makes Complex Genomes More Accessible

inferred← citeshttps://doi.org/10.1007/978-94-017-7543-4_16openalex-snapshot

Heterogeneity of Hepatocellular Carcinoma

inferred← citeshttps://doi.org/10.1007/978-981-13-1562-6_2openalex-snapshot

Next-Generation Sequencing: Technology, Advancements, and Applications

inferred← citeshttps://doi.org/10.1007/978-981-15-3151-4_13openalex-snapshot

Role of Biotechnology in the Exploration of Soil and Plant Microbiomes

inferred← citeshttps://doi.org/10.1007/978-981-16-1313-5_37-1openalex-snapshot

Targeting DNA Junctions with Small Molecules for Therapeutic Applications in Oncology

inferred← citeshttps://doi.org/10.1007/978-981-16-3993-7_23openalex-snapshot

Application of Metagenomics in Improvement of Rice

inferred← citeshttps://doi.org/10.1007/978-981-19-9776-1_37openalex-snapshot

Targeting DNA Junctions with Small Molecules for Therapeutic Applications in Oncology

inferred← citeshttps://doi.org/10.1007/978-981-96-4585-5_23openalex-snapshot

Application of Next-Generation Sequencing (NGS) Technology for Individualization in Forensic Context

inferred← citeshttps://doi.org/10.1007/978-981-96-4620-3_10openalex-snapshot

Genomic Approaches to Validate the Pathogenicity of Bacterial Fish Pathogens

inferred← citeshttps://doi.org/10.1007/978-981-97-3165-7_9openalex-snapshot

Genomics Data Analysis Techniques in Bioinformatics

inferred← citeshttps://doi.org/10.1007/s00122-013-2177-7openalex-snapshot

Copy number polymorphism in plant genomes

inferred← citeshttps://doi.org/10.1007/s00122-018-3218-zopenalex-snapshot

Identification of a gene responsible for cytoplasmic male-sterility in onions (Allium cepa L.) using comparative analysis of mitochondrial genome sequences of two recently diverged cytoplasms

inferred← citeshttps://doi.org/10.1007/s00122-023-04301-5openalex-snapshot

Structural variation of GL1 gene determines the trichome formation in Brassica juncea

inferred← citeshttps://doi.org/10.1007/s00204-025-04211-zopenalex-snapshot

Targeting cobra venom cytotoxin: a linear 40-mer ssDNA aptamer-based antivenom confers neutralisation potentials against cobra venom-induced cytotoxicity

inferred← citeshttps://doi.org/10.1007/s00216-018-0982-1openalex-snapshot

Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter

inferred← citeshttps://doi.org/10.1007/s00239-016-9741-0openalex-snapshot

Genomic Landscape of Long Terminal Repeat Retrotransposons (LTR-RTs) and Solo LTRs as Shaped by Ectopic Recombination in Chicken and Zebra Finch

inferred← citeshttps://doi.org/10.1007/s00251-017-1048-9openalex-snapshot

Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing

inferred← citeshttps://doi.org/10.1007/s00253-022-11963-6openalex-snapshot

Machine learning: its challenges and opportunities in plant system biology

inferred← citeshttps://doi.org/10.1007/s00277-019-03626-wopenalex-snapshot

Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT)

inferred← citeshttps://doi.org/10.1007/s00285-016-0982-8openalex-snapshot

Periodic power spectrum with applications in detection of latent periodicities in DNA sequences

inferred← citeshttps://doi.org/10.1007/s00335-016-9671-6openalex-snapshot

Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing

inferred← citeshttps://doi.org/10.1007/s00335-026-10205-8openalex-snapshot

Genome assembly of the Neotropical marsh rat Holochilus nanus (Cricetidae: Sigmodontinae) brings insights on B and sex chromosome evolution

inferred← citeshttps://doi.org/10.1007/s00412-013-0416-yopenalex-snapshot

Alteration of poly(ADP-ribose) metabolism affects murine sperm nuclear architecture by impairing pericentric heterochromatin condensation

inferred← citeshttps://doi.org/10.1007/s00412-014-0499-0openalex-snapshot

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

inferred← citeshttps://doi.org/10.1007/s00412-016-0601-xopenalex-snapshot

The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA

inferred← citeshttps://doi.org/10.1007/s00412-017-0646-5openalex-snapshot

New high copy tandem repeat in the content of the chicken W chromosome

inferred← citeshttps://doi.org/10.1007/s00412-019-00721-9openalex-snapshot

DNA transposon invasion and microsatellite accumulation guide W chromosome differentiation in a Neotropical fish genome

inferred← citeshttps://doi.org/10.1007/s00412-019-00729-1openalex-snapshot

Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars

inferred← citeshttps://doi.org/10.1007/s00417-023-06243-6openalex-snapshot

Nanopore sequencing method for CTG18.1 expansion in TCF4 in late-onset Fuchs endothelial corneal dystrophy and a comparison of the structural features of cornea with first-degree relatives

inferred← citeshttps://doi.org/10.1007/s00425-022-03898-zopenalex-snapshot

Coffea cytogenetics: from the first karyotypes to the meeting with genomics

inferred← citeshttps://doi.org/10.1007/s00438-014-0891-8openalex-snapshot

Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome

inferred← citeshttps://doi.org/10.1007/s00438-016-1225-9openalex-snapshot

Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum

inferred← citeshttps://doi.org/10.1007/s00438-016-1286-9openalex-snapshot

Tandem repeats of Allium fistulosum associated with major chromosomal landmarks

inferred← citeshttps://doi.org/10.1007/s00438-025-02270-6openalex-snapshot

Chromosome scale assembly unveils genomic structure and gene families of Calotropis procera

inferred← citeshttps://doi.org/10.1007/s00438-026-02489-xopenalex-snapshot

Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context

inferred← citeshttps://doi.org/10.1007/s00439-017-1769-8openalex-snapshot

The Y chromosomes of the great apes

inferred← citeshttps://doi.org/10.1007/s00439-019-02064-yopenalex-snapshot

Long-read sequencing in deciphering human genetics to a greater depth

inferred← citeshttps://doi.org/10.1007/s00453-021-00819-6openalex-snapshot

Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds

inferred← citeshttps://doi.org/10.1007/s00521-021-06188-zopenalex-snapshot

New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies

inferred← citeshttps://doi.org/10.1007/s10142-012-0293-0openalex-snapshot

Chromosomes in the flow to simplify genome analysis

inferred← citeshttps://doi.org/10.1007/s10142-026-01999-6openalex-snapshot

Dual-reference projection defines a callable core and reference-sensitive shell in a Qiantang River Megalobrama draft assembly

inferred← citeshttps://doi.org/10.1007/s10142-026-02060-2openalex-snapshot

Comprehensive genome-based characterization and pan-genome analysis of Bacillus paranthracis SM02 isolated from a fermented food ecosystem

inferred← citeshttps://doi.org/10.1007/s10327-022-01097-yopenalex-snapshot

Genomic resources of Colletotrichum fungi: development and application

inferred← citeshttps://doi.org/10.1007/s10404-015-1685-yopenalex-snapshot

Optical mapping and nanocoding approaches to whole-genome analysis

inferred← citeshttps://doi.org/10.1007/s10404-017-1889-4openalex-snapshot

From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis

inferred← citeshttps://doi.org/10.1007/s10489-015-0650-5openalex-snapshot

A novel locally guided genome reassembling technique using an artificial ant system

inferred← citeshttps://doi.org/10.1007/s10555-013-9426-8openalex-snapshot

Do mutator mutations fuel tumorigenesis?

inferred← citeshttps://doi.org/10.1007/s10577-014-9424-xopenalex-snapshot

A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome

inferred← citeshttps://doi.org/10.1007/s10577-016-9547-3openalex-snapshot

The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals

inferred← citeshttps://doi.org/10.1007/s10689-026-00559-yopenalex-snapshot

Vaccine strategies for cancer prevention in Lynch syndrome: the potential of dendritic cell-based therapy

inferred← citeshttps://doi.org/10.1007/s10709-016-9902-5openalex-snapshot

A comparative cytogenetic study of Drosophila parasitoids (Hymenoptera, Figitidae) using DNA-binding fluorochromes and FISH with 45S rDNA probe

inferred← citeshttps://doi.org/10.1007/s10722-017-0567-4openalex-snapshot

Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species

inferred← citeshttps://doi.org/10.1007/s10722-024-02186-xopenalex-snapshot

Genome-wide survey of Crataegus scabrifolia provides new insights into its genetic evolution and adaptation mechanisms

inferred← citeshttps://doi.org/10.1007/s10815-023-02999-2openalex-snapshot

Identification of cryptic balanced translocations in couples with unexplained recurrent pregnancy loss based upon embryonic PGT-A results

inferred← citeshttps://doi.org/10.1007/s11032-013-9997-7openalex-snapshot

Genome-wide single nucleotide polymorphism and Insertion-Deletion discovery through next-generation sequencing of reduced representation libraries in common bean

inferred← citeshttps://doi.org/10.1007/s11032-016-0558-8openalex-snapshot

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

inferred← citeshttps://doi.org/10.1007/s11032-017-0643-7openalex-snapshot

TILLING, high-resolution melting (HRM), and next-generation sequencing (NGS) techniques in plant mutation breeding

inferred← citeshttps://doi.org/10.1007/s11033-021-06189-0openalex-snapshot

The nearly complete mitogenome of the Southeast Asian firefly Pteroptyx tener (Coleoptera: Lampyridae)

inferred← citeshttps://doi.org/10.1007/s11033-022-07919-8openalex-snapshot

Genome sequence assembly algorithms and misassembly identification methods

inferred← citeshttps://doi.org/10.1007/s11033-022-08151-0openalex-snapshot

Characterization of highly polymorphic microsatellite markers for the chinese monal (Lophophorus lhuysii, Galliformes) using Illumina MiSeq sequencing

inferred← citeshttps://doi.org/10.1007/s11103-016-0508-1openalex-snapshot

Elucidating and mining the Tulipa and Lilium transcriptomes

inferred← citeshttps://doi.org/10.1007/s11262-026-02250-xopenalex-snapshot

Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae

inferred← citeshttps://doi.org/10.1007/s11265-019-01452-xopenalex-snapshot

Towards Accelerated Genome Informatics on Parallel HPC Platforms: The ReneGENE-GI Perspective

inferred← citeshttps://doi.org/10.1007/s11274-025-04375-xopenalex-snapshot

How genomics can help unravel the evolution of endophytic fungi

inferred← citeshttps://doi.org/10.1007/s11357-018-00050-2openalex-snapshot

Progerin expression induces a significant downregulation of transcription from human repetitive sequences in iPSC-derived dopaminergic neurons

inferred← citeshttps://doi.org/10.1007/s11557-026-02166-8openalex-snapshot

Whole-genome assemblies and comparative genomics of Fusarium oxysporum f. sp. capsici

inferred← citeshttps://doi.org/10.1007/s11627-019-10021-7openalex-snapshot

Spike morphology alternations in androgenic progeny of hexaploid triticale (× Triticosecale Wittmack) caused by nullisomy of 2R and 5R chromosomes

inferred← citeshttps://doi.org/10.1007/s11831-025-10337-1openalex-snapshot

Identification of Tandem Repeats in DNA Sequences Using Signal Processing Algorithms: A Review

inferred← citeshttps://doi.org/10.1007/s11882-016-0665-yopenalex-snapshot

Epigenetic Changes During Food-Specific Immunotherapy

inferred← citeshttps://doi.org/10.1007/s12038-016-9630-0openalex-snapshot

Identifying wrong assemblies in de novo short read primary sequence assembly contigs

inferred← citeshttps://doi.org/10.1007/s12281-017-0276-7openalex-snapshot

Harnessing Whole Genome Sequencing in Medical Mycology

inferred← citeshttps://doi.org/10.1007/s12304-017-9301-zopenalex-snapshot

Composite Agency: Semiotics of Modularity and Guiding Interactions

inferred← citeshttps://doi.org/10.1007/s13205-019-1614-yopenalex-snapshot

Comparative transcriptomics reveals potential genes involved in the vegetative growth of Morchella importuna

inferred← citeshttps://doi.org/10.1007/s13205-020-02513-wopenalex-snapshot

Comparative analysis of genomic- and EST-SSRs in European plum (Prunus domestica L.): implications for the diversity analysis of polyploids

inferred← citeshttps://doi.org/10.1007/s13258-019-00891-xopenalex-snapshot

Whole-genome resequencing analysis of 20 Micro-pigs

inferred← citeshttps://doi.org/10.1007/s13258-025-01708-wopenalex-snapshot

The role of Alu elements in causing BRCA1 structural variation and breast cancer susceptibility

inferred← citeshttps://doi.org/10.1007/s13313-026-01197-9openalex-snapshot

Diverse structural features and putative functional roles of early-stage Austropuccinia psidii effector proteins

inferred← citeshttps://doi.org/10.1007/s13577-017-0168-8openalex-snapshot

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

inferred← citeshttps://doi.org/10.1007/s40140-016-0185-2openalex-snapshot

The Genetics of Pain

inferred← citeshttps://doi.org/10.1007/s40484-016-0064-3openalex-snapshot

Combinatorial pooled sequencing: experiment design and decoding

inferred← citeshttps://doi.org/10.1007/s40484-019-0166-9openalex-snapshot

Current challenges and solutions of de novo assembly

inferred← citeshttps://doi.org/10.1007/s42995-022-00144-zopenalex-snapshot

An expectation–maximization algorithm for estimating proportions of deletions among bacterial populations with application to study antibiotic resistance gene transfer in Enterococcus faecalis

inferred← citeshttps://doi.org/10.1016/b978-0-08-100596-5.22700-5openalex-snapshot

Applying Genomics to Track Antimicrobial Resistance in the Food Chain

inferred← citeshttps://doi.org/10.1016/b978-0-12-420196-5.00022-8openalex-snapshot

Genomic Applications in Forensic Medicine

inferred← citeshttps://doi.org/10.1016/b978-0-12-800105-9.00001-9openalex-snapshot

The Newly Emerging View of the Genome

inferred← citeshttps://doi.org/10.1016/b978-0-12-800886-7.00041-8openalex-snapshot

Whole Genome Sequencing in the Molecular Pathology Laboratory

inferred← citeshttps://doi.org/10.1016/b978-0-12-802395-2.00022-5openalex-snapshot

Genetics of neurodegenerative diseases: an overview

inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20206-9openalex-snapshot

Next Generation Sequence Analysis

inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20227-6openalex-snapshot

Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses?

inferred← citeshttps://doi.org/10.1016/b978-0-12-812433-8.00015-0openalex-snapshot

Methods for Analysis of DNA Methylation

inferred← citeshttps://doi.org/10.1016/b978-0-12-814085-7.00002-7openalex-snapshot

The epigenetics of pluripotent stem cells

inferred← citeshttps://doi.org/10.1016/b978-0-12-822521-9.00202-1openalex-snapshot

Food Safety Applications of Genomic Technologies

inferred← citeshttps://doi.org/10.1016/b978-0-12-822824-1.00012-2openalex-snapshot

Whole-exome and whole-genome sequencing in the molecular diagnostic laboratory

inferred← citeshttps://doi.org/10.1016/b978-0-323-91172-6.00024-8openalex-snapshot

Digital healthcare data management using blockchain technology in genomics and COVID-19

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