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DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

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What this work says

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

inferredcites →https://doi.org/10.1007/11554714_3openalex-snapshot
Maximizing Synteny Blocks to Identify Ancestral Homologs
inferredcites →https://doi.org/10.1007/11557067openalex-snapshot
Algorithms in Bioinformatics
inferredcites →https://doi.org/10.1007/978-3-642-04241-6_19openalex-snapshot
Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes
inferredcites →https://doi.org/10.1007/bfb0045092openalex-snapshot
The median problem for breakpoints in comparative genomics
inferredcites →https://doi.org/10.1016/j.cub.2005.07.063openalex-snapshot
Evolution in Action: Following Function in Duplicated Floral Homeotic Genes
inferredcites →https://doi.org/10.1016/j.pbi.2006.01.007openalex-snapshot
Paleopolyploidy and gene duplication in soybean and other legumes
inferredcites →https://doi.org/10.1016/s0959-437x(00)00253-7openalex-snapshot
Gene and genome duplication
inferredcites →https://doi.org/10.1016/s1369-5274(99)00015-6openalex-snapshot
Yeast genome evolution in the post-genome era
inferredcites →https://doi.org/10.1038/35048692openalex-snapshot
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/35072009openalex-snapshot
Yesterday's polyploids and the mystery of diploidization
inferredcites →https://doi.org/10.1038/42711openalex-snapshot
Molecular evidence for an ancient duplication of the entire yeast genome
inferredcites →https://doi.org/10.1038/nature01521openalex-snapshot
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
inferredcites →https://doi.org/10.1038/nature02424openalex-snapshot
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1038/nature03025openalex-snapshot
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
inferredcites →https://doi.org/10.1038/nature04300openalex-snapshot
Genome sequencing and analysis of Aspergillus oryzae
inferredcites →https://doi.org/10.1038/nature05230openalex-snapshot
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
inferredcites →https://doi.org/10.1038/nbt1208-1336openalex-snapshot
Automated de novo protein sequencing of monoclonal antibodies
inferredcites →https://doi.org/10.1038/ng.2007.9openalex-snapshot
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
inferredcites →https://doi.org/10.1038/sj.emboj.7600024openalex-snapshot
Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments
inferredcites →https://doi.org/10.1073/pnas.0608218104openalex-snapshot
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
inferredcites →https://doi.org/10.1073/pnas.1932072100openalex-snapshot
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
inferredcites →https://doi.org/10.1089/cmb.2007.0048openalex-snapshot
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.492openalex-snapshot
GRIMM: genome rearrangements web server
inferredcites →https://doi.org/10.1093/bioinformatics/btg1005openalex-snapshot
Glocal alignment: finding rearrangements during alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btg1008openalex-snapshot
Fast identification and statistical evaluation of segmental homologies in comparative maps
inferredcites →https://doi.org/10.1093/bioinformatics/btg378openalex-snapshot
GRIL: genome rearrangement and inversion locator
inferredcites →https://doi.org/10.1093/bioinformatics/bth397openalex-snapshot
DAGchainer: a tool for mining segmental genome duplications and synteny
inferredcites →https://doi.org/10.1093/bioinformatics/bti168openalex-snapshot
Statistical detection of chromosomal homology using shared-gene density alone
inferredcites →https://doi.org/10.1093/bioinformatics/btm449openalex-snapshot
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
inferredcites →https://doi.org/10.1093/molbev/msh114openalex-snapshot
Fugu Genome Analysis Provides Evidence for a Whole-Genome Duplication Early During the Evolution of Ray-Finned Fishes
inferredcites →https://doi.org/10.1093/molbev/msl049openalex-snapshot
Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes
inferredcites →https://doi.org/10.1093/nar/28.20.4029openalex-snapshot
Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping
inferredcites →https://doi.org/10.1093/nar/30.1.38openalex-snapshot
The Ensembl genome database 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.076554.108openalex-snapshot
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
inferredcites →https://doi.org/10.1101/gr.082784.108openalex-snapshot
Breakpoint graphs and ancestral genome reconstructions
inferredcites →https://doi.org/10.1101/gr.187101openalex-snapshot
Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly
inferredcites →https://doi.org/10.1101/gr.1975204openalex-snapshot
Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes
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/10.1101/gr.2657504openalex-snapshot
A novel method for multiple alignment of sequences with repeated and shuffled elements
inferredcites →https://doi.org/10.1101/gr.400202openalex-snapshot
The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice
inferredcites →https://doi.org/10.1101/gr.4825606openalex-snapshot
Widespread genome duplications throughout the history of flowering plants
inferredcites →https://doi.org/10.1101/gr.5383506openalex-snapshot
Reconstructing contiguous regions of an ancestral genome
inferredcites →https://doi.org/10.1101/gr.5396706openalex-snapshot
SyMAP: A system for discovering and viewing syntenic regions of FPC maps
inferredcites →https://doi.org/10.1101/gr.7088808openalex-snapshot
Short read fragment assembly of bacterial genomes
inferredcites →https://doi.org/10.1101/gr.7337908openalex-snapshot
ALLPATHS: De novo assembly of whole-genome shotgun microreads
inferredcites →https://doi.org/10.1101/gr.751803openalex-snapshot
A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
inferredcites →https://doi.org/10.1101/gr.757503openalex-snapshot
Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes
inferredcites →https://doi.org/10.1101/gr.814403openalex-snapshot
LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics
inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
inferredcites →https://doi.org/10.1104/pp.108.124867openalex-snapshot
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
inferredcites →https://doi.org/10.1105/tpc.12.7.1093openalex-snapshot
Extensive Duplication and Reshuffling in the Arabidopsis Genome
inferredcites →https://doi.org/10.1109/icde.2007.367902openalex-snapshot
GString: A Novel Approach for Efficient Search in Graph Databases
inferredcites →https://doi.org/10.1126/science.1095781openalex-snapshot
The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome
inferredcites →https://doi.org/10.1126/science.290.5499.2114openalex-snapshot
The Origins of Genomic Duplications in Arabidopsis
inferredcites →https://doi.org/10.1128/jb.187.18.6488-6498.2005openalex-snapshot
Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition
inferredcites →https://doi.org/10.1186/1471-2105-8-82openalex-snapshot
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms
inferredcites →https://doi.org/10.1186/1745-6150-2-23openalex-snapshot
Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?
inferredcites →https://doi.org/10.1186/gb-2004-5-12-250openalex-snapshot
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids.
inferredcites →https://doi.org/10.1371/journal.pcbi.0020073openalex-snapshot
Parametric Alignment of Drosophila Genomes
inferredcites →https://doi.org/10.1371/journal.pcbi.0020075openalex-snapshot
An Integrative Method for Accurate Comparative Genome Mapping
inferredcites →https://doi.org/10.1371/journal.pgen.1000485openalex-snapshot
Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

What points at this work

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

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Applying Machine Learning to Classify the Origins of Gene Duplications
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Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data
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Whole-Genome Alignment
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Analysis of Gene Order Evolution Beyond Single-Copy Genes
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Whole-Genome Alignment
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Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes
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Manifold de Bruijn Graphs
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Genome Alignment
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Genome Alignment
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DNA sequences and DNA codes
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The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation
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A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms
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Molecular cytogenetic and genomic insights into chromosomal evolution
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Reconstructing the genome of the most recent common ancestor of flowering plants
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Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
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Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway
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Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis
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The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution
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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance
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Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance
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Capital investment of overseas Vietnamese to the economy of the Socialist Republic of Vietnam
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Assembly of long error-prone reads using de Bruijn graphs
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Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits
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Positional orthology: putting genomic evolutionary relationships into context
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GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions
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A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
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Mapping ancestral genomes with massive gene loss: A matrix sandwich problem
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Reconstructing the architecture of the ancestral amniote genome
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Evaluating synteny for improved comparative studies
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Ragout—a reference-assisted assembly tool for bacterial genomes
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TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
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/gigascience/giaa047openalex-snapshot
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
inferred← citeshttps://doi.org/10.1093/gigascience/giaa048openalex-snapshot
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
inferred← citeshttps://doi.org/10.1093/molbev/msaa114openalex-snapshot
Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies
inferred← citeshttps://doi.org/10.1093/molbev/msac041openalex-snapshot
IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios
inferred← citeshttps://doi.org/10.1093/nar/gkr955openalex-snapshot
i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets
inferred← citeshttps://doi.org/10.1093/nar/gkw310openalex-snapshot
Synteny Portal: a web-based application portal for synteny block analysis
inferred← citeshttps://doi.org/10.1093/nar/gkw330openalex-snapshot
SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species
inferred← citeshttps://doi.org/10.1101/2024.02.07.579356openalex-snapshot
Multi-genome synteny detection using minimizer graph mappings
inferred← citeshttps://doi.org/10.1101/2025.01.08.631874openalex-snapshot
Phylogenomic synteny analysis tracks conserved ancient polyploid-derived triplicated genomic blocks across Asteraceae genomes
inferred← citeshttps://doi.org/10.1101/215988openalex-snapshot
Panaconda: Application of pan-synteny graph models to genome content analysis
inferred← citeshttps://doi.org/10.1101/696245openalex-snapshot
Revisiting the landscape of evolutionary breakpoints across human genome using multi-way comparison
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Chromosome assembly of large and complex genomes using multiple references
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Computational Synteny Block: A framework to identify evolutionary events
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Exploring Frequented Regions in Pan-Genomic Graphs
inferred← citeshttps://doi.org/10.1109/tcbb.2021.3062068openalex-snapshot
StLiter: A Novel Algorithm to Iteratively Build the Compacted de Bruijn Graph From Many Complete Genomes
inferred← citeshttps://doi.org/10.1109/tcbb.2023.3340251openalex-snapshot
MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping
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Computational Synteny Block: A Framework to Identify Evolutionary Events
inferred← citeshttps://doi.org/10.1111/nph.14113openalex-snapshot
Reconciling the evolutionary origin of bread wheat (Triticum aestivum)
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Tracing 100 million years of grass genome evolutionary plasticity
inferred← citeshttps://doi.org/10.1142/s021972001343004xopenalex-snapshot
HOMOLOGOUS SYNTENY BLOCK DETECTION BASED ON SUFFIX TREE ALGORITHMS
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Exploring Frequented Regions in Pan-Genomic Graphs
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PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees
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Genome alignment with graph data structures: a comparison
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What is the difference between the breakpoint graph and the de Bruijn graph?
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Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events
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MLGO: phylogeny reconstruction and ancestral inference from gene-order data
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Resolution effects in reconstructing ancestral genomes
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Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.
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Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction
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Inter-chromosomal k-mer distances
inferred← citeshttps://doi.org/10.1186/s12915-023-01643-wopenalex-snapshot
Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
inferred← citeshttps://doi.org/10.1186/s12915-025-02455-wopenalex-snapshot
ntSynt: multi-genome synteny detection using minimizer graph mappings
inferred← citeshttps://doi.org/10.1186/s13015-022-00210-2openalex-snapshot
Fast characterization of segmental duplication structure in multiple genome assemblies
inferred← citeshttps://doi.org/10.1186/s13059-019-1627-1openalex-snapshot
Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA
inferred← citeshttps://doi.org/10.1186/s13059-026-04128-5openalex-snapshot
MGA: a tool for haplotype-mixed assembly of long and accurate reads
inferred← citeshttps://doi.org/10.1371/journal.pone.0180198openalex-snapshot
High precision detection of conserved segments from synteny blocks
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Contributions to computing and modeling multiple whole-genome alignments
inferred← citeshttps://doi.org/10.18174/456296openalex-snapshot
Synteny-based phylogenomic networks for comparative genomics
inferred← citeshttps://doi.org/10.21203/rs.3.rs-140488/v1openalex-snapshot
Inter-chromosomal K-mer Distances
inferred← citeshttps://doi.org/10.3389/fpls.2017.01843openalex-snapshot
Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.)
inferred← citeshttps://doi.org/10.3390/a14050152openalex-snapshot
Predicting the Evolution of Syntenies—An Algorithmic Review
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An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice
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Additional file 1 of Inter-chromosomal k-mer distances
inferred← citeshttps://doi.org/10.6084/m9.figshare.23730934openalex-snapshot
Additional file 1 of Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
inferred← citeshttps://doi.org/10.6084/m9.figshare.23730937openalex-snapshot
Additional file 2 of Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
inferred← citeshttps://doi.org/10.64898/2025.12.15.694404openalex-snapshot
On Deriving Synteny Blocks by Compacting Elements
inferred← citeshttps://doi.org/10.70675/1e1d281ezc0f7z4f31z8e50zb22eb5be7746openalex-snapshot
Nouvelles approches pour l'exploitation des données de séquences génomique haut débit
inferred← citeshttps://doi.org/10.70675/335aaf0bz9f74z46cfzbdaezaa3b2ba7d16copenalex-snapshot
Lien entre les réarrangements chromosomiques et la structure de la chromatine chez la Drosophile
inferred← citeshttps://doi.org/10.70675/55c62e58z6b80z4886z924az32c393094eacopenalex-snapshot
Étude de l'évolution de l'ordre des gènes de vertébrés par simulation
inferred← citeshttps://doi.org/10.7287/peerj.6526v0.1/reviews/1openalex-snapshot
Peer Review #1 of "TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6526v0.1/reviews/2openalex-snapshot
Peer Review #2 of "TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 (v0.1)"
inferred← citeshttps://doi.org/10.7717/peerj.6526openalex-snapshot
TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
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.