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Probabilistic recovery of cryptic haplotypes from metagenomic data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/11557067_11openalex-snapshot
On the Complexity of Several Haplotyping Problems
inferredcites →https://doi.org/10.1007/3-540-44676-1_15openalex-snapshot
SNPs Problems, Complexity, and Algorithms
inferredcites →https://doi.org/10.1007/978-3-540-30219-3_23openalex-snapshot
Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction
inferredcites →https://doi.org/10.1016/0304-4076(81)90071-3openalex-snapshot
Likelihood of a model and information criteria
inferredcites →https://doi.org/10.1016/j.copbio.2011.11.013openalex-snapshot
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
inferredcites →https://doi.org/10.1016/j.mib.2014.11.016openalex-snapshot
Ten years of pan-genome analyses
inferredcites →https://doi.org/10.1038/ismej.2016.172openalex-snapshot
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome
inferredcites →https://doi.org/10.1038/ismej.2017.34openalex-snapshot
Erratum: Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome
inferredcites →https://doi.org/10.1038/nature11711openalex-snapshot
Genomic variation landscape of the human gut microbiome
inferredcites →https://doi.org/10.1038/nbt.3416openalex-snapshot
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
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.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrm2698openalex-snapshot
The second wave of synthetic biology: from modules to systems
inferredcites →https://doi.org/10.1038/nrmicro.2016.93openalex-snapshot
Extracellular electron transfer mechanisms between microorganisms and minerals
inferredcites →https://doi.org/10.1038/srep23012openalex-snapshot
Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms
inferredcites →https://doi.org/10.1051/ro/2015037openalex-snapshot
Algorithmic approaches for the single individual haplotyping problem
inferredcites →https://doi.org/10.1073/pnas.0903507106openalex-snapshot
The genomic basis of trophic strategy in marine bacteria
inferredcites →https://doi.org/10.1089/cmb.2012.0084openalex-snapshot
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data
inferredcites →https://doi.org/10.1089/cmb.2012.0232openalex-snapshot
Probabilistic Inference of Viral Quasispecies Subject to Recombination
inferredcites →https://doi.org/10.1093/bib/3.1.23openalex-snapshot
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem
inferredcites →https://doi.org/10.1093/bib/bbw126openalex-snapshot
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq411openalex-snapshot
A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem
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/btu484openalex-snapshot
Probabilistic single-individual haplotyping
inferredcites →https://doi.org/10.1093/bioinformatics/btu754openalex-snapshot
ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing
inferredcites →https://doi.org/10.1093/femsec/fiv137openalex-snapshot
Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass
inferredcites →https://doi.org/10.1093/nar/gks678openalex-snapshot
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
inferredcites →https://doi.org/10.1093/nar/gku537openalex-snapshot
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
inferredcites →https://doi.org/10.1093/nar/gkv1290openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/ve/vew022openalex-snapshot
Challenges in the analysis of viral metagenomes
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.213462.116openalex-snapshot
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
inferredcites →https://doi.org/10.1109/tcbb.2013.145openalex-snapshot
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model
inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
inferredcites →https://doi.org/10.1186/1742-4690-11-56openalex-snapshot
Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants
inferredcites →https://doi.org/10.1186/gb-2012-13-12-r122openalex-snapshot
Ray Meta: scalable de novo metagenome assembly and profiling
inferredcites →https://doi.org/10.1186/s12859-015-0651-8openalex-snapshot
Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm
inferredcites →https://doi.org/10.1371/journal.pbio.1002251openalex-snapshot
Extremely High Mutation Rate of HIV-1 In Vivo
inferredcites →https://doi.org/10.1371/journal.pone.0169662openalex-snapshot
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
inferredcites →https://doi.org/10.1534/g3.114.015784openalex-snapshot
Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I 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/10.3390/md8061920openalex-snapshot
Research and Application of Marine Microbial Enzymes: Status and Prospects
inferredcites →https://doi.org/10.4155/fmc.12.68openalex-snapshot
Dihydrofolate Reductase As A Therapeutic Target for Infectious Diseases: Opportunities And Challenges
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41564-019-0494-6openalex-snapshot
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
inferred← citeshttps://doi.org/10.1038/s41564-019-0643-yopenalex-snapshot
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota
inferred← citeshttps://doi.org/10.1101/527796openalex-snapshot
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
inferred← citeshttps://doi.org/10.1590/1678-4685-gmb-2019-0401openalex-snapshot
Skin transcriptional profiles in Oophaga poison frogs
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