Paper · 28360232

Genome graphs and the evolution of genome inference.

Paten B and 3 others. Genome Res, 2017. Cited by 214 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. Genome graphs and the evolution of genome inference. Papers, record 28360232. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/28360232

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title: Genome graphs and the evolution of genome inference.; PubMed
Journal: Genome Res; PubMed
Year: 2017; PubMed
Publication types: Journal Article, Review, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural; PubMed
PubMed: https://pubmed.ncbi.nlm.nih.gov/28360232/; PubMed
DOI: https://doi.org/10.1101/gr.214155.116; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC5411762/; PubMed
The journal: https://conductscience.org/library/journal-index/9518021; PubMed
Citations, by iCite: 214; iCite
Relative citation ratio, by iCite: 6.41; iCite
Revised in PubMed: 2023-11-12; PubMed

Authors4

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

Order	Author	Forename
1	Paten B	Benedict
2	Novak AM	Adam M
3	Eizenga JM	Jordan M
4	Garrison E	Erik

Source PubMed

Topics5

NLM's MeSH indexing of the paper, its major topics first.

MeSH term	Major
Genome, Human	Major topic
Genome-Wide Association Study	Major topic
Genomics	Major topic
Humans
Polymorphism, Genetic

Source PubMed

Grants1

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes it	Agency	Country	NIH project	Stated by
U54 HG007990	NHGRI NIH HHS	United States	U54HG007990	PubMed and NIH

Source NIH RePORTER

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References52

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

Order	PMID	Title	Journal	Year	In Papers	Source
1	27,560,171	Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.	Nat Protoc	2016	https://conductscience.org/library/papers/27560171	PubMed
2	27,792,722	High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.	PLoS Comput Biol	2016	https://conductscience.org/library/papers/27792722	PubMed
3	19,761,611	Simultaneous alignment of short reads against multiple genomes.	Genome Biol	2009	https://conductscience.org/library/papers/19761611	PubMed
4	28,702,075	A graph extension of the positional Burrows-Wheeler transform and its applications.	Algorithms Mol Biol	2017	https://conductscience.org/library/papers/28702075	PubMed
5	26,432,246	An integrated map of structural variation in 2,504 human genomes.	Nature	2015	https://conductscience.org/library/papers/26432246	PubMed
6	19,808,877	Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.	Bioinformatics	2009	https://conductscience.org/library/papers/19808877	PubMed
7	26,042,914	The future of personalized and precision perinatal medicine. Foreword.	Clin Perinatol	2015	https://conductscience.org/library/papers/26042914	PubMed
8	21,750,661	Modernizing reference genome assemblies.	PLoS Biol	2011	https://conductscience.org/library/papers/21750661	PubMed
9	11,504,945	An Eulerian path approach to DNA fragment assembly.	Proc Natl Acad Sci U S A	2001	https://conductscience.org/library/papers/11504945	PubMed
10	26,220,960	Canonical, stable, general mapping using context schemes.	Bioinformatics	2015	https://conductscience.org/library/papers/26220960	PubMed

1 to 10 of 52

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Cited by178

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 214 citations.

PMID	Title	Journal	Year	In Papers	Source
42,930,755	Perspective: Evolutionary Genetics Is the Backbone of Genomic Epidemiology in Fungal Pathogens.	J Fungi (Basel)	2026	https://conductscience.org/library/papers/42930755	PubMed
42,903,307	From plant pangenome assemblies to operational graph references.	Front Plant Sci	2026	https://conductscience.org/library/papers/42903307	PubMed
42,793,079	Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.	Biomolecules	2026	https://conductscience.org/library/papers/42793079	PubMed
42,777,077	Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.	PLoS Comput Biol	2026	https://conductscience.org/library/papers/42777077	PubMed
42,618,781	An Icelandic pangenome reference.	Nature	2026	https://conductscience.org/library/papers/42618781	PubMed
42,591,269	Genomic epidemiology and phylogenomics of Magnusiomyces clavatus: a comparative analysis of novel italian and publicly available genomes.	Front Cell Infect Microbiol	2026	https://conductscience.org/library/papers/42591269	PubMed
42,565,874	Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context.	Mol Genet Genomics	2026	https://conductscience.org/library/papers/42565874	PubMed
42,561,951	Telomere-to-telomere genome assembly and a pangenome for the rat.	Cell Genom	2026	https://conductscience.org/library/papers/42561951	PubMed
42,561,913	A complete diploid human genome benchmark for personalized genomics.	Cell	2026	https://conductscience.org/library/papers/42561913	PubMed
42,463,514	Building and applying pangenome references to capture genetic diversity.	Nat Rev Genet	2026	https://conductscience.org/library/papers/42463514	PubMed

1 to 10 of 178

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Genes3

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

Gene	NCBI Gene ID	Linked by	In Genes	Source
DGCR	1,714	PubTator's text mining	https://conductscience.org/library/genes/1714	NCBI Gene
GUCY1A2	2,977	PubTator's text mining	https://conductscience.org/library/genes/2977	NCBI Gene
HLA-A	3,105	PubTator's text mining	https://conductscience.org/library/genes/3105	NCBI Gene

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed: 2026-11-06; PubMed
iCite: 2026-11-05; iCite
PMC's ID file: 2026-11-05; PMC's ID file
NIH RePORTER's grant and paper links: 2026-11-01; NIH RePORTER's grant and paper links
Trials: 2026-11-12
Gene search: 2026-11-11
Pipelines: 2026-09-18

Sources 11

ChEMBL, through Open TargetsCC BY-SA 3.0
ClinicalTrials.govNo license stated
HGNCCC0
iCiteCC BY 4.0
NCBI GenePublic domain (US government)
NIH RePORTER's grant and paper linksPublic domain
Open TargetsCC0 1.0
PMC's ID filePublic domain (US government)
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0

Each source's terms

ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
ClinicalTrials.govnone stated
HGNCCC0: https://www.genenames.org/about/license/
iCiteCC BY 4.0
NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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