Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (634 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
A form of gene library containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Genomic Libraries; Libraries, Genomic; Library, Genomic; Genome Library; Genome Libraries; Libraries, Genome; Library, Genome.
Where it fits in the MeSH classification
- Broader topics
- Gene Library; Genome
- See also
- DNA, Recombinant; Human Genome Project; Chromosomes, Artificial, Yeast
Related concepts
- Gene Library
Research landscape
PubMed indexes 5,505 records tagged with the MeSH heading “Genomic Library” (counts retrieved 2026-10-29). 89 of them (1.6%) were published from 2020 onward, and the busiest period so far is through 1999 with 3,429 records.
Reviews account for 229 records (4.2%) and meta-analyses for 0. Randomized controlled trials number 1 (0.0%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 3,429 |
| 2000-2009 | 1,346 |
| 2010-2019 | 641 |
| 2020 onward | 89 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 229 | 4.2% |
| Meta-analyses | 0 | 0.0% |
| Randomized controlled trials | 1 | 0.0% |
Method: PubMed query "Genomic Library"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in genetics and genomics
Genetic findings vary widely in strength. A variant linked to a condition in one study may not replicate in other ancestries, and most common variants have small effects that are meaningful only in aggregate. Studies of rare, high-impact variants can support strong causal claims about a gene, while association studies describe statistical links that need functional and independent replication. Check the sample size, the ancestry of participants, whether results were replicated, and whether a laboratory or clinical outcome was actually measured.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities | 2018 | Research article Design not recorded in structured metadata | 1,032 | cc by PMID 30575746 · DOI · PMC6303322 |
| Chromosome-scale shotgun assembly using an in vitro method for long-range linkage | 2016 | Research article Design not recorded in structured metadata | 678 | cc by PMID 26848124 · DOI · PMC4772016 |
| Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens | 2017 | Research article Design not recorded in structured metadata | 365 | cc by PMID 28474669 · DOI · PMC5424143 |
| Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries | 2022 | Research article Design not recorded in structured metadata | 10 | cc by PMID 35255806 · DOI · PMC8900324 |
Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities [1]
Abstract reading summary — source excerpts
- Opening excerpt
- The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function.
- Closing excerpt
- Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (146 words)
The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function. Here, we show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we present genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese), and show in negative selection screens that Dolcetto, with fewer sgRNAs per gene, outperforms existing CRISPRi libraries and achieves comparable performance to CRISPRko in detecting essential genes. We also perform positive selection CRISPRa screens and demonstrate that Calabrese outperforms the SAM approach at identifying vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 30575746 · DOI · PMC6303322
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage [2]
Abstract reading summary — source excerpts
- Opening excerpt
- Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics.
- Closing excerpt
- With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (164 words)
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach ("Chicago") based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline ("HiRise") that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 26848124 · DOI · PMC4772016
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens [3]
Abstract reading summary — source excerpts
- Opening excerpt
- CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and off-target sites, likely due to DNA damage.
- Closing excerpt
- Our results demonstrate a simple strategy for high-throughput evaluation of target specificity and nuclease toxicity in Cas9 screens.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (151 words)
CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on- and off-target sites, likely due to DNA damage. Here, to test potential solutions to this issue, we design and analyse a CRISPR-Cas9 library with 10 variable-length guides per gene and thousands of negative controls targeting non-functional, non-genic regions (termed safe-targeting guides), in addition to non-targeting controls. We find this library has excellent performance in identifying genes affecting growth and sensitivity to the ricin toxin. The safe-targeting guides allow for proper control of toxicity from on-target DNA damage. Using this toxicity as a proxy to measure off-target cutting, we demonstrate with tens of thousands of guides both the nucleotide position-dependent sensitivity to single mismatches and the reduction of off-target cutting using truncated guides. Our results demonstrate a simple strategy for high-throughput evaluation of target specificity and nuclease toxicity in Cas9 screens.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 28474669 · DOI · PMC5424143
Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries [4]
Abstract reading summary — source excerpts
- Opening excerpt
- BackgroundA variety of protocols exist for producing whole genome run-on transcription datasets.
- Closing excerpt
- However, these batch effects have only limited impact on our ability to infer which regulators underlie the observed transcriptional changes.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (173 words)
BackgroundA variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries.ResultsUsing run-on transcription datasets generated from the same biological system, we show that a variety of GRO- and PRO-seq preparation methods leave identifiable signatures within each library. Specifically we show that the library preparation method results in differences in quality control metrics, as well as differences in the signal distribution at the 5 ' end of transcribed regions. These shifts lead to disparities in eRNA identification, but do not impact analyses aimed at inferring the key regulators involved in changes to transcription.ConclusionsRun-on sequencing protocol variations result in technical signatures that can be used to identify both the enrichment and library preparation method of a particular data set. These technical signatures are batch effects that limit detailed comparisons of pausing ratios and eRNAs identified across protocols. However, these batch effects have only limited impact on our ability to infer which regulators underlie the observed transcriptional changes.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 35255806 · DOI · PMC8900324
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article DNA-encoded chemistry: enabling the deeper sampling of chemical space [5]
- Research article Improving plant breeding with exotic genetic libraries [6]
- Research article The evolution of cell adhesion [7]
- Research article Retroposons--seeds of evolution [8]
- Research article Development and applications of a molecular genetic linkage map of the mouse genome [9]
- Research article Drosophila melanogaster G protein-coupled receptors [10]
References
- Sanson KR, Hanna RE, Hegde M, Donovan KF, Strand C, Sullender ME, et al.. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. . 2018. PMID 30575746 · DOI · PMC6303322
- Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, et al.. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. . 2016. PMID 26848124 · DOI · PMC4772016
- Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, et al.. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. . 2017. PMID 28474669 · DOI · PMC5424143
- Hunter S, Sigauke RF, Stanley JT, Allen MA, Dowell RD. Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. . 2022. PMID 35255806 · DOI · PMC8900324
- Goodnow RA, Dumelin CE, Keefe AD. DNA-encoded chemistry: enabling the deeper sampling of chemical space. Nat Rev Drug Discov. 2017. PMID 27932801 · DOI
- Zamir D. Improving plant breeding with exotic genetic libraries. Nat Rev Genet. 2001. PMID 11733751 · DOI
- Hynes RO, Zhao Q. The evolution of cell adhesion. J Cell Biol. 2000. PMID 10908592 · DOI · PMC2180234
- Brosius J. Retroposons--seeds of evolution. Science. 1991. PMID 1990437 · DOI
- Copeland NG, Jenkins NA. Development and applications of a molecular genetic linkage map of the mouse genome. Trends Genet. 1991. PMID 2068781 · DOI
- Brody T, Cravchik A. Drosophila melanogaster G protein-coupled receptors. J Cell Biol. 2000. PMID 10908591 · DOI · PMC2180217
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.