Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (Q24534193)

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English	Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes	scientific article

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4 July 2017

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (English)

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4 July 2017

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Jakob Skou Pedersen

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Angie S. Hinrichs

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David Haussler

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Webb Miller

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Kate R. Rosenbloom

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Kate Rosenbloom

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Gill Bejerano

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W James Kent

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Ladeana W Hillier

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Richard K. Wilson

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Richard K Wilson

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Richard A Gibbs

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Richard A Gibbs

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John Spieth

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Minmei Hou

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Stephen Richards

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15 July 2005

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Genome Research

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8

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1034-1050

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4 July 2017

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Highly conserved non-coding sequences are associated with vertebrate development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results

1 reference

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24 March 2017

Human MicroRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

MicroRNA targets in Drosophila

1 reference

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24 March 2017

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

1 reference

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24 March 2017

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Human-mouse alignments with BLASTZ

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Rfam: an RNA family database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Computational discovery of sense-antisense transcription in the human and mouse genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

BLAT—The BLAST-Like Alignment Tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Untranslated regions of mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Noncoding RNA gene detection using comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Gene ontology: tool for the unification of biology

1 reference

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24 March 2017

A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Mutation rates differ among regions of the mammalian genome

1 reference

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24 March 2017

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

1 reference

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24 March 2017

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Ultraconserved Elements in the Human Genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Sequencing and comparison of yeast species to identify genes and regulatory elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Initial sequencing and comparative analysis of the mouse genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Combinatorial microRNA target predictions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

MicroRNA-directed cleavage of HOXB8 mRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

In search of antisense

1 reference

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24 March 2017

Scanning Human Gene Deserts for Long-Range Enhancers

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24 March 2017

Nervous system targets of RNA editing identified by comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Mechanisms of alternative pre-messenger RNA splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

The UCSC Genome Browser Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

Evolutionarily conserved sequences on human chromosome 21

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

PipMaker--a web server for aligning two genomic DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

A Hidden Markov Model approach to variation among sites in rate of evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

24 March 2017

The ENCODE (ENCyclopedia Of DNA Elements) Project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Aligning multiple genomic sequences with the threaded blockset aligner

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Comparative genomics of the eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Comparative analyses of multi-species sequences from targeted genomic regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Widespread occurrence of antisense transcription in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Origin of a substantial fraction of human regulatory sequences from transposable elements

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7 April 2017

VISTA : visualizing global DNA sequence alignments of arbitrary length

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

7 April 2017

Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser

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27 September 2017

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

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27 September 2017

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Naturally occurring antisense: transcriptional leakage or real overlap?

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27 September 2017

Evolution and functional classification of vertebrate gene deserts

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Mulan: multiple-sequence local alignment and visualization for studying function and evolution

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27 September 2017

Evidence for turnover of functional noncoding DNA in mammalian genome evolution

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27 September 2017

A comparative method for finding and folding RNA secondary structures within protein-coding regions

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27 September 2017

Efficient identification of regulatory sequences in the chicken genome by a powerful combination of embryo electroporation and genome comparison

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

1 reference

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27 September 2017

MAVID: constrained ancestral alignment of multiple sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Characterization of evolutionary rates and constraints in three Mammalian genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Transcriptome and genome conservation of alternative splicing events in humans and mice.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional

1 reference

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27 September 2017

Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci.

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27 September 2017

WormBase: a multi-species resource for nematode biology and genomics

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27 September 2017

Identification and characterization of multi-species conserved sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Mutation rate variation in the mammalian genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Intronic sequences flanking alternatively spliced exons are conserved between human and mouse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

27 September 2017

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

1 reference

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27 September 2017

NCBI Reference Sequence project: update and current status

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27 September 2017

Regulatory functions of 3'UTRs.

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27 September 2017

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

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27 September 2017

Selective constraint in intergenic regions of human and mouse genomes.

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27 September 2017

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

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27 September 2017

Cuticle collagen genes. Expression in Caenorhabditis elegans

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27 September 2017

Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions

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27 September 2017

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

1 reference

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27 September 2017

Making (anti)sense of non-coding sequence conservation

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27 September 2017

Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression

1 reference

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27 September 2017

A space-time process model for the evolution of DNA sequences.

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27 September 2017

Control of messenger RNA stability in higher eukaryotes

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27 September 2017

Mobile elements inserted in the distant past have taken on important functions

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30 May 2018

Megabase deletions of gene deserts result in viable mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

The share of human genomic DNA under selection estimated from human-mouse genomic alignments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Into the heart of darkness: large-scale clustering of human non-coding DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Evolutionary conservation of a 2-kb intronic sequence flanking a tissue-specific alternative exon in the PTBP2 gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

The FlyBase database of the Drosophila genome projects and community literature.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

The search for meaning in noncoding DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182216

29 November 2018

Pattern of selective constraint in C. elegans and C. briggsae genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/16024819

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/16024819

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.3715005

1 reference

Europe PubMed Central

PubMed publication ID

4 July 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 July 2017

ResearchGate publication ID

0 references

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