Managing References

Reference can be stored in a variety of formats, the most common are listed in the following table:

File Format Application
.ris Mendeley, Papers, Zotero
.enw EndNote
.bibtex BibTex
.txt Medlars, RefWorks
Table 1: File types for storing references

Examples of each type can be found in the following tabset:

Provider: Silverchair
Database: Oxford University Press
Content: text/plain; charset="UTF-8"

TY  - JOUR
AU  - Sanges, Remo
AU  - Hadzhiev, Yavor
AU  - Gueroult-Bellone, Marion
AU  - Roure, Agnes
AU  - Ferg, Marco
AU  - Meola, Nicola
AU  - Amore, Gabriele
AU  - Basu, Swaraj
AU  - Brown, Euan R.
AU  - De Simone, Marco
AU  - Petrera, Francesca
AU  - Licastro, Danilo
AU  - Strähle, Uwe
AU  - Banfi, Sandro
AU  - Lemaire, Patrick
AU  - Birney, Ewan
AU  - Müller, Ferenc
AU  - Stupka, Elia
T1  - Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development
PY  - 2013
Y1  - 2013/04/01
DO  - 10.1093/nar/gkt030
JO  - Nucleic Acids Research
JA  - Nucleic Acids Res
VL  - 41
IS  - 6
SP  - 3600
EP  - 3618
SN  - 0305-1048
AB  - Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’.
Y2  - 4/9/2024
UR  - https://doi.org/10.1093/nar/gkt030
ER  - 
%0 Journal Article
%A Sanges, Remo
%A Hadzhiev, Yavor
%A Gueroult-Bellone, Marion
%A Roure, Agnes
%A Ferg, Marco
%A Meola, Nicola
%A Amore, Gabriele
%A Basu, Swaraj
%A Brown, Euan R.
%A De Simone, Marco
%A Petrera, Francesca
%A Licastro, Danilo
%A Strähle, Uwe
%A Banfi, Sandro
%A Lemaire, Patrick
%A Birney, Ewan
%A Müller, Ferenc
%A Stupka, Elia
%T Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development
%B Nucleic Acids Research
%D 2013
%R 10.1093/nar/gkt030
%J Nucleic Acids Research
%V 41
%N 6
%P 3600-3618
%@ 0305-1048
%X Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’.
%[ 4/9/2024
%U https://doi.org/10.1093/nar/gkt030
@article{10.1093/nar/gkt030,
    author = {Sanges, Remo and Hadzhiev, Yavor and Gueroult-Bellone, Marion and Roure, Agnes and Ferg, Marco and Meola, Nicola and Amore, Gabriele and Basu, Swaraj and Brown, Euan R. and De Simone, Marco and Petrera, Francesca and Licastro, Danilo and Strähle, Uwe and Banfi, Sandro and Lemaire, Patrick and Birney, Ewan and Müller, Ferenc and Stupka, Elia},
    title = "{Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development}",
    journal = {Nucleic Acids Research},
    volume = {41},
    number = {6},
    pages = {3600-3618},
    year = {2013},
    month = {02},
    abstract = "{Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkt030},
    url = {https://doi.org/10.1093/nar/gkt030},
    eprint = {https://academic.oup.com/nar/article-pdf/41/6/3600/16943005/gkt030.pdf},
}
RT Journal Article
A1 Sanges, Remo
A1 Hadzhiev, Yavor
A1 Gueroult-Bellone, Marion
A1 Roure, Agnes
A1 Ferg, Marco
A1 Meola, Nicola
A1 Amore, Gabriele
A1 Basu, Swaraj
A1 Brown, Euan R.
A1 De Simone, Marco
A1 Petrera, Francesca
A1 Licastro, Danilo
A1 Strähle, Uwe
A1 Banfi, Sandro
A1 Lemaire, Patrick
A1 Birney, Ewan
A1 Müller, Ferenc
A1 Stupka, Elia
T1 Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development
JF Nucleic Acids Research
JO Nucleic Acids Res
YR 2013
DO 10.1093/nar/gkt030
VO 41
IS 6
SP 3600
OP 3618
SN 0305-1048
AB Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’.
RD 4/9/2024
UL https://doi.org/10.1093/nar/gkt030