This is the
list of accepted peer-reviewed papers I've put my hands in up to now.
Hopefully
this is up-to-date.
- The ENCODE Project Consortium (including Lagarde J).
A User's Guide to the Encyclopedia of DNA Elements
(ENCODE).
PLoS
Biol 9(4): e1001046. doi:10.1371/journal.pbio.1001046
- Djebali S (*),
Kapranov P (*),
Foissac S (*),
Lagarde J (*),
Reymond A (*),
Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud
F, Frankish A, Harrow J, Makrythanasis P, Vidal M, Calvo M,
Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigo R.
(*)
Equal contribution
Efficient
targeted transcript discovery via array-based normalization of RACE
libraries.
Nature
Methods. 2008; 5:
629-635.
- The ENCODE Project Consortium (including Lagarde J).
Identification and
analysis of
functional elements in 1% of the human genome by the ENCODE pilot
project.
Nature.
2007
Jun 14;447: 799-816.
Link to Nature's ENCODE portal with
free access to the main article.
- Washietl S, Pedersen JS,
Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J,
Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE,
Denoeud F, Lagarde
J, Drenkow J, Kapranov P, Gingeras TR, Snyder M, Gerstein MB,
Reymond A, Hofacker IL, Stadler PF.
Structured RNAs
in the ENCODE selected regions of the human genome.
Genome Research.
2007 Jun 14; 17: 852-864.
- Denoeud F, Kapranov P, Ucla
C, Frankish A, Castelo R, Drenkow D, Lagarde J,
Alioto
T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd
N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J,
Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE,
Reymond A.
Prominent use of
distal 5’ transcription start sites and discovery of a large number of
additional exons in ENCODE regions.
Genome
Research. 2007 Jun 14; 17: 746-759.
- Tress ML, Martelli PL,
Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M,
Hegyi H, Giorgetti A, Raimondo D, Lagarde J,
Laskowski
RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I,
Nagy A, Kai W, Storling Z, Orsini M, Assenov Y, Blankenburg H,
Huthmacher C, Ramirez F, Schlicker A, Denoeud F, Jones P, Kerrien S,
Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R,
Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy
L, Thornton JM, Tramontano A, Valencia A.
The implications
of alternative splicing in the ENCODE protein complement.
Proc Natl Acad Sci U S A.
2007
Mar 27;104(13):5495-500.
- Harrow J, Denoeud F, Frankish
A, Reymond A, Chen CK, Chrast J, Lagarde J,
Gilbert
JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T,
Antonarakis SE, Guigo R.
GENCODE:
producing a reference annotation for ENCODE.
Genome Biology.
2006;7 Suppl 1:S4.1-9.
- Guigo R, Flicek P, Abril JF,
Reymond A, Lagarde
J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E,
Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE,
Reese MG.
EGASP: the human
ENCODE Genome Annotation Assessment Project.
Genome Biology.
2006;7 Suppl 1:S2.1-31.
- The ENCODE Project Consortium
(including Lagarde
J).
The ENCODE
(ENCyclopedia Of DNA Elements) Project.
Science. 2004
Oct 22;306(5696):636-40.
- Jensen LJ, Lagarde J,
von
Mering C, Bork P.
ArrayProspector:
a web resource of functional associations inferred from microarray
expression data.
Nucleic Acids Research.
2004 Jul 1;32:W445-8.
