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Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

Denoeud, France; Kapranov, Philipp; Ucla, Catherine; Frankish, Adam; Castelo Valdueza, Robert; Drenkow, Jorg; Lagarde, Julien; Alioto, Tyler; Manzano, Caroline; Chrast, Jacqueline; Dike, Sujit; Wyss, Carine; Henrichsen, Charlotte N.; Holroyd, Nancy; Dickson, Mark C.; Taylor, Ruth; Hance, Zahra; Foissac, Sylvain; Myers, Richard M.; Rogers, Jane; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Gingeras, Thomas R.; Antonarakis, Stylianos E.; Reymond, Alexandre (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
A general definition and nomenclature for alternative splicing events

Guigó Serra, Roderic; Sammeth, Michael; Foissac, Sylvain (Public Library of Science (PLoS), 2008)
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

Guigó Serra, Roderic; Manichanh, Chaysavanh; Chapple, Charles E.; Frangeul, Lionel; Gloux, Karine; Dore, Joel (Oxford University Press, 2008)
Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD

Bosch Fusté, Elena; Laayouni, Hafid, 1968-; Morcillo Suárez, Carlos, 1969-; Casals López, Ferran; Moreno Estrada, Andrés; Ferrer Admetlla, Anna; Gardner, Michelle; Rosa, Araceli; Comas, David, 1969-; Graffelman, Jan; Calafell i Majó, Francesc; Bertranpetit, Jaume, 1952- (BioMed Central, 2009)
Structured RNAs in the ENCODE selected regions of the human genome

Washietl, Stefan; Pedersen, Jackob S.; Korbel, Jan O.; Stocsits, Claudia; Gruber, Andreas R.; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Reiche, Kristin; Tanzer, Andrea; Ucla, Catherine; Wyss, Carine; Antonarakis, Stylianos E.; Denoeud, France; Lagarde, Julien; Drenkow, Jorg; Kapranov, Philipp; Gingeras, Thomas R.; Guigó Serra, Roderic; Snyder, Michael; Gerstein, Mark B.; Reymond, Alexandre; Hofacker, Ivo L.; Stadler, Peter F. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
Topological comparison of methods for predicting transcriptional cooperativity in yeast

Aguilar, Daniel; Oliva Miguel, Baldomero (BioMed Central, 2008)
Comparative gene prediction in human and mouse

Parra Farré, Genís; Agarwal, Pankaj; Abril Ferrando, Josep Francesc; Wiehe, Thomas; Fickett, James W.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press-CSHL Press, 2003)
Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

Mendizábal Eceizabarrena, Isabel, 1981-; Sandoval Mendoza, Karla; Berniell Lee, Gemma; Calafell i Majó, Francesc; Salas, Antonio; Martínez Fuentes, Antonio; Comas, David, 1969- (BioMed Central, 2008)
Genetic characterization of the ABO blood group in Neandertals

Lalueza Fox, Carles, 1965-; Gigli, Elena, 1978-; Rasilla Vives, Marco de la; Fortea, Javier; Rosas, Antonio; Bertranpetit, Jaume, 1952-; Krause, Johannes (BioMed Central, 2008)
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Zheng, Deyou; Frankish, Adam; Baertsch, Robert; Kapranov, Philipp; Reymond, Alexandre; Choo, Siew Woh; Lu, Yontao; Denoeud, France; Antonarakis, Stylianos E.; Snyder, Michael; Ruan, Yijun; Wei, Chia-Lin; Gingeras, Thomas R.; Guigó Serra, Roderic; Harrow, Jennifer; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)