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ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

Baa-Puyoulet, Patrice; Parisot, Nicolas; Febvay, Gérard; Huerta Cepas, Jaime; Vellozo, Augusto F.; Gabaldón Estevan, Juan Antonio, 1973-; Calevro, Federica; Charles, Hubert; Colella, Stefano (Oxford University Press, 2016)
Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Cheng, Chao; Alexander, Roger; Min, Renqiang; Leng, Jing; Yip, Kevin Y.; Rozowsky, Joel S.; Yan, Koon-Kiu; Dong, Xianjun; Djebali, Sarah; Ruan, Yijun; Davis, Carrie A.; Carninci, Piero; Lassmann, Timo; Gingeras, Thomas R.; Guigó Serra, Roderic; Birney, Ewan; Weng, Zhiping; Snyder, Michael; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

Pryszcz, Leszek Piotr, 1985-; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2011)
Differential DNA mismatch repair underlies mutation rate variation across the human genome

Supek, Fran; Lehner, Ben, 1978- (Nature Publishing Group, 2015)
Use of ChIP-Seq data for the design of a multiple promoter-alignment method

Erb, Ionas; González-Vallinas Rostes, Juan, 1983-; Bussotti, Giovanni, 1983-; Blanco, Enrique; Eyras Jiménez, Eduardo; Notredame, Cedric (Oxford University Press, 2012)
An encyclopedia of mouse DNA elements (Mouse ENCODE)

Stamatoyannopoulos, John A.; Guigó Serra, Roderic; Djebali, Sarah; Lagarde, Julien; Adams, Leslie B. (BioMed Central, 2012)
PeSV-Fisher: identification of somatic and non-somatic structural variants using nextgeneration sequencing data

Escaramís, Geòrgia; Tornador Antolin, Cristian, 1979-; Bassaganyas Bars, Laia, 1985-; Rabionet, Raquel; Tubio, José M. C.; Martínez Fundichely, Alexander, 1978-; Cáceres Aguilar, Mario; Gut, Marta; Ossowski, Stephan; Estivill, Xavier, 1955- (Public Library of Science (PLoS), 2013)
The schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology

Silva, Larissa Lopes; Marcet Houben, Marina; Alves Nahum, Laila; Zerlotini, Adhemar; Gabaldón Estevan, Juan Antonio, 1973-; Oliveira, Guilherme (BioMed Central, 2012)
The tomato genome sequence provides insights into fleshy fruit evolution

Tomato Genome Consortium; Sato, S.; Guigó Serra, Roderic; Cámara, Francisco; Gianese, S. (Nature Publishing Group, 2012)
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

Minoche, André E.; Dohm, Juliane C.; Schneider, Jessica; Holtgräwe, Daniela; Viehöver, Prisca; Montfort, Magda; Sörensen, Thomas Rosleff; Weisshaar, Bernd; Himmelbauer, Heinz (BioMed Central, 2015)