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eggNOG v4.0: nested orthology inference across 3686 organisms

Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973-; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J.; Mering, Christian von; Bork, Peer (Oxford University Press, 2014)
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)
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)
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)
Differential DNA mismatch repair underlies mutation rate variation across the human genome

Supek, Fran; Lehner, Ben, 1978- (Nature Publishing Group, 2015)
The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

Sebé-Pedrós, Arnau; Ballaré, Cecilia Julia; Parra-Acero, Helena; Chiva, Cristina; Tena, Juan J.; Sabidó Aguadé, Eduard, 1981-; Gómez Skarmeta, José Luis; Di Croce, Luciano; Ruíz Trillo, Iñaki (Elsevier, 2016)
Unraveling the hidden universe of small proteins in bacterial genomes

Miravet Verde, Samuel; Ferrar, Tony; Espadas, Guadalupe; Mazzolini, Rocco; Gharrab, Anas; Sabidó Aguadé, Eduard, 1981-; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (Wiley Open Access, 2019)
Patterns of genomic variation in the opportunistic pathogen candida glabrata suggest the existence of mating and a secondary association with humans

Carreté Muñoz, Laia, 1990-; Ksiezopolska, Ewa; Pegueroles Queralt, Maria Cinta; Gómez-Molero, Emilia; Saus Martínez, Ester; Iraola Guzman, Susana; Loska, Damian; Bader, Olivier; Fairhead, Cécile; Gabaldón Estevan, Juan Antonio, 1973- (Elsevier, 2018)
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Ferreira, Pedro G.; González-Pérez, Abel; Knowles, David G.; Monlong, Jean; Johnson, Rory; Djebali, Sarah; Papasaikas, Panagiotis; Tamborero Noguera, David; Gouin, Anaïs; López Bigas, Núria; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)