MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes
Cantarel, Brandi L, Korf, Ian, Robb, Sofia M C, Parra, Genis, Ross, Eric, Moore, Barry, Holt, Carson, Sánchez Alvarado, Alejandro, Yandell, Mark
Published in Genome Research (01.01.2008)
Published in Genome Research (01.01.2008)
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Journal Article
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution
Roscito, Juliana G, Sameith, Katrin, Parra, Genis, Langer, Bjoern E, Petzold, Andreas, Moebius, Claudia, Bickle, Marc, Rodrigues, Miguel Trefaut, Hiller, Michael
Published in Nature communications (09.11.2018)
Published in Nature communications (09.11.2018)
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Journal Article
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
Kovach, Allen, Wegrzyn, Jill L, Parra, Genis, Holt, Carson, Bruening, George E, Loopstra, Carol A, Hartigan, James, Yandell, Mark, Langley, Charles H, Korf, Ian, Neale, David B
Published in BMC genomics (07.07.2010)
Published in BMC genomics (07.07.2010)
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Journal Article
Genomic Validation of Endometrial Cancer Patient-Derived Xenograft Models as a Preclinical Tool
Villafranca-Magdalena, Beatriz, Masferrer-Ferragutcasas, Carina, Lopez-Gil, Carlos, Coll-de la Rubia, Eva, Rebull, Marta, Parra, Genis, García, Ángel, Reques, Armando, Cabrera, Silvia, Colas, Eva, Gil-Moreno, Antonio, Moiola, Cristian P
Published in International journal of molecular sciences (03.06.2022)
Published in International journal of molecular sciences (03.06.2022)
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Journal Article
Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo
García, Alicia, Aguado, Encarni, Parra, Genis, Manzano, Susana, Martínez, Cecilia, Megías, Zoraida, Cebrián, Gustavo, Romero, Jonathan, Beltrán, Sergi, Garrido, Dolores, Jamilena, Manuel
Published in Frontiers in plant science (03.08.2018)
Published in Frontiers in plant science (03.08.2018)
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Journal Article
The C250T Mutation of TERTp Might Grant a Better Prognosis to Glioblastoma by Exerting Less Biological Effect on Telomeres and Chromosomes Than the C228T Mutation
Gorria, Teresa, Crous, Carme, Pineda, Estela, Hernandez, Ainhoa, Domenech, Marta, Sanz, Carolina, Jares, Pedro, Muñoz-Mármol, Ana María, Arpí-Llucía, Oriol, Melendez, Bárbara, Gut, Marta, Esteve, Anna, Esteve-Codina, Anna, Parra, Genis, Alameda, Francesc, Carrato, Cristina, Aldecoa, Iban, Mallo, Mar, de la Iglesia, Nuria, Balana, Carmen
Published in Cancers (09.02.2024)
Published in Cancers (09.02.2024)
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Journal Article
Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer
Díaz-Gay, Marcos, Franch-Expósito, Sebastià, Arnau-Collell, Coral, Park, Solip, Supek, Fran, Muñoz, Jenifer, Bonjoch, Laia, Gratacós-Mulleras, Anna, Sánchez-Rojas, Paula A, Esteban-Jurado, Clara, Ocaña, Teresa, Cuatrecasas, Miriam, Vila-Casadesús, Maria, Lozano, Juan José, Parra, Genis, Laurie, Steve, Beltran, Sergi, Castells, Antoni, Bujanda, Luis, Cubiella, Joaquín, Balaguer, Francesc, Castellví-Bel, Sergi
Published in Cancers (13.03.2019)
Published in Cancers (13.03.2019)
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Journal Article
Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment
Rubio-Perez, Carlota, Planas-Rigol, Ester, Trincado, Juan L, Bonfill-Teixidor, Ester, Arias, Alexandra, Marchese, Domenica, Moutinho, Catia, Serna, Garazi, Pedrosa, Leire, Iurlaro, Raffaella, Martínez-Ricarte, Francisco, Escudero, Laura, Cordero, Esteban, Cicuendez, Marta, Ruiz, Sara, Parra, Genís, Nuciforo, Paolo, Gonzalez, Josep, Pineda, Estela, Sahuquillo, Juan, Tabernero, Josep, Heyn, Holger, Seoane, Joan
Published in Nature communications (08.03.2021)
Published in Nature communications (08.03.2021)
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Journal Article
Patterns of coding variation in the complete exomes of three Neandertals
Castellano, Sergi, Parra, Genís, Sánchez-Quinto, Federico A., Racimo, Fernando, Kuhlwilm, Martin, Kircher, Martin, Sawyer, Susanna, Fu, Qiaomei, Heinze, Anja, Nickel, Birgit, Dabney, Jesse, Siebauer, Michael, White, Louise, Burbano, Hernán A., Renaud, Gabriel, Stenzel, Udo, Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajković, Dejana, Kucan, Željko, Gušic, Ivan, Shunkov, Michael V., Derevianko, Anatoli P., Viola, Bence, Meyer, Matthias, Kelso, Janet, Andrés, Aida M., Pääbo, Svante
Published in Proceedings of the National Academy of Sciences - PNAS (06.05.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (06.05.2014)
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Journal Article
Using geneid to Identify Genes
Alioto, Tyler, Blanco, Enrique, Parra, Genís, Guigó, Roderic
Published in Current protocols in bioinformatics (01.12.2018)
Published in Current protocols in bioinformatics (01.12.2018)
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Journal Article
Are splicing mutations the most frequent cause of hereditary disease?
López-Bigas, Núria, Audit, Benjamin, Ouzounis, Christos, Parra, Genís, Guigó, Roderic
Published in FEBS letters (28.03.2005)
Published in FEBS letters (28.03.2005)
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Journal Article
A critical spotlight on the paradigms of FFPE-DNA sequencing
Steiert, Tim A, Parra, Genís, Gut, Marta, Arnold, Norbert, Trotta, Jean-Rémi, Tonda, Raúl, Moussy, Alice, Gerber, Zuzana, Abuja, Peter M, Zatloukal, Kurt, Röcken, Christoph, Folseraas, Trine, Grimsrud, Marit M, Vogel, Arndt, Goeppert, Benjamin, Roessler, Stephanie, Hinz, Sebastian, Schafmayer, Clemens, Rosenstiel, Philip, Deleuze, Jean-François, Gut, Ivo G, Franke, Andre, Forster, Michael
Published in Nucleic acids research (11.08.2023)
Published in Nucleic acids research (11.08.2023)
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Journal Article
Gene finding in the chicken genome
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, Huckle, Elizabeth J, Parra, Genis, Shteynberg, David D, Wyss, Carine, Rogers, Jane, Antonarakis, Stylianos E, Birney, Ewan, Guigo, Roderic, Brent, Michael R
Published in BMC bioinformatics (30.05.2005)
Published in BMC bioinformatics (30.05.2005)
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Journal Article
Assessing the gene space in draft genomes
Parra, Genis, Bradnam, Keith, Ning, Zemin, Keane, Thomas, Korf, Ian
Published in Nucleic acids research (01.01.2009)
Published in Nucleic acids research (01.01.2009)
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Journal Article
Germline NPAT inactivating variants as cause of hereditary colorectal cancer
Terradas, Mariona, Schubert, Stephanie A, Viana-Errasti, Julen, Ruano, Dina, Aiza, Gemma, Nielsen, Maartje, Marciel, Paula, Tops, Carli M, Parra, Genís, Morreau, Hans, Torrents, David, van Leerdam, Monique E, Capellá, Gabriel, de Miranda, Noel F C C, Valle, Laura, van Wezel, Tom
Published in European journal of human genetics : EJHG (01.07.2024)
Published in European journal of human genetics : EJHG (01.07.2024)
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Journal Article
Long-Term Balancing Selection in LAD1 Maintains a Missense Trans-Species Polymorphism in Humans, Chimpanzees, and Bonobos
Teixeira, João C, de Filippo, Cesare, Weihmann, Antje, Meneu, Juan R, Racimo, Fernando, Dannemann, Michael, Nickel, Birgit, Fischer, Anne, Halbwax, Michel, Andre, Claudine, Atencia, Rebeca, Meyer, Matthias, Parra, Genís, Pääbo, Svante, Andrés, Aida M
Published in Molecular biology and evolution (01.05.2015)
Published in Molecular biology and evolution (01.05.2015)
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Journal Article
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
Olson, Nathan D., Wagner, Justin, McDaniel, Jennifer, Stephens, Sarah H., Westreich, Samuel T., Prasanna, Anish G., Johanson, Elaine, Boja, Emily, Maier, Ezekiel J., Serang, Omar, Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Kyriakidis, Konstantinos, Malousi, Andigoni, Shafin, Kishwar, Pesout, Trevor, Jain, Miten, Paten, Benedict, Chang, Pi-Chuan, Kolesnikov, Alexey, Nattestad, Maria, Baid, Gunjan, Goel, Sidharth, Yang, Howard, Carroll, Andrew, Eveleigh, Robert, Bourgey, Mathieu, Bourque, Guillaume, Li, Gen, Ma, ChouXian, Tang, LinQi, Du, YuanPing, Zhang, ShaoWei, Morata, Jordi, Tonda, Raúl, Parra, Genís, Trotta, Jean-Rémi, Brueffer, Christian, Demirkaya-Budak, Sinem, Kabakci-Zorlu, Duygu, Turgut, Deniz, Kalay, Özem, Budak, Gungor, Narcı, Kübra, Arslan, Elif, Brown, Richard, Johnson, Ivan J., Dolgoborodov, Alexey, Semenyuk, Vladimir, Jain, Amit, Tetikol, H. Serhat, Jain, Varun, Ruehle, Mike, Lajoie, Bryan, Roddey, Cooper, Catreux, Severine, Mehio, Rami, Ahsan, Mian Umair, Liu, Qian, Wang, Kai, Ebrahim Sahraeian, Sayed Mohammad, Fang, Li Tai, Mohiyuddin, Marghoob, Hung, Calvin, Jain, Chirag, Feng, Hanying, Li, Zhipan, Chen, Luoqi, Sedlazeck, Fritz J., Zook, Justin M.
Published in Cell genomics (11.05.2022)
Published in Cell genomics (11.05.2022)
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Journal Article
Tandem chimerism as a means to increase protein complexity in the human genome
Parra, Genís, Reymond, Alexandre, Dabbouseh, Noura, Dermitzakis, Emmanouil T, Castelo, Robert, Thomson, Timothy M, Antonarakis, Stylianos E, Guigó, Roderic
Published in Genome Research (01.01.2006)
Published in Genome Research (01.01.2006)
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Journal Article
Recent Selection Changes in Human Genes under Long-Term Balancing Selection
de Filippo, Cesare, Key, Felix M, Ghirotto, Silvia, Benazzo, Andrea, Meneu, Juan R, Weihmann, Antje, Parra, Genís, Green, Eric D, Andrés, Aida M
Published in Molecular biology and evolution (01.06.2016)
Published in Molecular biology and evolution (01.06.2016)
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Journal Article