Search Results - "Gut, Ivo"

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species by Nater, Alexander, Mattle-Greminger, Maja P., Nurcahyo, Anton, Nowak, Matthew G., de Manuel, Marc, Desai, Tariq, Groves, Colin, Pybus, Marc, Sonay, Tugce Bilgin, Roos, Christian, Lameira, Adriano R., Wich, Serge A., Askew, James, Davila-Ross, Marina, Fredriksson, Gabriella, de Valles, Guillem, Casals, Ferran, Prado-Martinez, Javier, Goossens, Benoit, Verschoor, Ernst J., Warren, Kristin S., Singleton, Ian, Marques, David A., Pamungkas, Joko, Perwitasari-Farajallah, Dyah, Rianti, Puji, Tuuga, Augustine, Gut, Ivo G., Gut, Marta, Orozco-terWengel, Pablo, van Schaik, Carel P., Bertranpetit, Jaume, Anisimova, Maria, Scally, Aylwyn, Marques-Bonet, Tomas, Meijaard, Erik, Krützen, Michael

“…Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos…”
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Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells by Habibi, Ehsan, Brinkman, Arie B., Arand, Julia, Kroeze, Leonie I., Kerstens, Hindrik H.D., Matarese, Filomena, Lepikhov, Konstantin, Gut, Marta, Brun-Heath, Isabelle, Hubner, Nina C., Benedetti, Rosaria, Altucci, Lucia, Jansen, Joop H., Walter, Jörn, Gut, Ivo G., Marks, Hendrik, Stunnenberg, Hendrik G.

“…The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite…”
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Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses by Metzger, Julia, Karwath, Matthias, Tonda, Raul, Beltran, Sergi, Águeda, Lídia, Gut, Marta, Gut, Ivo Glynne, Distl, Ottmar

“…Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show…”
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DNA methylation analysis by pyrosequencing by Tost, Jörg, Gut, Ivo G

“…Pyrosequencing is a sequencing-by-synthesis method that quantitatively monitors the real-time incorporation of nucleotides through the enzymatic conversion of…”
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Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate by Sardina, Jose Luis, Collombet, Samuel, Tian, Tian V., Gómez, Antonio, Di Stefano, Bruno, Berenguer, Clara, Brumbaugh, Justin, Stadhouders, Ralph, Segura-Morales, Carolina, Gut, Marta, Gut, Ivo G., Heath, Simon, Aranda, Sergi, Di Croce, Luciano, Hochedlinger, Konrad, Thieffry, Denis, Graf, Thomas

“…Here, we report DNA methylation and hydroxymethylation dynamics at nucleotide resolution using C/EBPα-enhanced reprogramming of B cells into induced…”
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Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation by Vilarrasa-Blasi, Roser, Soler-Vila, Paula, Verdaguer-Dot, Núria, Russiñol, Núria, Di Stefano, Marco, Chapaprieta, Vicente, Clot, Guillem, Farabella, Irene, Cuscó, Pol, Kulis, Marta, Agirre, Xabier, Prosper, Felipe, Beekman, Renée, Beà, Silvia, Colomer, Dolors, Stunnenberg, Hendrik G., Gut, Ivo, Campo, Elias, Marti-Renom, Marc A., Martin-Subero, José Ignacio

“…To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic…”
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Benchmarking single-cell RNA-sequencing protocols for cell atlas projects by Mereu, Elisabetta, Lafzi, Atefeh, Moutinho, Catia, Ziegenhain, Christoph, McCarthy, Davis J., Álvarez-Varela, Adrián, Batlle, Eduard, Sagar, Grün, Dominic, Lau, Julia K., Boutet, Stéphane C., Sanada, Chad, Ooi, Aik, Jones, Robert C., Kaihara, Kelly, Brampton, Chris, Talaga, Yasha, Sasagawa, Yohei, Tanaka, Kaori, Hayashi, Tetsutaro, Braeuning, Caroline, Fischer, Cornelius, Sauer, Sascha, Trefzer, Timo, Conrad, Christian, Adiconis, Xian, Nguyen, Lan T., Regev, Aviv, Levin, Joshua Z., Parekh, Swati, Janjic, Aleksandar, Wange, Lucas E., Bagnoli, Johannes W., Enard, Wolfgang, Gut, Marta, Sandberg, Rickard, Nikaido, Itoshi, Gut, Ivo, Stegle, Oliver, Heyn, Holger

“…Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are…”
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Machine learning and multi-omics data in chronic lymphocytic leukemia: the future of precision medicine? by Tsagiopoulou, Maria, Gut, Ivo G

“…Chronic lymphocytic leukemia is a complex and heterogeneous hematological malignancy. The advance of high-throughput multi-omics technologies has significantly…”
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Distinct DNA methylomes of newborns and centenarians by Heyn, Holger, Li, Ning, Ferreira, Humberto J., Moran, Sebastian, Pisano, David G., Gomez, Antonio, Diez, Javier, Sanchez-Mut, Jose V., Setien, Fernando, Carmona, F. Javier, Puca, Annibale A., Sayols, Sergi, Pujana, Miguel A., Serra-Musach, Jordi, Iglesias-Platas, Isabel, Formiga, Francesc, Fernandez, Agustin F., Fraga, Mario F., Heath, Simon C., Valencia, Alfonso, Gut, Ivo G., Wang, Jun, Esteller, Manel

“…Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means of explaining age-associated…”
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Impact of DNA methylation on 3D genome structure by Buitrago, Diana, Labrador, Mireia, Arcon, Juan Pablo, Lema, Rafael, Flores, Oscar, Esteve-Codina, Anna, Blanc, Julie, Villegas, Nuria, Bellido, David, Gut, Marta, Dans, Pablo D., Heath, Simon C., Gut, Ivo G., Brun Heath, Isabelle, Orozco, Modesto

“…Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic…”
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bigSCale: an analytical framework for big-scale single-cell data by Iacono, Giovanni, Mereu, Elisabetta, Guillaumet-Adkins, Amy, Corominas, Roser, Cuscó, Ivon, Rodríguez-Esteban, Gustavo, Gut, Marta, Pérez-Jurado, Luis Alberto, Gut, Ivo, Heyn, Holger

“…Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of…”
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Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data by Rueda, Manuel, Leist, Ivo C., Gut, Ivo G.

“…[Display omitted] Efficient sharing and integration of phenotypic data is crucial for advancing biomedical research and enhancing patient outcomes in precision…”
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A critical spotlight on the paradigms of FFPE-DNA sequencing by 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

“…Abstract In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still…”
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Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer by Stobbe, Miranda D, Thun, Gian A, Diéguez-Docampo, Andrea, Oliva, Meritxell, Whalley, Justin P, Raineri, Emanuele, Gut, Ivo G

“…The sheer size of the human genome makes it improbable that identical somatic mutations at the exact same position are observed in multiple tumours solely by…”
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Transcriptome and genome sequencing uncovers functional variation in humans by Lappalainen, Tuuli, Sammeth, Michael, Friedländer, Marc R., ‘t Hoen, Peter A. C., Monlong, Jean, Rivas, Manuel A., Gonzàlez-Porta, Mar, Kurbatova, Natalja, Griebel, Thasso, Ferreira, Pedro G., Barann, Matthias, Wieland, Thomas, Greger, Liliana, van Iterson, Maarten, Almlöf, Jonas, Ribeca, Paolo, Pulyakhina, Irina, Esser, Daniela, Giger, Thomas, Tikhonov, Andrew, Sultan, Marc, Bertier, Gabrielle, MacArthur, Daniel G., Lek, Monkol, Lizano, Esther, Buermans, Henk P. J., Padioleau, Ismael, Schwarzmayr, Thomas, Karlberg, Olof, Ongen, Halit, Kilpinen, Helena, Beltran, Sergi, Gut, Marta, Kahlem, Katja, Amstislavskiy, Vyacheslav, Stegle, Oliver, Pirinen, Matti, Montgomery, Stephen B., Donnelly, Peter, McCarthy, Mark I., Flicek, Paul, Strom, Tim M., Lehrach, Hans, Schreiber, Stefan, Sudbrak, Ralf, Carracedo, Ángel, Antonarakis, Stylianos E., Häsler, Robert, Syvänen, Ann-Christine, van Ommen, Gert-Jan, Brazma, Alvis, Meitinger, Thomas, Rosenstiel, Philip, Guigó, Roderic, Gut, Ivo G., Estivill, Xavier, Dermitzakis, Emmanouil T.

“…Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for…”
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DNA sequencing – spanning the generations by McGinn, Steven, Gut, Ivo Glynne

“…Nucleic acid sequencing is the mainstay of biological research. There are several generations of DNA sequencing technologies that can be well characterized…”
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Selective single molecule sequencing and assembly of a human Y chromosome of African origin by Kuderna, Lukas F. K., Lizano, Esther, Julià, Eva, Gomez-Garrido, Jessica, Serres-Armero, Aitor, Kuhlwilm, Martin, Alandes, Regina Antoni, Alvarez-Estape, Marina, Juan, David, Simon, Heath, Alioto, Tyler, Gut, Marta, Gut, Ivo, Schierup, Mikkel Heide, Fornas, Oscar, Marques-Bonet, Tomas

“…Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic…”
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gemBS: high throughput processing for DNA methylation data from bisulfite sequencing by Merkel, Angelika, Fernández-Callejo, Marcos, Casals, Eloi, Marco-Sola, Santiago, Schuyler, Ronald, Gut, Ivo G, Heath, Simon C

“…Abstract Motivation DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by…”
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Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage by Queirós, Ana C., Beekman, Renée, Vilarrasa-Blasi, Roser, Duran-Ferrer, Martí, Clot, Guillem, Merkel, Angelika, Raineri, Emanuele, Russiñol, Nuria, Castellano, Giancarlo, Beà, Sílvia, Navarro, Alba, Kulis, Marta, Verdaguer-Dot, Núria, Jares, Pedro, Enjuanes, Anna, Calasanz, María José, Bergmann, Anke, Vater, Inga, Salaverría, Itziar, van de Werken, Harmen J.G., Wilson, Wyndham H., Datta, Avik, Flicek, Paul, Royo, Romina, Martens, Joost, Giné, Eva, Lopez-Guillermo, Armando, Stunnenberg, Hendrik G., Klapper, Wolfram, Pott, Christiane, Heath, Simon, Gut, Ivo G., Siebert, Reiner, Campo, Elías, Martín-Subero, José I.

“…We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B…”
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MetaTrans: an open-source pipeline for metatranscriptomics by Martinez, Xavier, Pozuelo, Marta, Pascal, Victoria, Campos, David, Gut, Ivo, Gut, Marta, Azpiroz, Fernando, Guarner, Francisco, Manichanh, Chaysavanh

“…To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we…”
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