Publications

Alex Cornean, Jakob Gierten, Bettina Welz, Juan L. Mateo, Thomas Thumberger, Joachim Wittbrodt (2022). Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. eLife 11:e72124.

PDF Code DOI ACEofBASEs

Paula Masiá, Juan L. Mateo, Andrés Arias, Marlene Bartolomé, Carmen Blanco, Karim Erzini, François Le Loc'h, Jean Hervé Mve Beh, Deborah Power, Noemi Rodriguez, Gauthier Schaal, Gonzalo Machado-Schiaffino, Eva Garcia-Vazquez (2021). Potential microplastics impacts on African fishing resources. Sci Total Environ 806.

Max D. Knickmeyer, Juan L. Mateo, Stephan Heermann (2021). BMP Signaling Interferes with Optic Chiasm Formation and Retinal Ganglion Cell Pathfinding in Zebrafish. Int. J. Mol. Sci. 22(9).

Javier Vázquez-Marín, Jose Arturo Gutierrez-Triana, María Almuedo-Castillo, Lorena Buono, José Luis Gómez-Skarmeta, Juan L. Mateo, Joachim Wittbrodt, Juan Ramón Martínez-Morales (2019). Yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets. Development 146(13).

Mariko Kikuchi, Toshiya Nishimura, Daisuke Saito, Shuji Shigenobu, Ritsuko Takada, Jose Arturo Gutierrez-Triana, Juan L. Mateo, Shinji Takada, Joachim Wittbrodt, Mikita Suyama, Minoru Tanaka (2018). Novel components of germline sex determination acting downstream of foxl3 in medaka. Dev Biol 445(1).

Max D. Knickmeyer, Juan L. Mateo, Priska Eckert, Eleni Roussa, Belal Rahhal, Aimee Zuniga, Kerstin Krieglstein, Joachim Wittbrodt, Stephan Heermann (2018). TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism. Open Biol. 8.

Maurice Labuhn, Felix F. Adams, Michelle Ng, Sabine Knoess, Axel Schambach, Emmanuelle M. Charpentier, Adrian Schwarzer, Juan L. Mateo, Jan-Henning Klusmann, Dirk Heckl (2017). Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications. Nucl Acids Res 46(3).

Jose Arturo Gutierrez-Triana, Juan L. Mateo, David Ibberson, Soojin Ryu, Joachim Wittbrodt (2016). iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. Development 143.

Jubin N. Shah, Olga Kirioukhova, Pallavi Pawar, Muhammad Tayyab, Juan L. Mateo, Amal J. Johnston (2016). Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition. Front. Plant Sci. 7.

Juan I. Alonso-Barba, Raza-Ur Rahman, Joachim Wittbrodt, Juan L. Mateo (2016). MEPD: medaka expression pattern database, genes and more. Nucl Acids Res 44(D1).

Dirk Dolle, Juan L. Mateo, Michael P. Eichenlaub, Rebecca Sinn, Robert Reinhardt, Burkhard Höckendorf, Daigo Inoue, Lazaro Centanin, Laurence Ettwiller, Joachim Wittbrodt (2015). Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS ONE 10(10).

Bo Zhou, Jason M. Osinski, Juan L. Mateo, Ben Martynoga, Fraser J. Sim, Christine E. Campbell, François Guillemot, Michael Piper, Richard M. Gronostajski (2015). Loss of NFIX Transcription Factor Biases Postnatal Neural Stem/Progenitor Cells Toward Oligodendrogenesis. Stem Cells Dev 24 (18).

Manuel Stemmer, Thomas Thumberger, Maria del Sol Keyer, Joachim Wittbrodt, Juan L. Mateo (2015). CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE 12 (4).

PDF Code DOI CCTop

Juan L. Mateo, Debbie L.C. van den Berg, Maximilian Haeussler, Daniela Drechsel, Zachary B. Gaber, Diogo S. Castro, Paul Robson, Q. Richard Lu, Gregory E. Crawford, Paul Flicek, Laurence Ettwiller, Joachim Wittbrodt, François Guillemot, Ben Martynoga (2015). Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res. 25.

Ben Martynoga, Juan L. Mateo, Bo Zhou, Jimena Andersen, Angeliki Achimastou, Noelia Urbán, Debbie van den Berg, Dimitra Georgopoulou, Suzana Hadjur, Joachim Wittbrodt, Laurence Ettwiller, Michael Piper, Richard M. Gronostajski, François Guillemot (2013). Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence. Genes & Dev. 27.

José A. Gámez, Juan L. Mateo, José M. Puerta (2012). One iteration CHC algorithm for learning Bayesian networks: an effective and efficient algorithm for high dimensional problems. Prog Artif Intell 1, (4).

José A. Gámez, Juan L. Mateo, José M. Puerta (2010). Learning Bayesian networks by hill climbing: efficient methods based on progressive restriction of the neighborhood. Data Min Knowl Disc 22, (1-2).

Juan L. Mateo, Antonio Fernández-Caballero (2009). Finding out general tendencies in speckle noise reduction in ultrasound images. Expert Syst. Appl. 36(4).

M. Julia Flores, José A. Gámez, Juan L. Mateo (2008). Mining the ESROM: A study of breeding value classification in Manchego sheep by means of attribute selection and construction. Comput Electron Agric 60(2).

Luis delaOssa, M. Julia Flores, José A. Gámez, Juan L. Mateo, José M. Puerta (2007). Initial breeding value prediction on Manchego sheep by using rule-based systems. Expert Syst. Appl. 33(1).