Ylla Lab

Ylla Lab

Computational approaches to study genes, genomes, and gene regulatory networks

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publications

Towards understanding the molecular basis of cockroach tergal gland morphogenesis. A transcriptomic approach

Journal: Insect Biochemistry and Molecular Biology, 2015

Link to paper

Xavier Belles, Guillem Ylla, "Towards understanding the molecular basis of cockroach tergal gland morphogenesis. A transcriptomic approach." Insect Biochemistry and Molecular Biology, 2015. http://www.sciencedirect.com/science/article/pii/S0965174815300114

The microRNA toolkit of insects

Journal: Scientific Reports, 2016

Guillem Ylla, Bastian Fromm, Maria Piulachs, Xavier Belles, "The microRNA toolkit of insects." Scientific Reports, 2016.

Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types

Journal: BMC Genomics, 2017

Link to paper

Guillem Ylla, Maria Piulachs, Xavier Belles, "Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types." BMC Genomics, 2017. https://doi.org/10.1186/s12864-017-4177-5

Hemimetabolous genomes reveal molecular basis of termite eusociality

Journal: Nature Ecology and Evolution, 2018

Mark Harrison, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel Hughes, Ann Huylmans, Carsten Kemena, Lukas Kremer, Sandra Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose Monroy-Kuhn, Annabell Moser, Shwetha Murali, Donna Muzny, Saria Otani, Maria Piulachs, Monica Poelchau, Jiaxin Qu, Florentine Schaub, Ayako Wada-Katsumata, Kim Worley, Qiaolin Xie, Guillem Ylla, Michael Poulsen, Richard Gibbs, Coby Schal, Stephen Richards, Xavier Belles, Judith Korb, Erich Bornberg-Bauer, "Hemimetabolous genomes reveal molecular basis of termite eusociality." Nature Ecology and Evolution, 2018.

Comparative transcriptomics in two extreme neopterans reveal general trends in the evolution of modern insects

Journal: iScience, 2018

Link to paper

Guillem Ylla, Maria-Dolors Piulachs, Xavier Belles, "Comparative transcriptomics in two extreme neopterans reveal general trends in the evolution of modern insects." iScience, 2018. https://linkinghub.elsevier.com/retrieve/pii/S2589004218300725

Diversity of piRNA expression patterns during the ontogeny of the German cockroach

Journal: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2018

Link to paper

Natalia Llonga, Guillem Ylla, Josep Bau, Xavier Belles, Maria Piulachs, "Diversity of piRNA expression patterns during the ontogeny of the German cockroach." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2018. http://doi.wiley.com/10.1002/jez.b.22815

Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest

Journal: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2018

Link to paper

Mark Harrison, Nicolas Arning, Lukas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg-Bauer, Ann Huylmans, Evelien Jongepier, Maria Piulachs, Stephen Richards, Coby Schal, "Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2018. http://doi.wiley.com/10.1002/jez.b.22824

siRNA enrichment in Argonaute 2-depleted Blattella germanica

Journal: Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 2021

Link to paper

José Montañés, Carlos Rojano, Guillem Ylla, Maria Piulachs, José Maestro, "siRNA enrichment in Argonaute 2-depleted Blattella germanica." Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 2021. https://linkinghub.elsevier.com/retrieve/pii/S1874939921000225

Molecular characterization of genetic diversity in apricot cultivars: Current situation and future perspectives

Journal: Agronomy, 2021

Link to paper

Sara Herrera, José Hormaza, Jorge Lora, Guillem Ylla, Javier Rodrigo, "Molecular characterization of genetic diversity in apricot cultivars: Current situation and future perspectives." Agronomy, 2021. https://www.mdpi.com/2073-4395/11/9/1714/htm

Evolution of a Cytoplasmic Determinant: Evidence for the Biochemical Basis of Functional Evolution of the Novel Germ Line Regulator Oskar

Journal: Molecular Biology and Evolution, 2021

Link to paper

Leo Blondel, Savandara Besse, Emily Rivard, Guillem Ylla, Cassandra Extavour, "Evolution of a Cytoplasmic Determinant: Evidence for the Biochemical Basis of Functional Evolution of the Novel Germ Line Regulator Oskar." Molecular Biology and Evolution, 2021. https://academic.oup.com/mbe/article/38/12/5491/6373905

Insights into the genomic evolution of insects from cricket genomes

Journal: Communications Biology, 2021

Link to paper

Guillem Ylla, Taro Nakamura, Takehiko Itoh, Rei Kajitani, Atsushi Toyoda, Sayuri Tomonari, Tetsuya Bando, Yoshiyasu Ishimaru, Takahito Watanabe, Masao Fuketa, Yuji Matsuoka, Austen Barnett, Sumihare Noji, Taro Mito, Cassandra Extavour, "Insights into the genomic evolution of insects from cricket genomes." Communications Biology, 2021. http://www.nature.com/articles/s42003-021-02197-9

Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster

Journal: G3 GenestextbarGenomestextbarGenetics, 2022

Link to paper

Shreeharsha Tarikere, Guillem Ylla, Cassandra Extavour, "Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster." G3 GenestextbarGenomestextbarGenetics, 2022. https://doi.org/10.1093/g3journal/jkab305

Genomics and genome editing techniques of crickets, an emerging model insect for biology and food science

Journal: Current Opinion in Insect Science, 2022

Taro Nakamura, Guillem Ylla, Cassandra Extavour, "Genomics and genome editing techniques of crickets, an emerging model insect for biology and food science." Current Opinion in Insect Science, 2022.

Two avian Plasmodium species trigger different transcriptional responses on their vector Culex pipiens

Journal: Molecular Ecology, 2023

Link to paper

Marta Garrigós, Guillem Ylla, Josué Puente, Jordi Figuerola, María Ruiz-López, "Two avian Plasmodium species trigger different transcriptional responses on their vector Culex pipiens." Molecular Ecology, 2023. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.17240

Reduction of embryonic E93 expression as a hypothetical driver of the evolution of insect metamorphosis

Journal: Proceedings of the National Academy of Sciences, 2023

Link to paper

Ana Fernandez-Nicolas, Gabriela Machaj, Alba Ventos-Alfonso, Viviana Pagone, Toshinori Minemura, Takahiro Ohde, Takaaki Daimon, Guillem Ylla, Xavier Belles, "Reduction of embryonic E93 expression as a hypothetical driver of the evolution of insect metamorphosis." Proceedings of the National Academy of Sciences, 2023. https://www.pnas.org/doi/abs/10.1073/pnas.2216640120

oskar acts with the transcription factor Creb to regulate long-term memory in crickets

Journal: Proceedings of the National Academy of Sciences, 2023

Link to paper

Arpita Kulkarni, Ben Ewen-Campen, Kanta Terao, Yukihisa Matsumoto, Yaolong Li, Takayuki Watanabe, Jonchee Kao, Swapnil Parhad, Guillem Ylla, Makoto Mizunami, Cassandra Extavour, "oskar acts with the transcription factor Creb to regulate long-term memory in crickets." Proceedings of the National Academy of Sciences, 2023. https://www.pnas.org/doi/10.1073/pnas.2218506120

Dysregulated iron homeostasis in dystrophin-deficient cardiomyocytes: correction by gene editing and pharmacological treatment

Journal: Cardiovascular Research, 2024

Link to paper

Kalina Andrysiak, Gabriela Machaj, Dominik Priesmann, Olga Woźnicka, Alicja Martyniak, Guillem Ylla, Marcus Krüger, Elżbieta Pyza, Anna Potulska-Chromik, Anna Kostera-Pruszczyk, Agnieszka Łoboda, Jacek Stępniewski, Józef Dulak, "Dysregulated iron homeostasis in dystrophin-deficient cardiomyocytes: correction by gene editing and pharmacological treatment." Cardiovascular Research, 2024. https://doi.org/10.1093/cvr/cvad182

Insights into the early transcriptomic response against watermelon mosaic virus in melon

Journal: BMC Plant Biology, 2024

Link to paper

María López-Martín, Javier Montero-Pau, Guillem Ylla, María Gómez-Guillamón, Belén Picó, Ana Pérez-de-Castro, "Insights into the early transcriptomic response against watermelon mosaic virus in melon." BMC Plant Biology, 2024. https://doi.org/10.1186/s12870-024-04745-x

Upregulation of utrophin improves the phenotype of Duchenne muscular dystrophy hiPSC-derived CMs

Journal: Molecular Therapy - Nucleic Acids, 2024

Link to paper

Kalina Andrysiak, Paweł Ferdek, Anna Sanetra, Gabriela Machaj, Luisa Schmidt, Izabela Kraszewska, Katarzyna Sarad, Katarzyna Palus-Chramiec, Olga Lis, Marta Targosz-Korecka, Marcus Krüger, Marian Lewandowski, Guillem Ylla, Jacek Stępniewski, Józef Dulak, "Upregulation of utrophin improves the phenotype of Duchenne muscular dystrophy hiPSC-derived CMs." Molecular Therapy - Nucleic Acids, 2024. https://www.cell.com/molecular-therapy-family/nucleic-acids/abstract/S2162-2531(24)00134-3

MCPIP1 modulates the miRNA‒mRNA landscape in keratinocyte carcinomas

Journal: Journal of Experimental & Clinical Cancer Research, 2024

Link to paper

Agata Lichawska-Cieslar, Weronika Szukala, Guillem Ylla, Gabriela Machaj, Faustyna Ploskonka, Iwona Chlebicka, Jacek Szepietowski, Jolanta Jura, "MCPIP1 modulates the miRNA‒mRNA landscape in keratinocyte carcinomas." Journal of Experimental & Clinical Cancer Research, 2024. https://doi.org/10.1186/s13046-024-03211-8

Establishment of CRISPR/Cas9-based knock-in in a hemimetabolous insect: targeted gene tagging in the cricket Gryllus bimaculatus

Journal: Development, 2025

Link to paper

Yuji Matsuoka, Taro Nakamura, Takahito Watanabe, Austen Barnett, Sayuri Tomonari, Guillem Ylla, Carrie Whittle, Sumihare Noji, Taro Mito, Cassandra Extavour, "Establishment of CRISPR/Cas9-based knock-in in a hemimetabolous insect: targeted gene tagging in the cricket Gryllus bimaculatus." Development, 2025. https://doi.org/10.1242/dev.199746

Chromosome-scale whole genome assembly and annotation of the Jamaican field cricket Gryllus assimilis

Journal: Scientific Data, 2025

Link to paper

Yuki Ito, Ryuto Sanno, Seiya Ashikari, Kei Yura, Toru Asahi, Guillem Ylla, Kosuke Kataoka, "Chromosome-scale whole genome assembly and annotation of the Jamaican field cricket Gryllus assimilis." Scientific Data, 2025. https://www.nature.com/articles/s41597-025-05197-0

talks

The new FBBB’s Laboratory of Bioinformatics and Genome Biology: computational approaches to study genes, genomes, gene regulatory networks

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Comparative genomics of insects to unveil the evolution of gene regulatory networks.

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Using bioinformatics to unveil the mysteries of animal evolution.

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Using bioinformatics to unveil the mysteries of animal evolution.

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Non-traditional insect models are key for understanding the evolution and regulation of insect metamorphosis

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A novel bioinformatics tool to annotate and analyze piRNAs.

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The transcriptomics of the evolution of insect metamorphosis.

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teaching

AT4BR - Advanced Toolkit for Bioinformatics Research

Summer semester (February - June) for students of the Jagiellonian University.