35 Works

Data from: Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery

Maria Jose Rebollo-Lopez, Joel Lelievre, Francisco Martínez-Jiménez, Marc A. Marti-Renom, George Papadatos, Grace Mugumbate & John P. Overington
As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on not only antitubercular potency but also on physicochemical characteristics. The 50 most attractive compounds were then progressed for evaluation in three different predictive computational...

Additional file 5 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 5: Table S4. Non-HhaI amplicons used for cell selection.

Additional file 3 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 3: Supplementary Table 1. Characteristics of the study participants with information for cognition outcomes. Mean and SD are shown for continuous variables. Supplementary Table 2. Characteristics of the study participants with information for neuroimaging outcomes. Mean and SD are shown for continuous variables. Supplementary Table 3. Characteristics of the study participants with information for CSF biomarkers. Mean and SD are shown for continuous variables.

Additional file 5 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 5: Supplementary Figure 1. Leave-one-out permutation analysis plot for AD signature among individuals at high genetic predisposition to AD obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest of the instrumental variables. Supplementary Figure 2. Leave-one-out permutation analysis plot for Aging signature among individuals at high genetic predisposition to AD, obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest...

Data for \"Eighty million years of rapid evolution of the primate Y chromosomes\"

Yang Zhou, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei Li, Marjolaine Marie C Rousselle, Meritxell Riera Belles, Lan Zhao, Miaoquan Fang, Qi Fang, Lukas Kuderna, Tomas Marques-Bonet, Haruka Kitayama, Takashi Hayakawa, Yong-Gang Yao, Huanming Yang, David N. Cooper, Xiaoguang Qi, Dong-Dong Wu, Mikkel Heide Schierup & Guojie Zhang
This folder contains data for "Eighty million years of rapid evolution of the primate Y chromosome" gene_set.zip contains gene annotation (GFF, CDS, PEP, POS.ADD) for the 30 species used in this study XY_location.zip contains the genomic coordinates for PAR, nonPARX and nonPARY (BED format). Species names are in the 4th column. gametolog_alignment.tar.gz contains gametolog alignment (PHY format) used to calculate pairwise dN/dS. S5.tree.zip contains alignment (FASTA format) and constructed phylogeny (NWK format) for each S5...

Additional file 2 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 2: Table S1. Design overview of the panel of targeted regions.

Additional file 4 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 4: Table S3. Complete list of CpG methylation-sensitive endonucleases potentially compatible with scTAM-seq.

Additional file 7 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 7: Table S6. Doublet detection details per sample and condition.

Additional file 1 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia & Marc Robinson-Rechavi
Additional file 1: Table S1-Table S6.

Additional file 1 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia & Marc Robinson-Rechavi
Additional file 1: Table S1-Table S6.

Additional file 3 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 3: Supplementary Table 1. Characteristics of the study participants with information for cognition outcomes. Mean and SD are shown for continuous variables. Supplementary Table 2. Characteristics of the study participants with information for neuroimaging outcomes. Mean and SD are shown for continuous variables. Supplementary Table 3. Characteristics of the study participants with information for CSF biomarkers. Mean and SD are shown for continuous variables.

Data from: The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives

Riccardo Aversano, Felice Contaldi, Maria Raffaella Ercolano, Valentina Grosso, Massimo Iorizzo, Filippo Tatino, Luciano Xumerle, Alessandra Dal Molin, Carla Avanzato, Alberto Ferrarini, Massimo Delledonne, Walter Sanseverino, Riccardo Aiese Cigliano, Salvador Capella-Gutierrez, Toni Gabaldón, Luigi Frusciante, James M. Bradeen & Domenico Carputo
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data...

Additional file 3 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 3: Table S2. Sequencing details per sample and condition.

Additional file 6 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 6: Table S5. PCR program for DNA digestion and targeted amplification steps.

Additional file 6 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 6: Table S5. PCR program for DNA digestion and targeted amplification steps.

Additional file 1 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 1: Supplementary Table 1. Characteristics of Single Nucleotide Polymorphisms (SNPs) associated with longer telomere length. The effect allele refers to the allele that is associated with longer telomere length. Chromosomal position of the SNPs (genome assembly GRCh37 (hg19)) according to the public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI) (dbSNP).

Additional file 4 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 4: Supplementary Table 1. Results of the effect of genetically predicted longer telomere length on AD endophenotypes in the entire sample. Supplementary Table 2. Results of the effect of genetically predicted longer telomere length on AD endophenotypes among APOE-ɛ4 carriers. Supplementary Table 3. Results of the effect of genetically predicted longer telomere length on AD endophenotypes among APOE-ɛ4 non-carriers. Supplementary Table 4. Results of the effect of genetically predicted longer telomere length on...

Additional file 5 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Blanca Rodríguez-Fernández, Natalia Vilor-Tejedor, Eider M. Arenaza-Urquijo, Gonzalo Sánchez-Benavides, Marc Suárez-Calvet, Grégory Operto, Carolina Minguillón, Karine Fauria, Gwendlyn Kollmorgen, Ivonne Suridjan, Manuel Castro de Moura, David Piñeyro, Manel Esteller, Kaj Blennow, Henrik Zetterberg, Immaculata De Vivo, José Luis Molinuevo, Arcadi Navarro, Juan Domingo Gispert, Aleix Sala-Vila & Marta Crous-Bou
Additional file 5: Supplementary Figure 1. Leave-one-out permutation analysis plot for AD signature among individuals at high genetic predisposition to AD obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest of the instrumental variables. Supplementary Figure 2. Leave-one-out permutation analysis plot for Aging signature among individuals at high genetic predisposition to AD, obtained by leaving out the SNP indicated and repeating the Inverse-Variance Weighted method with the rest...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait

Peter C. Zee, Helena Mendes-Soares, Yuen-Tsu Nicco Yu, Susanne A. Kraemer, Heike Keller, Stephan Ossowski, Korbinian Schneeberger & Gregory J. Velicer
While the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral...

Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes

Riddhiman Dhar, Tobias Bergmiller & Andreas Wagner
Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these...

Additional file 4 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 4: Table S3. Complete list of CpG methylation-sensitive endonucleases potentially compatible with scTAM-seq.

Additional file 7 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 7: Table S6. Doublet detection details per sample and condition.

Additional file 8 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 8: Table S7 and Table S8. Correlation analysis between target CpGs and gene expression.

Polygenic risk score in Africa populations: progress and challenges

Ezekiel Adebiyi, Yagoub Adam, Suraju Sadeeq, Judit Kumuthini, Olabode Ajayi, Gordon Wells, Rotimi Solomon, Olubanke Ogunlana, Emmanuel Adetiba, Emeka Iweala & Benedikt Brors
Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects SNPs that contribute to the disease with low effect size making it more precise at individual level risk prediction. PRS analysis addresses the shortfall of GWAS by taking into account the...

Registration Year

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Affiliations

  • Centre for Genomic Regulation
    35
  • Barcelona Institute for Science and Technology
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  • Pompeu Fabra University
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  • August Pi i Sunyer Biomedical Research Institute
    24
  • Institució Catalana de Recerca i Estudis Avançats
    15
  • Saarland University
    13
  • Max Planck Institute for Informatics
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  • Centro Nacional de Análisis Genómico
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  • University of Barcelona
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  • University College London
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