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Author Details

Ana Conesa
Institute for Integrative Systems Biology, Spanish National Research Council (CSIC)
2000
143
47
Gloria M Sheynkman (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37398077SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms.bioRxiv2023
37546854Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.bioRxiv2023
37577445Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems.Front Microbiol2023
35228596GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease.Sci Rep2022
35383181acorde unravels functionally interpretable networks of isoform co-usage from single cell data.Nat Commun2022
35840900Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species.BMC Genomics2022
35609982PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases.Nucleic Acids Res2022
35579358Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines.Genetics2022
36494864New roles for AP-1/JUNB in cell cycle control and tumorigenic cell invasion via regulation of cyclin E1 and TGF-β2.Genome Biol2022
36046619Reference-based comparison of adaptive immune receptor repertoires.Cell Rep Methods2022
36066904The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12.Metallomics2022
36302651Palmitate impairs circadian transcriptomics in muscle cells through histone modification of enhancers.Life Sci Alliance2022
35961013A roadmap for the functional annotation of protein families: a community perspective.Database (Oxford)2022
36124809ECCB2022: the 21st European Conference on Computational Biology.Bioinformatics2022
35241129Enhanced protein isoform characterization through long-read proteogenomics.Genome Biol2022
35238331MultiBaC: an R package to remove batch effects in multi-omic experiments.Bioinformatics2022
32963345A network approach to elucidate and prioritize microbial dark matter in microbial communities.ISME J2021
33747045STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline.Front Genet2021
34680315Global Methylome Scores Correlate with Histological Subtypes of Colorectal Carcinoma and Show Different Associations with Common Clinical and Molecular Features.Cancers (Basel)2021
33404927A multi-omic study for uncovering molecular mechanisms associated with hyperammonemia-induced cerebellar function impairment in rats.Cell Biol Toxicol2021
33479266Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients.Sci Rep2021
33478573Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes.Genome Biol2021
32423416tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.Genome Biol2020
33256589Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance.BMC Plant Biol2020
33271804Transcriptional Differences for COVID-19 Disease Map Genes between Males and Females Indicate a Different Basal Immunophenotype Relevant to the Disease.Genes (Basel)2020
33381847MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants.Bioinformatics2020
33381819Padhoc: a computational pipeline for pathway reconstruction on the fly.Bioinformatics2020
32555183Harmonization of quality metrics and power calculation in multi-omic studies.Nat Commun2020
32214166Assessment of unconventional antimicrobial compounds for the control of 'Candidatus Liberibacter asiaticus', the causative agent of citrus greening disease.Sci Rep2020
32109230A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6.Sci Data2020
32131696MultiBaC: A strategy to remove batch effects between different omic data types.Stat Methods Med Res2020
29040385A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies.Brief Bioinform2019
31672978Making multi-omics data accessible to researchers.Sci Data2019
31682608Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.PLoS Comput Biol2019
31680439Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs.EMBO Rep2019
31464424A Multiomics Study To Unravel the Effects of Developmental Exposure to Endosulfan in Rats: Molecular Explanation for Sex-Dependent Effects.ACS Chem Neurosci2019
30978178Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.PLoS Biol2019
31025430Differences in gene expression profiling and biomarkers between histological colorectal carcinoma subsets from the serrated pathway.Histopathology2019
30383328Changes in the uterine metabolome of the cow during the first 7 days after estrus.Mol Reprod Dev2019
29272325GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text.Bioinformatics2018
29913432Transcriptome analysis reveals novel insights into the response of low-dose benzo(a)pyrene exposure in male tilapia.Aquat Toxicol2018
30021829Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.G3 (Bethesda)2018
29967126Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.Genome Res2018
29988640Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia.Front Microbiol2018
29800320PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.Nucleic Acids Res2018
30097058Single-cell RNAseq for the study of isoforms-how is that possible?Genome Biol2018
30258954Gene expression profile and molecular pathway datasets resulting from benzo(a)pyrene exposure in the liver and testis of adult tilapia.Data Brief2018
29893833Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis.Genome Biol Evol2018
30588486Transcriptional profiling of the mutualistic bacterium <i>Vibrio fischeri</i> and an <i>hfq</i> mutant under modeled microgravity.NPJ Microgravity2018
30413173Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers.Clin Epigenetics2018
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Collaborators

Joaqu??n Dopazo
Andalusian Public Foundation Progress and Health-FPS
Co-authored papers 23
David Montaner
Co-authored papers 11
David Gomez-Cabrero
King Abdullah University of Science and Technology
Co-authored papers 10
Ali Mortazavi
Co-authored papers 9
Jesper Tegn??r
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 8
José Carbonell-Caballero
Co-authored papers 6
Ignacio Medina
Co-authored papers 5
Thomas Rattei
Co-authored papers 3
Patrick Concannon
Co-authored papers 3
Ivo Gut
Spain Universitat de Barcelona (UB)
Co-authored papers 3
Javier Santoyo
Co-authored papers 3
Christoph Bock
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 3
Gloria M Sheynkman (CM4AI)
University of Virginia
Co-authored papers 3
Val??rie de Cr??cy-Lagard
University of Florida
Co-authored papers 3
Niklas Blomberg
Universitat Tubingen, Institut fur Arbeitsmedizin
Co-authored papers 2
Charles Auffray
European Institute for Systems Biology and Medicine
Co-authored papers 2
Michael L Tress
Spanish National Cancer Research Centre (CNIO)
Co-authored papers 2
Pablo Villoslada
Hospital Clinic of Barcelona-Institut d'Investigacions
Co-authored papers 2
Imad Abugessaisa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Pedro Madrigal
Co-authored papers 2
Lennart Martens
Co-authored papers 2
Ioannis Tsamardinos
Co-authored papers 2
Thierry Sengstag
University of Basel
Co-authored papers 2
Kenneth Verheggen
Co-authored papers 2
Reinhard Schneider
Co-authored papers 2
Juan Antonio Vizca??no
EMBL-European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Konstantin Okonechnikov
Hopp Children's Cancer Center Heidelberg (KiTZ)
Co-authored papers 2
Antoine Danchin
University of Hong Kong
Co-authored papers 2
F??tima Al-Shahrour
Spanish National Cancer Research Centre (CNIO)
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Xuegong Zhang
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Release 1.2