José M. González
A5101741653- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Viral gastroenteritis research and epidemiology
- Olfactory and Sensory Function Studies
- Animal Virus Infections Studies
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Plant and Fungal Interactions Research
- Biochemical Analysis and Sensing Techniques
- Virus-based gene therapy research
- Crystallization and Solubility Studies
- Plant Virus Research Studies
- SARS-CoV-2 and COVID-19 Research
- Atomic and Subatomic Physics Research
- Advanced MRI Techniques and Applications
- X-ray Diffraction in Crystallography
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Neurobiology and Insect Physiology Research
- Poxvirus research and outbreaks
- Genomic variations and chromosomal abnormalities
Spanish National Cancer Research Centre
2025
European Bioinformatics Institute
2017-2024
European Molecular Biology Laboratory
2022
Wellcome Sanger Institute
2012-2019
Duke University
2011-2019
Universidad Nacional de Colombia
2014-2018
Centro Nacional de Biotecnología
2001-2017
Consejo Superior de Investigaciones Científicas
2000-2014
University of California, Santa Cruz
2013
University of Cambridge
2013
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical experimental approaches to investigate these genes been hampered by the lack comprehensive lncRNA annotation. Here, we present analyze most complete annotation date, produced GENCODE consortium within framework ENCODE project comprising 9277 manually annotated producing 14,880 transcripts. Our analyses...
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since first public release this annotation data set, few new protein-coding loci have been added, yet number alternative splicing transcripts annotated has steadily increased. 7 contains 20,687 9640 long noncoding RNA 33,977 coding not represented UCSC genes RefSeq. It also most comprehensive (lncRNA) publicly available...
The accurate identification and description of the genes in human mouse genomes is a fundamental requirement for high quality analysis data informing both genome biology clinical genomics. Over last 15 years, GENCODE consortium has been producing reference gene annotations to provide this foundational resource. includes experimental computational groups who work together improve extend annotation. Specifically, we generate primary data, create bioinformatics tools support expert manual...
Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed efficiently deliver annotation at scale all eukaryotic life, it also provides deep comprehensive key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the new assemblies. Here, report release greatest annual number newly annotated genomes history...
Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed comprehensive annotation of gene structures, regulatory elements variants, enable comparative genomics by inferring the evolutionary history genes genomes. Our integrated are made available in a variety ways, including genome browsers, search interfaces, specialist tools such as Variant Effect Predictor, download files programmatic interfaces....
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation comparative genomics across the vertebrate subphylum key model organisms. pipeline capable of integrating experimental reference data from multiple providers into single integrated resource. Here, we present 94 newly annotated re-annotated genomes, bringing total number genomes offered by to 227. This represents largest expansion resource since its...
Abstract The GENCODE project annotates human and mouse genes transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology clinical genomics. annotation processes make use of primary bioinformatic tools analysis generated both within the consortium externally to support creation transcript structures determination their function. Here, we present improvements our infrastructure, bioinformatics tools, analysis, advances they in...
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms more than twenty years. During that time, our resources, services tools have continually evolved in line with both the publicly available genome data downstream research applications utilise platform. In recent years we witnessed a dramatic shift landscape. There been large increase number of reference genomes through global biodiversity initiatives. parallel, there major...
GENCODE produces high quality gene and transcript annotation for the human mouse genomes. All is supported by experimental data serves as a reference genome biology clinical genomics. The consortium generates targeted data, develops bioinformatic tools carries out analyses that, along with externally produced methods, support identification of structures determination their function. Here, we present an update on genes, including developments in tools, major collaborations which underpin...
Abstract Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, absence a standard for clinical reporting and browser display complicates process consistent interpretation reporting. To address these challenges, Ensembl/GENCODE 1 RefSeq 2 launched joint initiative, Matched Annotation from NCBI EMBL-EBI (MANE) collaboration, converge on human gene transcript jointly define high-value set transcripts corresponding proteins. Here, we...
Abstract Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates model organisms more than two decades. In recent years, there been dramatic shift in the landscape, with large increase number phylogenetic breadth of reference genomes, alongside major advances pan-genome representations higher species. order to support these efforts accelerate downstream research, continues focus on scaling rapid...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, consortium generated over 427 million sequences from complementary DNA direct RNA datasets, encompassing human, mouse manatee species. Developers utilized these data address challenges in transcript isoform detection, quantification de novo detection. study revealed that...
Abstract Genetic variants linked to autism are thought change cognition and behaviour by altering the structure function of brain. Although a substantial body literature has identified structural brain differences in autism, it is unknown whether autism-associated common genetic changes cortical macro- micro-structure. We investigated this using neuroimaging data from adults (UK Biobank, N = 31,748) children (ABCD, 4928). Using polygenic scores correlations we observe robust negative...
The construction of cDNA clones encoding large-size RNA molecules biological interest, like coronavirus genomes, which are among the largest mature known to biology, has been hampered by instability those cDNAs in bacteria. Herein, we show that application two strategies, cloning into a bacterial artificial chromosome and nuclear expression RNAs typically produced within cytoplasm, is useful for engineering large molecules. A an infectious genome cloned as chromosome. rescued conserved all...
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by National Center for Biotechnology Information (NCBI) Ensembl annotation pipelines. Identical annotations pass quality assurance tests tracked with stable identifier (CCDS ID). Members collaboration, who from NCBI, Wellcome Trust Sanger Institute University...
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in annotations produced independently by NCBI Ensembl group at EMBL-EBI. This is product an international collaboration includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics University California, Santa Cruz. Identically coding regions, which generated using automated pipeline pass multiple...
A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation a wide range tools are available to this end. McCarthy et al recently demonstrated the large differences in prediction loss-of-function (LoF) when RefSeq Ensembl transcripts used for annotation, highlighting importance reference on which variant based. We describe detailed analysis similarities between gene...
Abstract Mobile medical imaging devices are invaluable for clinical diagnostic purposes both in and outside healthcare institutions. Among the various modalities, only a few readily portable. Magnetic resonance (MRI), gold standard numerous conditions, does not traditionally belong to this group. Recently, low-field MRI technology companies have demonstrated first decisive steps towards portability within facilities vehicles. However, these scanners’ weight dimensions incompatible with more...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. consortium generated over 427 million sequences from cDNA and direct RNA datasets, encompassing human, mouse, manatee species, using different protocols sequencing platforms. These data were utilized by developers address challenges in transcript isoform detection quantification, as well de novo identification....
Experimental conditions that simulate the crowded bacterial cytoplasmic environment have been used to study assembly of essential cell division protein FtsZ from Escherichia coli. In solutions containing a suitable concentration physiological osmolytes, macromolecular crowding promotes GTP-dependent into dynamic two-dimensional polymers disassemble upon GTP depletion. Atomic force microscopy reveals these adopt shape ribbons are one subunit thick. When compared with filaments observed in...
Bacterial translocation is currently considered the main pathogenic mechanism leading to spontaneous bacterial peritonitis in patients with advanced cirrhosis and ascites. However, authors' knowledge there no information regarding characteristics of this process humans. The goals current study were pursue partially identified DNA blood (what authors consider molecular evidence translocation) through its relative quantification a 72-hour period by using real-time polymerase chain reaction...
FtsZ, the prokaryotic homologue of tubulin, is an essential cell division protein. In cell, it localizes at center, forming a ring that constricts during division. vitro, binds and hydrolyzes GTP polymerizes in GTP-dependent manner. We have used atomic force microscopy to study structure dynamics FtsZ polymer assembly on mica surface under buffer solution. The polymers were highly dynamic flexible, they continuously rearranged over surface. End-to-end joining filaments depolymerization from...