Marie‐Marthe Suner
A5088192191- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Neurobiology and Insect Physiology Research
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Insect Resistance and Genetics
- Genomics and Rare Diseases
- Plant Molecular Biology Research
- Plant Reproductive Biology
- CRISPR and Genetic Engineering
- Genetics, Bioinformatics, and Biomedical Research
- Insect Utilization and Effects
- Viral Infectious Diseases and Gene Expression in Insects
- Insect and Pesticide Research
- RNA Research and Splicing
- Genetics, Aging, and Longevity in Model Organisms
- Chemokine receptors and signaling
- Traumatic Brain Injury and Neurovascular Disturbances
- Insect and Arachnid Ecology and Behavior
- Mast cells and histamine
- Bioinformatics and Genomic Networks
- Animal Genetics and Reproduction
European Bioinformatics Institute
2017-2024
Wellcome Sanger Institute
2008-2019
Cornell University
2017
Burke Medical Research Institute
2017
Blythedale Children's Hospital
2017
University of California, Santa Cruz
2012-2013
Syngenta (Switzerland)
2004
Syngenta (United Kingdom)
2001
AstraZeneca (United Kingdom)
2000
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...
Defective Gene Detective Identifying genes that give rise to diseases is one of the major goals sequencing human genomes. However, putative loss-of-function genes, which are often some first identified targets genome and exome sequencing, have turned out be errors rather than true genetic variants. In order identify scope within genome, MacArthur et al. (p. 823 ; see Perspective by Quintana-Murci ) extensively validated genomes from 1000 Genomes Project, as well an additional European...
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...
Effective use of the human and mouse genomes requires reliable identification genes their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation genes, transcripts, proteins. The collaborative consensus coding sequence (CCDS) project tracks protein annotations on reference with a stable identifier (CCDS ID), ensures they consistently represented NCBI, Ensembl, UCSC Genome Browsers. Importantly,...
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 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...
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...
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....
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies methodologies allow us to catalog genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables identify large numbers of missing transcripts substantially improve existing models, our long non-coding RNA catalogs have undergone a dramatic expansion reconfiguration result. Meanwhile, we are...
Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen continued expansion in number represented, >4800 >31 300 prokaryotic genomes available. The new site, currently beta, develop, holding >2700 genome assemblies. site provides genome, gene, transcript, homology variation views, will replace current Rapid Release site; this...
The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing conservative set high quality, protein-coding region annotations for the human and mouse reference genome assemblies. CCDS data reflects 'gold standard' definition best supported protein annotations, corresponding genes, which pass standard series quality assurance checks are by manual curation. This supports use annotation information researchers effective experimental design,...
Abstract Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference human mouse genomes, becoming a foundation biomedical genomics communities worldwide. Nevertheless, collections of important yet poorly-understood classes like long non-coding RNAs (lncRNAs) remain incomplete scattered across multiple, uncoordinated catalogs, slowing down progress in field. To...
Abstract The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60–65% patients without molecular diagnosis. Here, we explore incompleteness transcript models used for exome genome analysis as one potential explanation lack current diagnoses. Therefore, have updated GENCODE gene annotation 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries other data...
Abstract The LCR/MEL system (Locus Control Region/Murine Erythroleukaemia cells) was employed to express and characterize the Locusta migratoria tyramine receptor (Tyr Loc ), an insect G protein‐coupled receptor. Functional agonist‐dependent responses were recorded in stable, expressing cell clones (MEL‐Tyr ). Tyramine elicited a dose‐dependent increase of cytosolic Ca 2+ ‐ions attenuation forskolin‐induced cyclic adenosine monophosphate (AMP) production. Octopamine shown be weak agonist for...
Summary Differential screening of two libraries made from whole, immature maize tassels was used to isolate six cDNAs which show enhanced levels expression in male flowers. MFS1, MFS2, MFS4, MFS10 and MFS18 , were isolated a 5 cm tassel library, are expressed throughout growth up until mature pollen is produced the anthers. MFS14 10–12 has narrower window associated with microsporogenesis declines as produced. mRNA accumulates glumes anther walls, paleas lemmas florets. particularly vascular...
Abstract Inducible, vector‐based, expression systems that allow fine control of transgene are gaining more and use in fundamental research as well therapeutic applications. In an effort to develop a tightly regulated heterologous system for Drosophila Schneider 2 cells, three different inducible reporter constructs were compared. These comprised six copies the glucocorticoid response element fused one distinct types gene promoters: (1) TATA‐box containing, (2) TATA‐less (3) bidirectional...
The HAVANA group from the Wellcome Trust Sanger Institute is responsible for manual annotation of coding, transcript and pseudogene loci on human, mouse zebrafish finished genomic sequence.The total number protein coding genes extent alternative splicing human genome still unclear.In collaboration with Ensembl, RefSeq at NCBI UCSC, CCDS project (Consensus CoDing Sequence) working to define a core set transcripts.Initially limited was recently extended include mouse.Any candidate transcripts...