Valérie Schneider
A5048156988- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Genomic variations and chromosomal abnormalities
- Molecular Biology Techniques and Applications
- Traumatic Ocular and Foreign Body Injuries
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Genomics and Rare Diseases
- Restraint-Related Deaths
- Genetic Associations and Epidemiology
- Poisoning and overdose treatments
- Genomics and Chromatin Dynamics
- Axon Guidance and Neuronal Signaling
- Zebrafish Biomedical Research Applications
- Genetic Mapping and Diversity in Plants and Animals
- Nerve injury and regeneration
- Autopsy Techniques and Outcomes
- CRISPR and Genetic Engineering
- HIV Research and Treatment
- Developmental Biology and Gene Regulation
- Cancer Genomics and Diagnostics
- Metabolism and Genetic Disorders
- Trauma Management and Diagnosis
- Epigenetics and DNA Methylation
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
Gender Studies
2023
Goethe University Frankfurt
2023
University of Passau
2023
Rosa Luxemburg Foundation
2023
United States National Library of Medicine
2022
Foundation for the National Institutes of Health
2022
NTL Institute for Applied Behavioral Science
2017
Charité - Universitätsmedizin Berlin
2004-2016
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published life science journals. Entrez system search retrieval operations most these data from 39 distinct databases. E-utilities serve as programming interface system. Augmenting many Web applications are custom implementations BLAST program optimized to specialized sets. New...
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing update since 2009; it reflects resolution roughly 1000 issues encompasses modifications ranging from thousands single base changes to megabase-scale path reorganizations, gap closures, localization previously orphaned sequences. We developed new approach sequence generation for targeted updates used data mapping technologies haplotype...
Abstract ClinVar is a freely available, public archive of human genetic variants and interpretations their relationships to diseases other conditions, maintained at the National Institutes Health (NIH). Submitted are aggregated made available on website (https://www.ncbi.nlm.nih.gov/clinvar/), as downloadable files via FTP through programmatic tools such NCBI’s E-utilities. The default view website, Variation page, was recently redesigned. new layout includes several sections that make it...
After two decades of improvements, the current human reference genome (GRCh38) is most accurate and complete vertebrate ever produced. However, no single chromosome has been finished end to end, hundreds unresolved gaps persist1,2. Here we present a assembly that surpasses continuity GRCh382, along with gapless, telomere-to-telomere chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing hydatidiform mole CHM13 genome, combined complementary technologies for...
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
I have read the journal's policy and following conflicts: Paul Flicek is married to deputy editor of PLoS Medicine, Melissa Norton. Evan Eichler on board Pacific Biosciences. Support for this work came from Intramural Research Program NIH, The National Library European Molecular Biology Laboratory, Wellcome Trust (grant number 077198), Howard Hughes Medical Institute (EEE). funders had no role in study design, data collection analysis, decision publish or preparation manuscript.
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 38 distinct databases. E-utilities serve as programming interface system. Augmenting many web applications are custom implementations BLAST program optimized to specialized sets. New...
Heart induction in Xenopus occurs paired regions of the dorsoanterior mesoderm response to signals from Spemann organizer and underlying endoderm. These tissues together are sufficient induce heart formation noncardiogenic ventral marginal zone mesoderm. Similarly, avians definitive endoderm induces cardiogenesis precardiac Heart-inducing factors amphibians not known, although certain BMPs FGFs can mimic aspects avians, neither full range activities elicited by inducing tissues. Here we...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface system. Custom implementations BLAST program provide sequence-based searching many specialized datasets. New released...
A spotlight on great ape genomes Most nonhuman primate generated to date have been “humanized” owing their many gaps and the reliance guidance by reference human genome. To remove this humanizing effect, Kronenberg et al. assembled long-read of a chimpanzee, an orangutan, two humans compared them with previously gorilla This analysis recognized genomic structural variation specific particular lineages. Comparisons between chimpanzee cerebral organoids showed down-regulation expression genes...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface New include Comparative Genome Resource (CGR) BLAST ClusteredNR database. Resources receiving significant updates past year PubMed, PMC, Bookshelf,...
Abstract Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese HX1 by single-molecule real-time (SMRT) long-read sequencing, construct physical map NanoChannel arrays and generate 2.93 Gb (contig N50: 8.3 Mb, scaffold 22.0 including 39.3 Mb N-bases), together 206 alternative haplotypes. The fully or partially fills 274 (28.4%) N-gaps reference genome GRCh38....
Abstract The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits continuation sequence assembly improvement efforts. We present new version chicken genome (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, improved physical maps. In overall assembled bases, we see gain 183 Mb, including 16.4 Mb in placed chromosomes with corresponding percentage intact repeat elements characterized. Of...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
The National Center for Biotechnology Information (NCBI) is an archive providing free access to a wide range and large volume of biological sequence data literature. Staff scientists at NCBI analyze user-submitted in the archive, producing gene SNP annotation generating alignment tools. NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation; integrated with other resources such as Gene, dbGaP, BLAST; provides platform customized analysis...
Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still many gaps and errors, does not represent biological genome as is blend multiple individuals 3,4 Recently, telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but derived from hydatidiform mole cell line nearly homozygous 5 To address these limitations, Human Pangenome...
Abstract The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface Resources receiving significant updates past year include PubMed, PMC, Bookshelf, SciENcv, NIH Comparative Genomics Resource (CGR), Virus,...
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant in new genomes. FCS-GX screens most genomes 0.1-10 min. Testing on artificially fragmented demonstrates high sensitivity specificity for diverse species. We used screen 1.6 million GenBank assemblies identified 36.8 Gbp contamination, comprising 0.16% total bases, with half from 161...
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant in new genomes. FCS-GX screens most genomes 0.1-10 minutes. Testing on artificially fragmented demonstrates sensitivity >95% for diverse species specificity >99.93%. We used screen 1.6 million GenBank assemblies identified 36.8 Gbp contamination (0.16% total bases), with half from 161...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence repository and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 31 distinct repositories knowledgebases. E-utilities serve as programming interface these. Resources receiving significant updates past year include PubMed, PubMed Central, Bookshelf, NIH Comparative Genomics...