A5091471463- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Geophysics and Gravity Measurements
- Earthquake Detection and Analysis
- Methane Hydrates and Related Phenomena
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Scientific Measurement and Uncertainty Evaluation
- Biomedical Text Mining and Ontologies
- CRISPR and Genetic Engineering
- Genetics, Bioinformatics, and Biomedical Research
- Analytical chemistry methods development
- Viral Infections and Immunology Research
- Genetic Associations and Epidemiology
- RNA Research and Splicing
- Analytical Chemistry and Sensors
- Natural Language Processing Techniques
- Semiconductor materials and devices
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Genetic factors in colorectal cancer
- Biosensors and Analytical Detection
Mitre (United States)
2022-2024
Stanford University
2014-2023
SLAC National Accelerator Laboratory
2018-2023
National Institute of Standards and Technology
2011-2022
Stanford Synchrotron Radiation Lightsource
2021
Material Measurement Laboratory
2015-2020
National Institute of Standards
2006-2019
Stanford Medicine
2019
Mayo Clinic in Florida
2018
SeraCare Life Sciences (United States)
2018
High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance different protocols platforms remain. We used newly developed pool 96 synthetic RNAs with various lengths, GC content covering 2 20 concentration range as spike-in controls to measure sensitivity, accuracy, biases in RNA-seq experiments well derive standard curves for quantifying abundance transcripts. observed linearity between read density...
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding organism-specific data of nucleic acid targets in the environment. Such are essential for characterizing interactions processes microbial communities, assessing contaminants environment (water, air, fomites), developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review...
Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the 'start codons' for initiation in Escherichia coli. Translation is typically not thought initiate from 61 remaining codons. Here, we quantified green fluorescent protein nanoluciferase E. coli all 64 triplet codons across range DNA copy number. We detected synthesis above measurement background 47 non-canonical ranged...
Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling methods. Here we use accurate linked long reads expand 7 samples include difficult-to-map regions segmental duplications that challenging for short reads. These add more than 300,000 SNVs 50,000 insertions or deletions (indels) 16% exonic variants, many challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, 92% of the autosomal GRCh38...
Abstract Translation regulation is critical for early mammalian embryonic development 1 . However, previous studies had been restricted to bulk measurements 2 , precluding precise determination of translation including allele-specific analyses. Here, address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized in single oocytes embryos during mouse development. We identified differential efficiency...
As whole exome sequencing (WES) and genome (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for methods analysis pipelines be technically accurate. The Genome in a Bottle Consortium has recently published set of benchmark SNV, indel, homozygous reference genotypes the pilot NIST Reference Material based on NA12878 genome. We examine relationship between human complexity genes/variants reported associated with disease. Specifically, we map regions...
The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural (SVs). High-quality benchmark variant calls for the pilot National Institute of Standards and Technology (NIST) Reference Material (NA12878) have been developed by Genome a Bottle Consortium, but no similar high-quality SV exist this genome. Since callers output highly discordant results, we methods combine multiple forms evidence sequencing technologies classify candidate...
Abstract Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long and linked now enable us construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - Major Histocompatibility Complex (MHC). Here, we develop genome benchmark derived from for openly-consented Genome in Bottle sample HG002. assemble single contig each...