Craig Pohl
A5009369753- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Gut microbiota and health
- Genomics and Chromatin Dynamics
- Genomics and Rare Diseases
- Acute Myeloid Leukemia Research
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Bat Biology and Ecology Studies
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Probiotics and Fermented Foods
- Diet and metabolism studies
- Genetics, Bioinformatics, and Biomedical Research
- Wildlife Ecology and Conservation
- FOXO transcription factor regulation
- Livestock and Poultry Management
- HIV Research and Treatment
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Evolution and Paleontology Studies
- Urinary Tract Infections Management
Washington University in St. Louis
2003-2023
University of Groningen
2016
University of Houston
2011
New York Genome Center
2008-2010
University of Washington
2007
Baylor College of Medicine
2007
Texas Biomedical Research Institute
2007
The full complement of DNA mutations that are responsible for the pathogenesis acute myeloid leukemia (AML) is not yet known.We used massively parallel sequencing to obtain a very high level coverage (approximately 98%) primary, cytogenetically normal, de novo genome AML with minimal maturation (AML-M1) and matched normal skin genome.We identified 12 acquired (somatic) within coding sequences genes 52 somatic point in conserved or regulatory portions genome. All appeared be heterozygous...
Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little past two decades, because most genetic events initiate remain undiscovered. Whole-genome sequencing now possible at reasonable cost and timeframe to use approach for unbiased discovery tumour-specific somatic mutations alter protein-coding genes. Here we present results obtained from typical acute genome, its...
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, monkeys most widely used nonhuman in basic applied biomedical research. We determined genome sequence Indian-origin Macaca mulatta female compared data with chimpanzees humans reveal structure ancestral genomes identify evidence for positive selection lineage-specific expansions...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits fascinating combination reptilian and mammalian characters. For example, platypuses have coat fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; males are equipped with venom similar that reptiles. Analysis first aligned these features genetic innovations. find reptile proteins been co-opted independently from same gene families; milk protein genes conserved despite...
News from the Inner Tube of Life A major initiative by U.S. National Institutes Health to sequence 900 genomes microorganisms that live on surfaces and orifices human body has established standardized protocols methods for such large-scale reference sequencing. By combining previously accumulated data with new data, Nelson et al. (p. 994 ) present an initial analysis 178 bacterial genomes. The sampling so far barely scratches surface microbial diversity found humans, but work provides...
The genome of the Southeast Asian great ape or orang-utan has been sequenced — specifically a draft assembly Sumatran female individual and short-read sequence data from five further Bornean orang-utan, Pongo abelii pygmaeus, respectively. Orang-utan species appear to have split around 400,000 years ago, more recent than most previous estimates suggested, resulting in an average Bornean–Sumatran nucleotide identity 99.68%. Structural evolution seems proceeded much slowly that other apes,...
CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we developed powerful tools marker-based and marker-free modifications Penicillium chrysogenum, model filamentous fungus industrially relevant cell factory. The toolbox is highly flexible allows new targets with minimal cloning efforts. Cas9 protein the sgRNA can be either delivered during transformation, preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed...
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome pipelines at a massive scale. The GMS framework provides detailed tracking samples and data coupled with reliable repeatable pipelines. also serves as platform for bioinformatics development, allowing large team to collaborate on analysis, or individual researcher leverage work others effectively within its system. Rather than separating ad-hoc from...
Detection of de novo variants (DNVs) is critical for studies disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Foundation Powering Autism Research (SPARK), 1000 Genomes Project (1000G) that were using DNA blood, saliva, lymphoblastoid cell lines (LCLs), respectively. The...
Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased rates at which they can generate data. In many environments, themselves also evolve a rapid fluid manner. These observations point importance of robust information management systems modern laboratory. Designing implementing such is non-trivial it appears that cases database project ultimately proves unserviceable. We describe general modeling framework for data its...
ABSTRACT Detection of de novo variants (DNVs) is critical for studies disease-related variation and mutation rates. We developed a GPU-based workflow to rapidly call DNVs (HAT) demonstrated its effectiveness by applying it 4,216 Simons Simplex Collection (SSC) whole-genome sequenced parent-child trios from DNA derived blood. In our SSC DNV data, we identified 78 ± 15 per individual, 18% 5% at CpG sites, 75% 9% phased the paternal chromosome origin, an average allele balance 0.49. These...
Rather than wait for the instrument manufacturer to provide 96-lane-per-gel capability, authors decided further develop a modification proposed by Clark Tibbetts in 1997, which entailed providing external control of CCD camera and collecting data with acquisition (Daq) card installed separate Windows 95 operated machine. Ideally, this combination could be used select any desired per-scan pixel density corresponding lane on gel. In practice, aimed increase model 377 gels 96, since number...
High-performance Computing (HPC) has been around for decades but maintaining software HPC with heterogeneous compute nodes remains a challenging task system administrators. Many package frameworks have developed over the years to ease installation tasks, example, EasyBuild [1], Spack [2], and GNU Guix [3]. Advances in virtualization technology, such as hypervisor container, dramatically changed computing world. Incorporating container technology into its own challenges, not mention adding on...