David Weisz
A5039103742- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- RNA Research and Splicing
- Plant and animal studies
- Molecular Biology Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Genetic Mapping and Diversity in Plants and Animals
- RNA and protein synthesis mechanisms
- Academic Publishing and Open Access
- Environmental DNA in Biodiversity Studies
- Animal Behavior and Reproduction
- Marine Sponges and Natural Products
- Cancer-related molecular mechanisms research
- SARS-CoV-2 and COVID-19 Research
- Advanced Proteomics Techniques and Applications
- Insect symbiosis and bacterial influences
- Plant Pathogens and Resistance
- Marine Biology and Environmental Chemistry
- Berry genetics and cultivation research
- Insect and Arachnid Ecology and Behavior
- Biomedical Text Mining and Ontologies
- Plant Disease Resistance and Genetics
- SARS-CoV-2 detection and testing
Baylor College of Medicine
2019-2025
Baylor Genetics
2024
Center for Theoretical Biological Physics
2020-2023
Rice University
2020-2023
Baylor University
2019
Icahn School of Medicine at Mount Sinai
2004
We investigated genome folding across the eukaryotic tree of life. find two types three-dimensional (3D) architectures at chromosome scale. Each type appears and disappears repeatedly during evolution. The architecture that an organism exhibits correlates with absence condensin II subunits. Moreover, depletion converts human to a state resembling seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together nucleoli, heterochromatin domains merge. propose...
Abstract The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create comprehensive catalog functional in the human genome. current database comprises more than 19000 genomics experiments across 1000 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape Homo sapiens Mus musculus genomes. All data, metadata, associated computational analyses created by ENCODE consortium are submitted Data...
Abstract Vertebrate genomes are partitioned into contact domains defined by enhanced internal frequency and formed two principal mechanisms: compartmentalization of transcriptionally active inactive domains, stalling chromosomal loop-extruding cohesin CTCF bound at domain boundaries. While Drosophila has widespread CTCF, it is currently unclear whether CTCF-dependent exist in flies. We genetically ablate examine impacts on genome folding transcriptional regulation the central nervous system....
Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms basis a valuable commercial fishery and plays key role coastal ecosystems food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which has evolved some immunity. molecular origins this immunity are interest evolutionary biologists, pharmaceutical companies, fisheries management. Findings Here we report genome assembly species,...
Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows virus most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this amplifies entirety genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only few loci. To achieve goal, combine enrichment developed by ARTIC...
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create comprehensive catalog functional in the human genome. current database comprises more than 19000 genomics experiments across 1000 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin a female woolly mammoth (†Mammuthus primigenius) died 52,000 years ago retained its architecture. We use PaleoHi-C map chromatin contacts assemble genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, inactive X chromosome (Xi) superdomains persist. The active...
Early-onset dystonia is an autosomal dominant movement disorder associated with deletion of a glutamic acid residue in torsinA. We generated four independent lines transgenic mice by overexpressing human ΔE-torsinA using neuron specific enolase promoter. The developed abnormal involuntary movements dystonic-appearing, self-clasping limbs, as early 3 weeks after birth. Animals also showed hyperkinesia and rapid bi-directional circling. Approximately 40% from each line demonstrated these...
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters their target genes. However, genome-wide depletions architectural proteins such as cohesin result in only limited changes expression, despite a loss contact domains and loops. Consequently, role contacts enhancer function remains debated. Here, we developed CRISPRi regulatory elements upon degron operation (CRUDO), novel approach measure how frequency impact effects on genes by...
Abstract Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows virus most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this amplifies entirety genome. This contrasts typical RT-PCR-based diagnostic tests, which amplify only few loci. To achieve goal, combine enrichment developed...
The structure of the genome shapes distribution genetic diversity and sequence divergence. To investigate how relationship between chromosome size recombination rate affects divergence species, we combined empirical analyses evolutionary simulations. We estimated pairwise among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, great apes—from chromosome-level assemblies. found a strong significant negative correlation in all comparisons within Peromyscus apes...
Abstract The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal chromosome painting experiments were valuable studying evolution of carnivoran genome architecture. research revealed that set similar to presumed ancestral karyotype Carnivora, which added additional value species. Using linked-read Hi-C sequencing, we generated chromosome-length assembly male (Gansu...
Advances in the sequencing and assembly of chromosome-level genome assemblies has enabled study non-model animals, providing further insights into evolution genomes chromosomes. Here, we present waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics chromosome evolution. Antelope evolutionary history been shaped by Robertsonian (Rb) fusions, with also showing variation karyotype due to two polymorphic Rb fusions. These polymorphisms are variable...
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions genome that are susceptible ("hot") and resistant ("cold") SHM, revealing susceptibility resistance often properties entire topologically associated domains (TADs). Comparison hot cold TADs reveals while levels transcription equivalent, enriched for cohesin loader NIPBL, super-enhancers, markers...
Abstract Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population subject of genetic rescue. understand, monitor, and modulate effects rescue on genome, chromosome-length genome high-density linkage map are required. Results We used combination Illumina, Oxford Nanopore, Hi-C sequencing technologies assemble honeyeater, comprising 906 scaffolds, with length 1.1 Gb scaffold N50...
Abstract We present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, separated most closely related Odonata with reference 150 ago. Using PacBio HiFi reads Hi-C data for scaffolding we produce one high-quality genomes to date. A scaffold N50 206.6 Mb single copy BUSCO score 96.2% indicate high contiguity completeness.
The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and Russian Far East. Chronic clonorchiasis cholangitis can induce a malignant cancer, called cholangiocarcinoma, biliary system. Control endemic is challenging, often relies largely on chemotherapy with one anthelmintic, praziquantel. Routine treatment carries significant risk inducing resistance to this anthelmintic such that discovery new...
Dramatic change in chromosomal DNA morphology between interphase and mitosis is a defining features of the eukaryotic cell cycle. Two types enzymes, namely cohesin condensin confer topology by extruding loops. While normally configures chromosomes exclusively during mitosis, does so interphase. The processivity cohesin’s loop extrusion limited regulatory factor called WAPL, which induces to dissociate from via mechanism that requires dissociation its kleisin neck SMC3. We show here related...
Abstract Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red idaeus), R. chingii, but very few genomic resources exist blackberries their relatives Rubus. Here we present a chromosome-length assembly annotation of diploid blackberry germplasm accession “Hillquist” argutus). is only known source...
Abstract We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have significant ecological impact, serving as food source for many mammals, reptiles, birds. are well known their massive emergences 1 to 3 species that appear in different locations eastern United States nearly every year. These year classes (“broods”) emerge dependably 13 or 17 yr given location. Recently, it has...
ABSTRACT Balanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome contribute substantial risk for developmental disorders (DDs). However, rarity lack systematic screening BCRs in population has precluded unbiased analyses genomic features mechanisms associated with DDs versus normal outcomes. Here, we sequenced analyzed 1,420 BCR breakpoints across 710 individuals, 406 DD cases first large-scale collection 304...
Abstract High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic demographic parameters relevant to the conservation biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations southern California, is a promising model studying how history shapes diversity, diversity turn may influence extinction risk. To facilitate these studies PPM, we combined PacBio HiFi long...
Abstract The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits intensive management, research, and collaboration save a species through ex situ conservation breeding reintroduction into its former range. However, remains at risk due possible inbreeding, disease susceptibility, multiple fertility challenges. Here, we report de novo genome assembly male generated combination linked-read sequencing, optical mapping, Hi-C proximity...
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates rays) hold a key phylogenetic position to explore the origin diversifications of jawed vertebrates. Here, we report integrate reference genomic, transcriptomic morphological data in small-spotted catshark