A5005001979- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Plant Molecular Biology Research
- Renal and related cancers
- Genomics and Chromatin Dynamics
- Plant Disease Resistance and Genetics
- Plant nutrient uptake and metabolism
- Toxin Mechanisms and Immunotoxins
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- Genetic Mapping and Diversity in Plants and Animals
- CRISPR and Genetic Engineering
- SARS-CoV-2 and COVID-19 Research
- Antibiotic Resistance in Bacteria
- Developmental Biology and Gene Regulation
- Reproductive Biology and Fertility
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Plant Reproductive Biology
- Pluripotent Stem Cells Research
- Bioenergy crop production and management
- Wheat and Barley Genetics and Pathology
- Plant pathogens and resistance mechanisms
- Genetics and Neurodevelopmental Disorders
Translational Genomics Research Institute
2020-2024
City Of Hope National Medical Center
2022-2024
City of Hope
2022-2024
J. Craig Venter Institute
2013-2023
Children's Hospital at Westmead
1999-2012
Cold Spring Harbor Laboratory
2009
University of Wyoming
2009
The University of Texas MD Anderson Cancer Center
1998-2007
Center for Genomic Science
2007
Orion Genomics (United States)
2003
As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of variations and narrow down search casual variants for disease phenotypes. Different classes at nucleotide level involved in human diseases, including substitutions, insertions, deletions, frameshifts, non-sense mutations. Frameshifts mutations likely cause a negative effect protein function....
Abstract Summary: We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using prediction tool PROVEAN. The provides rapid analysis protein variants from any organisms, also supports high-throughput for human mouse at both genomic levels. Availability implementation: is freely available open all users with no login requirements http://provean.jcvi.org. Contact: achan@jcvi.org Supplementary information: data are...
Summary The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of biology. A comprehensive annotation its genome paves the way understanding functions and activities all types transcripts, including mRNA , various classes non‐coding RNA small . TAIR 10 update had profound impact on but was released more than 5 years ago. Maintaining accuracy continues to be prerequisite future progress. Using an integrative pipeline, we assembled tissue‐specific ‐Seq...
Castor beans are best known as a source of industrial lubricants and the toxic bioterror threat, ricin, they have potential to provide biofuel. Chan et al. present draft sequence Ricinus communis genome, first for member Euphorbiaceae. bean (Ricinus communis) is an oilseed crop that belongs spurge (Euphorbiaceae) family, which comprises ∼6,300 species include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) physic nut (Jatropha curcas). It primarily economic interest castor oil,...
Medicago truncatula, a close relative of alfalfa, is preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The sequencing project began in 2003 with the goal to decipher sequences originated from euchromatic portion genome. initial approach was based on BAC tiling path, culminating BAC-based assembly (Mt3.5) as well an in-depth analysis genome published 2011. Here we describe further improved refined version M. truncatula (Mt4.0) de novo whole shotgun majority...
Abstract Sugarcane ( Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, interspecific genome poses challenges producing reference sequence. We exploited colinearity with sorghum to produce BAC-based monoploid sequence of sugarcane. A minimum tiling path 4660 sugarcane BAC that best covers the gene-rich part was selected based on whole-genome profiling, sequenced, assembled in 382-Mb single high-quality total 25,316...
Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard sequencing strategies are not readily adaptable to this type genome. Methodologies that enrich for genic might more rapidly generate useful results from complex genomes. Equivalent numbers clones selected by techniques called methylation filtering High C0t selection were sequenced approximately 200,000 reads (approximately 132 megabases), which...
The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide for construction of transcript assemblies. include sequence tags (ESTs) and full-length partial cDNAs, but exclude computationally predicted gene sequences. TA includes all plant species which more than 1000 EST or cDNA are publicly available. first clustered based on an all-versus-all pairwise comparison, followed by generation consensus (TAs)...
Humans are a diploid species that inherit one set of chromosomes paternally and homologous maternally. Unfortunately, most human sequencing initiatives ignore this fact in they do not directly delineate the nucleotide content maternal paternal copies 23 individuals possess (i.e., 'phase' genome) often because costs complexities doing so. We compared 11 different widely-used approaches to phasing genomes using publicly available 'Genome-In-A-Bottle' (GIAB) phased version NA12878 genome as...
Abstract Background Castor bean ( Ricinus communis ) is an agricultural crop and garden ornamental that widely cultivated has been introduced worldwide. Understanding population structure the distribution of castor cultivars challenging because limited genetic variability. We analyzed genetics R. in a worldwide collection plants from germplasm naturalized populations Florida, U.S. To assess diversity we conducted survey sequencing genomes seven diverse compared data to reference genome...
Abstract Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. pan-genomic studies used modest sample sizes of low diversity comparisons to a single reference genome, limiting our understanding gene order content. A consensus representation multiple genomes will provide better framework for comparison. large-scale comparative study identify genomic determinants associated with their adaptation as successful pathogen....
Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread drug-resistant bacterial pathogens causing a global crisis. To facilitate drug processes, we present large-scale study reference challenge transcriptome profiles, which included 37 antibiotics across 6 mechanisms actions (MOAs) and provide economical approach to aid in antimicrobial dereplication process. We demonstrate that classical MOAs can...
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative...
Abstract Background Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, annotation was submitted by multiple centers using inconsistent methods, making data difficult to use many applications. Results Over course three years, TIGR completed effort standardize structural and functional genome. Using both manual automated gene structures were refined products renamed assigned Gene...
The Arabidopsis Genome Sequencing Project was officially completed in late 2000, leading to the publication of a landmark paper describing, broad outline, many salient features genome (Arabidopsis Initiative [AGI], 2000).However, annotation, generated by individual sequencing centers, heterogeneous, both terms gene structure predictions and terminology used their description.In response, Institute for Genomic Research (TIGR) funded National Science Foundation carry out whole-genome...
Maize ( Zea mays or corn), both a major food source and an important cytogenetic model, evolved from tetraploid that arose about 4.8 million years ago (Mya). As result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb sequence spanning 17.4 cM short arm chromosome 1 6.6 (25.6 cM) long 9. Rice, which did not undergo similar whole genome duplication event, only orthologous region (4.9 Mb) on 3, can be used as...
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of unusual fatty acid ricinoleate, which has many industrial and medical applications. seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, gained relevance recent years due biosafety concerns. In order gain knowledge on global genetic diversity castor ultimately help development breeding forensic tools, we carried out extensive chloroplast sequence...
Genomic resources have significantly impacted plant biology research in recent years.Cell has been further enabled by an ongoing revolution visualization technologies.Using fluorescent proteins (FPs), we now unprecedented views of cellular architecture, and can study real-time dynamics cell structure, function, protein localization.To date, these technologies most widely used Arabidopsis (Arabidopsis thaliana); however, the grasses provide a unique opportunity to underlying mechanisms...
The CoV disease 2019 (COVID-19) infectious outbreak is having a dramatic global effect on public health and the economy. As of October 2020, SARS-CoV-2 has been detected in over 189 countries, infected 40 million people, responsible for more than 1 deaths.
dinucleotide repeat sequence –2.1 kbupstream of the transcription start site thealdose reductase gene has been found to bestrongly associated with human diabeticnephropathy and retinopathy (1,2) linked increasedexpression aldose (3). The current pro-ject was designed detect potential variants in putativepromoter encoding regions determine their poten-tial association early diabetic adoles-cents type 1 diabetes. A novel polymorphism pro-moter region identifie d ,which located at C(–106)T....
Summary Improvements in next‐generation sequencing technologies have resulted dramatically reduced costs. This has led to an explosion of ‘‐seq’‐based methods, which RNA ( ‐seq) for generating transcriptomic data is the most popular. By analysing global patterns gene expression organs/tissues/cells interest or response chemical environmental perturbations, researchers can better understand organism's biology. Tools designed work with large ‐seq sets enable analyses and visualizations help...