• Chengcang Charles Wu is a Chinese-born American scientist with expertise in the fields of genetics, bioinformatics, and genomics, particularly large fragment DNA cloning and BAC (Bacterial Artificial Chromosome) library technologies. (wikipedia.org)
  • Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
  • The database was originally used to support gene function analyses and oligonucleotide design, but has since grown to handle additional activities including microarray content design, SNP identification, genotyping platform design, comparative genomics, and the coupling of physical and genetic maps. (genomeweb.com)
  • The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. (biomedcentral.com)
  • In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. (biomedcentral.com)
  • Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. (tamu.edu)
  • Development of comparative physical gene maps for cattle, sheep, goat and deer by fluorescence in situ hybridisation (FISH) using ovine bacterial artificial chromosome (BAC) clones. (edu.au)
  • To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. (elsevierpure.com)
  • The sequence was used to map 110 ESTs and to predict new genes, including two GenScan gene predictions that overlapped ESTs and were shown to be differentially expressed in tumorigenic and suppressed A549 cell lines. (elsevierpure.com)
  • BAC libraries are essential elements in doing large-scale genome research such as screening for genes of target, biosynthetic gene cluster cloning, transgene identification, gene/gene cluster functional analyses, physical mapping and genome sequencing. (biost.com)
  • Bacterial artificial chromosome (BAC) cloning technology was developed in the early 1990s and quickly gained popularity among scientists whose requirement included developing a thorough understanding of gene network topology based effects, with particular emphasis on gene dosage and gene cassette orientation. (biost.com)
  • Because the STC resource permits the easy integration of genetic, physical, gene, and sequence maps for chromosomes, it will be a powerful tool for the initial analysis of the human genome and other complex genomes. (jcvi.org)
  • The database includes not only the research published by Close and his team, but the rest of the available mapping and gene data. (genomeweb.com)
  • lyrata (Lyre-leaved rock-cress) hypothetical protein (at5g25770) , arath-C7A10.830 Arabidopsis thaliana DNA chromosome 4,gene C7A10.830 No. 2 AT4G36530 , arath-F1N18.12 Arabidopsis thaliana (Mouse-ear cress) f1n18.12 AT1G29840 protein , arath-F1P2.110 Arabidopsis thaliana (Mouse-ear cress). (inrae.fr)
  • An allele frequency-dependent methodology for mapping and characterising a newly discovered major gene for self-compatibility in perennial ryegrass (Lolium perenne L. (aber.ac.uk)
  • Deletion mapping demonstrated single copy loss of a contiguous 1p36 terminal region encompassing many important neurodevelopmental genes, among them four HES genes implicated in regulating neural stem cell differentiation, and TP73 , a monoallelically expressed gene. (biomedcentral.com)
  • He suggested to introduce the term chromosomics being equal to cytogenomics to bring the three-dimensional morphologically of chromosomes into the focus of research, as this is essential for gene regulation. (frontiersin.org)
  • Chromosome localization and genomic structure of the KiSS-1 metastasis suppressor gene (KISS1). (shengsci.com)
  • The responsible gene has been mapped to band 12q24.1, which encodes the human transcription factor TBX5. (medscape.com)
  • A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. (tamu.edu)
  • Mapping quantitative trait loci (QTL) in cattle for meat quality, particularly fat and muscle metabolic traits. (edu.au)
  • Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. (elsevierpure.com)
  • Although this technology was developed much later than Yeast Artificial Chromosome (YAC) and cosmid/fosmid based genome library cloning technologies it soon became popular and tractable because of the technical advantages offered by BAC based cloning over YAC and cosmid/fosmid library cloning systems:1. (biost.com)
  • Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L. (frontiersin.org)
  • Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. (frontiersin.org)
  • The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. (frontiersin.org)
  • This sequence-based physical map will be useful to assemble the genome sequence of pea. (frontiersin.org)
  • In the current study, we have undertaken construction of a sequence-based physical map of pea to address the challenge in the assembly of these repetitive sequences and overcome the shortcomings of traditional restriction digestion based physical maps. (frontiersin.org)
  • WGP is designed based on the use of sequence tags generated by next generation sequencing (NGS) and is a powerful alternative to traditional DNA fingerprinting based physical mapping technologies, and also simultaneously generates a partial genome sequence. (frontiersin.org)
  • The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit. (biomedcentral.com)
  • In the absence of a finished quality genome sequence, insights into wheat genome structure and function have been accumulating through survey sequencing of individual chromosomes or chromosome-specific Bacterial Artificial Chromosome (BAC) libraries. (biomedcentral.com)
  • Our strategy is to develop bacterial artificial chromosome (BAC)-end sequence (BES) physical frameworks of the ten genome types of Oryza and align them to the reference sequence. (biomedcentral.com)
  • Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
  • Abstract: '[Researchers] have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. (harvard.edu)
  • P. 2194 middle column 2nd paragraph: 'Genome assembly relied on the use of several types of data, including clone-based sequence, whole-genome sequence from libraries with three insert sizes [2 kb, 10 kb, and 130 kb], and a Bacterial Artificial Chromosome (BAC)-based sequence-tagged site (STS) content map. (harvard.edu)
  • Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. (umn.edu)
  • The map-based reference genome sequence of barley cv. (umn.edu)
  • Dive into the research topics of 'Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.'. Together they form a unique fingerprint. (umn.edu)
  • The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. (inrae.fr)
  • In this study, we generated 42 simple sequence repeat (SSR) markers from the peach genome assembly v1.0 and an apricot bacterial artificial chromosome clone identified in the physical map of the PPV resistance locus previously defined in apricot. (rosaceae.org)
  • Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome. (jcvi.org)
  • The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes (BACs) with randomly cleaved inserts, sequencing both ends of each, and preparing a restriction enzyme fingerprint of each. (jcvi.org)
  • By reiterating this "sequence-then-map by computer analysis against the STC database" strategy, a minimum tiling path of clones can be sequenced at a rate that is primarily limited by the sequencing throughput of individual genome centers. (jcvi.org)
  • The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. (biomedcentral.com)
  • We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. (kent.ac.uk)
  • In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. (bvsalud.org)
  • Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. (biomedcentral.com)
  • 5 clones) that constitute ~95 % of the cumulative length of the map. (biomedcentral.com)
  • In addition, a 550-kbp contig composed of 6 BAC clones was constructed that encompassed two adjacent RFLP markers on chromosome 2. (johnshopkins.edu)
  • A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. (tamu.edu)
  • The STC resource, containing end sequences, fingerprints, and arrayed BACs, creates a map where the interrelationships of the individual BAC clones are resolved through their STCs as overlapping BAC clones are sequenced. (jcvi.org)
  • All chromosome imbalances were size mapped using BAC and PAC clones based on clone mapping databases ( www.ensembl.org , July 2003), except for case 9, which was size mapped using a chromosome 22 specific micro-array. (bmj.com)
  • We have tremendous experience with plant, animal, yeast and bacterial genomic BAC libraries. (biost.com)
  • Standard chromosome analysis by G-banding has a limited resolution, but molecular cytogenetic techniques, such as multi-subtelomeric FISH, microdeletion FISH, multicolour FISH and comparative genomic hybridisation (CGH), have played an important role for the diagnosis of MR during the past decade. (bmj.com)
  • We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. (biomedcentral.com)
  • BAC fingerprint analyses and alignments of BACs to the pre-existing linkage map have generated a BAC contig physical map of the genome. (kent.ac.uk)
  • To facilitate M. grisea genome analysis, physical mapping, and positional cloning, we have constructed a bacterial artificial chromosome (BAC) library from the rice infecting strain 70-15. (johnshopkins.edu)
  • The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. (biomedcentral.com)
  • Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. (biomedcentral.com)
  • The combination of these resources resulted in a set of ordered contigs spanning nearly all of the euchromatic region on each chromosome arm. (harvard.edu)
  • We present whole-genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. (ampliconexpress.com)
  • The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. (nature.com)
  • We've assigned over 6000 BACs to over 600 markers across almost all chicken chromosomes and linkage groups. (kent.ac.uk)
  • This involved multiplexing pools of bacterial artificial chromosomes (BACs) that had been manually prepared. (genomeweb.com)
  • After the sequencing was done, the researchers used the Velvet assembler to reassemble the BACs and then used CLARK , a supervised classification method, to assign the reassembled BACs to chromosome arms. (genomeweb.com)
  • Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. (pacb.com)
  • Whole-genome restriction mapping by 'subhaploid'-based RAD sequencing: An efficient and flexible approach for physical mapping and genome scaffolding. (pacb.com)
  • 19- 22 Yet none of these techniques is able to offer a high resolution screening of the whole genome for chromosome imbalances. (bmj.com)
  • The chicken genetic map is about 4000 cM, with 2000+ molecular markers mapped using three major reference families. (kent.ac.uk)
  • Both bacterial artificial chromosome (BAC) and small insert sequencing libraries have been constructed from DNA of a single female inbred Red Jungle Fowl, the nearest wild relative of domestic chickens. (kent.ac.uk)
  • Using a linkage mapping approach, we found SSR markers tightly linked to PPV resistance trait in all our progenies. (rosaceae.org)
  • Loss of heterozygosity for a locus on human chromosome 11q22-23 is observed at high frequency in non-small cell lung carcinoma (NSCLC). (elsevierpure.com)
  • Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. (biomedcentral.com)
  • 3- 16 However, these probes only reveal chromosome rearrangements located in the subtelomeric region. (bmj.com)
  • Routine chromosome analysis (450-500 bands) had failed to detect the rearrangements in all cases. (bmj.com)
  • Forschung und Innovation') 'sequencing barley chromosome 3H' to N.S. and U.S. (umn.edu)
  • National Science Foundation grant DBI 0321756 'Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome' to T.J.C. and S.L. (umn.edu)
  • We also constructed a bacterial artificial chromosome-based physical map that spans 13 Mb of the pericentromeric heterochromatin and a cytogenetic map that positions 11 Mb in specific chromosomal locations. (inrae.fr)
  • Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L. (tamu.edu)
  • Several other CBB resistance QTL have been identified but none of them have been physically mapped. (tamu.edu)
  • 2011. Comparative visualization of genetic and physical maps with Strudel . (hutton.ac.uk)
  • WGP TM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. (frontiersin.org)
  • Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for many species, including other avians. (kent.ac.uk)
  • Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. (pacb.com)
  • Despite the large chromosome fragments involved in the unbalanced translocation in this case, repeated standard G-band analysis could not reveal this rearrangement due to the similarity in the banding pattern of the chromosome fragments involved. (bmj.com)
  • We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. (inrae.fr)
  • Southern blot analysis of EcoRI-digested mouse cellular DNA with this probe detected four restriction fragments, all of which appear to be located on mouse chromosome 7, Northern blot analysis using the mouse probe demonstrated that related mRNA species were expressed in some normal adult mouse tissues. (shengsci.com)
  • In our scientific activity at the Division of Physical Chemistry 1 we find it essential to establish long-term goals and policies that are based on an unbiased analysis of the specific situation, rather than an uncritical following of the current trends. (lu.se)
  • Their approach, termed Synthetic Physical Interaction (SPI), is systematic, and does not depend on prior functional information about the proteins of interest. (microbialcell.com)
  • The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. (frontiersin.org)
  • The small fourth chromosome contains only ~1 Mb of euchromatin. (harvard.edu)
  • 31, 32 In this report we used a cDNA micro-array and two BAC clone micro-arrays on 10 previously identified cases containing 16 cryptic chromosome aberrations, to test their performance for the detection of small imbalances. (bmj.com)
  • Her research interests are in livestock molecular genetics and include the genome organization of Bovidae, genome mapping in Bovidae and genetics of lipid metabolism in cattle. (edu.au)
  • Construction and characterization of a bovine bacterial artificial chromosome library. (shengsci.com)
  • RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies. (pacb.com)
  • Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. (frontiersin.org)
  • Under this generic term, all chromosome-related studies should be summarized to introduce novel ideas and concepts in biology and medicine, thus having an integrative effect on the field. (frontiersin.org)
  • Chromosome specific micro-arrays have however been used in a few cases to determine the critical regions in microdeletion disorders. (bmj.com)