*  Research at the RBVI
Applications range from small, targeted sequencing projects to genome annotation to large-scale metagenomics analyses. ... TR&D 2: Software for Interactive Analysis of Large Molecular Assemblies. This project continues our successful development of ... Previously, large sequencing projects were the exclusive domain of a few dozen genome centers in the US and around the world. ... The DeRisi lab has several ongoing whole genome and metagenomic sequencing and assembly projects that can provide real-world, ...
  http://www.cgl.ucsf.edu/Research/index.html
*  The Cancer Genome Atlas API How To's | ProgrammableWeb
... is a project to improve the understanding of the molecular basis of cancer through the application of genome analysis ... Available information includes annotations, data matrices, data reports, project metadata, and biospecimen metadata. ... including large-scale genome sequencing. TCGA offers a collection of APIs that provide REST-based, programmatic access to its ...
  https://www.programmableweb.com/api/cancer-genome-atlas/how-to
*  Genome project - Wikipedia
... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... private company involved in genome sequencing Knome, private company offering genome analysis & sequencing Pevsner, Jonathan ( ... Genome Project Domestic Cow Bovine Genome Honey Bee Genome Sequencing Consortium Horse genome Human microbiome project ... a complete genome sequence will involve 46 separate chromosome sequences. The Human Genome Project was a landmark genome ...
  https://en.wikipedia.org/wiki/Genome_project
*  Symbiose Project Team - INRIA/Irisa - Fabrice LEGEAI
Its main goals are to supply the needs on automatically or manually annotation, genome browsing or genome comparative analyses ... Ollivier M., Legeai F., Rispe C. (2010) Comparative analysis of the Acyrthosiphon pisum genome and expressed sequence tag-based ... A centralized bioinformatic resource for annotation of the pea aphid genome. Insect Molecular Biology vol19,0,5-12 ... Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog. 2010 May 27;6(5). ...
  http://www.irisa.fr/symbiose/index2.php?option=com_content&task=view&id=70&pop=1&page=0
*  Frontiers | Genome-wide analysis of the CaHsp20 gene family in pepper: comprehensive sequence and expression profile analysis...
... were identified and renamed on the basis of their molecular weight, and then their gene structure, genome location, gene ... genome location, gene duplication, phylogenetic relationship and interaction network were also analyzed. The expression ... which provides the basis for further functional analyses of CaHsp20s in the formation of pepper acquired thermotoleance. ... were identified and renamed on the basis of their molecular weight, and then their gene structure, ...
  https://www.frontiersin.org/articles/10.3389/fpls.2015.00806/full
*  Project : USDA ARS
... four lines have been resequenced and the analysis of the sequences has been initiated. Knowledge of the genome sequence of ... Molecular, morphological and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome. 52:876-890. ... Create a population of insertional mutants, sets of diverse inbred lines and improved annotation of the genome sequence. Apply ... Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.. ...
  https://www.ars.usda.gov/research/project/?accnNo=418493&fy=2010
*  RPF1 Gene - GeneCards | RPF1 Protein | RPF1 Antibody
Genome research 2004) 3 4 58 * Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular ... The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58 ... The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) ... Molecular mass:. 40111 Da. Quaternary structure:. No Data Available SequenceCaution:. *Sequence=CAH71915.1; Type=Erroneous gene ...
  http://www.genecards.org/cgi-bin/carddisp.pl?gene=RPF1
*  SH2D1B - Wikipedia
Eissmann P, Watzl C (2006). "Molecular analysis of NTB-A signaling: a role for EAT-2 in NTB-A-mediated activation of human NK ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
  https://en.wikipedia.org/wiki/SH2D1B
*  Genomics - Wikipedia
The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching ... genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects ( ... sequencing. Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to ... This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared " ...
  https://en.wikipedia.org/wiki/Genomics
*  Agmatinase - Wikipedia
Human AGMAT genome location and AGMAT gene details page in the UCSC Genome Browser. Molecular and Cellular Biology portal. ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...
  https://en.wikipedia.org/wiki/Agmatinase
*  Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy...
... are members of a family of cysteine-rich low molecular weight polypeptides which play an important role in heavy metal ... Our analysis suggests presence of 11 class I MT genes in rice genome (Release 7 of the MSU Rice Genome Annotation Project) ... Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630-634PubMed ... Zhou G, Xu Y, Li J, Yang L, Liu JY (2006) Molecular analyses of the metallothionein gene family in rice (Oryza sativa L.). J ...
  https://link.springer.com/article/10.1007/s10142-012-0297-9
*  Palladin - Wikipedia
Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. ... 2004). "Molecular analysis of the interaction between palladin and alpha-actinin". FEBS Lett. 566 (1-3): 30-4. doi:10.1016/j. ... 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...
  https://en.wikipedia.org/wiki/Palladin
*  Frontiers | Brassinosteroids Regulate OFP1, a DLT Interacting Protein, to Modulate Plant Architecture and Grain Morphology in...
Genetic analysis showed that the regulation of plant architecture by OFP1 depends on DLT function. In addition, we found OFP1 ... Genetic analysis showed that the regulation of plant architecture by OFP1 depends on DLT function. In addition, we found OFP1 ... According to rice genome annotation project2, OFP1 (LOC_Os01g12690) is intronless and contains 1185-bp coding sequence, 44-bp 5 ... Vector Constructions and Transgenic Analysis. The DNA sequence containing the promoter and coding sequence of OFP1 was cloned ...
  https://www.frontiersin.org/articles/10.3389/fpls.2017.01698/full
*  Map Position and Expression of the Genes in the 38 Region of Drosophila | Genetics
Sequence analysis: Our molecular work was based on P1 and bacterial artificial chromosome (BAC) genomic sequences produced by ... 1996 Around the genomes: the Drosophila genome project. Genome Res. 6: 71-79. ... additional sequence annotations were carried out to identify sequence similarities with those in the public domain. Each ... Biological information must now be extracted from the genome sequence by systematic functional analysis of genes. Computer ...
  http://www.genetics.org/content/158/4/1597
*  MGI-Collaborators and Acknowledgements for Mouse Genome Informatics Projects
... and the Knockout Mouse Project (KOMP).. IMAGE Consortium (Integrated Molecular Analysis of Genomes and their Expression) and ... The miRBase Sequence Database contains all published miRNA sequences, genomic locations, and associated annotation.. Mouse ... The Genome Sequencing Center two-year project will produce expressed tag sequences (ESTs) from approximately 400,000 mouse ... We based the MGI Mouse Genome Browser, a tool for manipulating and displaying genome annotations, on JBrowse, a generic genome ...
  http://www.informatics.jax.org/mgihome/other/collab_and_acknow.shtml
*  The Drosophila Gene taranis Encodes a Novel Trithorax Group Member Potentially Linked to the Cell Cycle Regulatory Apparatus |...
2001), analysis of the recently completed Drosophila genome sequence (Adamset al. 2000) allowed us to identify 10 other P ... The Drosophila protein and annotation databases were searched at the Berkeley Drosophila Genome Project (BDGP; http://www. ... The tara gene structure suggests a possible molecular mechanism of action. Our molecular analysis of the twin TARA proteins ... Sequence of the alternative tara mRNAs and proteins. The nucleotide sequence and deduced amino acid sequence for a putative ...
  http://www.genetics.org/content/160/2/547
*  DUSP18 - Wikipedia
2005). "A genome annotation-driven approach to cloning the human ORFeome". Genome Biol. 5 (10): R84. doi:10.1186/gb-2004-5-10- ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ... 2003). "Molecular cloning and characterization of a novel dual-specificity phosphatase18 gene from human fetal brain". Biochim ...
  https://en.wikipedia.org/wiki/DUSP18
*  Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.) | BMC Genomics |...
Most of the current molecular markers for the yam genome by Mignouna et al. are based on AFLP and RAPD [14, 15]. However, for ... Sequence assembly, analysis and annotation. *a.. Preliminary sequencing data analysis: The Sanger sequences were analyzed using ... Mapman analysis: For data analysis by MapMan software version 3.5.0 BETA [34] http://gabi.rzpd.de/projects/MapMan/, the EST ... 454 sequence data analysis: The sequencing agency provided high quality raw reads as well as aligned EST sequences for three ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-100
*  IJMS | Free Full-Text | The MAPKKK Gene Family in Gossypium raimondii: Genome-Wide Identification, Classification and ...
Transcriptome sequencing data were used to investigate their transcript profiles in mature leaves, 0 day and 3 days post- ... for introns and additional domains were consistent with the evolutionary relationships inferred from the phylogenetic analysis ... In this study, we identified 78 putative MAPKKK genes in the genome of the diploid cotton, Gossypium raimondii. They were ... whereas Raf genes were distributed across the entire genome. Their conserved patterns observed ...
  http://www.mdpi.com/1422-0067/14/9/18740/htm
*  Frontiers | Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome...
Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in ... 3540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13778 genic Single Nucleotide Polymorphism (SNP) ... genome of chickpea (desi type) was downloaded from chickpea genome analysis project (Parween et al., 2015). All the four ... C) Molecular function. (D) Distribution of blast hit identified species.. Supplementary Figure 2. Annotation of differentially ...
  https://www.frontiersin.org/articles/10.3389/fpls.2017.00958/full
*  Plus it
The researchers sequenced the full coding exons of 64 commonly mutated cancer genes, performed genome-wide analyses of copy ... A second collaboration, the Cancer Genome Project's Cancer Cell Line Project, screened 639 tumor cell lines that included both ... "Now we can go to the Cell Line Encyclopedia and look up what the molecular basis of that might be." ... Golub says the team plans to increase its annotation of the cell lines in the collection, including proteomic and metabolic ...
  http://cancerdiscovery.aacrjournals.org/content/early/2012/04/11/2159-8290.CD-NB2012-037
*  Emerging Technologies to Study Long Non-coding RNAs | SpringerLink
2012). GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research, 22, 1760.Google Scholar ... 2001). Initial sequencing and analysis of the human genome. Nature, 409, 860. http://www.ncbi.nlm.nih.gov/pubmed/11237011. ... Functional Analysis. International Journal of Molecular Sciences, 13, 97.PubMedCrossRefGoogle Scholar ... 2009). Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19, 255.Google Scholar ...
  https://link.springer.com/chapter/10.1007/978-1-4614-8621-3_7
*  Metagenomic Analysis of Silage | Protocol (Translated to Chinese)
Bankevich, A., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. ... genome project classification. Nuc. Aci. Res. 43, (1), 1099-1106 (2015).. *Camacho, C., et al. BLAST+: architecture and ... Mikheyev, A. S., Tin, M. M. Y. A first look at the Oxford Nanopore MinION sequencer. Molecular Ecology Resources. 14, (6), 1097 ... Bose, T., Haque, M. M., Reddy, C., Mande, S. S. COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PLoS ...
  https://www.jove.com/video/54936/?language=Chinese
*  Genetic Modifiers: August 2010
The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified ... than alterations to protein sequence are central to the evolution of organisms has become something of a truism in molecular ... Northern blot analysis revealed that OB RNA is present at a high level in adipose tissue but at much lower levels in placenta ... Purifying selection is thought to purge TE insertions from the genome, and TE sequences are targeted by hosts for epigenetic ...
  http://geneticmodifiers.blogspot.com/2010/08/
*  ZCCHC17 - Wikipedia
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Chang WL, Lee DC, Leu S, Huang YM, Lu MC, Ouyang P (Aug 2003). "Molecular characterization of a novel nucleolar protein, pNO40 ...
  https://en.wikipedia.org/wiki/ZCCHC17