PPT-3D Genome Workshop - Overview of ENCODE

Dan Gilchrist National Human Genome Research Institute October 18 2016 The ENCODE Project 3D Data Access Through the ENCODE Portal The ENCODE Encyclopedia Tools for Investigating Genetic Variants. sequencing . for . identification,. detection, . and control of . Bactrocera dorsalis (. Hendel. ). and other Tephritid pests. Thomas Walk, Scott . Geib. USDA-ARS Pacific Basin Agricultural Research Center, Hilo HI. The Plot. Deepak . Purushotham. Hamid Reza . Hassanzadeh. Haozheng. . Tian. Juliette . Zerick. Lavanya. . Rishishwar. Piyush. . Ranjan. Lu Wang. The Outline. The Need & The Requirement. The Options. February . 27 2013. Fundamental Goals. Improve comprehensiveness and accuracy of gene annotation. Define novel protein coding and . noncoding. gene products, including variants. Define . noncoding. regulatory elements, including both sequence and epigenetic features. integrated encyclopedia of DNA elements in the human . genome”. ENCODE Project Consortium. . Nature . 2012 Sep 6; 489:57-74.. Michael . M. Hoffman. University of Washington. 12 September 2012. Major results. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. AKA:. why the ENCODE . project is full of it. by Matthew . Oberhardt. What is ENCODE?. from Biological . Problem to . Combinatorial Algorithms. (and back). Pavel Pevzner. Department of Computer . Science,. . University . of California at San Diego. What is the evolutionary scenario for transforming one genome into the other?. Basic Biology: DNA. Genetic information is stored in . deoxyribonucleic acid (DNA) . molecules.. A single DNA molecule is a sequence of . nucleotides. adenine (. A. ). cytosine (. C. ). guanine (. G. The Human Genome project sequenced “the human genome. ”. “the human genome” that we have labeled as such doesn’t actually . exist. What we call the human genome sequence is really just a . reference. Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. genomico. : implicaciones del proyecto ENCODE. 1. Rory Johnson. Bioinformatics and Genomics. Centre for Genomic Regulation. AEEH. 21 / 2 / 14. This talk:. Our view of the human genome today thanks to ENCODE. Encoding: Getting Information In. How We Encode. Automatic Processing. Parallel processing. Automatic processing. Space. Time. Frequency. Well-learned information. Encoding: Getting Information In. How We Encode. Genome: the total number of genes in an individual.. Human Genome- approx. 20,000 genes on the 46 human chromosomes.. Human Genome Project (HGP). Ongoing effort to completely map and sequence our genome.. from NHGRI’s . Planning . Workshop on the Future Opportunities . for . Genome Sequencing . & Beyond. Mark Gerstein & Rick Myers. Recommendations related to genome function. . Part 1: Workshop summary (Mark). G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy.