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DNA Sequencing Theory
DNA sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing and optimizing sequencing projects (known as "strategic genomics"), predicting project performance, troubleshooting experimental results, characterizing factors such as sequence bias and the effects of software processing algorithms, and comparing various sequencing methods to one another. In this sense, it could be considered a branch of systems engineering or operations research. The permanent archive of work is primarily mathematical, although numerical calculations are often conducted for particular problems too. DNA sequencing theory addresses ''physical processes'' related to sequencing DNA and should not be confused with theories of analyzing resultant DNA sequences, e.g. sequence alignment. Publications sometimes do not make a carefu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular func ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eric Lander
Eric Steven Lander (born February 3, 1957) is an American mathematician and geneticist who served as the 11th director of the Office of Science and Technology Policy and Science Advisor to the President, serving on the presidential Cabinet. Lander is a professor of biology at the Massachusetts Institute of Technology (MIT), a professor of systems biology at Harvard Medical School, a former member of the Whitehead Institute, and the founding director of the Broad Institute. He is a 1987 MacArthur Fellow and Rhodes Scholar. Lander co-chaired President Barack Obama's Council of Advisors on Science and Technology. Lander announced he would resign from the Biden Administration effective February 18, 2022 after allegations surfaced he had engaged in bullying and abusive conduct directed against his subordinates and other White House staff. Early life and education Lander was born in Brooklyn, New York City, to Jewish parents, the son of Rhoda G. Lander, a social studies teacher, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Celera
Celera is a subsidiary of Quest Diagnostics which focuses on genetic sequencing and related technologies. It was founded in 1998 as a business unit of Applera, spun off into an independent company in 2008, and finally acquired by Quest Diagnostics in 2011. History Originally headquartered in Rockville, Maryland (relocated to Alameda, California), it was established in May 1998 by PE Corporation (later renamed to Applera), with Dr. J. Craig Venter from The Institute for Genomic Research (TIGR) as its first president. While at TIGR, Venter and Hamilton Smith led the first successful effort to sequence an entire organism's genome, that of the ''Haemophilus influenzae'' bacterium. Celera was formed for the purpose of generating and commercializing genomic information. Its stock is a tracking stock of Applera, along with the tracking stock of Applera's larger Applied Biosystems Group business unit. Celera sequenced the human genome at a fraction of the cost of the publicly-funded H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shotgun Sequencing
In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The Sanger sequencing#Method, chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are sequence assembly, assembled to give the overall sequence. In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain ''reads''. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing was one of the precursor technologies that was res ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Leroy Hood
Leroy "Lee" Edward Hood (born October 10, 1938) is an American biologist who has served on the faculties at the California Institute of Technology (Caltech) and the University of Washington. Hood has developed ground-breaking scientific instruments which made possible major advances in the biological sciences and the medical sciences. These include the first gas phase protein sequencer (1982), for determining the sequence of amino acids in a given protein; a DNA synthesizer (1983), to synthesize short sections of DNA; a peptide synthesizer (1984), to combine amino acids into longer peptides and short proteins; the first automated DNA sequencer (1986), to identify the order of nucleotides in DNA; ink-jet oligonucleotide technology for synthesizing DNA and nanostring technology for analyzing single molecules of DNA and RNA. The protein sequencer, DNA synthesizer, peptide synthesizer, and DNA sequencer were commercialized through Applied Biosystems, Inc. and the ink-jet tec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proceedings Of The National Academy Of Sciences
''Proceedings of the National Academy of Sciences of the United States of America'' (often abbreviated ''PNAS'' or ''PNAS USA'') is a peer-reviewed multidisciplinary scientific journal. It is the official journal of the National Academy of Sciences, published since 1915, and publishes original research, scientific reviews, commentaries, and letters. According to ''Journal Citation Reports'', the journal has a 2021 impact factor of 12.779. ''PNAS'' is the second most cited scientific journal, with more than 1.9 million cumulative citations from 2008 to 2018. In the mass media, ''PNAS'' has been described variously as "prestigious", "sedate", "renowned" and "high impact". ''PNAS'' is a delayed open access journal, with an embargo period of six months that can be bypassed for an author fee ( hybrid open access). Since September 2017, open access articles are published under a Creative Commons license. Since January 2019, ''PNAS'' has been online-only, although print issues are a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Richard Arratia
Richard Alejandro Arratia is a mathematician noted for his work in combinatorics and probability theory. Contributions Arratia developed the ideas of interlace polynomials with Béla Bollobás and Gregory Sorkin,. found an equivalent formulation of the Stanley–Wilf conjecture as the convergence of a limit, and was the first to investigate the lengths of superpatterns of permutations. He has also written highly cited papers on the Chen–Stein method on distances between probability distributions,.. on random walks with exclusion,. and on sequence alignment... He is a coauthor of the book ''Logarithmic Combinatorial Structures: A Probabilistic Approach''.. Education and employment Arratia earned his Ph.D. in 1979 from the University of Wisconsin–Madison under the supervision of David Griffeath. He is currently a professor of mathematics at the University of Southern California , mottoeng = "Let whoever earns the palm bear it" , religious_affiliation = Nonsectarian ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bob Waterston
Robert Hugh "Bob" Waterston, (born September 17, 1943) is an American biologist. He is best known for his work on the Human Genome Project, for which he was a pioneer along with John Sulston. Education Waterston attended Princeton as an undergraduate where he majored in engineering; he wrote his senior dissertation on the plays of Eugene O'Neill. While on a visit to Germany he took courses in biology – in German – and returned to take up a place at the school of medicine of the University of Chicago. In 1972, he acquired both MD and PhD degrees, with his thesis focusing on immunology. Career Following a postdoctoral position in the laboratory of Sydney Brenner at the MRC Laboratory of Molecular Biology (LMB) in Cambridge, he joined the Washington University in St. Louis as assistant professor of anatomy and neurobiology in 1976. A few years later, he switched to the Department of Genetics, where by 1991 he became chair. In the mid-1980s he made a sabbatical visit to the LMB, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Michael Christopher Wendl
Michael Christopher Wendl is a mathematician and biomedical engineer who has worked on DNA sequencing theory, covering and matching problems in probability, theoretical fluid mechanics, and co-wrote Phred. He was a scientist on the Human Genome Project and has done bioinformatics and biostatistics work in cancer. Wendl is of ethnic German heritage and is the son of the aerospace engineer Michael J. Wendl.P Hummel and N Fuhry: "Sackelhausen im Banat" Volume 3, published by Heimatsortsgemeinschaft Sackelhausen, Reutlingen FRG, 2007, pages 2236-2237. Research Work Theoretical Fluid Mechanics The problem of low Reynolds number flow in the gap between 2 infinite cylinders, so-called Couette flow, was solved in 1845 by Stokes. Wendl reported the generalization of this solution for finite-length cylinders, which can actually be built for experimental work, in 1999, as a series of modified Bessel functions I_1 and K_1. He also examined a variety of other low Reynolds number rotationa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jared Roach
Jared C. Roach is an American biologist who invented the pairwise end sequencing strategy while a graduate student at the University of Washington. Education and early career Roach attended Cornell University, where he received his Bachelor of Science in Biology in 1990. He then attended the University of Washington, where he received his PhD in Immunology in 1998, and his MD in 1999. He trained in Internal Medicine at the University of Utah through 2001. Career Starting as a graduate student in the 1990s, Roach worked on the Human Genome Project from its early days through its conclusion in 2003. He invented pairwise end-sequencing while a graduate student in Leroy Hood's laboratory. Roach was a Senior Fellow at the Department of Molecular Biotechnology at the University of Washington from 1999-2000. In 2001, he became a Research Scientist at the Institute for Systems Biology. In 2009, Roach was first author on a project which sequenced the whole genomes of a family of f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Contig
A contig (from ''contiguous'') is a set of overlapping DNA segments that together represent a consensus region of DNA.Gregory, S. ''Contig Assembly''. Encyclopedia of Life Sciences, 2005. In bottom-up sequencing projects, a contig refers to overlapping sequence data ( reads); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly.Dear, P. H. ''Genome Mapping''. Encyclopedia of Life Sciences, 2005. . Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments) contained in clones depending on the context. Original definition of contig In 1980, Staden wrote: ''In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig". A contig is a set of gel readings that are related to one another by overlap of their sequences. All gel readings belong to one and only one con ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
