Genomics - Knowledge (XXG) (2024)

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especially because the availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved hom*ologs. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or

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acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity; with an optimal configuration, the ultimate throughput of the instrument depends only on the

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1146:. 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 is a random sampling process, requiring over-sampling to ensure a given1251:

so that local clonal colonies, initially coined "DNA colonies", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. Unlike pyrosequencing, the DNA chains are extended one nucleotide at a time and image

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Next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study populations. When combined with new informatics approaches that integrate many kinds of data with genomic data in disease research, this allows

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assembly paradigm there are two primary strategies for assembly, Eulerian path strategies, and overlap-layout-consensus (OLC) strategies. OLC strategies ultimately try to create a Hamiltonian path through an overlap graph which is an NP-hard problem. Eulerian path strategies are computationally more

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sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome: Overall, this method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from

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to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its power 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

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for finding similarities, and then annotating genomes based on hom*ologues. More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use

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which sequence dozens of terabases a year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop

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infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights

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is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches,

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or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods

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technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used. Third generation sequencing technologies such as PacBio or Oxford Nanopore routinely generate sequencing reads 10-100 kb in length; however,

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the sequencing process, producing thousands or millions of sequences at once. High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis

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in early 2001, creating much fanfare. This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared "finished" (less than one error in 20,000 bases and all chromosomes assembled). In the years since then, the genomes of many other

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gel (called polyacrylamide gel electrophoresis) and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and was a big improvement, but was still very laborious. Nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the

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and his colleagues played a key role in the development of DNA sequencing techniques that enabled the establishment of comprehensive genome sequencing projects. In 1975, he and Alan Coulson published a sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the

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with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput

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Environmental Shotgun Sequencing (ESS) is a key technique in metagenomics. (A) Sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and

1815:. Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further1766:. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying1296:

829:, which has resulted in a pronounced bias in their phylogenetic distribution compared to the breadth of microbial diversity. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast (1770:

evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of

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analyses. However, the Sanger method remains in wide use, primarily for smaller-scale projects and for obtaining especially long contiguous DNA sequence reads (>500 nucleotides). Chain-termination methods require a single-stranded DNA template, a DNA

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An alternative approach, ion semiconductor sequencing, is based on standard DNA replication chemistry. This technology measures the release of a hydrogen ion each time a base is incorporated. A microwell containing template DNA is flooded with a single

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Rossi, M.J; Kuntala, P.K; Lai, W.K.M; Yamada, N; Badjatia, N; Mittal, C; Kuzu, G; Bocklund, K; Farrell, N.P; Blanda, T.R; Mairose, J.D; Basting, A.V; Mistretta, K.S; Rocco, D.J; Perkinson, E.S; Kellogg, G.D; Mahony, S; Pugh, B.F (March 2021).

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After an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation.

1639:. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p.475). Two of the most characterized epigenetic modifications are1137:

Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a

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assembly, for genomes which are not similar to any sequenced in the past, and comparative assembly, which uses the existing sequence of a closely related organism as a reference during assembly. Relative to comparative assembly,

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has developed as a popular field of research, where genomic sequencing methods are used to conduct large-scale comparisons of DNA sequences among populations - beyond the limits of genetic markers such as short-range

1044:, among others) to claim that it has been oversold, it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the constituents of a system. In the study of1070:

Overview of a genome project. First, the genome must be selected, which involves several factors including cost and relevance. Second, the sequence is generated and assembled at a given sequencing center (such as

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Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, etal. (April 1976). "Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene".

706:) of DNA sequencing, involving the preferential cleavage of DNA at known bases, a less efficient method. For their groundbreaking work in the sequencing of nucleic acids, Gilbert and Sanger shared half the 19803179:

Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (December 2003). "Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique".

1439:, as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification. Ideally, these approaches co-exist and complement each other in the same annotation1142:. Since gel electrophoresis sequencing can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain686:), which formed the basis of the techniques of DNA sequencing, genome mapping, data storage, and bioinformatic analysis most widely used in the following quarter-century of research. In the same year2100:

and to detect patterns in variation throughout a given population, conservationists can formulate plans to aid a given species without as many variables left unknown as those unaddressed by standard

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Ohyama K, f*ckuzawa H, Kohchi T, Shirai H, Sano T, Sano S, etal. (1986). "Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA".

461:, "gene" (gamma, epsilon, nu, epsilon) meaning "become, create, creation, birth", and subsequent variants: genealogy, genesis, genetics, genic, genomere, genotype, genus etc. While the word1455:

genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g.

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coat protein. Fiers' group expanded on their MS2 coat protein work, determining the complete nucleotide-sequence of bacteriophage MS2-RNA (whose genome encodes just four genes in 3569

1048:, for example, researchers which were once limited to the study of a single gene product can now simultaneously compare the total complement of several types of biological molecules.4827:, Kawashima EH, Farinelli L, Mayer P, "Method of nucleic acid amplification", published 12 May 2005, issued 26 July 2011, assigned to Solexa Ltd Great Britain.7301:

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Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, etal. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd".

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776:(12.1 Mb), and since then genomes have continued being sequenced at an exponentially growing pace. As of October2011, the complete sequences are available for: 2,7191572:

1193:, normal deoxynucleosidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation. These chain-terminating nucleotides lack a 3'-1276:

is present in the template sequence multiple nucleotides will be incorporated in a single flood cycle, and the detected electrical signal will be proportionally higher.

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researchers to better understand the genetic bases of drug response and disease. Early efforts to apply the genome to medicine included those by a Stanford team led by

6147:"Two Boston Health Systems Enter the Growing Direct-to-Consumer Gene Sequencing Market by Opening Preventative Genomics Clinics, but Can Patients Afford the Service?"943:

resources from a large international collaboration. The continued analysis of human genomic data has profound political and social repercussions for human societies.

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Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, etal. (April 1981). "Sequence and organization of the human mitochondrial genome".

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research program aims to collect genome sequence data from 1 million participants to become a critical component of the precision medicine research platform.

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to a protein of known structure or based on chemical and physical principles for a protein with no hom*ology to any known structure. As opposed to traditional

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Conservationists can use the information gathered by genomic sequencing in order to better evaluate genetic factors key to species conservation, such as the

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3504:, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, etal. (May 1992). "The complete DNA sequence of yeast chromosome III".6264:

Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (December 2003). "The power and promise of population genomics: from genotyping to genome typing".

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through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in

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The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to

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has come to refer generally to the study of large, comprehensive biological data sets. While the growth in the use of the term has led some scientists (

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to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and

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of a population or whether an individual is heterozygous for a recessive inherited genetic disorder. By using genomic data to evaluate the effects of

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Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, etal. (May 1978). "Complete nucleotide sequence of SV40 DNA".

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The Illumina dye sequencing method is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical Research Institute, by

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1268:, if the nucleotide is complementary to the template strand it will be incorporated and a hydrogen ion will be released. This release triggers an3128:

Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, etal. (February 1977). "Nucleotide sequence of bacteriophage phi X174 DNA".

1647:. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in1103:

sequencers has come within reach of the average academic laboratory. On the whole, genome sequencing approaches fall into two broad categories,

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Yue GH, Lo LC, Zhu ZY, Lin G, Feng F (April 2006). "The complete nucleotide sequence of the mitochondrial genome of Tetraodon nigroviridis".

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1655:. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.7764:

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between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated. The ddNTPs may be radioactively or

658:. This involved two closely related methods that generated short oligonucleotides with defined 3' termini. These could be fractionated by7991:

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Min Jou W, Haegeman G, Ysebaert M, Fiers W (May 1972). "Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein".

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Sams, K.L; Mukai, C; Marks, B.A; Mittal, C; Demeter, E.A; Nelissen, S; Grenier, J.K; Tate, A.E; Ahmed, F; Coonrod, S.A (October 2022).

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4302:"A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers"2130:

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Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, etal. (March 1965). "Structure of a Ribonucleic Acid".

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samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional

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Illumina Genome Analyzer II System. Illumina technologies have set the standard for high-throughput massively parallel sequencing.

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Gallego, L.D; Schneider, M; Mittal, C; Romanuska, Anete; Gudino Carrillo, R.M; Schubert, T; Pugh, B.F; Kohler, A (March 2020).

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is represented in the reconstructed sequence; the average number of reads by which a genome is over-sampled is referred to as

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2337:"Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories"1974:

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Sanger F, Coulson AR (May 1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase".

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The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that

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for which a total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six

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nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle.

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of a human, providing a simplified overview of the human genome. It is a graphical representation of the idealized human

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1459:) rely on both curated data sources as well as a range of software tools in their automated genome annotation pipeline.1222:

4543:"The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation"1961:

who developed the first tools for the medical interpretation of a human genome. The Genomes2People research program at

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5773:"Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences"4908:

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and Harvard Medical School was established in 2012 to conduct empirical research in translating genomics into health.

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For much of its history, the technology underlying shotgun sequencing was the classical chain-termination method or '

392:, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to3606:

Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, etal. (October 1996). "Life with 6000 genes".

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An ABI PRISM 3100 Genetic Analyzer. Such capillary sequencers automated early large-scale genome sequencing efforts.

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The number of genome projects has increased as technological improvements continue to lower the cost of sequencing.

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The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that

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and Laurent Farinelli. In this method, DNA molecules and primers are first attached on a slide and amplified with

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the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of

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they have a high error rate at approximately 1 percent. Typically the short fragments, called reads, result from

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Frankham R (1 September 2010). "Challenges and opportunities of genetic approaches to biological conservation".

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Satzinger H (March 2008). "Theodor and Marcella Boveri: chromosomes and cytoplasm in heredity and development".

1588:. This genome-based approach allows for a high-throughput method of structure determination by a combination of643:

shared half of the 1980 Nobel Prize in Chemistry for Independently developing methods for the sequencing of DNA.

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of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of

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Gladyshev VN, Zhang Y (2013). "Chapter 16 Comparative Genomics Analysis of the Metallomes". In Banci L (ed.).

1209:. Typically, these machines can sequence up to 96 DNA samples in a single batch (run) in up to 48 runs a day.758:(1.8 Mb [megabase]) in 1995. The following year a consortium of researchers from laboratories across726:

The advent of these technologies resulted in a rapid intensification in the scope and speed of completion of

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genes and their roles in inheritance, genomics aims at the collective characterization and quantification of

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1079:). Third, the genome sequence is annotated at several levels: DNA, protein, gene pathways, or comparatively.845:

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A free, self-study course in genomic medicine. Resources include audio lectures and selected lecture notes.

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Ankeny RA (June 2003). "Sequencing the genome from nematode to human: changing methods, changing science".

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Allendorf FW, Hohenlohe PA, Luikart G (October 2010). "Genomics and the future of conservation genetics".

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5592:"Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes"3411:"The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression"2140:

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to use genomic methods to identify relationships between patterns of environmental and genetic variation.

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Finished genomes are defined as having a single contiguous sequence with no ambiguities representing each

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Multiple, fragmented sequence reads must be assembled together on the basis of their overlapping areas.

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Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, etal. (September 1986).

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Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, etal. (October 2009).

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Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, etal. (2012). Liu Z (ed.).

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Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, etal. (December 2009).

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229:

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Laird PW (March 2010). "Principles and challenges of genomewide DNA methylation analysis".

2862:

Nirenberg M, Leder P, Bernfield M, Brimacombe R, Trupin J, Rottman F, O'Neal C (May 1965).

1506:

that attempts to make use of the vast wealth of data produced by genomic projects (such as

421:

to facilitate understanding of even the most complex biological systems such as the brain.

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Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, etal. (March 2014).

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An example of a protein structure determined by the Midwest Center for Structural Genomics

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919:

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715:

659:

521:

466:

418:

5067:"Steady progress and recent breakthroughs in the accuracy of automated genome annotation"2241:

Franklin RE, Gosling RG (April 1953). "Molecular configuration in sodium thymonucleate".

2059:

of a population. Population genomic methods are used for many different fields including

6224:

5407:

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4688:

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4002:

3945:

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895:) are interesting because of their small and compact genomes, which contain very little819:

Most of the microorganisms whose genomes have been completely sequenced are problematic

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Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, etal. (July 2012).

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2048:

1989:

The growth of genomic knowledge has enabled increasingly sophisticated applications of

1915:

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815:

The cost in USD to sequence a 3,000 Mb (human-sized) genome on a log-transformed scale.

727:

687:

663:

640:

414:

410:

277:

202:

27:

5995:

5721:

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4355:

3310:

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The field also includes studies of intragenomic (within the genome) phenomena such as

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Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, etal. (May 2010).

5558:

5129:

Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, etal. (January 2013).

4519:

3643:

2186:

1937:

1863:

1829:

1823:

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960:

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759:

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525:

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536:

sequence of insulin in 1955, nucleic acid sequencing became a major target of early

7884:

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7809:

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7554:

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7544:

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7247:

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5527:

5348:

3873:"Dog Genome Assembled: Canine Genome Now Available to Research Community Worldwide"3541:

3487:

3392:

3165:

3061:

3010:

2958:

2278:

2181:

2068:

2052:

1941:

1714:

1691:

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1408:

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1005:

951:

927:

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752:(315 kb) was sequenced. The first free-living organism to be sequenced was that of738:(16,568 bp, about 16.6 kb [kilobase]), was reported in 1981, and the first572:

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473:

267:

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sequence in order to reconstruct the original sequence. This is needed as current

6609:

6320:

6045:

5608:

4567:

3627:

2864:"RNA codewords and protein synthesis, VII. On the general nature of the RNA code"1315:

Paired end reads of next generation sequencing data mapped to a reference genome.

8125:

7934:

7929:

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7739:

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2155:

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1958:

1652:

1648:

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1301:

Overlapping reads form contigs; contigs and gaps of known length form scaffolds.

1273:

739:

707:

691:

612:

529:

6658:: Looks at the development and use of the science and technologies of genomics.5465:

4824:

4792:

4743:

3280:

Proceedings of the National Academy of Sciences of the United States of America

3221:

Proceedings of the National Academy of Sciences of the United States of America

2868:

Proceedings of the National Academy of Sciences of the United States of America

2468:

2392:

2115:

770:

announced the completion of the first complete genome sequence of a eukaryote,

674:, completing the first fully sequenced DNA-based genome. The refinement of the8140:

8135:

8028:

7919:

7914:

7859:

7844:

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7749:

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2111:

2056:

1904:

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1551:

1539:

1265:

1248:

1147:

1098:, centralized facilities (ranging from large independent institutions such as1021:

1001:

968:

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544:

and colleagues published the first nucleic acid sequence ever determined, the

533:

485:

429:

197:

111:

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66:

4318:

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3723:

1381:

tractable because they try to find a Eulerian path through a deBruijn graph.

869:

is used for many developmental studies on the molecular level, and the plant

8032:

7834:

7819:

7804:

7754:

7729:

7001:

Matrix-assisted laser desorption ionization-time of flight mass spectrometer

6869:

6621:

4990:

4420:

4222:"An interdependent metabolic patchwork in the nested symbiosis of mealybugs"3576:

3241:

2336:

2171:

1998:

1925:

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6652:: The first Korean Genome published and the sequence is available freely.6400:

5788:

4636:"Advanced sequencing technologies and their wider impact in microbiology"4474:

4389:

4188:

3319:

3260:

3157:

3053:

2206:

1933:

1914:

chromosome pairs, both the female (XX) and male (XY) versions of the two

1772:

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1376:), making it less favourable for short-read NGS technologies. Within the1194:

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1025:

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26:"Genome biology" redirects here. For the journal with the same name, see6165:"NIH-funded genome centers to accelerate precision medicine discoveries"3953:

3768:

384:

focusing on the structure, function, evolution, mapping, and editing of

8120:

7939:

7669:

7539:

6830:

6511:

5287:

4777:"Massively parallel sequencing: the next big thing in genetic medicine"4652:

4635:

4609:. San Diego, California, USA: Illumina, Inc. p.12. Archived from2514:

2064:

1892:

1705:, early environmental gene sequencing cloned specific genes (often the1515:

1456:

1373:

1139:

781:

649:

In addition to his seminal work on the amino acid sequence of insulin,

584:

549:

7477:

6496:"Translating cancer genomes and transcriptomes for precision oncology"1530:, as opposed to the static aspects of the genomic information such as1161:', which is based on the selective incorporation of chain-terminating7604:

7216:

7191:

6080:"Clinical interpretation and implications of whole-genome sequencing"5332:

5035:

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3986:

3525:

3479:

3376:

3149:

3045:

2994:

2942:

2772:"Nucleotide sequences in the yeast alanine transfer ribonucleic acid"2617:

2262:

2044:

2008:

1759:

1585:

1419:

1344:

1181:

1013:

956:

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568:

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385:

106:

81:

6695:

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6277:

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Stein L (July 2001). "Genome annotation: from sequence to biology".

2369:"A high-resolution protein architecture of the budding yeast genome"2305:

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is used to address the objects of study of such fields, such as the

504:

on the mapping of the human genome in 1986. First as the name for a

6184:

Regenesis: how synthetic biology will reinvent nature and ourselves

5821:

5695:

Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H (June 2003).

1713:

in a natural sample. Such work revealed that the vast majority of

587:) were the first to determine the sequence of a gene: the gene for5392:"Phase separation directs ubiquitination of gene-body nucleosomes"3745:"A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea"1882:

1767:

1662:

1471:

consists of attaching biological information to genomic elements.

1269:

1234:

1122:

980:

950:

935:

individuals have been sequenced, partly under the auspices of the

798:

793:

777:

767:

580:

4405:"Shotgun DNA sequencing using cloned DNase I-generated fragments"3930:"An integrated map of genetic variation from 1,092 human genomes"3872:

3712:"Scientists Start a Genomic Catalog of Earth's Abundant Microbes"2688:"A decade of GigaScience: A perspective on conservation genetics"19:

This article is about the scientific field. For the journal, see

6410:"Genomics meets proteomics: identifying the culprits in disease"6385:(3rded.). New York: Oxford University Press. p.544.1755:

1511:

1415:

identifying portions of the genome that do not code for proteins

596:

552:

7980:

7481:

7097:

6704:

4967:"Genomics. Genome project standards in a new era of sequencing"849:

has been a very important tool (notably in early pre-molecular

7186:

7181:

5182:. Methods in Molecular Biology. Vol.453. pp.v–vi.1635:

modifications on the genetic material of a cell, known as the

1463:

consists of the identification of genomic elements, primarily

1332:

389:

76:

71:

4115:"Here"s an Omical Tale: Scientists Discover Spreading Suffix"3102:"Nobel lecture: Determination of nucleotide sequences in DNA"1932:

Genomics has provided applications in many fields, including

1550:

during various conditions. The most important tools here are

5823:

The Cyanobacteria: Molecular Biology, Genomics and Evolution

5319:

Brenner SE (October 2001). "A tour of structural genomics".

4947:

811:

The cost in US Dollars (USD) to sequence one million bases.

807:

Exponential growth of genome sequence databases since 1995.

7093:

6700:

6209:"Synthetic genomes: The next step for the synthetic genome"1997:

announced the creation of a partially synthetic species of

1592:. The principal difference between structural genomics and996:

informally refers to a field of study in biology ending in

575:

and his team at the Laboratory of Molecular Biology of the

4356:"A strategy of DNA sequencing employing computer programs"6638:

6169:

National Institutes of Health: All of Us Research Program

5929:

Lu YF, Goldstein DB, Angrist M, Cavalleri G (July 2014).

4459:"Genome assembly reborn: recent computational challenges"2445:(10thed.). San Francisco: Pearson Education. 2012.1973:

opened a Preventive Genomics Clinic in August 2019, with

1746:

have played and continue to play a key role in bacterial

1363:

Assembly can be broadly categorized into two approaches:

567:

and were able to determine the sequences of 54 out of 64

4929:

4603:

An Introduction to Next-Generation Sequencing Technology

4064:"Badomics words and the power and peril of the ome-meme"3903:

Drawing the map of life: inside the Human Genome Project

2647:"The wholeness in suffix -omics, -omes, and the word om"1535:

rather than a more traditional "gene-by-gene" approach.

742:

genomes followed in 1986. In 1992, the first eukaryotic

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Holley RW, Everett GA, Madison JT, Zamir A (May 1965).

923:) are all important model animals in medical research.6632:

2476:. Macmillan Science Library. Macmillan Reference USA.1450:

Traditionally, the basic level of annotation is using

1433:

Automatic annotation tools try to perform these steps

1176:. Recently, shotgun sequencing has been supplanted by5980:"Clinical assessment incorporating a personal genome"2499:"Genomics and proteomics in solving brain complexity"8113:

8092:

8076:

8050:

7948:

7436:

7335:

7286:

7230:

7169:

7024:

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6933:

6821:

6738:

6171:. National Institutes of Health. 25 September 2018.5931:"Personalized medicine and human genetic diversity"5668:

Metagenomics: Current Innovations and Future Trends

5541:Hugenholtz P, Goebel BM, Pace NR (September 1998).4173:"Making the most of "omics" for symbiosis research"1538:A major branch of genomics is still concerned with1429:

attaching biological information to these elements.

1256:rate of the camera. The camera takes images of the528:'s publication of the structure of DNA in 1953 and4267:

4265:

3900:

3217:"DNA sequencing with chain-terminating inhibitors"2564:

2467:

6453:"Cancer genomics and pathology: all together now"3215:Sanger F, Nicklen S, Coulson AR (December 1977).520:'s confirmation of the helical structure of DNA,5367:Epigenetics: the ultimate mystery of inheritance3894:

3892:

1631:Epigenomics is the study of the complete set of955:General schema showing the relationships of the436:(hybrid vigour), and other interactions between6569:: CS1 maint: DOI inactive as of January 2024 (5360:

5358:

2624:(Thirded.). Oxford University Press. 20081180:methods, especially for large-scale, automated875:is a model organism for flowering plants. The6153:. The Dark Intelligence Group. 3 January 2020.5643:Metagenomics: Theory, Methods and Applications5219:Marsden RL, Lewis TA, Orengo CA (March 2007).4775:Tucker T, Marra M, Friedman JM (August 2009).4349:

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4030:

3331:

3329:

3123:

3121:

2571:(2nded.). Hoboken, NJ: Wiley-Blackwell.2558:

2556:

2554:

2552:

2550:

2548:

2546:

2544:

2542:

2047:-wide effects to improve our understanding of1758:structure and gene regulation. Also the first7992:

7493:

7109:

6716:

5747:Bacteriophage: Genetics and Molecular Biology4675:Church GM (January 2006). "Genomes for all".2497:Kadakkuzha BM, Puthanveettil SV (July 2013).1613:, i.e. determining protein function from its678:method resulted in the chain-termination, or496:), over beers with Jim Womack, Tom Shows and358:

8:

6610:Annual Review of Genomics and Human Genetics4852:Annual Review of Genomics and Human Genetics4220:McCutcheon JP, von Dohlen CD (August 2011).3987:"Genomics: In search of rare human variants"508:and then as a whole new science discipline.388:. A genome is an organism's complete set of6996:Matrix-assisted laser desorption ionization6668:MIT OpenCourseWare HST.512 Genomic Medicine5935:Cold Spring Harbor Perspectives in Medicine4452:

4450:

4448:

2427:. World Health Organization. Archived from1467:and their localisation, or gene structure.899:compared to most species. The mammals dog (8084:International Society of Genetic Genealogy7999:

7985:

7977:

7500:

7486:

7478:

7116:

7102:

7094:

7064:

6723:

6709:

6701:

5701:Microbiology and Molecular Biology Reviews2425:"WHO definitions of genetics and genomics"1580:Structural genomics seeks to describe the730:. The first complete genome sequence of a432:(one gene affecting more than one trait),365:

351:

32:

7966:Timeline of biology and organic chemistry6676:Machine learning approaches to genomics.6519:

6468:

6433:

6232:

6103:

6054:

6044:

6003:

5954:

5905:

5864:

5796:

5720:

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5607:

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5295:

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5154:

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4800:

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3434:

3309:

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2787:

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2400:

1754:. Historically, they were used to define1483:have important applications in genomics.1444:

1032:as used in molecular biology refers to a5888:O'Donnell CJ, Nabel EG (December 2011).5826:(1sted.). Caister Academic Press.5750:(1sted.). Caister Academic Press.5744:McGrath S, van Sinderen D, eds. (2007).4845:"Next-generation DNA sequencing methods"4726:ten Bosch JR, Grody WW (November 2008).4041:. Chicago: University of Chicago Press.3869:National Human Genome Research Institute1875:to the genomes that have been analyzed.1571:

1065:

7449:List of genetics research organizations6408:Stunnenberg HG, Hubner NC (June 2014).5272:"Expectations from structural genomics"3342:The Stanford Encyclopedia of Philosophy2466:Culver KW, Labow MA (8 November 2002).2233:

1871:, or estimation of the contribution of1372:assembly is computationally difficult (1331:and merging fragments of a much longer683:

40:

6688:Genomics: Scitable by nature education6562:

6494:Roychowdhury S, Chinnaiyan AM (2016).2567:Bioinformatics and functional genomics1721:methods. Recent studies use "shotgun"1197:group required for the formation of a7961:Nobel Prize in Physiology or Medicine7038:European Molecular Biology Laboratory6645:JCVI Comprehensive Microbial Resource5270:Brenner SE, Levitt M (January 2000).4864:10.1146/annurev.genom.9.081307.1643594171:Chaston J, Douglas AE (August 2012).3274:Maxam AM, Gilbert W (February 1977).1899:. It shows dark and white regions on1094:Historically, sequencing was done in7:

5890:"Genomics of cardiovascular disease"5849:"Genomics, health care, and society"4732:The Journal of Molecular Diagnostics2021:Population and conservation genomics1985:Synthetic biology and bioengineering1903:. Each row is vertically aligned at1590:experimental and modeling approaches1584:of every protein encoded by a given1546:, mainly concerned with patterns of1411:, and consists of three main steps:6683:Global map of genomics laboratories5894:The New England Journal of Medicine5853:The New England Journal of Medicine4907:(September–October). Archived from4640:The Journal of Experimental Biology4600:Illumina, Inc. (28 February 2012).3079:(7ed.). London: McGraw Hill.2776:The Journal of Biological Chemistry1232:operations may be run in parallel.746:, chromosome III of brewer's yeast603:DNA-sequencing technology developed563:revealed the triplet nature of the6641:: US government's genome institute5820:Herrero A, Flores E, eds. (2008).4781:American Journal of Human Genetics3427:10.1002/j.1460-2075.1986.tb04464.x2651:Journal of Biomolecular Techniques2594:Intermediate Greek-English Lexicon2341:European Journal of Histochemistry1843:-fixing filamentous cyanobacteria1502:Functional genomics is a field of1475:Sequencing pipelines and databases859:is an often used simple model for14:

5178:Keith JM (2008). Keith JM (ed.).4697:10.1038/scientificamerican0106-463276:"A new method for sequencing DNA"2131:Hi-C (genomic analysis technique)1686:material recovered directly from1594:traditional structural prediction428:(effect of one gene on another),380:is an interdisciplinary field of8154:

8153:

7462:

7461:

7076:

7075:

7063:

6470:10.1111/j.1440-1827.2012.02855.x5707:(2): 238–76, table of contents.5559:10.1128/JB.180.18.4765-4774.19984901:"Powering Preventative Medicine"4039:Genomes and what to make of them2114:

1867:into the evolutionary origin of1308:

1294:

623:

611:

599:in 1976 and 1978, respectively.332:

331:

218:

217:

48:

7016:Chromosome conformation capture6696:Learn All About Genetics Online4146:Scudellari M (1 October 2011).571:in their experiments. In 1972,396:, which refers to the study of6635:: An openfree genomics portal.5713:10.1128/MMBR.67.2.238-276.20034274:"Benchtop sequencers ship off"2158:, an mRNA profiling technology2043:. Population genomics studies1975:Massachusetts General Hospital484:was coined by Tom Roderick, a1:

7044:National Institutes of Health6662:Institute for Genome Sciences6547:10.1007/978-94-007-5561-10_165996:10.1016/S0140-6736(10)60452-74272:Baker M (14 September 2012).3710:Zimmer C (29 December 2009).3194:10.1016/j.jbiotec.2003.08.0082833:10.1126/science.147.3664.14622789:10.1016/S0021-9258(18)97435-12749:10.1016/S0160-9327(03)00061-91993:. In 2010 researchers at the1977:following a month later. The1678:Metagenomics is the study of835:) has long been an important7408:Missing heritability problem6549:(inactive 31 January 2024).6321:10.1016/j.biocon.2010.05.0116127:Robbins R (16 August 2019).6046:10.1371/journal.pgen.10022805847:Hudson KL (September 2011).5609:10.1371/journal.pbio.00500824952:Oxford Nanopore Technologies4568:10.1371/journal.pone.00488374520:10.1016/0022-2836(75)90213-24508:Journal of Molecular Biology3907:. New York NY: Basic Books.3628:10.1126/science.274.5287.5462592:Liddell HG, Scott R (2013).1971:Brigham and Women's Hospital1963:Brigham and Women’s Hospital1730:of the entire living world.1528:protein–protein interactions1418:identifying elements on the1327:Sequence assembly refers to1223:Ion semiconductor sequencing698:independently developed the6960:Structure-based drug design6624:: A BMC journal on Genomics6219:(7347): 403, 405–403, 408.6182:Church GM, Regis E (2012).5947:10.1101/cshperspect.a0085815141:(Database issue): D48–D55.4463:Briefings in Bioinformatics3801:"Human gene number slashed"3686:"Genome Project Statistics"3661:"Complete genomes: Viruses"3614:(5287): 546, 563–546, 567.3336:Darden L, Tabery J (2010).2704:10.1093/gigascience/giac0552335:Cremer T, Cremer C (2006).1649:differentiation/development1028:) respectively. The suffix480:as early as 1926, the term8200:

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1794:strains, seven marine1762:to be sequenced was a1725:or massively parallel1715:microbial biodiversity1669:

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755:Haemophilus influenzae532:'s publication of the16:Discipline in genetics7660:Developmental biology7635:Computational biology7615:Cellular microbiology7444:List of genetic codes7011:Isotope affinity tags6965:Expression proteomics5907:10.1056/NEJMra11052395866:10.1056/NEJMra10105175666:Marco D, ed. (2011).5641:Marco D, ed. (2010).4421:10.1093/nar/9.13.30154081:10.1186/2047-217X-1-63690:Entrez Genome Project3344:(Fall 2010ed.).3340:. In Zalta EN (ed.).3301:10.1073/pnas.74.2.5602014:Mycoplasma genitalium1924:Further information:1886:

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4036:

4035:

4028:

3984:

3983:

3979:

3940:(7422): 56–65.3927:

3926:

3922:

3915:

3898:

3897:

3890:

3881:

3879:

3867:

3866:

3862:

3824:

3823:

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3810:

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3799:

3798:

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3726:

3709:

3708:

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3679:

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3668:

3659:

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3654:

3648:

3605:

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3554:

3553:

3549:

3512:(6373): 38–46.3500:

3499:

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3457:

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3452:

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3407:

3403:

3397:

3354:

3353:

3349:

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3327:

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3214:

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3094:

3087:

3074:

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3069:

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2971:

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2966:

2929:(5350): 82–88.2920:

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2861:

2860:

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2769:

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2364:

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2334:

2333:

2329:

2306:10.1038/nrg23112291:

2290:

2286:

2249:(4356): 740–1.2240:

2239:

2235:

2231:

2226:

2222:Thomas Roderick2202:Transcriptomics2120:

2113:

2110:

2037:microsatellites2023:

1987:

1967:Broad Institute1954:

1946:social sciences1928:

1916:sex chromosomes1881:

1842:

1818:Prochlorococcus1791:Prochlorococcus1782:

1741:

1736:

1676:

1661:

1641:DNA methylation1629:

1623:

1570:

1564:

1548:gene expression1500:

1494:

1489:

1477:

1424:gene prediction1405:

1399:

1387:

1361:

1325:

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1322:

1318:

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1304:

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1225:

1215:

1174:DNA replication1135:

1121:

1113:next-generation1109:high-throughput1092:

1086:

1060:

1054:

1052:Genome analysis987:

979:Main articles:949:

920:Pan troglodytes841:eukaryotic cell724:

716:recombinant DNA704:chemical method660:electrophoresis647:

646:

645:

644:

633:

632:

631:

628:

620:

619:

616:

605:

597:Simian virus 40522:James D. Watson514:

498:Stephen O’Brien455:

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419:systems biology371:

330:

323:

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8024:Types of tests8021:

8015:

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7807:

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7760:Marine biology7757:

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7570:Bioinformatics7567:

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7258:Immunogenetics7255:

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7209:

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7170:Key components7167:

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6420:(6): 689–700.6414:Human Genetics6405:

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5282:(1): 197–200.5262:

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5180:Bioinformatics5170:

5131:"Ensembl 2013"5121:

5057:

5030:(7): 493–503.5014:

4957:

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4921:

4891:

4835:

4825:US 200501009004816:

4787:(2): 142–154.4767:

4738:(6): 484–492.4718:

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2347:(3): 161–176.2327:

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1727:pyrosequencing1694:and microbial1672:Main article:1660:

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1556:bioinformatics1510:) to describe1496:Main article:1493:

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1207:DNA sequencers1191:DNA polymerase1167:DNA polymerase1131:Main article:1120:

1117:

1115:) sequencing.1090:DNA Sequencing1088:Main article:1085:

1082:

1058:Genome project1056:Main article:1053:

1050:

1042:Jonathan Eisen948:

945:

941:bioinformatics905:), brown rat (837:model organism723:

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688:Walter Gilbert676:Plus and Minus664:polyacrylamide641:Walter Gilbert635:

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1811:

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1799:

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1797:Synechococcus1793:

1792:

1787:

1786:cyanobacteria1780:Cyanobacteria1779:

1777:

1774:

1769:

1765:

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1653:tumorigenesis1650:

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1204:

1203:fluorescently1200:

1196:

1192:

1188:

1183:

1179:

1175:

1172:

1168:

1164:

1160:

1159:Sanger method1155:

1153:

1149:

1145:

1141:

1134:

1125:

1118:

1116:

1114:

1110:

1106:

1101:

1097:

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1083:

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1019:

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986:

982:

974:

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929:

924:

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916:

915:

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898:

897:noncoding DNA894:

893:

888:

884:

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868:

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858:

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760:North America757:

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721:

719:

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713:

709:

705:

701:

700:Maxam-Gilbert697:

693:

689:

685:

681:

680:Sanger method677:

673:

670:

669:bacteriophage665:

661:

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652:

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582:

578:

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570:

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526:Francis Crick523:

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329:

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105:

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98:

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65:

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55:

51:

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46:

43:

39:

35:

34:

29:

22:

8158:

7885:Sociobiology7865:Protistology7830:Photobiology7825:Pharmacology7815:Parasitology7810:Paleontology7790:Neuroscience7770:Microbiology7709:

7680:Epidemiology7650:Cytogenetics7610:Cell biology7590:Biosemiotics7580:Biomechanics7560:Biogeography7555:Biochemistry7550:Bacteriology7545:Astrobiology7368:Genetic code7362:

7302:the Americas7278:Quantitative7248:Cytogenetics7243:Conservation7136:Introduction7080:

7068:

6890:Microbiomics6885:Metabolomics6846:Connectomics6805:

6778:Metagenomics6731:

6633:Genomics.org6622:BMC Genomics6538:

6506:(1): 75–88.6503:

6499:

6460:

6456:

6417:

6413:

6382:

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6329:

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5766:

5746:

5739:

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5667:

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5596:PLOS Biology5595:

5585:

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