Literatura académica sobre el tema "Tandem duplication"

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Artículos de revistas sobre el tema "Tandem duplication"

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Pluciennik, Anna, Ravi R. Iyer, Pawel Parniewski y Robert D. Wells. "Tandem Duplication". Journal of Biological Chemistry 275, n.º 37 (30 de junio de 2000): 28386–97. http://dx.doi.org/10.1074/jbc.m000154200.

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Takahashi, Tadashi, Atsushi Sato, Masahiro Ogawa, Yoshiki Hanya y Tetsuya Oguma. "Targeted Tandem Duplication of a Large Chromosomal Segment in Aspergillus oryzae". Applied and Environmental Microbiology 80, n.º 15 (16 de mayo de 2014): 4547–58. http://dx.doi.org/10.1128/aem.00300-14.

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ABSTRACTWe describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment inAspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5′-deletedpyrGupstream of the region targeted for tandem chromosomal duplication and a 3′-deletedpyrGdownstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.
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Pan, Deng y Liqing Zhang. "Tandemly Arrayed Genes in Vertebrate Genomes". Comparative and Functional Genomics 2008 (2008): 1–11. http://dx.doi.org/10.1155/2008/545269.

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Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.
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Lin, Ming-Tseh, Li-Hui Tseng, Katie Beierl, Antony Hsieh, Michele Thiess, Nadine Chase, Amanda Stafford, Mark J. Levis, James R. Eshleman y Christopher D. Gocke. "Tandem Duplication PCR". Diagnostic Molecular Pathology 22, n.º 3 (septiembre de 2013): 149–55. http://dx.doi.org/10.1097/pdm.0b013e31828308a1.

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Broughton, R. E. y T. E. Dowling. "Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera." Genetics 138, n.º 1 (1 de septiembre de 1994): 179–90. http://dx.doi.org/10.1093/genetics/138.1.179.

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Abstract Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation.
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Naseeb, Samina, Ryan M. Ames, Daniela Delneri y Simon C. Lovell. "Rapid functional and evolutionary changes follow gene duplication in yeast". Proceedings of the Royal Society B: Biological Sciences 284, n.º 1861 (23 de agosto de 2017): 20171393. http://dx.doi.org/10.1098/rspb.2017.1393.

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Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of Saccharomyces cerevisiae carrying tandem and non-tandem duplications of the singleton gene IFA38 to monitor (i) the fate of the duplicates in different conditions, including time scale and asymmetry of gene loss, and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes, but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem IFA38 gene copy in a surprisingly short time, within only a few generations. This gene loss appears to be asymmetric and dependent on genome location, since the original IFA38 copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
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Fernandes, Gustavo, Mirela Souto, Frederico Costa, Edite Oliveira y Bernardo Garicochea. "Familial Lymphoproliferative Malignancies and Tandem Duplication of NF1 Gene". Case Reports in Oncological Medicine 2014 (2014): 1–4. http://dx.doi.org/10.1155/2014/685857.

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Background. Neurofibromatosis type 1 is a genetic disorder caused by loss-of-function mutations in a tumor suppressor gene (NF1) which codifies the protein neurofibromin. The frequent genetic alterations that modify neurofibromin function are deletions and insertions. Duplications are rare and phenotype in patients bearing duplication of NF1 gene is thought to be restricted to developmental abnormalities, with no reference to cancer susceptibility in these patients. We evaluated a patient who presented with few clinical signs of neurofibromatosis type 1 and a conspicuous personal and familiar history of different types of cancer, especially lymphoproliferative malignancies. The coding region of the NF-1 gene was analyzed by real-time polymerase chain reaction and direct sequencing. Multiplex ligation-dependent probe amplification was performed to detect the number of mutant copies. The NF1 gene analysis showed the following alterations: mosaic duplication of NF1, TRAF4, and MYO1D. Fluorescence in situ hybridization using probes (RP5-1002G3 and RP5-92689) flanking NF1 gene in 17q11.2 and CEP17 for 17q11.11.1 was performed. There were three signals (RP5-1002G3conRP5-92689) in the interphases analyzed and two signals (RP5-1002G3conRP5-92689) in 93% of cells. These findings show a tandem duplication of 17q11.2.Conclusion. The case suggests the possibility that NF1 gene duplication may be associated with a phenotype characterized by lymphoproliferative disorders.
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BENSON, GARY. "Sequence Alignment with Tandem Duplication". Journal of Computational Biology 4, n.º 3 (enero de 1997): 351–67. http://dx.doi.org/10.1089/cmb.1997.4.351.

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Yang, J. "On Counting Tandem Duplication Trees". Molecular Biology and Evolution 21, n.º 6 (12 de febrero de 2004): 1160–63. http://dx.doi.org/10.1093/molbev/msh115.

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Penso-Dolfin, L., T. Wu y C. D. Greenman. "The combinatorics of tandem duplication". Discrete Applied Mathematics 194 (octubre de 2015): 1–22. http://dx.doi.org/10.1016/j.dam.2015.05.014.

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Tesis sobre el tema "Tandem duplication"

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Bertrand, Denis. "Étude et inférence d'arbres de duplication en tandem". Montpellier 2, 2005. http://www.theses.fr/2005MON20180.

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Dorrance, Adrienne M. "The Partial Tandem Duplication of the MLL (MLL PTD)in Leukemogenesis". The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1203712889.

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Dorrance, Adrienne M. "The role of the partial tandem duplication of the MLL (MLL PTD) in leukemogenesis". Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1203712889.

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Austin, Stephen J. "The prognostic significance of the mixed lineage leukaemia partial tandem duplication in acute myeloid leukaemia". Thesis, Cardiff University, 2010. http://orca.cf.ac.uk/54154/.

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This study concerns a specific molecular genetic mutation, the mixed lineage leukaemia partial tandem duplication ( MLL PTD). MLL is a transcriptional regulator that known to be instrumental in both normal haematopoiesis and in leukaemogenesis. This study aimed to evaluate the prognostic importance of this abnormality through investigation of its influence on clinical outcome, its utility as a marker of minimal residual disease (MRD) and the downstream effects of its expression. A qualitative PCR assay was established and determined the frequency of MLL PTD to be 5.2% in de novo AML. MLL PTD was found to be a useful independent marker being associated with a greater risk of relapse and a reduction of relapse free survival and overall survival. A quantitative PCR (QPCR) assay was developed that reliably distinguished AML-related MLL PTDs from the low level of background MLL PTDs occurring normally. Despite a high rate of cytogenetic clonal evolution MLL PTD expression remained stabled between diagnosis and relapse, making it a suitable marker for MRD. Results also suggested the QPCR assay could determine onset of remission and prediction of relapse. Gene expression profiling was used to identify a gene signature unique to the MLL PTD and was found to be distinct from that associated with MLL translocation. Analysis of the gene signature also identified three candidate chemotherapy compounds predicted to antagonise the effects of the MLL PTD. The results of this study could prove instrumental in improving the treatment of MLL PTD patients.
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Audemard, Eric. "Détection des duplications en tandem au niveau nucléique à l'aide de la théorie des flots". Toulouse 3, 2011. http://thesesups.ups-tlse.fr/1448/.

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Après un rappel des notions fondamentales de biologie moléculaire et plus particulièrement des duplications en tandem, la thèse présente un panorama des outils existants permettant de détecter des régions homologues à grande échelle, en se focalisant sur les méthodes de chaînage d'ancres. Le document introduit alors un formalisme général de modélisation basé sur les graphes. Une nouvelle méthode de chaînage, capable de produire un ensemble de chaînes de score optimal et satisfaisant des contraintes de cohérences assurant une interprétation aisée des résultats est formulée, en exploitant la théorie des flots de coût minimum. Cette méthode est évaluée sur des problèmes de détection de duplications segmentales chez les plantes puis intégrée dans un pipeline de détection de grande régions dupliquées en tandem directement à partir de la séquence génomique. Cet outil est évalué sur le génome de la plante modèle Arabidopsis thaliana et confronté à l'annotation du génome, montrant ses capacités à détecter des régions dupliquées impliquant des éléments non-codants
After a quick introduction to molecular biology and more specifically tandem duplications, the thesis presents an overview of existing tools for detecting large scale homologuous regions, witha focus on anchor chaining methods. The thesis introduces a new graph-based general modelling formalism. A new chaining method, which is able to produce an optimal set of chains that satisfies specific consistency constraints that aim at easier interpretation is described, using minimum cost flow theory. This method is evaluated on segmental duplications detection in plants and then integrated in a pipeline targeted at tandem duplication detection directly from DNA. This tool is evaluated on the Arabidopsis thaliana genome and compared to the annotation, showing that it is able to detect tandem duplicated regions involving non coding elements
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Sagit, Rauan. "Variation in length of proteins by repeats and disorder regions". Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-88553.

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Protein-coding genes evolve together with their genome and acquire changes, some of which affect the length of their protein products. This explains why equivalent proteins from different species can exhibit length differences. Variation in length of proteins during evolution arguably presents a large number of possibilities for improvement and innovation of protein structure and function. In order to contribute to an increased understanding of this process, we have studied variation caused by tandem domain duplications and insertions or deletions of intrinsically disordered residues. The study of two proteins, Nebulin and Filamin, together with a broader study of long repeat proteins (>10 domain repeats), began by confirming that tandem domains evolve by internal duplications. Next, we show that vertebrate Nebulins evolved by duplications of a seven-domain unit, yet the most recent duplications utilized different gene parts as duplication units. However, Filamin exhibits a checkered duplication pattern, indicating that duplications were followed by similarity erosions that were hindered at particular domains due to the presence of equivalent binding motifs. For long repeat proteins, we found that human segmental duplications are over-represented in long repeat genes. Additionally, domains that have formed long repeats achieved this primarily by duplications of two or more domains at a time. The study of homologous protein pairs from the well-characterized eukaryotes nematode, fruit fly and several fungi, demonstrated a link between variation in length and variation in the number of intrinsically disordered residues. Next, insertions and deletions (indels) estimated from HMM-HMM pairwise alignments showed that disordered residues are clearly more frequent among indel than non-indel residues. Additionally, a study of raw length differences showed that more than half of the variation in fungi proteins is composed of disordered residues. Finally, a model of indels and their immediate surroundings suggested that disordered indels occur in already disordered regions rather than in ordered regions.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: In press. Paper 4: Manuscript.

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Yavaş, Gökhan. "Algorithms for Characterizing Structural Variation in Human Genome". Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1279345476.

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Garcia, Joana Cristina. "Evolution of respiratory adaptations in hydrothermal vent scale-worms (Polynoidae)". Paris 6, 2009. http://hal.upmc.fr/tel-01112539.

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Hydrothermal vents (HV) are deep-sea ecosystems where hypoxia/anoxia is one of the major constraints. Respiratory pigments play a key function in the adaptation to hypoxia. HV polynoids are abundant, diverse and widely distributed and are the only ones to possess hemoglobins (Hb), and these are unique among annelids. The goal of this work was to know their evolutionary history. There are 2 types of Hb in HV polynoids: 1- and 4-domains. While they are extracellular, they are more related to intracellular globins that to annelid extracellular ones, indicating a distinct origin. We studied the evolutionary history of the 4-domain gene Hb and found that originated from the tandem duplication of a myoglobin-like ancestral. Both globin types possess residues in the heme pocket that are responsible for the high oxygen affinity in other organisms' Hb. But the adaptive value of these Hb probably resides in their expression at high levels. Plus, some amino acid sites were shown to be under positive selection (PS). Some are located in the heme pocket where they might affect functional properties. Others are in areas where they can affect interactions between subunits and domains.
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Thomas, Antoine. "Problèmes de réarrangement avec marqueurs génomiques dupliqués". Phd thesis, Université des Sciences et Technologie de Lille - Lille I, 2014. http://tel.archives-ouvertes.fr/tel-01067114.

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La compréhension de la dynamique des réarrangements génomiques est importante en phylogénie. La phylogénie est l'étude de l'évolution des espèces. Un but majeur est d'établir les relations d'évolution au sein d'un groupe d'espèces, pour déterminer la topologie de l'arbre d'évolution formé par ce groupe et des ancêtres communs à certains sous-ensembles. Pour ce faire, il est naturellement très utile de disposer d'un moyen d'évaluer les distances évolutionnaires relatives entre des espèces, ou encore d'être capable d'inférer à un groupe d'espèces le génome d'un ancêtre commun à celles-ci. Ce travail de thèse, dans la lignée d'autres travaux, consiste à élaborer de tels moyens, ici dans des cas particuliers où les génomes possèdent des gènes en multiples copies, ce qui complique les choses. Plusieurs hypotèses explicatives de la présence de duplications ont été considérées, des formules de distance ainsi que des algorithmes de calcul de scénarios ont été élaborés, accompagnés de preuves de complexité.
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Messer, Philipp W. [Verfasser]. "Tandem Duplications in the Human Genome / Philipp Messer". Berlin : Freie Universität Berlin, 2008. http://d-nb.info/102286713X/34.

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Libros sobre el tema "Tandem duplication"

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Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima y Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.

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Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.
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Capítulos de libros sobre el tema "Tandem duplication"

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Taylor, William R. y Michael I. Sadowski. "Protein Products of Tandem Gene Duplication: A Structural View". En Evolution after Gene Duplication, 133–62. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9780470619902.ch7.

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Zhang, Louxin, Bin Ma y Lusheng Wang. "Efficient Methods for Inferring Tandem Duplication History". En Lecture Notes in Computer Science, 97–111. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45784-4_8.

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Bernt, Matthias, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao y Martin Middendorf. "Finding All Sorting Tandem Duplication Random Loss Operations". En Combinatorial Pattern Matching, 301–13. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02441-2_27.

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Bertrand, Denis y Olivier Gascuel. "Topological Rearrangements and Local Search Method for Tandem Duplication Trees". En Lecture Notes in Computer Science, 374–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30219-3_32.

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Cicalese, Ferdinando y Nicolò Pilati. "The Tandem Duplication Distance Problem Is Hard over Bounded Alphabets". En Lecture Notes in Computer Science, 179–93. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-79987-8_13.

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Sammeth, Michael, Thomas Weniger, Dag Harmsen y Jens Stoye. "Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)". En Lecture Notes in Computer Science, 276–90. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11557067_23.

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Elemento, Olivier y Olivier Gascuel. "An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees". En Combinatorial Pattern Matching, 96–108. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/3-540-44888-8_8.

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Choi, Eun-Young, Keyur Patel, Marie Reine Haddad, Ling Yi, Courtney Holmes, David S. Goldstein, Amalia Dutra, Evgenia Pak y Stephen G. Kaler. "Tandem Duplication of Exons 1–7 Neither Impairs ATP7A Expression Nor Causes a Menkes Disease Phenotype". En JIMD Reports, 57–63. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/8904_2014_391.

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Zhu, Binhai. "Tandem Duplications, Segmental Duplications and Deletions, and Their Applications". En Computer Science – Theory and Applications, 79–102. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-50026-9_6.

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Poulton, J., M. E. Deadman, M. Solymar, S. Ramcharan y R. M. Gardiner. "Direct tandem duplications of mitochondrial DNA in mitochondrial myopathy". En Molecular Basis of Neurological Disorders and Their Treatment, 191–99. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3114-8_18.

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Actas de conferencias sobre el tema "Tandem duplication"

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Benson, Gary. "Sequence alignment with tandem duplication". En the first annual international conference. New York, New York, USA: ACM Press, 1997. http://dx.doi.org/10.1145/267521.267526.

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Jain, Siddharth, Farzad Farnoud y Jehoshua Bruck. "Capacity and expressiveness of genomic tandem duplication". En 2015 IEEE International Symposium on Information Theory (ISIT). IEEE, 2015. http://dx.doi.org/10.1109/isit.2015.7282795.

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Tang, Mengxiang, Michael Waterman y Shibu Yooseph. "Zinc finger gene clusters and tandem gene duplication". En the fifth annual international conference. New York, New York, USA: ACM Press, 2001. http://dx.doi.org/10.1145/369133.369241.

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Liu, Xuan, Shing-Wan Choi, Thomas K. F. Wong, Tak-Wah Lam y Siu-Ming Yiu. "Detection of novel tandem duplication with next-generation sequencing". En the 2nd ACM Conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2147805.2147861.

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Tang, Yuanyuan y Farzad Farnoud. "Error-correcting Codes for Short Tandem Duplication and Substitution Errors". En 2020 IEEE International Symposium on Information Theory (ISIT). IEEE, 2020. http://dx.doi.org/10.1109/isit44484.2020.9174444.

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Yehezkeally, Yonatan y Moshe Schwartz. "Uncertainty of Reconstructing Multiple Messages from Uniform-Tandem-Duplication Noise". En 2020 IEEE International Symposium on Information Theory (ISIT). IEEE, 2020. http://dx.doi.org/10.1109/isit44484.2020.9174322.

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Yehezkeally, Yonatan y Moshe Schwartz. "Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors". En 2018 IEEE International Symposium on Information Theory (ISIT). IEEE, 2018. http://dx.doi.org/10.1109/isit.2018.8437731.

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Chaudhuri, Kamalika, Kevin Chen, Radu Mihaescu y Satish Rao. "On the tandem duplication-random loss model of genome rearrangement". En the seventeenth annual ACM-SIAM symposium. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1109557.1109619.

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SIROTININA, E. A., E. V. ROMANOVA y D. YU SHERBAKOV. "TANDEM DUPLICATION RANDOM LOSS EVENTS INFLUENCED TO GENE ORDER CHANGES IN BAIKALIAN AMPHIPODS". En 5TH MOSCOW INTERNATIONAL CONFERENCE "MOLECULAR PHYLOGENETICSAND BIODIVERSITY BIOBANKING". TORUS PRESS, 2018. http://dx.doi.org/10.30826/molphy2018-71.

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Hampton, Oliver A., Navin Rustagi, Jie Li, Liu Xi, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel y David A. Wheeler. "Abstract 4856: ITD Assembler: An algorithm for internal tandem duplication discovery from short-read sequencing data". En Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4856.

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