Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Daniel A. Dalquen"'
Autor:
Adrian M. Altenhoff, Maximilian J. Telford, Bartlomiej Tomiczek, David Dylus, Natasha Glover, Steven Müller, Christophe Dessimoz, Daniel A. Dalquen, Magdalena Zarowiecki, Jeremy Levy, Alex Warwick Vesztrocy
Publikováno v:
Genome research, vol. 29, no. 7, pp. 1152-1163
Genome Research, 29 (7)
Genome Research, 29 (7)
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4442f9b3c272fc14662bff06e39acaeb
https://doi.org/10.1101/gr.243212.118
https://doi.org/10.1101/gr.243212.118
Publikováno v:
PLoS ONE, Vol 8, Iss 2, p e56925 (2013)
The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology infer
Externí odkaz:
https://doaj.org/article/3bca8898af154b70a6ae8c4a6a98c501
Publikováno v:
Bayesian Anal. 13, no. 4 (2018), 1037-1063
We discuss a few principles to guide the design of efficient Metropolis–Hastings proposals for well-behaved target distributions without deeply divided modes. We illustrate them by developing and evaluating novel proposal kernels using a variety of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b8af74e2aa695c73f815ac58b70bead2
https://doi.org/10.1214/17-ba1084
https://doi.org/10.1214/17-ba1084
Autor:
Maximilian J. Telford, David Dylus, Magdalena Zarowiecki, Jeremy Levy, Natasha Glover, Daniel A. Dalquen, Adrian M. Altenhoff, Steven Müller, Bartlomiej Tomiczek, Christophe Dessimoz, Alex Warwick Vesztrocy
Publikováno v:
Genome Res
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0239d474a022249836dd4365e0bc1b20
https://doi.org/10.1101/gr.266809.120
https://doi.org/10.1101/gr.266809.120
Autor:
Christophe Dessimoz, Daniel A. Dalquen
Publikováno v:
Genome Biology and Evolution
Genome biology and evolution
Genome biology and evolution
Bidirectional best hits (BBH), which entails identifying the pairs of genes in two different genomes that are more similar to each other than either is to any other gene in the other genome, is a simple and widely used method to infer orthology. A re
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2aed7b46be72a165d392b8a81e7e85f1
http://europepmc.org/articles/PMC3814191
http://europepmc.org/articles/PMC3814191
Autor:
Leszek P. Pryszcz, Peer Bork, Adrian M. Altenhoff, Kimmen Sjölander, Toni Gabaldón, Christian von Mering, Odile Lecompte, Todd DeLuca, Clément-Marie Train, Maria Jesus Martin, Brigitte Boeckmann, Cécile Pereira, Kristoffer Forslund, Matthieu Muffato, Christophe Dessimoz, Suzanna E. Lewis, Salvador Capella-Gutierrez, Erik L. L. Sonnhammer, Paul Thomas, Benjamin Linard, Jaime Huerta-Cepas, Fabian Schreiber, Damian Szklarczyk, Ioannis Xenarios, Alan Wilter Sousa da Silva, Lars Juhl Jensen, Daniel A. Dalquen
Publikováno v:
Altenhoff, A M, Boeckmann, B, Capella-Gutierrez, S, Dalquen, D A, DeLuca, T, Forslund, K, Huerta-Cepas, J, Linard, B, Pereira, C, Pryszcz, L P, Schreiber, F, da Silva, A S, Szklarczyk, D, Train, C-M, Bork, P, Lecompte, O, von Mering, C, Xenarios, I, Sjölander, K, Jensen, L J, Martin, M J, Muffato, M, Gabaldón, T, Lewis, S E, Thomas, P D, Sonnhammer, E, Dessimoz, C & Quest for Orthologs consortium 2016, ' Standardized benchmarking in the quest for orthologs ', Nature Methods, vol. 13, pp. 425-30 . https://doi.org/10.1038/nmeth.3830
Nature Methods
Nature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Nature Methods, 13 (5)
Altenhoff, AM; Boeckmann, B; Capella-Gutierrez, S; Dalquen, DA; DeLuca, T; Forslund, K; et al.(2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5), 425-430. doi: 10.1038/nmeth.3830. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/59r1v5ts
Nature Methods, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Recercat. Dipósit de la Recerca de Catalunya
instname
Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Nature Methods, 13 (5)
Altenhoff, AM; Boeckmann, B; Capella-Gutierrez, S; Dalquen, DA; DeLuca, T; Forslund, K; et al.(2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5), 425-430. doi: 10.1038/nmeth.3830. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/59r1v5ts
Nature Methods, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Recercat. Dipósit de la Recerca de Catalunya
instname
Nature methods
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications acr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60866a263954de38b31c376023291243
https://curis.ku.dk/ws/files/187625712/nmeth.3830.pdf
https://curis.ku.dk/ws/files/187625712/nmeth.3830.pdf
Publikováno v:
Mol Biol Evol
Molecular Biology and Evolution
Molecular Biology and Evolution
In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9ae9805830c2ebd2f9825ac25e6519ab
http://mbe.oxfordjournals.org/content/29/4/1115
http://mbe.oxfordjournals.org/content/29/4/1115
Publikováno v:
Systematic biology. 66(3)
We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4ee4271da38d9a26ed8bfd0d24bc4b16
https://pubmed.ncbi.nlm.nih.gov/27486180
https://pubmed.ncbi.nlm.nih.gov/27486180
Publikováno v:
2006 Digest of Technical Papers International Conference on Consumer Electronics.
This paper evaluates hybrid hardware-software structures for acceleration and power savings in audio coding algorithms. Using the well known MPEG I/II layer 3 (mp3) decoder as example, we demonstrate the general principles and trade-offs. The results
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7cb9ab36505f0b583eae6052722ba15d
https://doi.org/10.1109/icce.2006.1598421
https://doi.org/10.1109/icce.2006.1598421
Publikováno v:
Schirrmeister, B E, Dalquen, D A, Anisimova, M & Bagheri, H C 2012, ' Gene copy number variation and its significance in cyanobacterial phylogeny ', BMC Microbiology, vol. 12, 177 . https://doi.org/10.1186/1471-2180-12-177
BMC Microbiology, Vol 12, Iss 1, p 177 (2012)
BMC Microbiology
BMC Microbiology, 12
BMC Microbiology, Vol 12, Iss 1, p 177 (2012)
BMC Microbiology
BMC Microbiology, 12
Background In eukaryotes, variation in gene copy numbers is often associated with deleterious effects, but may also have positive effects. For prokaryotes, studies on gene copy number variation are rare. Previous studies have suggested that high numb
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e1f5cbbbe2e7961df5ac17829f5e9f0
https://doi.org/10.1186/1471-2180-12-177
https://doi.org/10.1186/1471-2180-12-177