OMA standalone: orthology inference among public and custom genomes and transcriptomes

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)

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

Designing Simple and Efficient Markov Chain Monte Carlo Proposal Kernels

Autor: Ziheng Yang, Daniel A. Dalquen, Yuttapong Thawornwattana

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

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https://doi.org/10.1214/17-ba1084

Standardized benchmarking in the quest for orthologs

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

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

Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species

Autor: Tianqi Zhu, Ziheng Yang, Daniel A. Dalquen

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

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https://pubmed.ncbi.nlm.nih.gov/27486180

Gene copy number variation and its significance in cyanobacterial phylogeny

Autor: Bettina E. Schirrmeister, Maria Anisimova, Homayoun C. Bagheri, Daniel A. Dalquen

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

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