Posada D - Search Results

1

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data.

Edrisi M, Valecha MV, Chowdary SBV, Robledo S, Ogilvie HA, Posada D, Zafar H, Nakhleh L. Edrisi M, et al. Among authors: posada d. Bioinformatics. 2022 Jun 24;38(Suppl 1):i195-i202. doi: 10.1093/bioinformatics/btac254. Bioinformatics. 2022. PMID: 35758771 Free PMC article.

2

ProtTest 3: fast selection of best-fit models of protein evolution.

Darriba D, Taboada GL, Doallo R, Posada D. Darriba D, et al. Among authors: posada d. Bioinformatics. 2011 Apr 15;27(8):1164-5. doi: 10.1093/bioinformatics/btr088. Epub 2011 Feb 17. Bioinformatics. 2011. PMID: 21335321 Free PMC article.

3

jmodeltest.org: selection of nucleotide substitution models on the cloud.

Santorum JM, Darriba D, Taboada GL, Posada D. Santorum JM, et al. Among authors: posada d. Bioinformatics. 2014 May 1;30(9):1310-1. doi: 10.1093/bioinformatics/btu032. Epub 2014 Jan 21. Bioinformatics. 2014. PMID: 24451621 Free PMC article.

4

A comparison of tools for the simulation of genomic next-generation sequencing data.

Escalona M, Rocha S, Posada D. Escalona M, et al. Among authors: posada d. Nat Rev Genet. 2016 Aug;17(8):459-69. doi: 10.1038/nrg.2016.57. Epub 2016 Jun 20. Nat Rev Genet. 2016. PMID: 27320129 Free PMC article. Review.

5

NGSphy: phylogenomic simulation of next-generation sequencing data.

Escalona M, Rocha S, Posada D. Escalona M, et al. Among authors: posada d. Bioinformatics. 2018 Jul 15;34(14):2506-2507. doi: 10.1093/bioinformatics/bty146. Bioinformatics. 2018. PMID: 29534152

6

Sensitivity to sequencing depth in single-cell cancer genomics.

Alves JM, Posada D. Alves JM, et al. Among authors: posada d. Genome Med. 2018 Apr 16;10(1):29. doi: 10.1186/s13073-018-0537-2. Genome Med. 2018. PMID: 29661213 Free PMC article.

7

CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples.

Posada D. Posada D. Mol Biol Evol. 2020 May 1;37(5):1535-1542. doi: 10.1093/molbev/msaa025. Mol Biol Evol. 2020. PMID: 32027371 Free PMC article.

8

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.

Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Sapoval N, et al. Among authors: posada d. bioRxiv [Preprint]. 2020 Jul 2:2020.07.02.184481. doi: 10.1101/2020.07.02.184481. bioRxiv. 2020. PMID: 32637955 Free PMC article. Updated. Preprint.

9

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.

Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. Sapoval N, et al. Among authors: posada d. Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120. Epub 2021 Feb 18. Genome Res. 2021. PMID: 33602693 Free PMC article.

10

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data.

Kozlov A, Alves JM, Stamatakis A, Posada D. Kozlov A, et al. Among authors: posada d. Genome Biol. 2022 Jan 26;23(1):37. doi: 10.1186/s13059-021-02583-w. Genome Biol. 2022. PMID: 35081992 Free PMC article.

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