Mirarab S - Search Results

1

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Mirarab S, Warnow T. Mirarab S, et al. Bioinformatics. 2015 Jun 15;31(12):i44-52. doi: 10.1093/bioinformatics/btv234. Bioinformatics. 2015. PMID: 26072508 Free PMC article.

2

The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.

Rachtman E, Balaban M, Bafna V, Mirarab S. Rachtman E, et al. Among authors: mirarab s. Mol Ecol Resour. 2020 May;20(3). doi: 10.1111/1755-0998.13135. Epub 2020 Feb 4. Mol Ecol Resour. 2020. PMID: 31943790

3

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Zhu Q, et al. Among authors: mirarab s. Nat Commun. 2019 Dec 2;10(1):5477. doi: 10.1038/s41467-019-13443-4. Nat Commun. 2019. PMID: 31792218 Free PMC article.

4

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. Asnicar F, et al. Among authors: mirarab s. Nat Commun. 2020 May 19;11(1):2500. doi: 10.1038/s41467-020-16366-7. Nat Commun. 2020. PMID: 32427907 Free PMC article.

5

FastSP: linear time calculation of alignment accuracy.

Mirarab S, Warnow T. Mirarab S, et al. Bioinformatics. 2011 Dec 1;27(23):3250-8. doi: 10.1093/bioinformatics/btr553. Epub 2011 Oct 7. Bioinformatics. 2011. PMID: 21984754

6

SEPP: SATé-enabled phylogenetic placement.

Mirarab S, Nguyen N, Warnow T. Mirarab S, et al. Pac Symp Biocomput. 2012:247-58. doi: 10.1142/9789814366496_0024. Pac Symp Biocomput. 2012. PMID: 22174280

7

MRL and SuperFine+MRL: new supertree methods.

Nguyen N, Mirarab S, Warnow T. Nguyen N, et al. Among authors: mirarab s. Algorithms Mol Biol. 2012 Jan 26;7(1):3. doi: 10.1186/1748-7188-7-3. Algorithms Mol Biol. 2012. PMID: 22280525 Free PMC article.

8

Inferring optimal species trees under gene duplication and loss.

Bayzid MS, Mirarab S, Warnow T. Bayzid MS, et al. Among authors: mirarab s. Pac Symp Biocomput. 2013:250-61. doi: 10.1142/9789814447973_0025. Pac Symp Biocomput. 2013. PMID: 23424130

9

ASTRAL: genome-scale coalescent-based species tree estimation.

Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. Mirarab S, et al. Bioinformatics. 2014 Sep 1;30(17):i541-8. doi: 10.1093/bioinformatics/btu462. Bioinformatics. 2014. PMID: 25161245 Free PMC article.

10

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

Mirarab S, Bayzid MS, Warnow T. Mirarab S, et al. Syst Biol. 2016 May;65(3):366-80. doi: 10.1093/sysbio/syu063. Epub 2014 Aug 26. Syst Biol. 2016. PMID: 25164915

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