Fuhrman JA - Search Results

1

A network-based integrated framework for predicting virus-prokaryote interactions.

Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. Wang W, et al. Among authors: fuhrman ja. NAR Genom Bioinform. 2020 Jun;2(2):lqaa044. doi: 10.1093/nargab/lqaa044. Epub 2020 Jun 23. NAR Genom Bioinform. 2020. PMID: 32626849 Free PMC article.

2

A dynamic programming algorithm for binning microbial community profiles.

Ruan Q, Steele JA, Schwalbach MS, Fuhrman JA, Sun F. Ruan Q, et al. Among authors: fuhrman ja. Bioinformatics. 2006 Jun 15;22(12):1508-14. doi: 10.1093/bioinformatics/btl114. Epub 2006 Mar 27. Bioinformatics. 2006. PMID: 16567364

3

Ruan Q, Dutta D, Schwalbach MS, Steele JA, Fuhrman JA, Sun F. Ruan Q, et al. Among authors: fuhrman ja. Bioinformatics. 2006 Oct 15;22(20):2532-8. doi: 10.1093/bioinformatics/btl417. Epub 2006 Jul 31. Bioinformatics. 2006. PMID: 16882654

4

Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Kim DY, Chow CE, Sachdeva R, Jones AC, Schwalbach MS, Rose JM, Hewson I, Patel A, Sun F, Caron DA, Fuhrman JA. Steele JA, et al. Among authors: fuhrman ja. ISME J. 2011 Sep;5(9):1414-25. doi: 10.1038/ismej.2011.24. Epub 2011 Mar 24. ISME J. 2011. PMID: 21430787 Free PMC article.

5

Accurate genome relative abundance estimation based on shotgun metagenomic reads.

Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F. Xia LC, et al. Among authors: fuhrman ja. PLoS One. 2011;6(12):e27992. doi: 10.1371/journal.pone.0027992. Epub 2011 Dec 6. PLoS One. 2011. PMID: 22162995 Free PMC article.

6

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, Fuhrman JA, Sun F. Xia LC, et al. Among authors: fuhrman ja. BMC Syst Biol. 2011;5 Suppl 2(Suppl 2):S15. doi: 10.1186/1752-0509-5-S2-S15. Epub 2011 Dec 14. BMC Syst Biol. 2011. PMID: 22784572 Free PMC article.

7

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data.

Xia LC, Ai D, Cram J, Fuhrman JA, Sun F. Xia LC, et al. Among authors: fuhrman ja. Bioinformatics. 2013 Jan 15;29(2):230-7. doi: 10.1093/bioinformatics/bts668. Epub 2012 Nov 23. Bioinformatics. 2013. PMID: 23178636 Free PMC article.

8

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes.

Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA. Cram JA, et al. Among authors: fuhrman ja. ISME J. 2015 Dec;9(12):2573-86. doi: 10.1038/ismej.2015.76. Epub 2015 May 19. ISME J. 2015. PMID: 25989373 Free PMC article.

9

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

Xia LC, Ai D, Cram JA, Liang X, Fuhrman JA, Sun F. Xia LC, et al. Among authors: fuhrman ja. BMC Bioinformatics. 2015 Sep 21;16:301. doi: 10.1186/s12859-015-0732-8. BMC Bioinformatics. 2015. PMID: 26390921 Free PMC article.

10

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

Lu YY, Chen T, Fuhrman JA, Sun F. Lu YY, et al. Among authors: fuhrman ja. Bioinformatics. 2017 Mar 15;33(6):791-798. doi: 10.1093/bioinformatics/btw290. Bioinformatics. 2017. PMID: 27256312

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