Rasko DA - Search Results

1

Best practices on the differential expression analysis of multi-species RNA-seq.

Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Chung M, et al. Among authors: rasko da. Genome Biol. 2021 Apr 29;22(1):121. doi: 10.1186/s13059-021-02337-8. Genome Biol. 2021. PMID: 33926528 Free PMC article. Review.

2

Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate MRSA-M2.

Harro JM, Daugherty S, Bruno VM, Jabra-Rizk MA, Rasko DA, Shirtliff ME. Harro JM, et al. Among authors: rasko da. Genome Announc. 2013 Jan;1(1):e00037-12. doi: 10.1128/genomeA.00037-12. Epub 2013 Jan 31. Genome Announc. 2013. PMID: 23405318 Free PMC article.

3

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Dugan VG, et al. PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014. PLoS One. 2014. PMID: 24936976 Free PMC article.

4

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.

Crabtree J, Agrawal S, Mahurkar A, Myers GS, Rasko DA, White O. Crabtree J, et al. Among authors: rasko da. Bioinformatics. 2014 Nov 1;30(21):3125-7. doi: 10.1093/bioinformatics/btu505. Epub 2014 Jul 29. Bioinformatics. 2014. PMID: 25075113 Free PMC article.

5

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates.

Hazen TH, Daugherty SC, Shetty A, Mahurkar AA, White O, Kaper JB, Rasko DA. Hazen TH, et al. Among authors: rasko da. Front Microbiol. 2015 Jun 12;6:569. doi: 10.3389/fmicb.2015.00569. eCollection 2015. Front Microbiol. 2015. PMID: 26124752 Free PMC article.

6

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.

Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. Chibucos MC, et al. Among authors: rasko da. Nat Commun. 2016 Jul 22;7:12218. doi: 10.1038/ncomms12218. Nat Commun. 2016. PMID: 27447865 Free PMC article.

7

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli.

Hazen TH, Michalski J, Luo Q, Shetty AC, Daugherty SC, Fleckenstein JM, Rasko DA. Hazen TH, et al. Among authors: rasko da. Sci Rep. 2017 Jun 14;7(1):3513. doi: 10.1038/s41598-017-03489-z. Sci Rep. 2017. PMID: 28615618 Free PMC article.

8

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions.

Hazen TH, Daugherty SC, Shetty AC, Nataro JP, Rasko DA. Hazen TH, et al. Among authors: rasko da. mSystems. 2017 Jul 25;2(4):e00024-17. doi: 10.1128/mSystems.00024-17. eCollection 2017 Jul-Aug. mSystems. 2017. PMID: 28766584 Free PMC article.

9

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC. Robinson KM, et al. Among authors: rasko da. Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep. Microb Genom. 2017. PMID: 29114401 Free PMC article.

10

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses.

Chung M, Teigen L, Liu H, Libro S, Shetty A, Kumar N, Zhao X, Bromley RE, Tallon LJ, Sadzewicz L, Fraser CM, Rasko DA, Filler SG, Foster JM, Michalski ML, Bruno VM, Dunning Hotopp JC. Chung M, et al. Among authors: rasko da. Sci Rep. 2018 Sep 6;8(1):13377. doi: 10.1038/s41598-018-31420-7. Sci Rep. 2018. PMID: 30190541 Free PMC article.

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