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Items: 27

1.

Direct detection of early-stage cancers using circulating tumor DNA.

Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MW, Woodward BD, Murphy D, Parpart-Li S, Riley D, Nesselbush M, Sengamalay N, Georgiadis A, Li QK, Madsen MR, Mortensen FV, Huiskens J, Punt C, van Grieken N, Fijneman R, Meijer G, Husain H, Scharpf RB, Diaz LA Jr, Jones S, Angiuoli S, Ørntoft T, Nielsen HJ, Andersen CL, Velculescu VE.

Sci Transl Med. 2017 Aug 16;9(403). pii: eaan2415. doi: 10.1126/scitranslmed.aan2415.

PMID:
28814544
2.

Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease.

Lin M, Bachman K, Cheng Z, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y.

Microb Biotechnol. 2017 Jul;10(4):933-957. doi: 10.1111/1751-7915.12731. Epub 2017 Jun 6.

3.

Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility.

Price EP, Smith ML, Paxinos EE, Tallon LJ, Sadzewicz L, Sengamalay N, Baird RW, Currie BJ, Sarovich DS.

Genome Announc. 2017 Apr 6;5(14). pii: e00053-17. doi: 10.1128/genomeA.00053-17.

4.

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions.

Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C.

Sci Rep. 2016 Oct 18;6:35284. doi: 10.1038/srep35284.

5.

Concurrent Mutations in ATM and Genes Associated with Common γ Chain Signaling in Peripheral T Cell Lymphoma.

Simpson HM, Khan RZ, Song C, Sharma D, Sadashivaiah K, Furusawa A, Liu X, Nagaraj S, Sengamalay N, Sadzewicz L, Tallon LJ, Chen QC, Livak F, Rapoport AP, Kimball A, Banerjee A.

PLoS One. 2015 Nov 4;10(11):e0141906. doi: 10.1371/journal.pone.0141906. eCollection 2015.

6.

Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements.

Chancey ST, Bai X, Kumar N, Drabek EF, Daugherty SC, Colon T, Ott S, Sengamalay N, Sadzewicz L, Tallon LJ, Fraser CM, Tettelin H, Stephens DS.

PLoS One. 2015 Feb 19;10(2):e0116254. doi: 10.1371/journal.pone.0116254. eCollection 2015.

7.

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.

Ioannidis P, Lu Y, Kumar N, Creasy T, Daugherty S, Chibucos MC, Orvis J, Shetty A, Ott S, Flowers M, Sengamalay N, Tallon LJ, Pick L, Dunning Hotopp JC.

BMC Genomics. 2014 Aug 29;15:738. doi: 10.1186/1471-2164-15-738.

8.

Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00203-14. doi: 10.1128/genomeA.00203-14.

9.

Genome sequences of rhinovirus B isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00202-14. doi: 10.1128/genomeA.00202-14.

10.

Genome sequences of rhinovirus a isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00200-14. doi: 10.1128/genomeA.00200-14.

11.

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.

Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J.

Microbiome. 2014 Feb 24;2(1):6. doi: 10.1186/2049-2618-2-6.

12.

Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842.

Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM.

Genome Announc. 2014 Jan 23;2(1). pii: e01180-13. doi: 10.1128/genomeA.01180-13.

13.

Simultaneous transcriptional profiling of bacteria and their host cells.

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengamalay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GS.

PLoS One. 2013 Dec 4;8(12):e80597. doi: 10.1371/journal.pone.0080597. eCollection 2013.

14.

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum.

Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O'Brien K, Sengamalay NA, Tallon LJ, Smith AD, Rayko E, Ahmed I, Le Crom S, Farrant GK, Sgro JY, Olson SA, Bondurant SS, Allen AE, Rabinowicz PD, Sussman MR, Bowler C, Tirichine L.

Nat Commun. 2013;4:2091. doi: 10.1038/ncomms3091. Erratum in: Nat Commun. 2014;5:3028. Allen, Andrew [corrected to Allen, Andrew E].

PMID:
23820484
15.

Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains.

Eppinger M, Daugherty S, Agrawal S, Galens K, Sengamalay N, Sadzewicz L, Tallon L, Cebula TA, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Fraser CM, Ravel J.

Genome Announc. 2013 Feb 28;1(2):e0013412. doi: 10.1128/genomeA.00134-12.

16.

Genomic insights into the emerging human pathogen Mycobacterium massiliense.

Tettelin H, Sampaio EP, Daugherty SC, Hine E, Riley DR, Sadzewicz L, Sengamalay N, Shefchek K, Su Q, Tallon LJ, Conville P, Olivier KN, Holland SM, Fraser CM, Zelazny AM.

J Bacteriol. 2012 Oct;194(19):5450. doi: 10.1128/JB.01200-12.

17.

Draft genome sequences of the diarrheagenic Escherichia coli collection.

Hazen TH, Sahl JW, Redman JC, Morris CR, Daugherty SC, Chibucos MC, Sengamalay NA, Fraser-Liggett CM, Steinsland H, Whittam TS, Whittam B, Manning SD, Rasko DA.

J Bacteriol. 2012 Jun;194(11):3026-7. doi: 10.1128/JB.00426-12.

18.

Genetic deletion of trkB.T1 increases neuromuscular function.

Dorsey SG, Lovering RM, Renn CL, Leitch CC, Liu X, Tallon LJ, Sadzewicz LD, Pratap A, Ott S, Sengamalay N, Jones KM, Barrick C, Fulgenzi G, Becker J, Voelker K, Talmadge R, Harvey BK, Wyatt RM, Vernon-Pitts E, Zhang C, Shokat K, Fraser-Liggett C, Balice-Gordon RJ, Tessarollo L, Ward CW.

Am J Physiol Cell Physiol. 2012 Jan 1;302(1):C141-53. doi: 10.1152/ajpcell.00469.2010. Epub 2011 Oct 5.

19.

Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States.

Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Sengamalay N, Ghedin E, Miller MA, Simonsen L, Viboud C, Holmes EC.

PLoS Pathog. 2008 Aug 22;4(8):e1000133. doi: 10.1371/journal.ppat.1000133. Erratum in: PLoS Pathog. 2008 Dec;4(12). doi.org//10.1371/annotation/1391941e-93d3-48d3-8c9a-b7c6d98f9527.. Sengamalay, Naomi [added].

20.

The evolutionary genetics and emergence of avian influenza viruses in wild birds.

Dugan VG, Chen R, Spiro DJ, Sengamalay N, Zaborsky J, Ghedin E, Nolting J, Swayne DE, Runstadler JA, Happ GM, Senne DA, Wang R, Slemons RD, Holmes EC, Taubenberger JK.

PLoS Pathog. 2008 May 30;4(5):e1000076. doi: 10.1371/journal.ppat.1000076.

21.

Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918.

Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, St George K, Taylor J, Spiro DJ, Sengamalay NA, Ghedin E, Taubenberger JK, Holmes EC.

PLoS Pathog. 2008 Feb 29;4(2):e1000012. doi: 10.1371/journal.ppat.1000012.

22.

Viral genome sequencing by random priming methods.

Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ.

BMC Genomics. 2008 Jan 7;9:5. doi: 10.1186/1471-2164-9-5.

23.

Genome analysis linking recent European and African influenza (H5N1) viruses.

Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Dung do H, Guercio A, Joannis T, Maken Ali AS, Osmani A, Padalino I, Saad MD, Savić V, Sengamalay NA, Yingst S, Zaborsky J, Zorman-Rojs O, Ghedin E, Capua I.

Emerg Infect Dis. 2007 May;13(5):713-8.

24.

Detection of HHV-6B in post-mortem central nervous system tissue of a post-bone marrow transplant recipient: a multi-virus array analysis.

Yao K, Akyani N, Donati D, Sengamalay N, Fotheringham J, Ghedin E, Bishop M, Barrett J, Kashanchi F, Jacobson S.

J Clin Virol. 2006 Dec;37 Suppl 1:S57-62.

PMID:
17276371
25.

Stochastic processes are key determinants of short-term evolution in influenza a virus.

Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC.

PLoS Pathog. 2006 Dec;2(12):e125. Erratum in: PLoS Pathog. 2006 Dec;2(12):e138. Ghedi, Elodie [corrected to Ghedin, Elodie].

26.

Differential HHV-6A gene expression in T cells and primary human astrocytes based on multi-virus array analysis.

Yao K, Mandel M, Akyani N, Maynard K, Sengamalay N, Fotheringham J, Ghedin E, Kashanchi F, Jacobson S.

Glia. 2006 Jun;53(8):789-98.

PMID:
16541415
27.

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL.

Nature. 2005 Oct 20;437(7062):1162-6. Epub 2005 Oct 5.

PMID:
16208317

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