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Items: 39

1.

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC.

Microb Genom. 2020 Jan;6(1). doi: 10.1099/mgen.0.000320.

2.

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics.

Chung M, Teigen LE, Libro S, Bromley RE, Olley D, Kumar N, Sadzewicz L, Tallon LJ, Mahurkar A, Foster JM, Michalski ML, Dunning Hotopp JC.

mSystems. 2019 Dec 3;4(6). pii: e00596-19. doi: 10.1128/mSystems.00596-19.

3.

TwinBLAST: When Two Is Better than One.

Dunning Hotopp JC, Matsumura J, Bromley RE, Riley DR, Agrawal S, Sparklin B, Mattick J, Crabtree J, Mahurkar A.

Microbiol Resour Announc. 2019 Aug 29;8(35). pii: e00842-19. doi: 10.1128/MRA.00842-19.

4.

Dual RNA-Seq of Chlamydia and Host Cells.

Marsh JW, Hayward RJ, Shetty A, Mahurkar A, Humphrys MS, Myers GSA.

Methods Mol Biol. 2019;2042:123-135. doi: 10.1007/978-1-4939-9694-0_9.

PMID:
31385273
5.

Whole blood transcriptomic profiles can differentiate vulnerability to chronic low back pain.

Dorsey SG, Renn CL, Griffioen M, Lassiter CB, Zhu S, Huot-Creasy H, McCracken C, Mahurkar A, Shetty AC, Jackson-Cook CK, Kim H, Henderson WA, Saligan L, Gill J, Colloca L, Lyon DE, Starkweather AR.

PLoS One. 2019 May 16;14(5):e0216539. doi: 10.1371/journal.pone.0216539. eCollection 2019.

6.

CD34 defines melanocyte stem cell subpopulations with distinct regenerative properties.

Joshi SS, Tandukar B, Pan L, Huang JM, Livak F, Smith BJ, Hodges T, Mahurkar AA, Hornyak TJ.

PLoS Genet. 2019 Apr 24;15(4):e1008034. doi: 10.1371/journal.pgen.1008034. eCollection 2019 Apr.

7.

The miRNA Expression Profile of Experimental Autoimmune Encephalomyelitis Reveals Novel Potential Disease Biomarkers.

Venkatesha SH, Dudics S, Song Y, Mahurkar A, Moudgil KD.

Int J Mol Sci. 2018 Dec 11;19(12). pii: E3990. doi: 10.3390/ijms19123990.

8.

A comparative analysis of library prep approaches for sequencing low input translatome samples.

Song Y, Milon B, Ott S, Zhao X, Sadzewicz L, Shetty A, Boger ET, Tallon LJ, Morell RJ, Mahurkar A, Hertzano R.

BMC Genomics. 2018 Sep 21;19(1):696. doi: 10.1186/s12864-018-5066-2.

9.

Metaviz: interactive statistical and visual analysis of metagenomic data.

Wagner J, Chelaru F, Kancherla J, Paulson JN, Zhang A, Felix V, Mahurkar A, Elmqvist N, Corrada Bravo H.

Nucleic Acids Res. 2018 Apr 6;46(6):2777-2787. doi: 10.1093/nar/gky136.

10.

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.

Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep.

11.

Identification of a gene expression signature associated with the metastasis suppressor function of NME1: prognostic value in human melanoma.

Leonard MK, McCorkle JR, Snyder DE, Novak M, Zhang Q, Shetty AC, Mahurkar AA, Kaetzel DM.

Lab Invest. 2018 Mar;98(3):327-338. doi: 10.1038/labinvest.2017.108. Epub 2017 Oct 23.

12.

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Nov 9;551(7679):256. doi: 10.1038/nature24485. Epub 2017 Oct 12.

PMID:
29022944
13.

Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20. Erratum in: Nature. 2017 Oct 12;:.

14.

Corrigendum: Brain feminization requires active repression of masculinization via DNA methylation.

Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, Russo SJ, Devine SE, McCarthy MM.

Nat Neurosci. 2017 May 25;20(6):896. doi: 10.1038/nn0617-896a. No abstract available.

PMID:
28542152
15.

Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments.

Marsh JW, Hayward RJ, Shetty AC, Mahurkar A, Humphrys MS, Myers GSA.

Brief Bioinform. 2018 Nov 27;19(6):1115-1129. doi: 10.1093/bib/bbx043.

16.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

Agrawal S, Arze C, Adkins RS, Crabtree J, Riley D, Vangala M, Galens K, Fraser CM, Tettelin H, White O, Angiuoli SV, Mahurkar A, Fricke WF.

BMC Genomics. 2017 Apr 27;18(1):332. doi: 10.1186/s12864-017-3717-3.

17.

Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing.

Reho JJ, Shetty A, Dippold RP, Mahurkar A, Fisher SA.

Physiol Rep. 2015 Jul;3(7). pii: e12450. doi: 10.14814/phy2.12450.

18.

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.

Front Microbiol. 2015 Jun 12;6:569. doi: 10.3389/fmicb.2015.00569. eCollection 2015.

19.

Functional dynamics of the gut microbiome in elderly people during probiotic consumption.

Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, Mahurkar A, Ravel J, Haverkamp M, Fiorino AM, Botelho C, Andreyeva I, Hibberd PL, Fraser CM.

mBio. 2015 Apr 14;6(2). pii: e00231-15. doi: 10.1128/mBio.00231-15.

20.

New signaling pathways govern the host response to C. albicans infection in various niches.

Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM.

Genome Res. 2015 May;25(5):679-89. doi: 10.1101/gr.187427.114. Epub 2015 Apr 9.

21.

Brain feminization requires active repression of masculinization via DNA methylation.

Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, Russo SJ, Devine SE, McCarthy MM.

Nat Neurosci. 2015 May;18(5):690-7. doi: 10.1038/nn.3988. Epub 2015 Mar 30. Erratum in: Nat Neurosci. 2017 May 25;20(6):896.

22.

Map of open and closed chromatin domains in Drosophila genome.

Milon B, Sun Y, Chang W, Creasy T, Mahurkar A, Shetty A, Nurminsky D, Nurminskaya M.

BMC Genomics. 2014 Nov 18;15:988. doi: 10.1186/1471-2164-15-988.

23.

MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL.

Landon AL, Muniandy PA, Shetty AC, Lehrmann E, Volpon L, Houng S, Zhang Y, Dai B, Peroutka R, Mazan-Mamczarz K, Steinhardt J, Mahurkar A, Becker KG, Borden KL, Gartenhaus RB.

Nat Commun. 2014 Nov 18;5:5413. doi: 10.1038/ncomms6413.

24.

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.

25.

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

Crabtree J, Agrawal S, Mahurkar A, Myers GS, Rasko DA, White O.

Bioinformatics. 2014 Nov 1;30(21):3125-7. doi: 10.1093/bioinformatics/btu505. Epub 2014 Jul 29.

26.

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.

27.

MetaRef: a pan-genomic database for comparative and community microbial genomics.

Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N.

Nucleic Acids Res. 2014 Jan;42(Database issue):D617-24. doi: 10.1093/nar/gkt1078. Epub 2013 Nov 6.

28.

Cardiomyocyte-specific perilipin 5 overexpression leads to myocardial steatosis and modest cardiac dysfunction.

Wang H, Sreenivasan U, Gong DW, O'Connell KA, Dabkowski ER, Hecker PA, Ionica N, Konig M, Mahurkar A, Sun Y, Stanley WC, Sztalryd C.

J Lipid Res. 2013 Apr;54(4):953-65. doi: 10.1194/jlr.M032466. Epub 2013 Jan 23.

29.

Microtubules underlie dysfunction in duchenne muscular dystrophy.

Khairallah RJ, Shi G, Sbrana F, Prosser BL, Borroto C, Mazaitis MJ, Hoffman EP, Mahurkar A, Sachs F, Sun Y, Chen YW, Raiteri R, Lederer WJ, Dorsey SG, Ward CW.

Sci Signal. 2012 Aug 7;5(236):ra56. doi: 10.1126/scisignal.2002829.

30.

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.

Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG.

Stand Genomic Sci. 2011 Apr 29;4(2):244-51. doi: 10.4056/sigs.1223234. Epub 2011 Apr 25.

31.

Natural genetic variation caused by small insertions and deletions in the human genome.

Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE.

Genome Res. 2011 Jun;21(6):830-9. doi: 10.1101/gr.115907.110. Epub 2011 Apr 1.

32.

Ergatis: a web interface and scalable software system for bioinformatics workflows.

Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV.

Bioinformatics. 2010 Jun 15;26(12):1488-92. doi: 10.1093/bioinformatics/btq167. Epub 2010 Apr 22.

33.

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.

Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N.

Nucleic Acids Res. 2010 Jan;38(Database issue):D754-64. doi: 10.1093/nar/gkp832. Epub 2009 Oct 22.

34.

IDEA: Interactive Display for Evolutionary Analyses.

Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC.

BMC Bioinformatics. 2008 Dec 8;9:524. doi: 10.1186/1471-2105-9-524.

35.

Study of the spread of a cold instantaneous heavy gas release with surface heat transfer and variable entrainment.

Kumar A, Mahurkar A, Joshi A.

J Hazard Mater. 2003 Jul 18;101(2):157-77.

PMID:
12927733
36.

Constructing retinal fundus photomontages. A new computer-based method.

Mahurkar AA, Vivino MA, Trus BL, Kuehl EM, Datiles MB 3rd, Kaiser-Kupfer MI.

Invest Ophthalmol Vis Sci. 1996 Jul;37(8):1675-83.

PMID:
8675411
37.

Scheimpflug photography and postcataract surgery posterior capsule opacification.

Lasa MS, Datiles MB 3rd, Magno BV, Mahurkar A.

Ophthalmic Surg. 1995 Mar-Apr;26(2):110-3.

PMID:
7596535
38.

Quantitative analysis of retroillumination images.

Vivino MA, Mahurkar A, Trus B, Lopez ML, Datiles M.

Eye (Lond). 1995;9 ( Pt 1):77-84.

PMID:
7713254
39.

Reproducibility study of posterior subcapsular opacities on the NEI retroillumination image analysis system.

Lopez ML, Datiles MB 3rd, Podgor MJ, Vivino MA, Mahurkar AA, Lasa SM.

Eye (Lond). 1994;8 ( Pt 6):657-61.

PMID:
7867822

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