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Items: 1 to 50 of 83

1.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.

Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ.

Microbiome. 2018 Dec 17;6(1):226. doi: 10.1186/s40168-018-0605-2.

2.

Curcumin gum formulation for prevention of oral cavity head and neck squamous cell carcinoma.

Boven L, Holmes SP, Latimer B, McMartin K, Ma X, Moore-Medlin T, Khandelwal AR, McLarty J, Nathan CO.

Laryngoscope. 2018 Nov 13. doi: 10.1002/lary.27542. [Epub ahead of print]

PMID:
30421467
3.

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.

Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A, Thomas BC, Shaw GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA.

Genome Res. 2018 Oct;28(10):1467-1480. doi: 10.1101/gr.236000.118. Epub 2018 Sep 19.

PMID:
30232199
4.

Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses.

Kronstad LM, Seiler C, Vergara R, Holmes SP, Blish CA.

J Immunol. 2018 Oct 1;201(7):2117-2131. doi: 10.4049/jimmunol.1800161. Epub 2018 Aug 24.

PMID:
30143589
6.

Latent variable modeling for the microbiome.

Sankaran K, Holmes SP.

Biostatistics. 2018 Jun 3. doi: 10.1093/biostatistics/kxy018. [Epub ahead of print]

PMID:
29868846
7.

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow.

Proctor DM, Fukuyama JA, Loomer PM, Armitage GC, Lee SA, Davis NM, Ryder MI, Holmes SP, Relman DA.

Nat Commun. 2018 Feb 14;9(1):681. doi: 10.1038/s41467-018-02900-1.

8.

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing.

Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW.

J Infect Dis. 2017 Aug 1;216(3):387-391. doi: 10.1093/infdis/jix338.

9.

Induced Pluripotent Stem Cell-Derived Neural Stem Cell Therapy Enhances Recovery in an Ischemic Stroke Pig Model.

Baker EW, Platt SR, Lau VW, Grace HE, Holmes SP, Wang L, Duberstein KJ, Howerth EW, Kinder HA, Stice SL, Hess DC, Mao H, West FD.

Sci Rep. 2017 Aug 30;7(1):10075. doi: 10.1038/s41598-017-10406-x.

10.

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Callahan BJ, DiGiulio DB, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9966-9971. doi: 10.1073/pnas.1705899114. Epub 2017 Aug 28.

11.

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.

Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman DA, Holmes SP.

PLoS Comput Biol. 2017 Aug 18;13(8):e1005706. doi: 10.1371/journal.pcbi.1005706. eCollection 2017 Aug.

12.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.

Callahan BJ, McMurdie PJ, Holmes SP.

ISME J. 2017 Dec;11(12):2639-2643. doi: 10.1038/ismej.2017.119. Epub 2017 Jul 21.

13.

Comparison of ultrasonography and magnetic resonance imaging to arthroscopy for diagnosing medial meniscal lesions in dogs with cranial cruciate ligament deficiency.

Franklin SP, Cook JL, Cook CR, Shaikh LS, Clarke KM, Holmes SP.

J Am Vet Med Assoc. 2017 Jul 1;251(1):71-79. doi: 10.2460/javma.251.1.71.

PMID:
28621599
14.

The effect of platelet-rich plasma on osseous healing in dogs undergoing high tibial osteotomy.

Franklin SP, Burke EE, Holmes SP.

PLoS One. 2017 May 16;12(5):e0177597. doi: 10.1371/journal.pone.0177597. eCollection 2017.

15.

Evaluation of magnetic resonance imaging for the differentiation of inflammatory, neoplastic, and vascular intradural spinal cord diseases in the dog.

Masciarelli AE, Griffin JF 4th, Fosgate GT, Hecht S, Mankin JM, Holmes SP, Platt SR, Kent M, Pancotto TE, Chen AV, Levine JM.

Vet Radiol Ultrasound. 2017 Jul;58(4):444-453. doi: 10.1111/vru.12501. Epub 2017 Apr 18.

PMID:
28421647
16.

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.

Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, Günthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KCE, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW.

EBioMedicine. 2017 Apr;18:225-235. doi: 10.1016/j.ebiom.2017.03.024. Epub 2017 Mar 19.

17.

Utility of MRI for Characterizing Articular Cartilage Pathology in Dogs with Medial Coronoid Process Disease.

Franklin SP, Burke EE, Holmes SP.

Front Vet Sci. 2017 Feb 24;4:25. doi: 10.3389/fvets.2017.00025. eCollection 2017.

18.

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2017 Jan 19;6. pii: e24879. doi: 10.7554/eLife.24879. No abstract available.

19.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP.

Version 2. F1000Res. 2016 Jun 24 [revised 2016 Jan 1];5:1492. eCollection 2016.

20.

Cranioplasty Using Titanium Mesh After Skull Tumor Resection in Five Dogs.

Rosselli DD, Platt SR, Freeman C, O'Neill J, Kent M, Holmes SP.

Vet Surg. 2017 Jan;46(1):67-74. doi: 10.1111/vsu.12577. Epub 2016 Nov 2.

PMID:
27805731
21.

Hydrocephalus secondary to obstruction of the lateral apertures in two dogs.

Kent M, Glass EN, Haley AC, Shaikh LS, Sequel M, Blas-Machado U, Bishop TM, Holmes SP, Platt SR.

Aust Vet J. 2016 Nov;94(11):415-422. doi: 10.1111/avj.12510.

PMID:
27785804
22.

MRI-Based Assessment of Intralesional Delivery of Bone Marrow-Derived Mesenchymal Stem Cells in a Model of Equine Tendonitis.

Scharf A, Holmes SP, Thoresen M, Mumaw J, Stumpf A, Peroni J.

Stem Cells Int. 2016;2016:8610964. Epub 2016 Sep 26.

23.

Evaluation of a New Surgical Treatment for Equine Hind Limb Proximal Suspensory Desmitis.

Brokken MT, Schneider RK, Roberts GD, Holmes SP, Gavin PR, Sampson SN, Farnsworth KD, Dahlgren LA.

Vet Surg. 2016 Oct;45(7):868-878. doi: 10.1111/vsu.12527. Epub 2016 Aug 22.

PMID:
27545972
24.

DADA2: High-resolution sample inference from Illumina amplicon data.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP.

Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23.

25.

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation.

Rhee SY, Sankaran K, Varghese V, Winters MA, Hurt CB, Eron JJ, Parkin N, Holmes SP, Holodniy M, Shafer RW.

J Virol. 2016 Jun 10;90(13):6058-6070. doi: 10.1128/JVI.00495-16. Print 2016 Jul 1.

26.

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle.

Gorvitovskaia A, Holmes SP, Huse SM.

Microbiome. 2016 Apr 12;4:15. doi: 10.1186/s40168-016-0160-7.

27.

MANDIBULAR SQUAMOUS CELL CARCINOMA IN A BOBCAT (LYNX RUFUS).

Sladakovic I, Burnum A, Blas-Machado U, Kelly LS, Garner BC, Holmes SP, Divers SJ.

J Zoo Wildl Med. 2016 Mar;47(1):370-3. doi: 10.1638/2015-0197.1.

PMID:
27010306
28.

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2016 Feb 15;5. pii: e10670. doi: 10.7554/eLife.10670. Erratum in: Elife. 2017 Jan 19;6:.

29.

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea.

Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA.

Nat Commun. 2016 Feb 3;7:10516. doi: 10.1038/ncomms10516.

30.

A SURVEY OF RADIOLOGISTS AND REFERRING VETERINARIANS REGARDING IMAGING REPORTS.

Weissman A, Solano M, Taeymans O, Holmes SP, Jiménez D, Barton B.

Vet Radiol Ultrasound. 2016 Mar-Apr;57(2):124-9. doi: 10.1111/vru.12310. Epub 2015 Dec 17.

PMID:
26677167
31.

FOCUSED ASSESSMENT WITH SONOGRAPHY AS AN AID FOR THE DIAGNOSIS OF GASTROINTESTINAL PERFORATION IN A BOBCAT ( FELIS RUFUS ).

Mejia-Fava J, Mayer J, Divers SJ, Cohen EB, Schmiedt C, Holmes SP.

J Zoo Wildl Med. 2015 Dec;46(4):921-4. doi: 10.1638/2013-0116.1.

PMID:
26667552
32.

IMAGING DIAGNOSIS-VERTEBRAL POLYOSTOTIC LYMPHOMA IN A GERIATRIC DOG.

Kornder J, Platt SR, Eagleson J, Kent M, Holmes SP.

Vet Radiol Ultrasound. 2016 Jul;57(4):E42-5. doi: 10.1111/vru.12312. Epub 2015 Nov 23.

PMID:
26592800
33.

Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.

Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA.

PLoS One. 2015 Nov 13;10(11):e0142825. doi: 10.1371/journal.pone.0142825. eCollection 2015.

34.

Use of a Nitinol Wire Stent for Management of Severe Tracheal Stenosis in an Eclectus Parrot (Eclectus roratus).

Mejia-Fava J, Holmes SP, Radlinsky M, Johnson D, Ellis AE, Mayer J, Schnellbacher R, Divers SJ.

J Avian Med Surg. 2015 Sep;29(3):238-49. doi: 10.1647/2013-041.

PMID:
26378671
35.

IMAGING DIAGNOSIS--RADIOGRAPHIC, ULTRASONOGRAPHIC, COMPUTED TOMOGRAPHIC, AND FLUOROSCOPIC APPEARANCE OF A DISTAL PELVIC LIMB ARTERIOVENOUS MALFORMATION IN A YOUNG GERMAN SHEPHERD DOG.

Shaikh LS, Holmes SP, Selberg KT, Jarrett C, Holladay SD, Thomason J, Coleman AE.

Vet Radiol Ultrasound. 2016 Mar-Apr;57(2):E16-21. doi: 10.1111/vru.12290. Epub 2015 Sep 7.

PMID:
26346616
36.

Temporal and spatial variation of the human microbiota during pregnancy.

DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11060-5. doi: 10.1073/pnas.1502875112. Epub 2015 Aug 17.

37.

Functional metastatic parathyroid adenocarcinoma in a dog.

Kishi EN, Holmes SP, Abbott JR, Bacon NJ.

Can Vet J. 2014 Apr;55(4):383-8. Erratum in: Can Vet J. 2014 May;55(5):494.

38.

Development and characterization of a Yucatan miniature biomedical pig permanent middle cerebral artery occlusion stroke model.

Platt SR, Holmes SP, Howerth EW, Duberstein KJJ, Dove CR, Kinder HA, Wyatt EL, Linville AV, Lau VW, Stice SL, Hill WD, Hess DC, West FD.

Exp Transl Stroke Med. 2014 Mar 23;6(1):5. doi: 10.1186/2040-7378-6-5.

39.

Evaluation of standard magnetic resonance characteristics used to differentiate neoplastic, inflammatory, and vascular brain lesions in dogs.

Young BD, Fosgate GT, Holmes SP, Wolff CA, Chen-Allen AV, Kent M, Platt SR, Savage MY, Schatzberg SJ, Levine JM.

Vet Radiol Ultrasound. 2014 Jul-Aug;55(4):399-406. doi: 10.1111/vru.12137. Epub 2014 Jan 28.

PMID:
24467341
40.

Gait analysis in a pre- and post-ischemic stroke biomedical pig model.

Duberstein KJ, Platt SR, Holmes SP, Dove CR, Howerth EW, Kent M, Stice SL, Hill WD, Hess DC, West FD.

Physiol Behav. 2014 Feb 10;125:8-16. doi: 10.1016/j.physbeh.2013.11.004. Epub 2013 Nov 25.

PMID:
24286894
41.

HIV-1 transmission networks in a small world.

Pennings PS, Holmes SP, Shafer RW.

J Infect Dis. 2014 Jan 15;209(2):180-2. doi: 10.1093/infdis/jit525. Epub 2013 Oct 22. No abstract available.

42.

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota.

Kashyap PC, Marcobal A, Ursell LK, Smits SA, Sonnenburg ED, Costello EK, Higginbottom SK, Domino SE, Holmes SP, Relman DA, Knight R, Gordon JI, Sonnenburg JL.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):17059-64. doi: 10.1073/pnas.1306070110. Epub 2013 Sep 23.

43.

Canine vaginal leiomyoma diagnosed by CT vaginourethrography.

Weissman A, Jiménez D, Torres B, Cornell K, Holmes SP.

J Am Anim Hosp Assoc. 2013 Nov-Dec;49(6):394-7. doi: 10.5326/JAAHA-MS-5922. Epub 2013 Sep 19.

PMID:
24051257
44.

Detection of cytomegalovirus drug resistance mutations by next-generation sequencing.

Sahoo MK, Lefterova MI, Yamamoto F, Waggoner JJ, Chou S, Holmes SP, Anderson MW, Pinsky BA.

J Clin Microbiol. 2013 Nov;51(11):3700-10. doi: 10.1128/JCM.01605-13. Epub 2013 Aug 28.

45.

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1.

Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW.

Antimicrob Agents Chemother. 2013 Sep;57(9):4290-4299. doi: 10.1128/AAC.00614-13. Epub 2013 Jun 24.

46.

Adrenal gland function in a dog following unilateral complete adrenalectomy and contralateral partial adrenalectomy.

Larson RN, Schmiedt CW, Wang A, Lawrence J, Howerth EW, Holmes SP, Grey SW.

J Am Vet Med Assoc. 2013 May 15;242(10):1398-404. doi: 10.2460/javma.242.10.1398.

PMID:
23634685
47.

Differential tolerance to copper, but no evidence of population-level genetic differences in a widely-dispersing native barnacle.

Gall ML, Holmes SP, Dafforn KA, Johnston EL.

Ecotoxicology. 2013 Jul;22(5):929-37. doi: 10.1007/s10646-013-1063-z. Epub 2013 Mar 19.

PMID:
23508295
48.

PRC2/EED-EZH2 complex is up-regulated in breast cancer lymph node metastasis compared to primary tumor and correlates with tumor proliferation in situ.

Yu H, Simons DL, Segall I, Carcamo-Cavazos V, Schwartz EJ, Yan N, Zuckerman NS, Dirbas FM, Johnson DL, Holmes SP, Lee PP.

PLoS One. 2012;7(12):e51239. doi: 10.1371/journal.pone.0051239. Epub 2012 Dec 10.

49.

Bilateral lumbar hernias in a domestic shorthair cat.

Olin SJ, Holmes SP, Jeffs A, Cornell KK.

J Am Vet Med Assoc. 2012 Dec 1;241(11):1495-8. doi: 10.2460/javma.241.11.1495.

PMID:
23176243
50.

Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment.

Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW.

Antimicrob Agents Chemother. 2013 Jan;57(1):343-9. doi: 10.1128/AAC.01601-12. Epub 2012 Oct 31.

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