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Items: 23

1.

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ.

mSystems. 2019 Feb 12;4(1). pii: e00337-18. doi: 10.1128/mSystems.00337-18. eCollection 2019 Jan-Feb.

2.

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.

Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L.

Front Microbiol. 2018 Oct 30;9:2559. doi: 10.3389/fmicb.2018.02559. eCollection 2018.

3.

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.

Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R.

Clin Gastroenterol Hepatol. 2019 Jan;17(2):218-230. doi: 10.1016/j.cgh.2018.09.017. Epub 2018 Sep 18. Review.

4.

Are microbiome studies ready for hypothesis-driven research?

Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R.

Curr Opin Microbiol. 2018 Aug;44:61-69. doi: 10.1016/j.mib.2018.07.002. Epub 2018 Jul 27. Review.

PMID:
30059804
5.

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.

BMC Syst Biol. 2018 Jun 11;12(1):66. doi: 10.1186/s12918-018-0587-5.

6.

American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

7.

Creating a 3D microbial and chemical snapshot of a human habitat.

Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC.

Sci Rep. 2018 Feb 27;8(1):3669. doi: 10.1038/s41598-018-21541-4.

8.

Bringing the Dynamic Microbiome to Life with Animations.

Vázquez-Baeza Y, Gonzalez A, Smarr L, McDonald D, Morton JT, Navas-Molina JA, Knight R.

Cell Host Microbe. 2017 Jan 11;21(1):7-10. doi: 10.1016/j.chom.2016.12.009.

9.

Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy.

Smarr L, Hyde ER, McDonald D, Sandborn WJ, Knight R.

Methods Inf Med. 2017;56(6):442-447. doi: 10.3414/ME17-01-0036. Epub 2018 Feb 10. No abstract available.

PMID:
29582916
10.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

OMICS. 2014 Jan;18(1):10-4. doi: 10.1089/omi.2013.0149.

11.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, MacNealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

Big Data. 2013 Dec;1(4):196-201. doi: 10.1089/big.2013.0039.

PMID:
27447251
12.

Quantifying your body: a how-to guide from a systems biology perspective.

Smarr L.

Biotechnol J. 2012 Aug;7(8):980-91. doi: 10.1002/biot.201100495.

PMID:
22887886
13.

CAMERA: a community resource for metagenomics.

Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M.

PLoS Biol. 2007 Mar;5(3):e75. No abstract available.

14.

Reforming the malpractice system.

Smarr LE.

Front Health Serv Manage. 2003 Fall;20(1):27-30; discussion 39-42. No abstract available.

PMID:
14510315
15.

Head-on collision of two equal mass black holes.

Anninos P, Hobill D, Seidel E, Smarr L, Suen WM.

Phys Rev D Part Fields. 1995 Aug 15;52(4):2044-2058. No abstract available.

PMID:
10019425
16.

Dynamics of Apparent and Event Horizons.

Anninos P, Bernstein D, Brandt S, Libson J, Massó J, Seidel E, Smarr L, Suen WM, Walker P.

Phys Rev Lett. 1995 Jan 30;74(5):630-633. No abstract available.

PMID:
10058808
17.

Malpractice claims. Does the past predict the future?

Smarr LE.

JAMA. 1994 Nov 9;272(18):1453-4. No abstract available.

PMID:
7933429
18.

Numerically generated axisymmetric black hole spacetimes: Numerical methods and code tests.

Bernstein D, Hobill D, Seidel E, Smarr L, Towns J.

Phys Rev D Part Fields. 1994 Oct 15;50(8):5000-5024. No abstract available.

PMID:
10018152
19.

Dynamics of black hole apparent horizons.

Anninos P, Bernstein D, Brandt SR, Hobill D, Seidel E, Smarr L.

Phys Rev D Part Fields. 1994 Sep 15;50(6):3801-3815. No abstract available.

PMID:
10018023
20.

Initial data for the black hole plus Brill wave spacetime.

Bernstein D, Hobill D, Seidel E, Smarr L.

Phys Rev D Part Fields. 1994 Sep 15;50(6):3760-3782. No abstract available.

PMID:
10018019
21.

Collision of two black holes.

Anninos P, Hobill D, Seidel E, Smarr L, Suen WM.

Phys Rev Lett. 1993 Nov 1;71(18):2851-2854. No abstract available.

PMID:
10054795
22.

Numerically generated black-hole spacetimes: Interaction with gravitational waves.

Abrahams A, Bernstein D, Hobill D, Seidel E, Smarr L.

Phys Rev D Part Fields. 1992 May 15;45(10):3544-3558. No abstract available.

PMID:
10014249
23.

An approach to complexity: numerical computations.

Smarr LL.

Science. 1985 Apr 26;228(4698):403-8.

PMID:
17746870

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