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Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria.

Riniker S, Landrum GA, Montanari F, Villalba SD, Maier J, Jansen JM, Walters WP, Shelat AA.

Version 2. F1000Res. 2017 Jul 17 [revised 2018 Jan 1];6:1136. doi: 10.12688/f1000research.11905.2. eCollection 2017.


D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.


Ecotracer: analyzing concentration of contaminants and radioisotopes in an aquatic spatial-dynamic food web model.

Walters WJ, Christensen V.

J Environ Radioact. 2018 Jan;181:118-127. doi: 10.1016/j.jenvrad.2017.11.008. Epub 2017 Nov 13.


Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites.

Reddivari L, Veeramachaneni DNR, Walters WA, Lozupone C, Palmer J, Hewage MKK, Bhatnagar R, Amir A, Kennett MJ, Knight R, Vanamala JKP.

mSystems. 2017 Oct 10;2(5). pii: e00093-17. doi: 10.1128/mSystems.00093-17. eCollection 2017 Sep-Oct.


Dynamics of the human gut microbiome in inflammatory bowel disease.

Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK.

Nat Microbiol. 2017 Feb 13;2:17004. doi: 10.1038/nmicrobiol.2017.4.


Curcumin decreases malignant characteristics of glioblastoma stem cells via induction of reactive oxygen species.

Gersey ZC, Rodriguez GA, Barbarite E, Sanchez A, Walters WM, Ohaeto KC, Komotar RJ, Graham RM.

BMC Cancer. 2017 Feb 4;17(1):99. doi: 10.1186/s12885-017-3058-2.


Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes.

Johnson EL, Heaver SL, Walters WA, Ley RE.

J Mol Med (Berl). 2017 Jan;95(1):1-8. doi: 10.1007/s00109-016-1492-2. Epub 2016 Nov 29. Review.


Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.


Understanding covariate shift in model performance.

McGaughey G, Walters WP, Goldman B.

Version 3. F1000Res. 2016 Apr 7 [revised 2016 Jan 1];5. pii: Chem Inf Sci-597. eCollection 2016.


Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.

Taylor DL, Walters WA, Lennon NJ, Bochicchio J, Krohn A, Caporaso JG, Pennanen T.

Appl Environ Microbiol. 2016 Nov 21;82(24):7217-7226. Print 2016 Dec 15.


D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK.

J Comput Aided Mol Des. 2016 Sep;30(9):651-668. Epub 2016 Sep 30.


Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia.

Singh J, Johnson RC, Schlett CD, Elassal EM, Crawford KB, Mor D, Lanier JB, Law NN, Walters WA, Teneza-Mora N, Bennett JW, Hall ER, Millar EV, Ellis MW, Merrell DS.

mSphere. 2016 Oct 5;1(5). pii: e00232-16. eCollection 2016 Sep-Oct.


Prediction of Protein Pairs Sharing Common Active Ligands Using Protein Sequence, Structure, and Ligand Similarity.

Chen YC, Tolbert R, Aronov AM, McGaughey G, Walters WP, Meireles L.

J Chem Inf Model. 2016 Sep 26;56(9):1734-45. doi: 10.1021/acs.jcim.6b00118. Epub 2016 Sep 2.


Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.

Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE, Hanson MR.

Microbiome. 2016 Jun 23;4(1):30. doi: 10.1186/s40168-016-0171-4.


The Soil Geochemistry in the Beardmore Glacier Region, Antarctica: Implications for Terrestrial Ecosystem History.

Lyons WB, Deuerling K, Welch KA, Welch SA, Michalski G, Walters WW, Nielsen U, Wall DH, Hogg I, Adams BJ.

Sci Rep. 2016 May 18;6:26189. doi: 10.1038/srep26189.


Direct Lifetime Measurements of the Excited States in (72)Ni.

Kolos K, Miller D, Grzywacz R, Iwasaki H, Al-Shudifat M, Bazin D, Bingham CR, Braunroth T, Cerizza G, Gade A, Lemasson A, Liddick SN, Madurga M, Morse C, Portillo M, Rajabali MM, Recchia F, Riedinger LL, Voss P, Walters WB, Weisshaar D, Whitmore K, Wimmer K, Tostevin JA.

Phys Rev Lett. 2016 Mar 25;116(12):122502. doi: 10.1103/PhysRevLett.116.122502. Epub 2016 Mar 22.


Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward.

Shoichet BK, Walters WP, Jiang H, Bajorath J.

J Med Chem. 2016 May 12;59(9):4033-4. doi: 10.1021/acs.jmedchem.6b00511. Epub 2016 Apr 7. No abstract available.


On the evolving open peer review culture for chemical information science.

Walters WP, Bajorath J.

F1000Res. 2015 Nov 25;4. pii: Chem Inf Sci-1350. doi: 10.12688/f1000research.7460.1. eCollection 2015.


Successful Medical Weight Loss in a Community Setting.

Carney D, Schultz S, Lim J, Walters W.

J Obes Weight Loss Ther. 2015 Feb;5(1). pii: 248. Epub 2015 Feb 27.


Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin.

Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG; Genographic Consortium.

PLoS One. 2015 Oct 8;10(10):e0139192. doi: 10.1371/journal.pone.0139192. eCollection 2015.


Nitrogen Isotope Composition of Thermally Produced NOx from Various Fossil-Fuel Combustion Sources.

Walters WW, Tharp BD, Fang H, Kozak BJ, Michalski G.

Environ Sci Technol. 2015 Oct 6;49(19):11363-71. doi: 10.1021/acs.est.5b02769. Epub 2015 Sep 9.


Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 Jul 31;3:34. doi: 10.1186/s40168-015-0098-1. eCollection 2015.


How Does the Local Electrostatic Field Influence Emitted Wavelengths and Bioluminescent Intensities of Modified Heteroaromatic Luciferins?

Zhou JG, Williams QL, Walters W Jr, Deng ZY.

J Phys Chem B. 2015 Aug 20;119(33):10399-405. doi: 10.1021/acs.jpcb.5b03827. Epub 2015 Aug 6.


Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 May 20;3:20. doi: 10.1186/s40168-015-0081-x. eCollection 2015. Erratum in: Microbiome. 2015;3:34.


A combination of chorea, myoclonus, and dystonia in a patient with pontocerebellar hypoplasia type 2: a video case presentation.

Gupta HV, Ramakrishnaiah RH, Sharp GB, Lee RW, Walters WD.

Acta Neurol Belg. 2015 Dec;115(4):783-5. doi: 10.1007/s13760-015-0461-9. Epub 2015 Apr 3. No abstract available.


Nitrogen stable isotope composition (δ15N) of vehicle-emitted NOx.

Walters WW, Goodwin SR, Michalski G.

Environ Sci Technol. 2015 Feb 17;49(4):2278-85. doi: 10.1021/es505580v. Epub 2015 Feb 6.


Caring for people with dementia in residential aged care: successes with a composite person-centered care model featuring Montessori-based activities.

Roberts G, Morley C, Walters W, Malta S, Doyle C.

Geriatr Nurs. 2015 Mar-Apr;36(2):106-10. doi: 10.1016/j.gerinurse.2014.11.003. Epub 2014 Dec 12.


Meta-analyses of human gut microbes associated with obesity and IBD.

Walters WA, Xu Z, Knight R.

FEBS Lett. 2014 Nov 17;588(22):4223-33. doi: 10.1016/j.febslet.2014.09.039. Epub 2014 Oct 13.


Acidic and basic drugs in medicinal chemistry: a perspective.

Charifson PS, Walters WP.

J Med Chem. 2014 Dec 11;57(23):9701-17. doi: 10.1021/jm501000a. Epub 2014 Sep 18. Review.


Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.


Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE.

Cell. 2014 Jul 17;158(2):250-262. doi: 10.1016/j.cell.2014.06.037.


Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R.

Front Microbiol. 2014 Jun 19;5:298. doi: 10.3389/fmicb.2014.00298. eCollection 2014.


Performance of a high-resolution mid-IR optical-parametric-oscillator transient absorption spectrometer.

Echebiri GO, Smarte MD, Walters WW, Mullin AS.

Opt Express. 2014 Jun 16;22(12):14885-95. doi: 10.1364/OE.22.014885.


Neuropathic pain-induced depressive-like behavior and hippocampal neurogenesis and plasticity are dependent on TNFR1 signaling.

Dellarole A, Morton P, Brambilla R, Walters W, Summers S, Bernardes D, Grilli M, Bethea JR.

Brain Behav Immun. 2014 Oct;41:65-81. doi: 10.1016/j.bbi.2014.04.003. Epub 2014 Jun 2.


Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples.

Green HC, Haugland RA, Varma M, Millen HT, Borchardt MA, Field KG, Walters WA, Knight R, Sivaganesan M, Kelty CA, Shanks OC.

Appl Environ Microbiol. 2014 May;80(10):3086-94. doi: 10.1128/AEM.04137-13. Epub 2014 Mar 7.


Technology and techniques for microbial ecology via DNA sequencing.

Walters WA, Knight R.

Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S16-20. doi: 10.1513/AnnalsATS.201306-160MG. Review.


Gut microbiota from twins discordant for obesity modulate metabolism in mice.

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI.

Science. 2013 Sep 6;341(6150):1241214. doi: 10.1126/science.1241214.


Activation of NF-κB in Schwann cells is dispensable for myelination in vivo.

Morton PD, Dellarole A, Theus MH, Walters WM, Berge SS, Bethea JR.

J Neurosci. 2013 Jun 12;33(24):9932-6. doi: 10.1523/JNEUROSCI.2483-12.2013.


Modeling, informatics, and the quest for reproducibility.

Walters WP.

J Chem Inf Model. 2013 Jul 22;53(7):1529-30. doi: 10.1021/ci400197w. Epub 2013 Jun 21.


From molecules to dynamic biological communities.

McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R.

Biol Philos. 2013 Mar;28(2):241-259. Epub 2013 Feb 5.


Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH.

PLoS One. 2013;8(2):e47879. doi: 10.1371/journal.pone.0047879. Epub 2013 Feb 8.


Global biogeography of highly diverse protistan communities in soil.

Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N.

ISME J. 2013 Mar;7(3):652-9. doi: 10.1038/ismej.2012.147. Epub 2012 Dec 13.


Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.


Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle.

Carey HV, Walters WA, Knight R.

Am J Physiol Regul Integr Comp Physiol. 2013 Jan 1;304(1):R33-42. doi: 10.1152/ajpregu.00387.2012. Epub 2012 Nov 14.


Collaborative cloud-enabled tools allow rapid, reproducible biological insights.

Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG.

ISME J. 2013 Mar;7(3):461-4. doi: 10.1038/ismej.2012.123. Epub 2012 Oct 25. No abstract available.


Computational chemistry and drug discovery: a call to action.

Jansen JM, Amaro RE, Cornell W, Tseng YJ, Walters WP.

Future Med Chem. 2012 Oct;4(15):1893-6. doi: 10.4155/fmc.12.137. No abstract available.


Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.

Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS.

Genome Res. 2012 Nov;22(11):2146-52. doi: 10.1101/gr.140608.112. Epub 2012 Oct 12.


Iterative refinement of a binding pocket model: active computational steering of lead optimization.

Varela R, Walters WP, Goldman BB, Jain AN.

J Med Chem. 2012 Oct 25;55(20):8926-42. doi: 10.1021/jm301210j. Epub 2012 Oct 9.


Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM.

PLoS One. 2012;7(8):e43052. doi: 10.1371/journal.pone.0043052. Epub 2012 Aug 15.

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