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Items: 1 to 50 of 240

1.

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL.

J Am Chem Soc. 2019 Mar 20;141(11):4711-4720. doi: 10.1021/jacs.8b13613. Epub 2019 Mar 11.

PMID:
30834751
2.

MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats.

Tuohy JM, Mueller-Spitz SR, Albert CM, Scholz-Ng SE, Wall ME, Noutsios GT, Gutierrez AJ, Sandrin TR.

Front Microbiol. 2018 Oct 15;9:2442. doi: 10.3389/fmicb.2018.02442. eCollection 2018.

3.

"Why Me?" Understanding the HCV Care Continuum Among People With Serious Mental Illness.

Arnold RM, Machover H, Wall ME, Ahmadizadeh I, Potts W, Himelhoch S.

Psychiatr Serv. 2018 Nov 1;69(11):1188-1190. doi: 10.1176/appi.ps.201700542. Epub 2018 Sep 17.

PMID:
30220243
4.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

Wall ME.

IUCrJ. 2018 Jan 25;5(Pt 2):172-181. doi: 10.1107/S2052252518000519. eCollection 2018 Mar 1.

5.

Interactions that know no boundaries.

Wall ME.

IUCrJ. 2018 Feb 26;5(Pt 2):120-121. doi: 10.1107/S2052252518002713. eCollection 2018 Mar 1.

6.

Bringing diffuse X-ray scattering into focus.

Wall ME, Wolff AM, Fraser JS.

Curr Opin Struct Biol. 2018 Jun;50:109-116. doi: 10.1016/j.sbi.2018.01.009. Epub 2018 Feb 16. Review.

7.

Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions.

Vesselinova N, Alexandrov BS, Wall ME.

PLoS One. 2016 Nov 8;11(11):e0165899. doi: 10.1371/journal.pone.0165899. eCollection 2016.

8.

Cell Signaling in Tenocytes: Response to Load and Ligands in Health and Disease.

Wall ME, Dyment NA, Bodle J, Volmer J, Loboa E, Cederlund A, Fox AM, Banes AJ.

Adv Exp Med Biol. 2016;920:79-95. doi: 10.1007/978-3-319-33943-6_7. Review.

PMID:
27535250
9.

Quantum crystallographic charge density of urea.

Wall ME.

IUCrJ. 2016 Jun 8;3(Pt 4):237-46. doi: 10.1107/S2052252516006242. eCollection 2016 Jul 1.

10.

Graph-based linear scaling electronic structure theory.

Niklasson AM, Mniszewski SM, Negre CF, Cawkwell MJ, Swart PJ, Mohd-Yusof J, Germann TC, Wall ME, Bock N, Rubensson EH, Djidjev H.

J Chem Phys. 2016 Jun 21;144(23):234101. doi: 10.1063/1.4952650.

PMID:
27334148
11.

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

Negre CF, Mniszewski SM, Cawkwell MJ, Bock N, Wall ME, Niklasson AM.

J Chem Theory Comput. 2016 Jul 12;12(7):3063-73. doi: 10.1021/acs.jctc.6b00154. Epub 2016 Jun 24.

PMID:
27267207
12.

Measuring and modeling diffuse scattering in protein X-ray crystallography.

Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4069-74. doi: 10.1073/pnas.1524048113. Epub 2016 Mar 28.

13.

The eighth q-bio conference: meeting report and special issue preface.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O.

Phys Biol. 2015 Dec 30;12(6):060401. doi: 10.1088/1478-3975/12/6/060401. No abstract available.

PMID:
26716953
14.

Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

Mniszewski SM, Cawkwell MJ, Wall ME, Mohd-Yusof J, Bock N, Germann TC, Niklasson AM.

J Chem Theory Comput. 2015 Oct 13;11(10):4644-54. doi: 10.1021/acs.jctc.5b00552. Epub 2015 Sep 29.

PMID:
26574255
15.

Fitness consequences of short- and long-distance pollinations in Phlox hirsuta, an endangered species.

Ruane LG, Dickens ME, Wall ME.

Am J Bot. 2015 Oct;102(10):1659-65. doi: 10.3732/ajb.1500270. Epub 2015 Oct 5.

16.

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1657-67. doi: 10.1107/S1399004715007415. Epub 2015 Jul 28.

17.

Tendon mechanobiology: Current knowledge and future research opportunities.

Lavagnino M, Wall ME, Little D, Banes AJ, Guilak F, Arnoczky SP.

J Orthop Res. 2015 Jun;33(6):813-22. doi: 10.1002/jor.22871. Epub 2015 Apr 27. Review.

18.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17887-92. doi: 10.1073/pnas.1416744111. Epub 2014 Dec 1.

19.

The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.

20.

Diffuse X-ray scattering to model protein motions.

Wall ME, Adams PD, Fraser JS, Sauter NK.

Structure. 2014 Feb 4;22(2):182-4. doi: 10.1016/j.str.2014.01.002.

21.

Cyclic tensile strain enhances osteogenesis and angiogenesis in mesenchymal stem cells from osteoporotic donors.

Charoenpanich A, Wall ME, Tucker CJ, Andrews DM, Lalush DS, Dirschl DR, Loboa EG.

Tissue Eng Part A. 2014 Jan;20(1-2):67-78. doi: 10.1089/ten.TEA.2013.0006. Epub 2013 Sep 19.

22.

Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.

PMID:
23735417
23.

Detection of protein catalytic sites in the biomedical literature.

Verspoor K, Mackinlay A, Cohn JD, Wall ME.

Pac Symp Biocomput. 2013:433-44.

24.

Literature mining of protein-residue associations with graph rules learned through distant supervision.

Ravikumar K, Liu H, Cohn JD, Wall ME, Verspoor K.

J Biomed Semantics. 2012 Oct 5;3 Suppl 3:S2. doi: 10.1186/2041-1480-3-S3-S2. Epub 2012 Oct 5.

25.

Text mining improves prediction of protein functional sites.

Verspoor KM, Cohn JD, Ravikumar KE, Wall ME.

PLoS One. 2012;7(2):e32171. doi: 10.1371/journal.pone.0032171. Epub 2012 Feb 29.

26.

Genome majority vote improves gene predictions.

Wall ME, Raghavan S, Cohn JD, Dunbar J.

PLoS Comput Biol. 2011 Nov;7(11):e1002284. doi: 10.1371/journal.pcbi.1002284. Epub 2011 Nov 17.

27.

Predicting binding sites by analyzing allosteric effects.

Ming D, Wall ME.

Methods Mol Biol. 2012;796:423-36. doi: 10.1007/978-1-61779-334-9_23.

PMID:
22052504
28.

Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.

Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

Phys Biol. 2011 Oct;8(5):050301. doi: 10.1088/1478-3975/8/5/050301. Epub 2011 Aug 10.

PMID:
21832800
30.

Consistency of gene starts among Burkholderia genomes.

Dunbar J, Cohn JD, Wall ME.

BMC Genomics. 2011 Feb 22;12:125. doi: 10.1186/1471-2164-12-125.

31.

Structure-function relations are subtle in genetic regulatory networks.

Wall ME.

Math Biosci. 2011 May;231(1):61-8. doi: 10.1016/j.mbs.2011.02.003. Epub 2011 Feb 15. Review.

PMID:
21329703
32.

The Third q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

IET Syst Biol. 2010 Nov;4(6):331-3. doi: 10.1049/iet-syb.2010.9133. No abstract available.

PMID:
21073232
33.

Model of transcriptional activation by MarA in Escherichia coli.

Wall ME, Markowitz DA, Rosner JL, Martin RG.

PLoS Comput Biol. 2009 Dec;5(12):e1000614. doi: 10.1371/journal.pcbi.1000614. Epub 2009 Dec 18.

34.

Methods and software for diffuse X-ray scattering from protein crystals.

Wall ME.

Methods Mol Biol. 2009;544:269-79. doi: 10.1007/978-1-59745-483-4_17.

PMID:
19488705
35.

Determinants of bistability in induction of the Escherichia coli lac operon.

Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME.

IET Syst Biol. 2008 Sep;2(5):293-303. doi: 10.1049/iet-syb:20080095.

PMID:
19045824
36.

Selected papers from the First q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Edwards JS, Faeder JR, Jiang Y, Wall ME.

IET Syst Biol. 2008 Sep;2(5):203-5. doi: 10.1049/iet-syb:20089018. No abstract available.

PMID:
19045816
37.

Activation of the Escherichia coli marA/soxS/rob regulon in response to transcriptional activator concentration.

Martin RG, Bartlett ES, Rosner JL, Wall ME.

J Mol Biol. 2008 Jul 4;380(2):278-84. doi: 10.1016/j.jmb.2008.05.015. Epub 2008 May 13.

38.

Isolation of human mesenchymal stem cells from bone and adipose tissue.

Bernacki SH, Wall ME, Loboa EG.

Methods Cell Biol. 2008;86:257-78. doi: 10.1016/S0091-679X(08)00011-3. No abstract available.

PMID:
18442651
39.

Hidden structure in protein energy landscapes.

Ming D, Anghel M, Wall ME.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Feb;77(2 Pt 1):021902. Epub 2008 Feb 4.

PMID:
18352046
40.

Fast dynamics perturbation analysis for prediction of protein functional sites.

Ming D, Cohn JD, Wall ME.

BMC Struct Biol. 2008 Jan 30;8:5. doi: 10.1186/1472-6807-8-5.

41.

Q-bio 2007: a watershed moment in modern biology.

Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I, Wall ME.

Mol Syst Biol. 2007;3:148. Epub 2007 Dec 4. No abstract available.

42.

Domain motions of Argonaute, the catalytic engine of RNA interference.

Ming D, Wall ME, Sanbonmatsu KY.

BMC Bioinformatics. 2007 Nov 30;8:470.

43.

Effects of oxygen plasma treatment on adipose-derived human mesenchymal stem cell adherence to poly(L-lactic acid) scaffolds.

Hanson AD, Wall ME, Pourdeyhimi B, Loboa EG.

J Biomater Sci Polym Ed. 2007;18(11):1387-400.

PMID:
17961322
44.

Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism.

Nemenman I, Escola GS, Hlavacek WS, Unkefer PJ, Unkefer CJ, Wall ME.

Ann N Y Acad Sci. 2007 Dec;1115:102-15. Epub 2007 Oct 9.

PMID:
17925356
45.

Human adipose-derived adult stem cells upregulate palladin during osteogenesis and in response to cyclic tensile strain.

Wall ME, Rachlin A, Otey CA, Loboa EG.

Am J Physiol Cell Physiol. 2007 Nov;293(5):C1532-8. Epub 2007 Aug 8.

46.

Alvaradoins E-N, antitumor and cytotoxic anthracenone C-glycosides from the leaves of Alvaradoa haitiensis.

Phifer SS, Lee D, Seo EK, Kim NC, Graf TN, Kroll DJ, Navarro HA, Izydore RA, Jiménez F, Garcia R, Rose WC, Fairchild CR, Wild R, Soejarto DD, Farnsworth NR, Kinghorn AD, Oberlies NH, Wall ME, Wani MC.

J Nat Prod. 2007 Jun;70(6):954-61. Epub 2007 Jun 7.

47.
48.

Connexin 43 is localized with actin in tenocytes.

Wall ME, Otey C, Qi J, Banes AJ.

Cell Motil Cytoskeleton. 2007 Feb;64(2):121-30.

PMID:
17183550
49.

Computer-assisted categorizing of head computed tomography reports for clinical decision rule research.

Wall SP, Mayorga O, Banfield CE, Wall ME, Aisic I, Auerbach C, Gennis P.

Ann Emerg Med. 2006 Nov;48(5):551-7, 557.e1-25. Epub 2006 Sep 25.

PMID:
16997422
50.

Interactions in native binding sites cause a large change in protein dynamics.

Ming D, Wall ME.

J Mol Biol. 2006 Apr 21;358(1):213-23. Epub 2006 Feb 14.

PMID:
16513135

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