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Items: 1 to 50 of 86

1.

Modular epitope binding predicts influenza quasispecies dominance and vaccine effectiveness: Application to 2018/19 season.

Bonomo ME, Kim RY, Deem MW.

Vaccine. 2019 May 27;37(24):3154-3158. doi: 10.1016/j.vaccine.2019.03.068. Epub 2019 May 3.

2.

Machine-learning approach to the design of OSDAs for zeolite beta.

Daeyaert F, Ye F, Deem MW.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3413-3418. doi: 10.1073/pnas.1818763116. Epub 2019 Feb 7.

3.

Corrigendum: Static and Dynamic Measures of Human Brain Connectivity Predict Complementary Aspects of Human Cognitive Performance.

Ramos-Nuñez AI, Fischer-Baum S, Martin RC, Yue Q, Ye F, Deem MW.

Front Hum Neurosci. 2018 Sep 7;12:345. doi: 10.3389/fnhum.2018.00345. eCollection 2018.

4.
5.

Reply to Xu and Ye: On the Sufficiency of the Pepitope Method.

Bonomo ME, Deem MW.

Clin Infect Dis. 2019 Jan 7;68(2):347. doi: 10.1093/cid/ciy561. No abstract available.

PMID:
29986011
6.

The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences.

Tripathi S, Deem MW.

J Mol Evol. 2018 Jul;86(6):325-339. doi: 10.1007/s00239-018-9852-x. Epub 2018 Jun 29.

PMID:
29959476
7.

Predicting Influenza H3N2 Vaccine Efficacy From Evolution of the Dominant Epitope.

Bonomo ME, Deem MW.

Clin Infect Dis. 2018 Sep 14;67(7):1129-1131. doi: 10.1093/cid/ciy323.

PMID:
29672670
8.

Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma.

Ye F, Jia D, Lu M, Levine H, Deem MW.

Oncotarget. 2018 Feb 22;9(19):15015-15026. doi: 10.18632/oncotarget.24551. eCollection 2018 Mar 13.

9.

The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas.

Bonomo ME, Deem MW.

Phys Biol. 2018 Apr 30;15(4):041002. doi: 10.1088/1478-3975/aab6d6. Review.

PMID:
29543191
10.

Single molecule sequencing of the M13 virus genome without amplification.

Zhao L, Deng L, Li G, Jin H, Cai J, Shang H, Li Y, Wu H, Xu W, Zeng L, Zhang R, Zhao H, Wu P, Zhou Z, Zheng J, Ezanno P, Yang AX, Yan Q, Deem MW, He J.

PLoS One. 2017 Dec 18;12(12):e0188181. doi: 10.1371/journal.pone.0188181. eCollection 2017.

11.

Static and Dynamic Measures of Human Brain Connectivity Predict Complementary Aspects of Human Cognitive Performance.

Ramos-Nuñez AI, Fischer-Baum S, Martin RC, Yue Q, Ye F, Deem MW.

Front Hum Neurosci. 2017 Aug 24;11:420. doi: 10.3389/fnhum.2017.00420. eCollection 2017. Erratum in: Front Hum Neurosci. 2018 Sep 07;12:345.

12.

Brain Modularity Mediates the Relation between Task Complexity and Performance.

Yue Q, Martin RC, Fischer-Baum S, Ramos-Nuñez AI, Ye F, Deem MW.

J Cogn Neurosci. 2017 Sep;29(9):1532-1546. doi: 10.1162/jocn_a_01142. Epub 2017 May 4.

PMID:
28471728
13.

Enantiomerically enriched, polycrystalline molecular sieves.

Brand SK, Schmidt JE, Deem MW, Daeyaert F, Ma Y, Terasaki O, Orazov M, Davis ME.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):5101-5106. doi: 10.1073/pnas.1704638114. Epub 2017 May 1.

14.

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats.

Han P, Deem MW.

J R Soc Interface. 2017 Feb;14(127). pii: 20160905. doi: 10.1098/rsif.2016.0905.

15.

A Pareto Algorithm for Efficient De Novo Design of Multi-functional Molecules.

Daeyaert F, Deem MW.

Mol Inform. 2017 Jan;36(1-2). doi: 10.1002/minf.201600044. Epub 2016 Jul 21.

PMID:
28124835
16.

T Cell Repertoire Diversity Is Decreased in Type 1 Diabetes Patients.

Tong Y, Li Z, Zhang H, Xia L, Zhang M, Xu Y, Wang Z, Deem MW, Sun X, He J.

Genomics Proteomics Bioinformatics. 2016 Dec;14(6):338-348. doi: 10.1016/j.gpb.2016.10.003. Epub 2016 Dec 24.

17.

Modular knowledge systems accelerate human migration in asymmetric random environments.

Wang D, Deem MW.

J R Soc Interface. 2016 Dec;13(125). pii: 20160778.

18.

Template-Framework Interactions in Tetraethylammonium-Directed Zeolite Synthesis.

Schmidt JE, Fu D, Deem MW, Weckhuysen BM.

Angew Chem Int Ed Engl. 2016 Dec 23;55(52):16044-16048. doi: 10.1002/anie.201609053. Epub 2016 Nov 22.

19.

Prediction of influenza B vaccine effectiveness from sequence data.

Pan Y, Deem MW.

Vaccine. 2016 Aug 31;34(38):4610-4617. doi: 10.1016/j.vaccine.2016.07.015. Epub 2016 Jul 26.

PMID:
27473305
20.

Influenza evolution and H3N2 vaccine effectiveness, with application to the 2014/2015 season.

Li X, Deem MW.

Protein Eng Des Sel. 2016 Aug;29(8):309-15. doi: 10.1093/protein/gzw017. Epub 2016 Jun 16.

21.

Single molecule targeted sequencing for cancer gene mutation detection.

Gao Y, Deng L, Yan Q, Gao Y, Wu Z, Cai J, Ji D, Li G, Wu P, Jin H, Zhao L, Liu S, Ge L, Deem MW, He J.

Sci Rep. 2016 May 19;6:26110. doi: 10.1038/srep26110.

22.

Modularity enhances the rate of evolution in a rugged fitness landscape.

Park JM, Chen M, Wang D, Deem MW.

Phys Biol. 2015 Mar 19;12(2):025001. doi: 10.1088/1478-3975/12/2/025001.

23.

In silico prediction of MOFs with high deliverable capacity or internal surface area.

Bao Y, Martin RL, Haranczyk M, Deem MW.

Phys Chem Chem Phys. 2015 May 14;17(18):11962-73. doi: 10.1039/c5cp00002e.

PMID:
25716343
24.

Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia.

Tripathi S, Deem MW.

Phys Biol. 2015 Feb 16;12(1):016016. doi: 10.1088/1478-3975/12/1/016016.

25.

Quasispecies theory for evolution of modularity.

Park JM, Niestemski LR, Deem MW.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Jan;91(1):012714. Epub 2015 Jan 28.

26.

Development of modularity in the neural activity of children's brains.

Chen M, Deem MW.

Phys Biol. 2015 Jan 26;12(1):016009. doi: 10.1088/1478-3975/12/1/016009.

27.

Discovery of optimal zeolites for challenging separations and chemical transformations using predictive materials modeling.

Bai P, Jeon MY, Ren L, Knight C, Deem MW, Tsapatsis M, Siepmann JI.

Nat Commun. 2015 Jan 21;6:5912. doi: 10.1038/ncomms6912.

28.

Synthesis of a specified, silica molecular sieve by using computationally predicted organic structure-directing agents.

Schmidt JE, Deem MW, Davis ME.

Angew Chem Int Ed Engl. 2014 Aug 4;53(32):8372-4. doi: 10.1002/anie.201404076. Epub 2014 Jun 24.

29.

Hierarchy of gene expression data is predictive of future breast cancer outcome.

Chen M, Deem MW.

Phys Biol. 2013 Oct;10(5):056006. doi: 10.1088/1478-3975/10/5/056006. Epub 2013 Oct 3.

30.

Evolution: life has evolved to evolve: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro.

Deem MW.

Phys Life Rev. 2013 Sep;10(3):333-5. doi: 10.1016/j.plrev.2013.07.010. Epub 2013 Jul 10. No abstract available.

31.

Evolutionary processes in finite populations.

Lorenz DM, Park JM, Deem MW.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022704. Epub 2013 Feb 13.

32.

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system.

Han P, Niestemski LR, Barrick JE, Deem MW.

Phys Biol. 2013 Apr;10(2):025004. doi: 10.1088/1478-3975/10/2/025004. Epub 2013 Mar 15.

33.

Prediction of heart rate response to conclusion of the spontaneous breathing trial by fluctuation dissipation theory.

Chen M, Niestemski LR, Prevost R, McRae M, Cholleti S, Najarro G, Buchman TG, Deem MW.

Phys Biol. 2013 Feb;10(1):016006. doi: 10.1088/1478-3975/10/1/016006. Epub 2013 Jan 30.

34.

Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats.

Zhang C, Deem MW.

J Chem Phys. 2013 Jan 21;138(3):034103. doi: 10.1063/1.4773435.

PMID:
23343264
35.

In silico screening of carbon-capture materials.

Lin LC, Berger AH, Martin RL, Kim J, Swisher JA, Jariwala K, Rycroft CH, Bhown AS, Deem MW, Haranczyk M, Smit B.

Nat Mater. 2012 May 27;11(7):633-41. doi: 10.1038/nmat3336.

PMID:
22635045
36.

A multi-scale model for correlation in B cell VDJ usage of zebrafish.

Pan K, Deem MW.

Phys Biol. 2011 Oct;8(5):055006. doi: 10.1088/1478-3975/8/5/055006. Epub 2011 Aug 10.

37.

Evolution of H3N2 influenza virus in a guinea pig model.

Long J, Bushnell RV, Tobin JK, Pan K, Deem MW, Nara PL, Tobin GJ.

PLoS One. 2011;6(7):e20130. doi: 10.1371/journal.pone.0020130. Epub 2011 Jul 22.

38.

Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation.

Pan K, Deem MW.

J Chem Theory Comput. 2011 May 10;7(5):1259-1272.

39.

Quantifying selection and diversity in viruses by entropy methods, with application to the haemagglutinin of H3N2 influenza.

Pan K, Deem MW.

J R Soc Interface. 2011 Nov 7;8(64):1644-53. doi: 10.1098/rsif.2011.0105. Epub 2011 May 4.

40.

A database of new zeolite-like materials.

Pophale R, Cheeseman PA, Deem MW.

Phys Chem Chem Phys. 2011 Jul 21;13(27):12407-12. doi: 10.1039/c0cp02255a. Epub 2011 Mar 18.

PMID:
21423937
41.

The emergence of modularity in biological systems.

Lorenz DM, Jeng A, Deem MW.

Phys Life Rev. 2011 Jun;8(2):129-60. doi: 10.1016/j.plrev.2011.02.003. Epub 2011 Feb 25. Review.

42.

Structure and response in the world trade network.

He J, Deem MW.

Phys Rev Lett. 2010 Nov 5;105(19):198701. Epub 2010 Nov 5.

PMID:
21231202
43.

A novel sequence-based antigenic distance measure for H1N1, with application to vaccine effectiveness and the selection of vaccine strains.

Pan K, Subieta KC, Deem MW.

Protein Eng Des Sel. 2011 Mar;24(3):291-9. doi: 10.1093/protein/gzq105. Epub 2010 Nov 30.

44.

Selective pressure to increase charge in immunodominant epitopes of the H3 hemagglutinin influenza protein.

Pan K, Long J, Sun H, Tobin GJ, Nara PL, Deem MW.

J Mol Evol. 2011 Jan;72(1):90-103. doi: 10.1007/s00239-010-9405-4. Epub 2010 Nov 18.

45.

Low-dimensional clustering detects incipient dominant influenza strain clusters.

He J, Deem MW.

Protein Eng Des Sel. 2010 Dec;23(12):935-46. doi: 10.1093/protein/gzq078. Epub 2010 Oct 29.

46.

Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats).

He J, Deem MW.

Phys Rev Lett. 2010 Sep 17;105(12):128102. Epub 2010 Sep 14.

PMID:
20867676
47.

Quasispecies theory for finite populations.

Park JM, Muñoz E, Deem MW.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 1):011902. Epub 2010 Jan 6.

48.

Theoretical aspects of immunity.

Deem MW, Hejazi P.

Annu Rev Chem Biomol Eng. 2010;1:247-76. doi: 10.1146/annurev-chembioeng-073009-100952. Review.

49.

Hierarchical evolution of animal body plans.

He J, Deem MW.

Dev Biol. 2010 Jan 1;337(1):157-61. doi: 10.1016/j.ydbio.2009.09.038. Epub 2009 Sep 30.

50.

Predicting clinical physiology: a Markov chain model of heart rate recovery after spontaneous breathing trials in mechanically ventilated patients.

Lu Y, Burykin A, Deem MW, Buchman TG.

J Crit Care. 2009 Sep;24(3):347-61. doi: 10.1016/j.jcrc.2009.01.014.

PMID:
19664524

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