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Items: 1 to 50 of 283

1.

Epidemic dynamics of respiratory syncytial virus in current and future climates.

Baker RE, Mahmud AS, Wagner CE, Yang W, Pitzer VE, Viboud C, Vecchi GA, Metcalf CJE, Grenfell BT.

Nat Commun. 2019 Dec 4;10(1):5512. doi: 10.1038/s41467-019-13562-y.

PMID:
31797866
2.

Functionally Overlapping Variants Control Tuberculosis Susceptibility in Collaborative Cross Mice.

Smith CM, Proulx MK, Lai R, Kiritsy MC, Bell TA, Hock P, Pardo-Manuel de Villena F, Ferris MT, Baker RE, Behar SM, Sassetti CM.

MBio. 2019 Nov 26;10(6). pii: e02791-19. doi: 10.1128/mBio.02791-19.

3.

Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression.

Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR.

BMC Bioinformatics. 2019 Nov 21;20(1):603. doi: 10.1186/s12859-019-3156-z.

4.

Testing Models of mRNA Localization Reveals Robustness Regulated by Reducing Transport between Cells.

Harrison JU, Parton RM, Davis I, Baker RE.

Biophys J. 2019 Dec 3;117(11):2154-2165. doi: 10.1016/j.bpj.2019.10.025. Epub 2019 Oct 24.

PMID:
31708163
5.

Accurate and efficient discretizations for stochastic models providing near agent-based spatial resolution at low computational cost.

Fadai NT, Baker RE, Simpson MJ.

J R Soc Interface. 2019 Oct 31;16(159):20190421. doi: 10.1098/rsif.2019.0421. Epub 2019 Oct 23.

PMID:
31640499
6.

An interdisciplinary approach to investigate collective cell migration in neural crest.

Giniūnaitė R, McLennan R, McKinney MC, Baker RE, Kulesa PM, Maini PK.

Dev Dyn. 2019 Oct 17. doi: 10.1002/dvdy.124. [Epub ahead of print]

PMID:
31622517
7.

Modelling collective cell migration: neural crest as a model paradigm.

Giniūnaitė R, Baker RE, Kulesa PM, Maini PK.

J Math Biol. 2019 Oct 5. doi: 10.1007/s00285-019-01436-2. [Epub ahead of print]

PMID:
31587096
8.

Continuum descriptions of spatial spreading for heterogeneous cell populations: Theory and experiment.

Matsiaka OM, Baker RE, Simpson MJ.

J Theor Biol. 2019 Dec 7;482:109997. doi: 10.1016/j.jtbi.2019.109997. Epub 2019 Sep 3.

PMID:
31491498
9.

A one-dimensional individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation.

Murphy RJ, Buenzli PR, Baker RE, Simpson MJ.

Proc Math Phys Eng Sci. 2019 Jul;475(2227):20180838. doi: 10.1098/rspa.2018.0838. Epub 2019 Jul 24.

PMID:
31423086
10.

Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy.

Bellerose MM, Baek SH, Huang CC, Moss CE, Koh EI, Proulx MK, Smith CM, Baker RE, Lee JS, Eum S, Shin SJ, Cho SN, Murray M, Sassetti CM.

MBio. 2019 Jul 30;10(4). pii: e00663-19. doi: 10.1128/mBio.00663-19.

11.

Self-assembly of biological networks via adaptive patterning revealed by avian intradermal muscle network formation.

Wu XS, Yeh CY, Harn HI, Jiang TX, Wu P, Widelitz RB, Baker RE, Chuong CM.

Proc Natl Acad Sci U S A. 2019 May 28;116(22):10858-10867. doi: 10.1073/pnas.1818506116. Epub 2019 May 9.

12.

Uniformization techniques for stochastic simulation of chemical reaction networks.

Beentjes CHL, Baker RE.

J Chem Phys. 2019 Apr 21;150(15):154107. doi: 10.1063/1.5081043.

PMID:
31005097
13.

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art.

Warne DJ, Baker RE, Simpson MJ.

J R Soc Interface. 2019 Feb 28;16(151):20180943. doi: 10.1098/rsif.2018.0943.

14.

Using Experimental Data and Information Criteria to Guide Model Selection for Reaction-Diffusion Problems in Mathematical Biology.

Warne DJ, Baker RE, Simpson MJ.

Bull Math Biol. 2019 Jun;81(6):1760-1804. doi: 10.1007/s11538-019-00589-x. Epub 2019 Feb 27.

PMID:
30815837
15.

Cell cycle-dependent association of polo kinase Cdc5 with CENP-A contributes to faithful chromosome segregation in budding yeast.

Mishra PK, Olafsson G, Boeckmann L, Westlake TJ, Jowhar ZM, Dittman LE, Baker RE, D'Amours D, Thorpe PH, Basrai MA.

Mol Biol Cell. 2019 Apr 1;30(8):1020-1036. doi: 10.1091/mbc.E18-09-0584. Epub 2019 Feb 6.

16.

A free boundary model of epithelial dynamics.

Baker RE, Parker A, Simpson MJ.

J Theor Biol. 2019 Nov 21;481:61-74. doi: 10.1016/j.jtbi.2018.12.025. Epub 2018 Dec 19.

17.

Klossiella equi infection in a Cheval Canadien Mare.

Baker RE, Schlipf JW Jr, Brady JV, Gorman ME.

Vet Clin Pathol. 2018 Dec;47(4):654-659. doi: 10.1111/vcp.12660. Epub 2018 Oct 15.

PMID:
30321471
18.

A Lysine Acetyltransferase Contributes to the Metabolic Adaptation to Hypoxia in Mycobacterium tuberculosis.

Rittershaus ESC, Baek SH, Krieger IV, Nelson SJ, Cheng YS, Nambi S, Baker RE, Leszyk JD, Shaffer SA, Sacchettini JC, Sassetti CM.

Cell Chem Biol. 2018 Dec 20;25(12):1495-1505.e3. doi: 10.1016/j.chembiol.2018.09.009. Epub 2018 Oct 11.

PMID:
30318462
19.

SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin.

Ohkuni K, Pasupala N, Peek J, Holloway GL, Sclar GD, Levy-Myers R, Baker RE, Basrai MA, Kerscher O.

Front Genet. 2018 Sep 18;9:379. doi: 10.3389/fgene.2018.00379. eCollection 2018.

20.

The impact of experimental design choices on parameter inference for models of growing cell colonies.

Parker A, Simpson MJ, Baker RE.

R Soc Open Sci. 2018 Aug 29;5(8):180384. doi: 10.1098/rsos.180384. eCollection 2018 Aug.

21.

Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time.

Engblom S, Wilson DB, Baker RE.

R Soc Open Sci. 2018 Aug 1;5(8):180379. doi: 10.1098/rsos.180379. eCollection 2018 Aug.

22.

A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A.

Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA.

Genetics. 2018 Sep;210(1):203-218. doi: 10.1534/genetics.118.301305. Epub 2018 Jul 16.

23.

Topology-dependent density optima for efficient simultaneous network exploration.

Wilson DB, Baker RE, Woodhouse FG.

Phys Rev E. 2018 Jun;97(6-1):062301. doi: 10.1103/PhysRevE.97.062301.

PMID:
30011429
24.

The impact of temporal sampling resolution on parameter inference for biological transport models.

Harrison JU, Baker RE.

PLoS Comput Biol. 2018 Jun 25;14(6):e1006235. doi: 10.1371/journal.pcbi.1006235. eCollection 2018 Jun.

25.

Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems.

Beentjes CHL, Baker RE.

Bull Math Biol. 2019 Aug;81(8):2931-2959. doi: 10.1007/s11538-018-0442-2. Epub 2018 May 25.

26.

Mechanistic models versus machine learning, a fight worth fighting for the biological community?

Baker RE, Peña JM, Jayamohan J, Jérusalem A.

Biol Lett. 2018 May;14(5). pii: 20170660. doi: 10.1098/rsbl.2017.0660. Review.

27.

N-terminal Sumoylation of Centromeric Histone H3 Variant Cse4 Regulates Its Proteolysis To Prevent Mislocalization to Non-centromeric Chromatin.

Ohkuni K, Levy-Myers R, Warren J, Au WC, Takahashi Y, Baker RE, Basrai MA.

G3 (Bethesda). 2018 Mar 28;8(4):1215-1223. doi: 10.1534/g3.117.300419.

28.

Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues.

Kursawe J, Baker RE, Fletcher AG.

J Theor Biol. 2018 Apr 14;443:66-81. doi: 10.1016/j.jtbi.2018.01.020. Epub 2018 Jan 31.

29.

Discrete and Continuum Approximations for Collective Cell Migration in a Scratch Assay with Cell Size Dynamics.

Matsiaka OM, Penington CJ, Baker RE, Simpson MJ.

Bull Math Biol. 2018 Apr;80(4):738-757. doi: 10.1007/s11538-018-0398-2. Epub 2018 Jan 25.

PMID:
29372496
30.

Optimal Quantification of Contact Inhibition in Cell Populations.

Warne DJ, Baker RE, Simpson MJ.

Biophys J. 2017 Nov 7;113(9):1920-1924. doi: 10.1016/j.bpj.2017.09.016. Epub 2017 Oct 13.

31.

DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion.

McLennan R, Bailey CM, Schumacher LJ, Teddy JM, Morrison JA, Kasemeier-Kulesa JC, Wolfe LA, Gogol MM, Baker RE, Maini PK, Kulesa PM.

J Cell Biol. 2017 Oct 2;216(10):3339-3354. doi: 10.1083/jcb.201612169. Epub 2017 Aug 15.

32.

Self-organization process in newborn skin organoid formation inspires strategy to restore hair regeneration of adult cells.

Lei M, Schumacher LJ, Lai YC, Juan WT, Yeh CY, Wu P, Jiang TX, Baker RE, Widelitz RB, Yang L, Chuong CM.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):E7101-E7110. doi: 10.1073/pnas.1700475114. Epub 2017 Aug 10.

33.

Semblance of Heterogeneity in Collective Cell Migration.

Schumacher LJ, Maini PK, Baker RE.

Cell Syst. 2017 Aug 23;5(2):119-127.e1. doi: 10.1016/j.cels.2017.06.006. Epub 2017 Jul 26.

34.

Using approximate Bayesian computation to quantify cell-cell adhesion parameters in a cell migratory process.

Ross RJH, Baker RE, Parker A, Ford MJ, Mort RL, Yates CA.

NPJ Syst Biol Appl. 2017 Mar 10;3:9. doi: 10.1038/s41540-017-0010-7. eCollection 2017.

35.

Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis.

Mishra BB, Lovewell RR, Olive AJ, Zhang G, Wang W, Eugenin E, Smith CM, Phuah JY, Long JE, Dubuke ML, Palace SG, Goguen JD, Baker RE, Nambi S, Mishra R, Booty MG, Baer CE, Shaffer SA, Dartois V, McCormick BA, Chen X, Sassetti CM.

Nat Microbiol. 2017 May 15;2:17072. doi: 10.1038/nmicrobiol.2017.72.

36.

Variable species densities are induced by volume exclusion interactions upon domain growth.

Ross RJH, Yates CA, Baker RE.

Phys Rev E. 2017 Mar;95(3-1):032416. doi: 10.1103/PhysRevE.95.032416. Epub 2017 Mar 27.

PMID:
28415323
37.

Continuum approximations for lattice-free multi-species models of collective cell migration.

Matsiaka OM, Penington CJ, Baker RE, Simpson MJ.

J Theor Biol. 2017 Jun 7;422:1-11. doi: 10.1016/j.jtbi.2017.04.009. Epub 2017 Apr 8.

PMID:
28400108
38.

Mechanocellular models of epithelial morphogenesis.

Fletcher AG, Cooper F, Baker RE.

Philos Trans R Soc Lond B Biol Sci. 2017 May 19;372(1720). pii: 20150519. doi: 10.1098/rstb.2015.0519. Review.

39.

Statistical analysis of genetic interactions in Tn-Seq data.

DeJesus MA, Nambi S, Smith CM, Baker RE, Sassetti CM, Ioerger TR.

Nucleic Acids Res. 2017 Jun 20;45(11):e93. doi: 10.1093/nar/gkx128.

40.
41.

Efficient parameter sensitivity computation for spatially extended reaction networks.

Lester C, Yates CA, Baker RE.

J Chem Phys. 2017 Jan 28;146(4):044106. doi: 10.1063/1.4973219.

PMID:
28147517
42.

Tuberculosis Susceptibility and Vaccine Protection Are Independently Controlled by Host Genotype.

Smith CM, Proulx MK, Olive AJ, Laddy D, Mishra BB, Moss C, Gutierrez NM, Bellerose MM, Barreira-Silva P, Phuah JY, Baker RE, Behar SM, Kornfeld H, Evans TG, Beamer G, Sassetti CM.

MBio. 2016 Sep 20;7(5). pii: e01516-16. doi: 10.1128/mBio.01516-16.

43.

An analytical method for disentangling the roles of adhesion and crowding for random walk models on a crowded lattice.

Ellery AJ, Baker RE, Simpson MJ.

Phys Biol. 2016 Sep 6;13(5):05LT02. doi: 10.1088/1478-3975/13/5/05LT02.

PMID:
27597573
44.

Goniometrie evaluation of standing extension and maximum flexion joint angles of llamas and alpacas.

Walters AL, Semevolos SA, Baker RE.

Am J Vet Res. 2016 Sep;77(9):1000-4. doi: 10.2460/ajvr.77.9.1000.

PMID:
27580112
45.

How domain growth is implemented determines the long-term behavior of a cell population through its effect on spatial correlations.

Ross RJ, Baker RE, Yates CA.

Phys Rev E. 2016 Jul;94(1-1):012408. doi: 10.1103/PhysRevE.94.012408. Epub 2016 Jul 14.

PMID:
27575165
46.

Extending the Multi-level Method for the Simulation of Stochastic Biological Systems.

Lester C, Baker RE, Giles MB, Yates CA.

Bull Math Biol. 2016 Aug;78(8):1640-77. doi: 10.1007/s11538-016-0178-9. Epub 2016 Aug 11.

PMID:
27515935
47.

Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches.

Taylor PR, Baker RE, Simpson MJ, Yates CA.

J R Soc Interface. 2016 Jul;13(120). pii: 20160336. doi: 10.1098/rsif.2016.0336.

48.

Exits in order: How crowding affects particle lifetimes.

Penington CJ, Baker RE, Simpson MJ.

J Chem Phys. 2016 Jun 28;144(24):244107. doi: 10.1063/1.4953913.

PMID:
27369497
49.

Multidisciplinary approaches to understanding collective cell migration in developmental biology.

Schumacher LJ, Kulesa PM, McLennan R, Baker RE, Maini PK.

Open Biol. 2016 Jun;6(6). pii: 160056. doi: 10.1098/rsob.160056. Review.

50.

Polo kinase Cdc5 associates with centromeres to facilitate the removal of centromeric cohesin during mitosis.

Mishra PK, Ciftci-Yilmaz S, Reynolds D, Au WC, Boeckmann L, Dittman LE, Jowhar Z, Pachpor T, Yeh E, Baker RE, Hoyt MA, D'Amours D, Bloom K, Basrai MA.

Mol Biol Cell. 2016 Jul 15;27(14):2286-300. doi: 10.1091/mbc.E16-01-0004. Epub 2016 May 25.

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