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Items: 1 to 50 of 79

1.

Physical and Emotional Burden of the Epley Maneuver in the Elderly.

Maas BDPJ, Bruintjes TD, van der Zaag-Loonen HJ, Winters SM, Masius-Olthof S, Colijn C, Benthem PPGV, van Leeuwen RB.

Otol Neurotol. 2019 Sep;40(8):1082-1087. doi: 10.1097/MAO.0000000000002326.

PMID:
31356487
2.

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.

Hall MD, Colijn C.

Mol Biol Evol. 2019 Jun 1;36(6):1333-1343. doi: 10.1093/molbev/msz058.

3.

Correction: Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil.

Mabud TS, de Lourdes Delgado Alves M, Ko AI, Basu S, Walter KS, Cohen T, Mathema B, Colijn C, Lemos E, Croda J, Andrews JR.

PLoS Med. 2019 Mar 1;16(3):e1002764. doi: 10.1371/journal.pmed.1002764. eCollection 2019 Mar.

4.

Phylogenies from dynamic networks.

Metzig C, Ratmann O, Bezemer D, Colijn C.

PLoS Comput Biol. 2019 Feb 26;15(2):e1006761. doi: 10.1371/journal.pcbi.1006761. eCollection 2019 Feb.

5.

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.

Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C.

Mol Biol Evol. 2019 Mar 1;36(3):587-603. doi: 10.1093/molbev/msy242.

PMID:
30690464
6.

Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil.

Mabud TS, de Lourdes Delgado Alves M, Ko AI, Basu S, Walter KS, Cohen T, Mathema B, Colijn C, Lemos E, Croda J, Andrews JR.

PLoS Med. 2019 Jan 24;16(1):e1002737. doi: 10.1371/journal.pmed.1002737. eCollection 2019 Jan. Erratum in: PLoS Med. 2019 Mar 1;16(3):e1002764.

7.

Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population.

Ayabina D, Ronning JO, Alfsnes K, Debech N, Brynildsrud OB, Arnesen T, Norheim G, Mengshoel AT, Rykkvin R, Dahle UR, Colijn C, Eldholm V.

Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000219. Epub 2018 Sep 14.

8.

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD, Harris SR.

Wellcome Open Res. 2018 Mar 23;3:33. doi: 10.12688/wellcomeopenres.14265.2. eCollection 2018.

9.

Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis.

Yang C, Lu L, Warren JL, Wu J, Jiang Q, Zuo T, Gan M, Liu M, Liu Q, DeRiemer K, Hong J, Shen X, Colijn C, Guo X, Gao Q, Cohen T.

Lancet Infect Dis. 2018 Jul;18(7):788-795. doi: 10.1016/S1473-3099(18)30218-4. Epub 2018 Apr 23.

10.

The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study.

Yaesoubi R, Trotter C, Colijn C, Yaesoubi M, Colombini A, Resch S, Kristiansen PA, LaForce FM, Cohen T.

PLoS Med. 2018 Jan 24;15(1):e1002495. doi: 10.1371/journal.pmed.1002495. eCollection 2018 Jan.

11.

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C.

PLoS One. 2017 Dec 27;12(12):e0189838. doi: 10.1371/journal.pone.0189838. eCollection 2017.

12.

Host population structure and treatment frequency maintain balancing selection on drug resistance.

Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M.

J R Soc Interface. 2017 Aug;14(133). pii: 20170295. doi: 10.1098/rsif.2017.0295.

13.

Erratum to: Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA).

Sartelli M, Weber DG, Ruppé E, Bassetti M, Wright BJ, Ansaloni L, Catena F, Coccolini F, Abu-Zidan FM, Coimbra R, Moore EE, Moore FA, Maier RV, De Waele JJ, Kirkpatrick AW, Griffiths EA, Eckmann C, Brink AJ, Mazuski JE, May AK, Sawyer RG, Mertz D, Montravers P, Kumar A, Roberts JA, Vincent JL, Watkins RR, Lowman W, Spellberg B, Abbott IJ, Adesunkanmi AK, Al-Dahir S, Al-Hasan MN, Agresta F, Althani AA, Ansari S, Ansumana R, Augustin G, Bala M, Balogh ZJ, Baraket O, Bhangu A, Beltrán MA, Bernhard M, Biffl WL, Boermeester MA, Brecher SM, Cherry-Bukowiec JR, Buyne OR, Cainzos MA, Cairns KA, Camacho-Ortiz A, Chandy SJ, Che Jusoh A, Chichom-Mefire A, Colijn C, Corcione F, Cui Y, Curcio D, Delibegovic S, Demetrashvili Z, De Simone B, Dhingra S, Diaz JJ, Di Carlo I, Dillip A, Di Saverio S, Doyle MP, Dorj G, Dogjani A, Dupont H, Eachempati SR, Enani MA, Egiev VN, Elmangory MM, Ferrada P, Fitchett JR, Fraga GP, Guessennd N, Giamarellou H, Ghnnam W, Gkiokas G, Goldberg SR, Gomes CA, Gomi H, Guzmán-Blanco M, Haque M, Hansen S, Hecker A, Heizmann WR, Herzog T, Hodonou AM, Hong SK, Kafka-Ritsch R, Kaplan LJ, Kapoor G, Karamarkovic A, Kees MG, Kenig J, Kiguba R, Kim PK, Kluger Y, Khokha V, Koike K, Kok KY, Kong V, Knox MC, Inaba K, Isik A, Iskandar K, Ivatury RR, Labbate M, Labricciosa FM, Laterre PF, Latifi R, Lee JG, Lee YR, Leone M, Leppaniemi A, Li Y, Liang SY, Loho T, Maegele M, Malama S, Marei HE, Martin-Loeches I, Marwah S, Massele A, McFarlane M, Melo RB, Negoi I, Nicolau DP, Nord CE, Ofori-Asenso R, Omari AH, Ordonez CA, Ouadii M, Pereira Júnior GA, Piazza D, Pupelis G, Rawson TM, Rems M, Rizoli S, Rocha C, Sakakushev B, Sanchez-Garcia M, Sato N, Segovia Lohse HA, Sganga G, Siribumrungwong B, Shelat VG, Soreide K, Soto R, Talving P, Tilsed JV, Timsit JF, Trueba G, Trung NT, Ulrych J, van Goor H, Vereczkei A, Vohra RS, Wani I, Uhl W, Xiao Y, Yuan KC, Zachariah SK, Zahar JR, Zakrison TL, Corcione A, Melotti RM, Viscoli C, Viale P.

World J Emerg Surg. 2017 Aug 2;12:35. doi: 10.1186/s13017-017-0147-0. eCollection 2017.

14.

A curated genome-scale metabolic model of Bordetella pertussis metabolism.

Fyson N, King J, Belcher T, Preston A, Colijn C.

PLoS Comput Biol. 2017 Jul 17;13(7):e1005639. doi: 10.1371/journal.pcbi.1005639. eCollection 2017 Jul.

15.

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

Klinkenberg D, Backer JA, Didelot X, Colijn C, Wallinga J.

PLoS Comput Biol. 2017 May 18;13(5):e1005495. doi: 10.1371/journal.pcbi.1005495. eCollection 2017 May.

16.

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.

AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25.

17.

A Metric on Phylogenetic Tree Shapes.

Colijn C, Plazzotta G.

Syst Biol. 2018 Jan 1;67(1):113-126. doi: 10.1093/sysbio/syx046.

18.

The Dizzy Patient: Consider a Second Diagnosis.

van Leeuwen RB, Colijn C, van Wensen E, Bruintjes TD.

Neurologist. 2017 May;22(3):69-71. doi: 10.1097/NRL.0000000000000116.

PMID:
28471892
19.

Toward Precision Healthcare: Context and Mathematical Challenges.

Colijn C, Jones N, Johnston IG, Yaliraki S, Barahona M.

Front Physiol. 2017 Mar 21;8:136. doi: 10.3389/fphys.2017.00136. eCollection 2017.

20.

treespace: Statistical exploration of landscapes of phylogenetic trees.

Jombart T, Kendall M, Almagro-Garcia J, Colijn C.

Mol Ecol Resour. 2017 Nov;17(6):1385-1392. doi: 10.1111/1755-0998.12676. Epub 2017 May 15.

21.

Declaring a tuberculosis outbreak over with genomic epidemiology.

Hatherell HA, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, Colijn C, Gardy JL.

Microb Genom. 2016 May 31;2(5):e000060. doi: 10.1099/mgen.0.000060. eCollection 2016 May.

22.

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.

Didelot X, Fraser C, Gardy J, Colijn C.

Mol Biol Evol. 2017 Apr 1;34(4):997-1007. doi: 10.1093/molbev/msw275.

23.

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.

24.

Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture.

Ayabina D, Hendon-Dunn C, Bacon J, Colijn C.

J R Soc Interface. 2016 Nov;13(124). pii: 20160745.

25.

Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA).

Sartelli M, Weber DG, Ruppé E, Bassetti M, Wright BJ, Ansaloni L, Catena F, Coccolini F, Abu-Zidan FM, Coimbra R, Moore EE, Moore FA, Maier RV, De Waele JJ, Kirkpatrick AW, Griffiths EA, Eckmann C, Brink AJ, Mazuski JE, May AK, Sawyer RG, Mertz D, Montravers P, Kumar A, Roberts JA, Vincent JL, Watkins RR, Lowman W, Spellberg B, Abbott IJ, Adesunkanmi AK, Al-Dahir S, Al-Hasan MN, Agresta F, Althani AA, Ansari S, Ansumana R, Augustin G, Bala M, Balogh ZJ, Baraket O, Bhangu A, Beltrán MA, Bernhard M, Biffl WL, Boermeester MA, Brecher SM, Cherry-Bukowiec JR, Buyne OR, Cainzos MA, Cairns KA, Camacho-Ortiz A, Chandy SJ, Che Jusoh A, Chichom-Mefire A, Colijn C, Corcione F, Cui Y, Curcio D, Delibegovic S, Demetrashvili Z, De Simone B, Dhingra S, Diaz JJ, Di Carlo I, Dillip A, Di Saverio S, Doyle MP, Dorj G, Dogjani A, Dupont H, Eachempati SR, Enani MA, Egiev VN, Elmangory MM, Ferrada P, Fitchett JR, Fraga GP, Guessennd N, Giamarellou H, Ghnnam W, Gkiokas G, Goldberg SR, Gomes CA, Gomi H, Guzmán-Blanco M, Haque M, Hansen S, Hecker A, Heizmann WR, Herzog T, Hodonou AM, Hong SK, Kafka-Ritsch R, Kaplan LJ, Kapoor G, Karamarkovic A, Kees MG, Kenig J, Kiguba R, Kim PK, Kluger Y, Khokha V, Koike K, Kok KY, Kong V, Knox MC, Inaba K, Isik A, Iskandar K, Ivatury RR, Labbate M, Labricciosa FM, Laterre PF, Latifi R, Lee JG, Lee YR, Leone M, Leppaniemi A, Li Y, Liang SY, Loho T, Maegele M, Malama S, Marei HE, Martin-Loeches I, Marwah S, Massele A, McFarlane M, Melo RB, Negoi I, Nicolau DP, Nord CE, Ofori-Asenso R, Omari AH, Ordonez CA, Ouadii M, Pereira Júnior GA, Piazza D, Pupelis G, Rawson TM, Rems M, Rizoli S, Rocha C, Sakakushev B, Sanchez-Garcia M, Sato N, Segovia Lohse HA, Sganga G, Siribumrungwong B, Shelat VG, Soreide K, Soto R, Talving P, Tilsed JV, Timsit JF, Trueba G, Trung NT, Ulrych J, van Goor H, Vereczkei A, Vohra RS, Wani I, Uhl W, Xiao Y, Yuan KC, Zachariah SK, Zahar JR, Zakrison TL, Corcione A, Melotti RM, Viscoli C, Viale P.

World J Emerg Surg. 2016 Jul 15;11:33. doi: 10.1186/s13017-016-0089-y. eCollection 2016. Review. Erratum in: World J Emerg Surg. 2017 Aug 2;12 :35.

26.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

Kendall M, Colijn C.

Mol Biol Evol. 2016 Oct;33(10):2735-43. doi: 10.1093/molbev/msw124. Epub 2016 Jun 24.

27.

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Aanensen DM, Feil EJ, Holden MT, Dordel J, Yeats CA, Fedosejev A, Goater R, Castillo-Ramírez S, Corander J, Colijn C, Chlebowicz MA, Schouls L, Heck M, Pluister G, Ruimy R, Kahlmeter G, Åhman J, Matuschek E, Friedrich AW, Parkhill J, Bentley SD, Spratt BG, Grundmann H; European SRL Working Group.

MBio. 2016 May 5;7(3). pii: e00444-16. doi: 10.1128/mBio.00444-16.

28.

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.

Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I.

BMC Med. 2016 Mar 23;14:21. doi: 10.1186/s12916-016-0566-x. Review.

29.

Effects of memory on the shapes of simple outbreak trees.

Plazzotta G, Kwan C, Boyd M, Colijn C.

Sci Rep. 2016 Feb 18;6:21159. doi: 10.1038/srep21159.

30.

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections.

Chindelevitch L, Colijn C, Moodley P, Wilson D, Cohen T.

PLoS Comput Biol. 2016 Feb 1;12(2):e1004475. doi: 10.1371/journal.pcbi.1004475. eCollection 2016 Feb. Erratum in: PLoS Comput Biol. 2016 Feb;12(2):e1004806.

31.

Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond.

Colijn C, Cohen T.

Lancet Respir Med. 2016 Jan;4(1):6-8. doi: 10.1016/S2213-2600(15)00510-X. Epub 2015 Dec 4. No abstract available.

32.

The Distribution of Fitness Costs of Resistance-Conferring Mutations Is a Key Determinant for the Future Burden of Drug-Resistant Tuberculosis: A Model-Based Analysis.

Knight GM, Colijn C, Shrestha S, Fofana M, Cobelens F, White RG, Dowdy DW, Cohen T.

Clin Infect Dis. 2015 Oct 15;61Suppl 3:S147-54. doi: 10.1093/cid/civ579.

33.

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance.

Colijn C, Cohen T.

Elife. 2015 Sep 22;4. pii: e10559. doi: 10.7554/eLife.10559.

34.

Spatio-temporal analysis of tuberculous infection risk among clients of a homeless shelter during an outbreak.

Crisan A, Wong HY, Johnston JC, Tang P, Colijn C, Otterstatter M, Hiscoe L, Parker R, Pollock SL, Gardy JL.

Int J Tuberc Lung Dis. 2015 Sep;19(9):1033-8, i-iii. doi: 10.5588/ijtld.14.0957.

PMID:
26260820
35.

Competition, coinfection and strain replacement in models of Bordetella pertussis.

Nicoli EJ, Ayabina D, Trotter CL, Turner KM, Colijn C.

Theor Popul Biol. 2015 Aug;103:84-92. doi: 10.1016/j.tpb.2015.05.003. Epub 2015 May 30.

36.

How could preventive therapy affect the prevalence of drug resistance? Causes and consequences.

Kunkel A, Colijn C, Lipsitch M, Cohen T.

Philos Trans R Soc Lond B Biol Sci. 2015 Jun 5;370(1670):20140306. doi: 10.1098/rstb.2014.0306.

37.

Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection.

Plazzotta G, Cohen T, Colijn C.

J Theor Biol. 2015 Mar 7;368:67-73. doi: 10.1016/j.jtbi.2014.12.009. Epub 2014 Dec 29.

38.

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.

Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M.

Genome Med. 2014 Nov 15;6(11):101. doi: 10.1186/s13073-014-0101-7. eCollection 2014.

39.

Intratympanic gentamicin treatment for Ménière's disease: a randomized, double-blind, placebo-controlled trial on dose efficacy - results of a prematurely ended study.

Bremer HG, van Rooy I, Pullens B, Colijn C, Stegeman I, van der Zaag-Loonen HJ, van Benthem PP, Klis SF, Grolman W, Bruintjes TD.

Trials. 2014 Aug 18;15:328. doi: 10.1186/1745-6215-15-328.

40.

Errors in reported degrees and respondent driven sampling: implications for bias.

Mills HL, Johnson S, Hickman M, Jones NS, Colijn C.

Drug Alcohol Depend. 2014 Sep 1;142:120-6. doi: 10.1016/j.drugalcdep.2014.06.015. Epub 2014 Jun 21.

41.

OutbreakTools: a new platform for disease outbreak analysis using the R software.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

42.

Phylogenetic tree shapes resolve disease transmission patterns.

Colijn C, Gardy J.

Evol Med Public Health. 2014 Jun 9;2014(1):96-108. doi: 10.1093/emph/eou018.

43.

Bayesian inference of infectious disease transmission from whole-genome sequence data.

Didelot X, Gardy J, Colijn C.

Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.

44.

Response to comment on "Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis".

Mills HL, Cohen T, Colijn C.

Sci Transl Med. 2013 Sep 25;5(204):204lr4. doi: 10.1126/scitranslmed.3007442.

45.

How the dynamics and structure of sexual contact networks shape pathogen phylogenies.

Robinson K, Fyson N, Cohen T, Fraser C, Colijn C.

PLoS Comput Biol. 2013;9(6):e1003105. doi: 10.1371/journal.pcbi.1003105. Epub 2013 Jun 20.

46.

HIV transmission from drug injectors to partners who do not inject, and beyond: modelling the potential for a generalized heterosexual epidemic in St. Petersburg, Russia.

Mills HL, White E, Colijn C, Vickerman P, Heimer R.

Drug Alcohol Depend. 2013 Nov 1;133(1):242-7. doi: 10.1016/j.drugalcdep.2013.04.028. Epub 2013 May 18.

47.

Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis.

Mills HL, Cohen T, Colijn C.

Sci Transl Med. 2013 Apr 10;5(180):180ra49. doi: 10.1126/scitranslmed.3005260.

48.

Influenza and RSV make a modest contribution to invasive pneumococcal disease incidence in the UK.

Nicoli EJ, Trotter CL, Turner KM, Colijn C, Waight P, Miller E.

J Infect. 2013 Jun;66(6):512-20. doi: 10.1016/j.jinf.2013.02.007. Epub 2013 Mar 5.

49.

Pathogen spread on coupled networks: effect of host and network properties on transmission thresholds.

Mills HL, Ganesh A, Colijn C.

J Theor Biol. 2013 Mar 7;320:47-57. doi: 10.1016/j.jtbi.2012.12.006. Epub 2012 Dec 14.

PMID:
23246458
50.

Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control.

Cohen T, van Helden PD, Wilson D, Colijn C, McLaughlin MM, Abubakar I, Warren RM.

Clin Microbiol Rev. 2012 Oct;25(4):708-19. doi: 10.1128/CMR.00021-12. Review.

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