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Items: 1 to 50 of 186

1.

The Third Annual Meeting of the European Virus Bioinformatics Center.

Hufsky F, Ibrahim B, Modha S, Clokie MRJ, Deinhardt-Emmer S, Dutilh BE, Lycett S, Simmonds P, Thiel V, Abroi A, Adriaenssens EM, Escalera-Zamudio M, Kelly JN, Lamkiewicz K, Lu L, Susat J, Sicheritz T, Robertson DL, Marz M.

Viruses. 2019 May 5;11(5). pii: E420. doi: 10.3390/v11050420.

2.

The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences.

Tapinos A, Constantinides B, Phan MVT, Kouchaki S, Cotten M, Robertson DL.

Viruses. 2019 Apr 26;11(5). pii: E394. doi: 10.3390/v11050394.

3.

Interpreting Viral Deep Sequencing Data with GLUE.

Singer JB, Thomson EC, Hughes J, Aranday-Cortes E, McLauchlan J, da Silva Filipe A, Tong L, Manso CF, Gifford RJ, Robertson DL, Barnes E, Ansari MA, Mbisa JL, Bibby DF, Bradshaw D, Smith D.

Viruses. 2019 Apr 3;11(4). pii: E323. doi: 10.3390/v11040323.

4.

The Association Between Hunter-Killed Deer and Lyme Disease in New Jersey, 2000-2014.

Robertson DL, Babin LM, Krall JR, von Fricken ME, Baghi H, Jacobsen KH.

Ecohealth. 2019 Jun;16(2):330-337. doi: 10.1007/s10393-019-01401-x. Epub 2019 Mar 1.

PMID:
30825021
5.

A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns.

Kouchaki S, Tapinos A, Robertson DL.

Sci Rep. 2019 Feb 15;9(1):2159. doi: 10.1038/s41598-018-38197-9.

6.

Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems.

Ravindran V, Nacher JC, Akutsu T, Ishitsuka M, Osadcenco A, Sunitha V, Bagler G, Schwartz JM, Robertson DL.

Sci Rep. 2019 Feb 14;9(1):2066. doi: 10.1038/s41598-018-38224-9.

7.

Clonal analysis of HIV-1 genotype and function associated with virologic failure in treatment-experienced persons receiving maraviroc: Results from the MOTIVATE phase 3 randomized, placebo-controlled trials.

Lewis M, Mori J, Toma J, Mosley M, Huang W, Simpson P, Mansfield R, Craig C, van der Ryst E, Robertson DL, Whitcomb JM, Westby M.

PLoS One. 2018 Dec 26;13(12):e0204099. doi: 10.1371/journal.pone.0204099. eCollection 2018.

8.

Using set theory to reduce redundancy in pathway sets.

Stoney RA, Schwartz JM, Robertson DL, Nenadic G.

BMC Bioinformatics. 2018 Oct 19;19(1):386. doi: 10.1186/s12859-018-2355-3.

9.

Mapping biological process relationships and disease perturbations within a pathway network.

Stoney R, Robertson DL, Nenadic G, Schwartz JM.

NPJ Syst Biol Appl. 2018 Jun 11;4:22. doi: 10.1038/s41540-018-0055-2. eCollection 2018.

10.

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

11.

Redefining the ancestral origins of the interleukin-1 superfamily.

Rivers-Auty J, Daniels MJD, Colliver I, Robertson DL, Brough D.

Nat Commun. 2018 Mar 20;9(1):1156. doi: 10.1038/s41467-018-03362-1.

12.

Male Stigma: Emotional and Behavioral Effects of a Negative Social Identity on a Group of Canadian Men.

Robertson DLH.

Am J Mens Health. 2018 Jul;12(4):1118-1130. doi: 10.1177/1557988318763661. Epub 2018 Mar 20.

13.

HIV-1 group P infection: towards a dead-end infection?

Alessandri-Gradt E, De Oliveira F, Leoz M, Lemee V, Robertson DL, Feyertag F, Ngoupo PA, Mauclere P, Simon F, Plantier JC.

AIDS. 2018 Jun 19;32(10):1317-1322. doi: 10.1097/QAD.0000000000001791.

PMID:
29547436
14.

Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism.

Jiang X, Feyertag F, Robertson DL.

PLoS One. 2017 Oct 19;12(10):e0185790. doi: 10.1371/journal.pone.0185790. eCollection 2017.

15.

Adaptive HIV-1 evolutionary trajectories are constrained by protein stability.

Olabode AS, Kandathil SM, Lovell SC, Robertson DL.

Virus Evol. 2017 Aug 1;3(2):vex019. doi: 10.1093/ve/vex019. eCollection 2017 Jul.

16.

Do the shuffle: Changes in Symbiodinium consortia throughout juvenile coral development.

Reich HG, Robertson DL, Goodbody-Gringley G.

PLoS One. 2017 Feb 9;12(2):e0171768. doi: 10.1371/journal.pone.0171768. eCollection 2017.

17.

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes.

Tsimpidis M, Bachoumis G, Mimouli K, Kyriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD.

BMC Bioinformatics. 2017 Jan 5;18(1):13. doi: 10.1186/s12859-016-1420-z.

18.

Challenges in the analysis of viral metagenomes.

Rose R, Constantinides B, Tapinos A, Robertson DL, Prosperi M.

Virus Evol. 2016 Aug 3;2(2):vew022. doi: 10.1093/ve/vew022. eCollection 2016 Jul. Review.

19.

A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

Duck G, Nenadic G, Filannino M, Brass A, Robertson DL, Stevens R.

PLoS One. 2016 Jun 22;11(6):e0157989. doi: 10.1371/journal.pone.0157989. eCollection 2016.

20.

Binding interface change and cryptic variation in the evolution of protein-protein interactions.

Ames RM, Talavera D, Williams SG, Robertson DL, Lovell SC.

BMC Evol Biol. 2016 Feb 18;16:40. doi: 10.1186/s12862-016-0608-1.

21.

Disentangling the multigenic and pleiotropic nature of molecular function.

Stoney RA, Ames RM, Nenadic G, Robertson DL, Schwartz JM.

BMC Syst Biol. 2015;9 Suppl 6:S3. doi: 10.1186/1752-0509-9-S6-S3. Epub 2015 Dec 9.

22.

Characterizing the Diverse Mutational Pathways Associated with R5-Tropic Maraviroc Resistance: HIV-1 That Uses the Drug-Bound CCR5 Coreceptor.

Jiang X, Feyertag F, Meehan CJ, McCormack GP, Travers SA, Craig C, Westby M, Lewis M, Robertson DL.

J Virol. 2015 Nov;89(22):11457-72. doi: 10.1128/JVI.01384-15. Epub 2015 Sep 2.

23.

The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon.

Leoz M, Feyertag F, Kfutwah A, Mauclère P, Lachenal G, Damond F, De Oliveira F, Lemée V, Simon F, Robertson DL, Plantier JC.

PLoS Pathog. 2015 Aug 4;11(8):e1005029. doi: 10.1371/journal.ppat.1005029. eCollection 2015 Aug.

24.

Ambiguity and variability of database and software names in bioinformatics.

Duck G, Kovacevic A, Robertson DL, Stevens R, Nenadic G.

J Biomed Semantics. 2015 Jun 29;6:29. doi: 10.1186/s13326-015-0026-0. eCollection 2015.

25.

Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak.

Olabode AS, Jiang X, Robertson DL, Lovell SC.

Virology. 2015 Aug;482:202-7. doi: 10.1016/j.virol.2015.03.029. Epub 2015 Apr 14.

26.

Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network.

Keith BP, Robertson DL, Hentges KE.

Front Genet. 2014 Dec 9;5:434. doi: 10.3389/fgene.2014.00434. eCollection 2014.

27.

Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.

Ghoshroy S, Robertson DL.

J Mol Evol. 2015 Jan;80(1):65-80. doi: 10.1007/s00239-014-9659-3. Epub 2014 Dec 11.

PMID:
25504421
28.

A logical model of HIV-1 interactions with the T-cell activation signalling pathway.

Oyeyemi OJ, Davies O, Robertson DL, Schwartz JM.

Bioinformatics. 2015 Apr 1;31(7):1075-83. doi: 10.1093/bioinformatics/btu787. Epub 2014 Nov 26.

PMID:
25431332
29.

Extracting patterns of database and software usage from the bioinformatics literature.

Duck G, Nenadic G, Brass A, Robertson DL, Stevens R.

Bioinformatics. 2014 Sep 1;30(17):i601-8. doi: 10.1093/bioinformatics/btu471.

30.

The pain interactome: connecting pain-specific protein interactions.

Jamieson DG, Moss A, Kennedy M, Jones S, Nenadic G, Robertson DL, Sidders B.

Pain. 2014 Nov;155(11):2243-52. doi: 10.1016/j.pain.2014.06.020. Epub 2014 Jun 28.

31.

The utility of different bioinformatics algorithms for genotypic HIV-1 tropism testing in a large clinical cohort with multiple subtypes.

Bartlett AD, MaCartney MJ, Conibear TC, Feyertag F, Smith CJ, Johnson MA, Hyams C, Garcia-Diaz A, McCormick AL, Booth C, Robertson DL, Webster DP.

AIDS. 2014 Jul 17;28(11):1611-7. doi: 10.1097/QAD.0000000000000288.

PMID:
24785955
32.

Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants.

Woo J, Robertson DL, Lovell SC.

Virology. 2014 Apr;454-455:34-9. doi: 10.1016/j.virol.2014.01.029. Epub 2014 Feb 22.

33.

Factors associated with siman immunodeficiency virus transmission in a natural African nonhuman primate host in the wild.

Ma D, Jasinska AJ, Feyertag F, Wijewardana V, Kristoff J, He T, Raehtz K, Schmitt CA, Jung Y, Cramer JD, Dione M, Antonio M, Tracy R, Turner T, Robertson DL, Pandrea I, Freimer N, Apetrei C; International Vervet Research Consortium.

J Virol. 2014 May;88(10):5687-705. doi: 10.1128/JVI.03606-13. Epub 2014 Mar 12.

34.

Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.

Gibson RM, Meyer AM, Winner D, Archer J, Feyertag F, Ruiz-Mateos E, Leal M, Robertson DL, Schmotzer CL, Quiñones-Mateu ME.

Antimicrob Agents Chemother. 2014;58(4):2167-85. doi: 10.1128/AAC.02710-13. Epub 2014 Jan 27.

35.

Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries.

Boissonneault KR, Henningsen BM, Bates SS, Robertson DL, Milton S, Pelletier J, Hogan DA, Housman DE.

BMC Mol Biol. 2013 Nov 1;14:25. doi: 10.1186/1471-2199-14-25.

36.

bioNerDS: exploring bioinformatics' database and software use through literature mining.

Duck G, Nenadic G, Brass A, Robertson DL, Stevens R.

BMC Bioinformatics. 2013 Jun 15;14:194. doi: 10.1186/1471-2105-14-194.

37.

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.

Jamieson DG, Roberts PM, Robertson DL, Sidders B, Nenadic G.

Database (Oxford). 2013 May 23;2013:bat033. doi: 10.1093/database/bat033. Print 2013.

38.

Modular biological function is most effectively captured by combining molecular interaction data types.

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.

39.

The role of protein interactions in mediating essentiality and synthetic lethality.

Talavera D, Robertson DL, Lovell SC.

PLoS One. 2013 Apr 29;8(4):e62866. doi: 10.1371/journal.pone.0062866. Print 2013.

40.

Alternative splicing and protein interaction data sets.

Talavera D, Robertson DL, Lovell SC.

Nat Biotechnol. 2013 Apr;31(4):292-3. doi: 10.1038/nbt.2540. No abstract available.

PMID:
23563420
41.

Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.

Weber J, Vazquez AC, Winner D, Gibson RM, Rhea AM, Rose JD, Wylie D, Henry K, Wright A, King K, Archer J, Poveda E, Soriano V, Robertson DL, Olivo PD, Arts EJ, Quiñones-Mateu ME.

J Clin Microbiol. 2013 May;51(5):1517-27. doi: 10.1128/JCM.00092-13. Epub 2013 Mar 13.

42.

SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations.

Ma D, Jasinska A, Kristoff J, Grobler JP, Turner T, Jung Y, Schmitt C, Raehtz K, Feyertag F, Martinez Sosa N, Wijewardana V, Burke DS, Robertson DL, Tracy R, Pandrea I, Freimer N, Apetrei C; International Vervet Research Consortium.

PLoS Pathog. 2013 Jan;9(1):e1003011. doi: 10.1371/journal.ppat.1003011. Epub 2013 Jan 17.

43.

The origins of the evolutionary signal used to predict protein-protein interactions.

Swapna LS, Srinivasan N, Robertson DL, Lovell SC.

BMC Evol Biol. 2012 Dec 6;12:238. doi: 10.1186/1471-2148-12-238.

44.

Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

Archer J, Weber J, Henry K, Winner D, Gibson R, Lee L, Paxinos E, Arts EJ, Robertson DL, Mimms L, Quiñones-Mateu ME.

PLoS One. 2012;7(11):e49602. doi: 10.1371/journal.pone.0049602. Epub 2012 Nov 14.

45.

MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES(1).

Ghoshroy S, Robertson DL.

J Phycol. 2012 Jun;48(3):768-83. doi: 10.1111/j.1529-8817.2012.01169.x.

PMID:
27011094
46.

Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database.

Jamieson DG, Gerner M, Sarafraz F, Nenadic G, Robertson DL.

Database (Oxford). 2012 Apr 23;2012:bas023. doi: 10.1093/database/bas023. Print 2012.

47.

Evolvability of yeast protein-protein interaction interfaces.

Talavera D, Williams SG, Norris MG, Robertson DL, Lovell SC.

J Mol Biol. 2012 Jun 22;419(5):387-96. doi: 10.1016/j.jmb.2012.03.021. Epub 2012 Apr 1.

PMID:
22472422
48.

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL.

BMC Bioinformatics. 2012 Mar 23;13:47. doi: 10.1186/1471-2105-13-47.

49.

Defining the role of essential genes in human disease.

Dickerson JE, Zhu A, Robertson DL, Hentges KE.

PLoS One. 2011;6(11):e27368. doi: 10.1371/journal.pone.0027368. Epub 2011 Nov 11.

50.

An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection.

MacPherson JI, Sidders B, Wieland S, Zhong J, Targett-Adams P, Lohmann V, Backes P, Delpuech-Adams O, Chisari F, Lewis M, Parkinson T, Robertson DL.

PLoS One. 2011;6(10):e25584. doi: 10.1371/journal.pone.0025584. Epub 2011 Oct 25.

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