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Items: 1 to 50 of 193

1.

Accuracy of Coupled Cluster Excited State Potential Energy Surfaces.

Tajti A, Stanton JF, Matthews DA, Szalay PG.

J Chem Theory Comput. 2018 Nov 13;14(11):5859-5869. doi: 10.1021/acs.jctc.8b00681. Epub 2018 Oct 23.

PMID:
30299948
2.

Fourth-order vibrational perturbation theory with the Watson Hamiltonian: Report of working equations and preliminary results.

Gong JZ, Matthews DA, Changala PB, Stanton JF.

J Chem Phys. 2018 Sep 21;149(11):114102. doi: 10.1063/1.5040360.

PMID:
30243279
3.

PITDB: a database of translated genomic elements.

Saha S, Chatzimichali EA, Matthews DA, Bessant C.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1223-D1228. doi: 10.1093/nar/gkx906.

4.

High throughput discovery of protein variants using proteomics informed by transcriptomics.

Saha S, Matthews DA, Bessant C.

Nucleic Acids Res. 2018 Jun 1;46(10):4893-4902. doi: 10.1093/nar/gky295.

5.

Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity.

Lum FM, Lee D, Chua TK, Tan JJL, Lee CYP, Liu X, Fang Y, Lee B, Yee WX, Rickett NY, Chia PY, Lim V, Leo YS, Matthews DA, Hiscox JA, Ng LFP.

mSphere. 2018 Mar 28;3(2). pii: e00120-18. doi: 10.1128/mSphereDirect.00120-18. eCollection 2018 Mar-Apr.

6.

Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde.

Morgan WJ, Matthews DA, Ringholm M, Agarwal J, Gong JZ, Ruud K, Allen WD, Stanton JF, Schaefer HF 3rd.

J Chem Theory Comput. 2018 Mar 13;14(3):1333-1350. doi: 10.1021/acs.jctc.7b01138. Epub 2018 Feb 23.

PMID:
29474074
7.

Proteomics technique opens new frontiers in mobilome research.

Davidson AD, Matthews DA, Maringer K.

Mob Genet Elements. 2017 Aug 1;7(4):1-9. doi: 10.1080/2159256X.2017.1362494. eCollection 2017.

8.

Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut.

Carroll MW, Haldenby S, Rickett NY, Pályi B, Garcia-Dorival I, Liu X, Barker G, Bore JA, Koundouno FR, Williamson ED, Laws TR, Kerber R, Sissoko D, Magyar N, Di Caro A, Biava M, Fletcher TE, Sprecher A, Ng LFP, Rénia L, Magassouba N, Günther S, Wölfel R, Stoecker K, Matthews DA, Hiscox JA.

mSphere. 2017 Aug 23;2(4). pii: e00325-17. doi: 10.1128/mSphereDirect.00325-17. eCollection 2017 Jul-Aug.

9.

Proteomics informed by transcriptomics for characterising differential cellular susceptibility to Nelson Bay orthoreovirus infection.

Mok L, Wynne JW, Tachedjian M, Shiell B, Ford K, Matthews DA, Bacic A, Michalski WP.

BMC Genomics. 2017 Aug 14;18(1):615. doi: 10.1186/s12864-017-3994-x.

10.

Comparison of protein expression during wild-type, and E1B-55k-deletion, adenovirus infection using quantitative time-course proteomics.

Fu YR, Turnell AS, Davis S, Heesom KJ, Evans VC, Matthews DA.

J Gen Virol. 2017 Jun;98(6):1377-1388. doi: 10.1099/jgv.0.000781. Epub 2017 Jun 20.

11.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

12.

A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus.

Bosworth A, Dowall SD, Garcia-Dorival I, Rickett NY, Bruce CB, Matthews DA, Fang Y, Aljabr W, Kenny J, Nelson C, Laws TR, Williamson ED, Stewart JP, Carroll MW, Hewson R, Hiscox JA.

Sci Rep. 2017 Feb 27;7:43144. doi: 10.1038/srep43144.

13.

Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.

Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD.

BMC Genomics. 2017 Jan 19;18(1):101. doi: 10.1186/s12864-016-3432-5.

14.

Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus.

Liu X, Speranza E, Muñoz-Fontela C, Haldenby S, Rickett NY, Garcia-Dorival I, Fang Y, Hall Y, Zekeng EG, Lüdtke A, Xia D, Kerber R, Krumkamp R, Duraffour S, Sissoko D, Kenny J, Rockliffe N, Williamson ED, Laws TR, N'Faly M, Matthews DA, Günther S, Cossins AR, Sprecher A, Connor JH, Carroll MW, Hiscox JA.

Genome Biol. 2017 Jan 19;18(1):4. doi: 10.1186/s13059-016-1137-3.

15.

Convergence of coupled cluster perturbation theory.

Eriksen JJ, Kristensen K, Matthews DA, Jørgensen P, Olsen J.

J Chem Phys. 2016 Dec 14;145(22):224104.

PMID:
27984892
16.

A new approach to approximate equation-of-motion coupled cluster with triple excitations.

Matthews DA, Stanton JF.

J Chem Phys. 2016 Sep 28;145(12):124102.

PMID:
27782677
17.

Assessment of the accuracy of coupled cluster perturbation theory for open-shell systems. II. Quadruples expansions.

Eriksen JJ, Matthews DA, Jørgensen P, Gauss J.

J Chem Phys. 2016 May 21;144(19):194103. doi: 10.1063/1.4948781.

PMID:
27208932
18.

Assessment of the accuracy of coupled cluster perturbation theory for open-shell systems. I. Triples expansions.

Eriksen JJ, Matthews DA, Jørgensen P, Gauss J.

J Chem Phys. 2016 May 21;144(19):194102. doi: 10.1063/1.4948780.

PMID:
27208931
19.

Density, Salinity, and Entry Depths of Municipal Wastewater in an Urban Lake.

Matthews DA, O'Donnell SM, Effler SW, Owens EM, Hurteau CA, Prestigiacomo AR.

Water Environ Res. 2016 Nov 1;88(11):2059-2069. doi: 10.2175/106143016X14609975745966. Epub 2016 Feb 2.

PMID:
27095460
20.

Communication: An accurate calculation of the S1 C2H2 cis-trans isomerization barrier height.

Baraban JH, Matthews DA, Stanton JF.

J Chem Phys. 2016 Mar 21;144(11):111102. doi: 10.1063/1.4943865.

PMID:
27004854
21.

A view on coupled cluster perturbation theory using a bivariational Lagrangian formulation.

Kristensen K, Eriksen JJ, Matthews DA, Olsen J, Jørgensen P.

J Chem Phys. 2016 Feb 14;144(6):064103. doi: 10.1063/1.4941605.

PMID:
26874478
22.

Real-time, portable genome sequencing for Ebola surveillance.

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sanchez A, Carter LL, Doerrbecker J, Enkirch T, Dorival IGG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallash E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Trina R, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner D, Pollakis G, Hiscox JA, Matthews DA, O'Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Woelfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keita S, Rambaut A, Formenty P, Gunther S, Carroll MW.

Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3.

23.

Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach.

Aljabr W, Touzelet O, Pollakis G, Wu W, Munday DC, Hughes M, Hertz-Fowler C, Kenny J, Fearns R, Barr JN, Matthews DA, Hiscox JA.

J Virol. 2016 Apr 29;90(10):4876-4888. doi: 10.1128/JVI.02349-15. Print 2016 May 15.

24.

Accelerating the convergence of higher-order coupled cluster methods.

Matthews DA, Stanton JF.

J Chem Phys. 2015 Nov 28;143(20):204103. doi: 10.1063/1.4936241.

PMID:
26627946
25.

Identification of Epstein-Barr Virus Replication Proteins in Burkitt's Lymphoma Cells.

Traylen C, Ramasubramanyan S, Zuo J, Rowe M, Almohammad R, Heesom K, Sweet SM, Matthews DA, Sinclair AJ.

Pathogens. 2015 Oct 29;4(4):739-51. doi: 10.3390/pathogens4040739.

26.

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.

Fan J, Saha S, Barker G, Heesom KJ, Ghali F, Jones AR, Matthews DA, Bessant C.

Mol Cell Proteomics. 2015 Nov;14(11):3087-93. doi: 10.1074/mcp.O115.048777. Epub 2015 Aug 12.

27.

Communication: The performance of non-iterative coupled cluster quadruples models.

Eriksen JJ, Matthews DA, Jørgensen P, Gauss J.

J Chem Phys. 2015 Jul 28;143(4):041101. doi: 10.1063/1.4927247.

PMID:
26233096
28.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions.

Thompson MC, Baraban JH, Matthews DA, Stanton JF, Weber JM.

J Chem Phys. 2015 Jun 21;142(23):234304. doi: 10.1063/1.4922609.

PMID:
26093556
29.

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman EN, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CE, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S.

Nature. 2015 Aug 6;524(7563):97-101. doi: 10.1038/nature14594. Epub 2015 Jun 17.

PMID:
26083749
30.

Stabilization of the Simplest Criegee Intermediate from the Reaction between Ozone and Ethylene: A High-Level Quantum Chemical and Kinetic Analysis of Ozonolysis.

Nguyen TL, Lee H, Matthews DA, McCarthy MC, Stanton JF.

J Phys Chem A. 2015 Jun 4;119(22):5524-33. doi: 10.1021/acs.jpca.5b02088. Epub 2015 May 21.

PMID:
25945650
31.

Zooplankton community changes confound the biodilution theory of methylmercury accumulation in a recovering mercury-contaminated lake.

Todorova S, Driscoll CT, Matthews DA, Effler SW.

Environ Sci Technol. 2015 Apr 7;49(7):4066-71. doi: 10.1021/es5044084. Epub 2015 Mar 17.

PMID:
25741879
32.

Non-orthogonal spin-adaptation of coupled cluster methods: A new implementation of methods including quadruple excitations.

Matthews DA, Stanton JF.

J Chem Phys. 2015 Feb 14;142(6):064108. doi: 10.1063/1.4907278.

PMID:
25681888
33.

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity.

Dowall SD, Matthews DA, Garcia-Dorival I, Taylor I, Kenny J, Hertz-Fowler C, Hall N, Corbin-Lickfett K, Empig C, Schlunegger K, Barr JN, Carroll MW, Hewson R, Hiscox JA.

Genome Biol. 2014;15(11):540.

34.

Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics.

Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA.

J Gen Virol. 2014 Nov;95(Pt 11):2504-11. doi: 10.1099/vir.0.068221-0. Epub 2014 Aug 5.

35.

Factors affecting de novo RNA synthesis and back-priming by the respiratory syncytial virus polymerase.

Noton SL, Aljabr W, Hiscox JA, Matthews DA, Fearns R.

Virology. 2014 Aug;462-463:318-27. doi: 10.1016/j.virol.2014.05.032. Epub 2014 Jul 8.

36.

High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells.

Chiu HC, Hannemann H, Heesom KJ, Matthews DA, Davidson AD.

PLoS One. 2014 Mar 26;9(3):e93305. doi: 10.1371/journal.pone.0093305. eCollection 2014.

37.

Changes in the long-term supply of mercury species to the upper mixed waters of a recovering lake.

Todorova SG, Driscoll CT, Effler SW, O'Donnell S, Matthews DA, Todorov DL, Gindlesperger S.

Environ Pollut. 2014 Feb;185:314-21. doi: 10.1016/j.envpol.2013.11.005. Epub 2013 Dec 5.

PMID:
24316069
38.

Revisitation of Nonorthogonal Spin Adaptation in Coupled Cluster Theory.

Matthews DA, Gauss J, Stanton JF.

J Chem Theory Comput. 2013 Jun 11;9(6):2567-72. doi: 10.1021/ct301024v. Epub 2013 May 24.

PMID:
26583853
39.

Whole-lake nitrate addition for control of methylmercury in mercury-contaminated Onondaga Lake, NY.

Matthews DA, Babcock DB, Nolan JG, Prestigiacomo AR, Effler SW, Driscoll CT, Todorova SG, Kuhr KM.

Environ Res. 2013 Aug;125:52-60. doi: 10.1016/j.envres.2013.03.011. Epub 2013 May 17.

PMID:
23683521
40.

Retrospective analyses of inputs of municipal wastewater effluent and coupled impacts on an urban lake.

Effler SW, O'Donnell SM, Prestigiacomo AR, Matthews DA, Auer MT.

Water Environ Res. 2013 Jan;85(1):13-26.

PMID:
23409450
41.

De novo derivation of proteomes from transcriptomes for transcript and protein identification.

Evans VC, Barker G, Heesom KJ, Fan J, Bessant C, Matthews DA.

Nat Methods. 2012 Dec;9(12):1207-11. doi: 10.1038/nmeth.2227. Epub 2012 Nov 11.

42.

Factors diminishing the effectiveness of phosphorus loading from municipal effluent: critical information for TMDL analyses.

Effler SW, Auer MT, Peng F, Perkins M, O'Donnell SM, Prestigiacomo AR, Matthews DA, DePetro PA, Lambert RS, Minott NM.

Water Environ Res. 2012 Mar;84(3):254-64.

PMID:
22755493
43.

Adenoviral protein V promotes a process of viral assembly through nucleophosmin 1.

Ugai H, Dobbins GC, Wang M, Le LP, Matthews DA, Curiel DT.

Virology. 2012 Oct 25;432(2):283-95. doi: 10.1016/j.virol.2012.05.028. Epub 2012 Jun 18.

44.

The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology.

Wu W, Tran KC, Teng MN, Heesom KJ, Matthews DA, Barr JN, Hiscox JA.

J Virol. 2012 Aug;86(15):7777-89. doi: 10.1128/JVI.00460-12. Epub 2012 May 16.

45.

Quantitative proteomics using SILAC coupled to LC-MS/MS reveals changes in the nucleolar proteome in influenza A virus-infected cells.

Emmott E, Wise H, Loucaides EM, Matthews DA, Digard P, Hiscox JA.

J Proteome Res. 2010 Oct 1;9(10):5335-45. doi: 10.1021/pr100593g.

PMID:
20701360
46.

Nucleolar proteomics and viral infection.

Hiscox JA, Whitehouse A, Matthews DA.

Proteomics. 2010 Nov;10(22):4077-86. doi: 10.1002/pmic.201000251. Review.

PMID:
20661956
47.

The effect of municipal wastewater effluent on nitrogen levels in Onondaga Lake, a 36-year record.

Effler SW, O'Donnel SM, Prestigiacomo AR, O'Donnell DM, Gelda RK, Matthews DA.

Water Environ Res. 2010 Jan;82(1):3-19.

PMID:
20112533
48.

In vitro dynamic visualization analysis of fluorescently labeled minor capsid protein IX and core protein V by simultaneous detection.

Ugai H, Wang M, Le LP, Matthews DA, Yamamoto M, Curiel DT.

J Mol Biol. 2010 Jan 8;395(1):55-78. doi: 10.1016/j.jmb.2009.10.034. Epub 2009 Oct 21.

49.

Proteomics analysis of the nucleolus in adenovirus-infected cells.

Lam YW, Evans VC, Heesom KJ, Lamond AI, Matthews DA.

Mol Cell Proteomics. 2010 Jan;9(1):117-30. doi: 10.1074/mcp.M900338-MCP200. Epub 2009 Oct 7.

50.

Evidence for regulation of monomethyl mercury by nitrate in a seasonally stratified, eutrophic lake.

Todorova SG, Driscoll CT Jr, Matthews DA, Effler SW, Hines ME, Henry EA.

Environ Sci Technol. 2009 Sep 1;43(17):6572-8.

PMID:
19764219

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