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A Genomic Perspective on the Origin and Emergence of SARS-CoV-2.

Zhang YZ, Holmes EC.

Cell. 2020 Mar 26. pii: S0092-8674(20)30328-7. doi: 10.1016/j.cell.2020.03.035. [Epub ahead of print]


Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins.

Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, Wei W, Cheung WY, Li WJ, Li LF, Leung GM, Holmes EC, Hu YL, Guan Y.

Nature. 2020 Mar 26. doi: 10.1038/s41586-020-2169-0. [Epub ahead of print]


Comparative analysis of RNA virome composition in rabbits and associated ectoparasites.

Mahar JE, Shi M, Hall RN, Strive T, Holmes EC.

J Virol. 2020 Mar 18. pii: JVI.02119-19. doi: 10.1128/JVI.02119-19. [Epub ahead of print]


OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R.

JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: 10.1200/CCI.19.00117.


Correction for Batovska et al., "Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes".

Batovska J, Buchmann JP, Holmes EC, Lynch SE.

Microbiol Resour Announc. 2020 Mar 5;9(10). pii: e00103-20. doi: 10.1128/MRA.00103-20. No abstract available.


Sleep and intrusive memories immediately after a traumatic event in emergency department patients.

Porcheret K, Iyadurai L, Bonsall MB, Goodwin GM, Beer SA, Darwent M, Holmes EA.

Sleep. 2020 Mar 5. pii: zsaa033. doi: 10.1093/sleep/zsaa033. [Epub ahead of print]


High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection.

Li CX, Li W, Zhou J, Zhang B, Feng Y, Xu CP, Lu YY, Holmes EC, Shi M.

Sci Rep. 2020 Mar 3;10(1):3963. doi: 10.1038/s41598-020-60992-6.


Metabonomics and the gut microbiome associated with primary response to anti-TNF therapy in Crohn's disease.

Ding NS, McDonald JAK, Perdones-Montero A, Rees DN, Adegbola SO, Misra R, Hendy P, Penez L, Marchesi JR, Holmes E, Sarafian MH, Hart AL.

J Crohns Colitis. 2020 Mar 2. pii: jjaa039. doi: 10.1093/ecco-jcc/jjaa039. [Epub ahead of print]


The use of taxon-specific reference databases compromises metagenomic classification.

R Marcelino V, Holmes EC, Sorrell TC.

BMC Genomics. 2020 Feb 27;21(1):184. doi: 10.1186/s12864-020-6592-2.


Speech spoken by familiar people is more resistant to interference by linguistically similar speech.

Holmes E, Johnsrude IS.

J Exp Psychol Learn Mem Cogn. 2020 Feb 27. doi: 10.1037/xlm0000823. [Epub ahead of print]


Properties and abundance of overlapping genes in viruses.

Schlub TE, Holmes EC.

Virus Evol. 2020 Feb 13;6(1):veaa009. doi: 10.1093/ve/veaa009. eCollection 2020 Jan.


We shouldn't worry when a virus mutates during disease outbreaks.

Grubaugh ND, Petrone ME, Holmes EC.

Nat Microbiol. 2020 Apr;5(4):529-530. doi: 10.1038/s41564-020-0690-4. No abstract available.


Emotional recognition training modifies neural response to emotional faces but does not improve mood in healthy volunteers with high levels of depressive symptoms.

Penton-Voak IS, Adams S, Button KS, Fluharty M, Dalili M, Browning M, Holmes EA, Harmer CJ, Munafò MR.

Psychol Med. 2020 Feb 17:1-9. doi: 10.1017/S0033291719004124. [Epub ahead of print]


Imaginator: A Proof-of-Concept Feasibility Trial of a Brief Imagery-Based Psychological Intervention for Young People Who Self-Harm.

Di Simplicio M, Appiah-Kusi E, Wilkinson P, Watson P, Meiser-Stedman C, Kavanagh DJ, Holmes EA.

Suicide Life Threat Behav. 2020 Feb 14:e12620. doi: 10.1111/sltb.12620. [Epub ahead of print]


A feasibility study of microwave therapy for precancerous actinic keratosis.

Jackson DN, Hogarth FJ, Sutherland D, Holmes EM, Donnan PT, Proby CM.

Br J Dermatol. 2020 Feb 6. doi: 10.1111/bjd.18935. [Epub ahead of print]


Characterisation of the Serum Metabolic Signature of Cholangiocarcinoma in a United Kingdom Cohort.

Alsaleh M, Leftley Z, Barbera TA, Koomson LK, Zabron A, Crossey MME, Reeves HL, Cramp M, Ryder S, Greer S, Prince M, Sithithaworn P, Shariff M, Khuntikeo N, Loilome W, Yongvanit P, Shen YL, Cox IJ, Williams R, Wadsworth CA, Holmes E, Nash K, Taylor-Robinson SD.

J Clin Exp Hepatol. 2020 Jan-Feb;10(1):17-29. doi: 10.1016/j.jceh.2019.06.001. Epub 2019 Jun 15.


Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction.

Dumenci OE, U AM, Khan SA, Holmes E, Taylor-Robinson SD.

J Hepatocell Carcinoma. 2020 Jan 7;7:1-9. doi: 10.2147/JHC.S239039. eCollection 2020.


Occurrence of cross-resistance and β-lactam seesaw effect in glycopeptide-, lipopeptide- and lipoglycopeptide-resistant MRSA correlates with membrane phosphatidylglycerol levels.

Hines KM, Shen T, Ashford NK, Waalkes A, Penewit K, Holmes EA, McLean K, Salipante SJ, Werth BJ, Xu L.

J Antimicrob Chemother. 2020 Feb 4. pii: dkz562. doi: 10.1093/jac/dkz562. [Epub ahead of print]


A new coronavirus associated with human respiratory disease in China.

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ.

Nature. 2020 Mar;579(7798):265-269. doi: 10.1038/s41586-020-2008-3. Epub 2020 Feb 3.


Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W.

Lancet. 2020 Feb 22;395(10224):565-574. doi: 10.1016/S0140-6736(20)30251-8. Epub 2020 Jan 30.


Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat.

Carrai M, Van Brussel K, Shi M, Li CX, Chang WS, Munday JS, Voss K, McLuckie A, Taylor D, Laws A, Holmes EC, Barrs VR, Beatty JA.

Viruses. 2020 Jan 20;12(1). pii: E124. doi: 10.3390/v12010124.


Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery.

West KA, Kanu C, Maric T, McDonald JAK, Nicholson JK, Li JV, Johnson MR, Holmes E, Savvidou MD.

Gut. 2020 Jan 21. pii: gutjnl-2019-319620. doi: 10.1136/gutjnl-2019-319620. [Epub ahead of print]


Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes.

Batovska J, Buchmann JP, Holmes EC, Lynch SE.

Microbiol Resour Announc. 2020 Jan 9;9(2). pii: e01476-19. doi: 10.1128/MRA.01476-19. Erratum in: Microbiol Resour Announc. 2020 Mar 5;9(10):.


Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits.

Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK.

Viruses. 2019 Dec 31;12(1). pii: E47. doi: 10.3390/v12010047.


Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases.

Cunha MDP, Duarte-Neto AN, Pour SZ, Ortiz-Baez AS, Černý J, Pereira BBS, Braconi CT, Ho YL, Perondi B, Sztajnbok J, Alves VAF, Dolhnikoff M, Holmes EC, Saldiva PHN, Zanotto PMA.

Sci Rep. 2019 Dec 31;9(1):20418. doi: 10.1038/s41598-019-56650-1.


Improving mental health and physiological stress responses in mothers following traumatic childbirth and in their infants: study protocol for the Swiss TrAumatic biRth Trial (START).

Sandoz V, Deforges C, Stuijfzand S, Epiney M, Vial Y, Sekarski N, Messerli-Bürgy N, Ehlert U, Bickle-Graz M, Morisod Harari M, Porcheret K, Schechter DS, Ayers S, Holmes EA, Horsch A; START Research Consortium.

BMJ Open. 2019 Dec 30;9(12):e032469. doi: 10.1136/bmjopen-2019-032469.


Characterisation of the Urinary Metabolic Profile of Liver Fluke-Associated Cholangiocarcinoma.

Alsaleh M, Sithithaworn P, Khuntikeo N, Loilome W, Yongvanit P, Chamadol N, Hughes T, O'Connor T, Andrews RH, Holmes E, Taylor-Robinson SD.

J Clin Exp Hepatol. 2019 Nov-Dec;9(6):657-675. doi: 10.1016/j.jceh.2019.06.005. Epub 2019 Jul 31.


Supporting people with type 2 diabetes in effective use of their medicine through mobile health technology integrated with clinical care (SuMMiT-D Feasibility): a randomised feasibility trial protocol.

Farmer A, Allen J, Bartlett K, Bower P, Chi Y, French D, Gudgin B, Holmes EA, Horne R, Hughes DA, Kenning C, Locock L, McSharry J, Miles L, Newhouse N, Rea R, Riga E, Tarassenko L, Velardo C, Williams N, Williams V, Yu LM; SuMMiT-D Collaborative Group.

BMJ Open. 2019 Dec 29;9(12):e033504. doi: 10.1136/bmjopen-2019-033504.


Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease.

Charon J, Grigg MJ, Eden JS, Piera KA, Rana H, William T, Rose K, Davenport MP, Anstey NM, Holmes EC.

PLoS Pathog. 2019 Dec 30;15(12):e1008216. doi: 10.1371/journal.ppat.1008216. eCollection 2019 Dec.


Validation study of randomly selected cases of PTSD diagnoses identified in a Swedish regional database compared with medical records: is the validity sufficient for epidemiological research?

Hollander AC, Askegård K, Iddon-Escalante C, Holmes EA, Wicks S, Dalman C.

BMJ Open. 2019 Dec 23;9(12):e031964. doi: 10.1136/bmjopen-2019-031964.


The Ecology and Evolution of Influenza Viruses.

Wille M, Holmes EC.

Cold Spring Harb Perspect Med. 2019 Dec 30. pii: a038489. doi: 10.1101/cshperspect.a038489. [Epub ahead of print]


Suicide attempt and suicide in refugees in Sweden - a nationwide population-based cohort study.

Amin R, Helgesson M, Runeson B, Tinghög P, Mehlum L, Qin P, Holmes EA, Mittendorfer-Rutz E.

Psychol Med. 2019 Dec 20:1-10. doi: 10.1017/S0033291719003167. [Epub ahead of print]


Distinct Lineages of Feline Parvovirus Associated with Epizootic Outbreaks in Australia, New Zealand and the United Arab Emirates.

Van Brussel K, Carrai M, Lin C, Kelman M, Setyo L, Aberdein D, Brailey J, Lawler M, Maher S, Plaganyi I, Lewis E, Hawkswell A, Allison AB, Meers J, Martella V, Beatty JA, Holmes EC, Decaro N, Barrs VR.

Viruses. 2019 Dec 13;11(12). pii: E1155. doi: 10.3390/v11121155.


Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain.

Benfield CT, MacKenzie F, Ritzefeld M, Mazzon M, Weston S, Tate E, Teo BH, Smith SE, Kellam P, Holmes EC, Marsh M.

Life Sci Alliance. 2019 Dec 11;3(1). pii: e201900542. doi: 10.26508/lsa.201900542. Print 2020 Jan.


Building a Patient-Centered Weight Management Program: A Mixed Methods Project to Obtain Patients' Information Needs and Ideas for Program Structure.

Arnold A, Holmes E, Rosenthal M.

Pharmacy (Basel). 2019 Dec 3;7(4). pii: E165. doi: 10.3390/pharmacy7040165.


Clinical and molecular evidence of accelerated ageing following very preterm birth.

Parkinson JRC, Emsley R, Adkins JLT, Longford N, Ozanne SE, Holmes E, Modi N.

Pediatr Res. 2019 Dec 7. doi: 10.1038/s41390-019-0709-9. [Epub ahead of print]


Using spatial release from masking to estimate the magnitude of the familiar-voice intelligibility benefit.

Domingo Y, Holmes E, Macpherson E, Johnsrude IS.

J Acoust Soc Am. 2019 Nov;146(5):3487. doi: 10.1121/1.5133628.


Intra-host growth kinetics of dengue virus in the mosquito Aedes aegypti.

Novelo M, Hall MD, Pak D, Young PR, Holmes EC, McGraw EA.

PLoS Pathog. 2019 Dec 2;15(12):e1008218. doi: 10.1371/journal.ppat.1008218. eCollection 2019 Dec.


The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP).

Gibson R, Lau CE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q.

Am J Clin Nutr. 2020 Feb 1;111(2):280-290. doi: 10.1093/ajcn/nqz293.


Emotional Mental Imagery Abnormalities in Monozygotic Twins With, at High-Risk of, and Without Affective Disorders: Present in Affected Twins in Remission but Absent in High-Risk Twins.

Di Simplicio M, Lau-Zhu A, Meluken I, Taylor P, Kessing LV, Vinberg M, Holmes EA, Miskowiak KW.

Front Psychiatry. 2019 Nov 8;10:801. doi: 10.3389/fpsyt.2019.00801. eCollection 2019.


Identification and evolution of avian endogenous foamy viruses.

Chen Y, Wei X, Zhang G, Holmes EC, Cui J.

Virus Evol. 2019 Nov 25;5(2):vez049. doi: 10.1093/ve/vez049. eCollection 2019 Jul.


Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics.

Porter AF, Shi M, Eden JS, Zhang YZ, Holmes EC.

Viruses. 2019 Nov 25;11(12). pii: E1092. doi: 10.3390/v11121092.


Human pegivirus in brain tissue of a patient with encephalitis.

Tuddenham R, Eden JS, Gilbey T, Dwyer DE, Jennings Z, Holmes EC, Branley JM.

Diagn Microbiol Infect Dis. 2020 Feb;96(2):114898. doi: 10.1016/j.diagmicrobio.2019.114898. Epub 2019 Oct 5.


Are father depression and masculinity associated with father perceptions of maternal gatekeeping?

Thomas CR, Holmes EK.

J Fam Psychol. 2019 Nov 21. doi: 10.1037/fam0000604. [Epub ahead of print]


Remediating reduced memory specificity in bipolar disorder: A case study using a Computerized Memory Specificity Training.

Martens K, Takano K, Barry TJ, Holmes EA, Wyckaert S, Raes F.

Brain Behav. 2019 Dec;9(12):e01468. doi: 10.1002/brb3.1468. Epub 2019 Nov 20.


An Ecosystems Perspective on Virus Evolution and Emergence.

French RK, Holmes EC.

Trends Microbiol. 2020 Mar;28(3):165-175. doi: 10.1016/j.tim.2019.10.010. Epub 2019 Nov 16. Review.


Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice.

Kundu P, Lee HU, Garcia-Perez I, Tay EXY, Kim H, Faylon LE, Martin KA, Purbojati R, Drautz-Moses DI, Ghosh S, Nicholson JK, Schuster S, Holmes E, Pettersson S.

Sci Transl Med. 2019 Nov 13;11(518). pii: eaau4760. doi: 10.1126/scitranslmed.aau4760.


Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe.

Pettersson JH, Shi M, Eden JS, Holmes EC, Hesson JC.

Viruses. 2019 Nov 6;11(11). pii: E1033. doi: 10.3390/v11111033.


Mass Spectrometry: A Guide for the Clinician.

Alsaleh M, Barbera TA, Andrews RH, Sithithaworn P, Khuntikeo N, Loilome W, Yongvanit P, Cox IJ, Syms RRA, Holmes E, Taylor-Robinson SD.

J Clin Exp Hepatol. 2019 Sep-Oct;9(5):597-606. doi: 10.1016/j.jceh.2019.04.053. Epub 2019 May 9. Review.


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