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Landscape of stimulation-responsive chromatin across diverse human immune cells.

Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu B, Trombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, Marson A, Pritchard JK.

Nat Genet. 2019 Sep 30. doi: 10.1038/s41588-019-0505-9. [Epub ahead of print]


Changes in the molecular and functional phenotype of bovine monocytes during T. parva infection.

Bastos RG, Sears K, Dinkel KD, Knowles DP, Fry LM.

Infect Immun. 2019 Sep 30. pii: IAI.00703-19. doi: 10.1128/IAI.00703-19. [Epub ahead of print]


Remodeling of the inter-domain allosteric linker upon membrane binding of CCTα pulls its active site close to the membrane surface.

Knowles DG, Lee J, Taneva SG, Cornell RB.

J Biol Chem. 2019 Sep 4. pii: jbc.RA119.009850. doi: 10.1074/jbc.RA119.009850. [Epub ahead of print]


Inter-domain communication in the phosphatidylcholine regulatory enzyme, CCTα, relies on a modular αE helix.

Taneva SG, Lee J, Knowles DG, Tishyadhigama C, Chen H, Cornell RB.

J Biol Chem. 2019 Sep 4. pii: jbc.RA119.009849. doi: 10.1074/jbc.RA119.009849. [Epub ahead of print]


Mycoplasma ovis infection in domestic sheep (Ovis aries) in the United States: Prevalence, distribution, associated risk factors, and associated outcomes.

Urie NJ, Highland MA, Knowles DP, Branan MA, Herndon DR, Marshall KL.

Prev Vet Med. 2019 Aug 24;171:104750. doi: 10.1016/j.prevetmed.2019.104750. [Epub ahead of print]


The use of modelling studies to inform planning of health services: case study of rapidly increasing endoscopy services in Australia.

Carter HE, Knowles D, Moroney T, Holtmann G, Rahman T, Appleyard M, Steele N, Zanco M, Graves N.

BMC Health Serv Res. 2019 Aug 29;19(1):608. doi: 10.1186/s12913-019-4438-x.


Infection dynamics of Theileria equi and Theileria haneyi, a newly discovered apicomplexan of the horse.

Sears KP, Kappmeyer LS, Wise LN, Silva M, Ueti MW, White S, Reif KE, Knowles DP.

Vet Parasitol. 2019 Jul;271:68-75. doi: 10.1016/j.vetpar.2019.06.009. Epub 2019 Jun 12.


Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.

Knowles DA, Bouchard G, Plevritis S.

PLoS Comput Biol. 2019 May 28;15(5):e1006743. doi: 10.1371/journal.pcbi.1006743. eCollection 2019 May.


Molecular and Antigenic Properties of Mammalian Cell-Expressed Theileria parva Antigen Tp9.

Bastos RG, Franceschi V, Tebaldi G, Connelley T, Morrison WI, Knowles DP, Donofrio G, Fry LM.

Front Immunol. 2019 Apr 29;10:897. doi: 10.3389/fimmu.2019.00897. eCollection 2019.


A recombinant bovine herpesvirus-4 vectored vaccine delivered via intranasal nebulization elicits viral neutralizing antibody titers in cattle.

Williams LBA, Fry LM, Herndon DR, Franceschi V, Schneider DA, Donofrio G, Knowles DP.

PLoS One. 2019 Apr 19;14(4):e0215605. doi: 10.1371/journal.pone.0215605. eCollection 2019.


Opportunities and challenges for transcriptome-wide association studies.

Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A.

Nat Genet. 2019 Apr;51(4):592-599. doi: 10.1038/s41588-019-0385-z. Epub 2019 Mar 29. Review.


Gene gun DNA immunization of cattle induces humoral and CD4 T-cell-mediated immune responses against the Theileria parva polymorphic immunodominant molecule.

Fry LM, Bastos RG, Stone BC, Williams LB, Knowles DP, Murphy SC.

Vaccine. 2019 Mar 14;37(12):1546-1553. doi: 10.1016/j.vaccine.2019.02.009. Epub 2019 Feb 16.


"Getting into it": People with intellectual disabilities' experiences and views of Behavioural Activation and Guided Self-Help for depression.

Knight R, Jahoda A, Scott K, Sanger K, Knowles D, Dagnan D, Hastings RP, Appleton K, Cooper SA, Melville C, Jones R, Williams C, Hatton C.

J Appl Res Intellect Disabil. 2019 Jul;32(4):819-830. doi: 10.1111/jar.12571. Epub 2019 Feb 14.


Predicting Splicing from Primary Sequence with Deep Learning.

Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB, Chow ED, Kanterakis E, Gao H, Kia A, Batzoglou S, Sanders SJ, Farh KK.

Cell. 2019 Jan 24;176(3):535-548.e24. doi: 10.1016/j.cell.2018.12.015. Epub 2019 Jan 17.


Evolution and diversity of the EMA families of the divergent equid parasites, Theileria equi and T. haneyi.

Wise LN, Kappmeyer LS, Knowles DP, White SN.

Infect Genet Evol. 2019 Mar;68:153-160. doi: 10.1016/j.meegid.2018.12.020. Epub 2018 Dec 18.


Exploring the underpinning mechanisms of the proximity effect within a competitive food environment.

Knowles D, Brown K, Aldrovandi S.

Appetite. 2019 Mar 1;134:94-102. doi: 10.1016/j.appet.2018.12.005. Epub 2018 Dec 12.


Behavioural activation versus guided self-help for depression in adults with learning disabilities: the BeatIt RCT.

Jahoda A, Hastings R, Hatton C, Cooper SA, McMeekin N, Dagnan D, Appleton K, Scott K, Fulton L, Jones R, McConnachie A, Zhang R, Knight R, Knowles D, Williams C, Briggs A, Melville C.

Health Technol Assess. 2018 Sep;22(53):1-130. doi: 10.3310/hta22530.


Supporting people with intellectual disabilities in psychological therapies for depression: A qualitative analysis of supporters' experiences.

Scott K, Hatton C, Knight R, Singer K, Knowles D, Dagnan D, Hastings RP, Appleton K, Cooper SA, Melville C, Jones R, Williams C, Jahoda A.

J Appl Res Intellect Disabil. 2019 Mar;32(2):323-335. doi: 10.1111/jar.12529. Epub 2018 Sep 28. Erratum in: J Appl Res Intellect Disabil. 2019 Jul;32(4):1006.


The feasibility and acceptability of a novel anxiety in bipolar disorder intervention compared to treatment as usual: A randomized controlled trial.

Jones SH, Knowles D, Tyler E, Holland F, Peters S, Lobban F, Langshaw B, Hilton C, Long R, Gantt K, Owen R, Roberts C, Riste L.

Depress Anxiety. 2018 Oct;35(10):953-965. doi: 10.1002/da.22781. Epub 2018 Jul 19.


Evaluation of glycoprotein Ov8 as a potential antigen for an OvHV-2-specific diagnostic assay.

Alhajri SM, Cunha CW, Knowles DP, Li H, Taus NS.

PLoS One. 2018 Jul 2;13(7):e0200130. doi: 10.1371/journal.pone.0200130. eCollection 2018.


Discovery of a novel species, Theileria haneyi n. sp., infective to equids, highlights exceptional genomic diversity within the genus Theileria: implications for apicomplexan parasite surveillance.

Knowles DP, Kappmeyer LS, Haney D, Herndon DR, Fry LM, Munro JB, Sears K, Ueti MW, Wise LN, Silva M, Schneider DA, Grause J, White SN, Tretina K, Bishop RP, Odongo DO, Pelzel-McCluskey AM, Scoles GA, Mealey RH, Silva JC.

Int J Parasitol. 2018 Aug;48(9-10):679-690. doi: 10.1016/j.ijpara.2018.03.010. Epub 2018 Jun 6.


Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes.

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y.

Elife. 2018 May 8;7. pii: e33480. doi: 10.7554/eLife.33480.


Assessment of Draxxin® (tulathromycin) as an inhibitor of in vitro growth of Babesia bovis, Babesia bigemina and Theileria equi.

Silva MG, Villarino NF, Knowles DP, Suarez CE.

Int J Parasitol Drugs Drug Resist. 2018 Aug;8(2):265-270. doi: 10.1016/j.ijpddr.2018.04.004. Epub 2018 Apr 17.


Stable transformation of Babesia bigemina and Babesia bovis using a single transfection plasmid.

Silva MG, Knowles DP, Mazuz ML, Cooke BM, Suarez CE.

Sci Rep. 2018 Apr 17;8(1):6096. doi: 10.1038/s41598-018-23010-4.


Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS.

PLoS One. 2018 Apr 16;13(4):e0195788. doi: 10.1371/journal.pone.0195788. eCollection 2018.


Exercise-induced pulmonary hemorrhage in barrel racing horses in the Pacific Northwest region of the United States.

Gold JR, Knowles DP, Coffey T, Bayly WM.

J Vet Intern Med. 2018 Mar;32(2):839-845. doi: 10.1111/jvim.15066. Epub 2018 Feb 20.


Impacts of licensed premises trading hour policies on alcohol-related harms.

Atkinson JA, Prodan A, Livingston M, Knowles D, O'Donnell E, Room R, Indig D, Page A, McDonnell G, Wiggers J.

Addiction. 2018 Jul;113(7):1244-1251. doi: 10.1111/add.14178. Epub 2018 Mar 2.


Annotation-free quantification of RNA splicing using LeafCutter.

Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK.

Nat Genet. 2018 Jan;50(1):151-158. doi: 10.1038/s41588-017-0004-9. Epub 2017 Dec 11.


Comparison of behavioural activation with guided self-help for treatment of depression in adults with intellectual disabilities: a randomised controlled trial.

Jahoda A, Hastings R, Hatton C, Cooper SA, Dagnan D, Zhang R, McConnachie A, McMeekin N, Appleton K, Jones R, Scott K, Fulton L, Knight R, Knowles D, Williams C, Briggs A, MacMahon K, Lynn H, Smith I, Thomas G, Melville C.

Lancet Psychiatry. 2017 Dec;4(12):909-919. doi: 10.1016/S2215-0366(17)30426-1. Epub 2017 Nov 16.


Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes.

Oliveira RD, Mousel MR, Pabilonia KL, Highland MA, Taylor JB, Knowles DP, White SN.

PLoS One. 2017 Nov 15;12(11):e0188054. doi: 10.1371/journal.pone.0188054. eCollection 2017.


Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression.

Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK.

Am J Hum Genet. 2017 Nov 2;101(5):686-699. doi: 10.1016/j.ajhg.2017.09.009. Epub 2017 Oct 26.


Harnessing advances in computer simulation to inform policy and planning to reduce alcohol-related harms.

Atkinson JA, Knowles D, Wiggers J, Livingston M, Room R, Prodan A, McDonnell G, O'Donnell E, Jones S, Haber PS, Muscatello D, Ezard N, Phung N, Freebairn L, Indig D, Rychetnik L, Ananthapavan J, Wutzke S; alcohol modelling consortium.

Int J Public Health. 2018 May;63(4):537-546. doi: 10.1007/s00038-017-1041-y. Epub 2017 Oct 19.


Verification of post-chemotherapeutic clearance of Theileria equi through concordance of nested PCR and immunoblot.

Wise LN, Kappmeyer LS, Silva MG, White SN, Grause JF, Knowles DP.

Ticks Tick Borne Dis. 2018 Feb;9(2):135-140. doi: 10.1016/j.ttbdis.2017.08.007. Epub 2017 Aug 25.


Assessment and optimization of Theileria parva sporozoite full-length p67 antigen expression in mammalian cells.

Tebaldi G, Williams LB, Verna AE, Macchi F, Franceschi V, Fry LM, Knowles DP, Donofrio G.

PLoS Negl Trop Dis. 2017 Aug 11;11(8):e0005803. doi: 10.1371/journal.pntd.0005803. eCollection 2017 Aug.


Underdominant KCC3b R31I association with blood sodium concentration in domestic sheep suggests role in oligomer function.

White SN, Oliveira RD, Mousel MR, Gonzalez MV, Highland MA, Herndon MK, Taylor JB, Knowles DP.

Anim Genet. 2017 Oct;48(5):626-627. doi: 10.1111/age.12585. Epub 2017 Jul 27. No abstract available.


Allele-specific expression reveals interactions between genetic variation and environment.

Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A.

Nat Methods. 2017 Jul;14(7):699-702. doi: 10.1038/nmeth.4298. Epub 2017 May 22.


Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot.

Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D.

Am J Bot. 2017 May;104(5):757-771. doi: 10.3732/ajb.1700054. Epub 2017 May 17.


Inhibition of the in vitro growth of Babesia bigemina, Babesia caballi and Theileria equi parasites by trifluralin analogues.

G Silva M, Knowles DP, Antunes S, Domingos A, Esteves MA, Suarez CE.

Ticks Tick Borne Dis. 2017 Jun;8(4):593-597. doi: 10.1016/j.ttbdis.2017.04.002. Epub 2017 Apr 10.


Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice.

Becker LA, Huang B, Bieri G, Ma R, Knowles DA, Jafar-Nejad P, Messing J, Kim HJ, Soriano A, Auburger G, Pulst SM, Taylor JP, Rigo F, Gitler AD.

Nature. 2017 Apr 20;544(7650):367-371. doi: 10.1038/nature22038. Epub 2017 Apr 12.


Assessing Feasibility and Acceptability of Web-Based Enhanced Relapse Prevention for Bipolar Disorder (ERPonline): A Randomized Controlled Trial.

Lobban F, Dodd AL, Sawczuk AP, Asar O, Dagnan D, Diggle PJ, Griffiths M, Honary M, Knowles D, Long R, Morriss R, Parker R, Jones S.

J Med Internet Res. 2017 Mar 24;19(3):e85. doi: 10.2196/jmir.7008.


Building Research Capacity: Results of a Feasibility Study Using a Novel mHealth Epidemiological Data Collection System Within a Gestational Diabetes Population.

McLean A, Osgood N, Newstead-Angel J, Stanley K, Knowles D, van der Kamp W, Qian W, Dyck R.

Stud Health Technol Inform. 2017;234:228-232.


Batch effects and the effective design of single-cell gene expression studies.

Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y.

Sci Rep. 2017 Jan 3;7:39921. doi: 10.1038/srep39921.


Transfected Babesia bovis Expressing a Tick GST as a Live Vector Vaccine.

Oldiges DP, Laughery JM, Tagliari NJ, Leite Filho RV, Davis WC, da Silva Vaz I Jr, Termignoni C, Knowles DP, Suarez CE.

PLoS Negl Trop Dis. 2016 Dec 2;10(12):e0005152. doi: 10.1371/journal.pntd.0005152. eCollection 2016 Dec.


BoHV-4-based vector delivering Ebola virus surface glycoprotein.

Rosamilia A, Jacca S, Tebaldi G, Tiberti S, Franceschi V, Macchi F, Cavirani S, Kobinger G, Knowles DP, Donofrio G.

J Transl Med. 2016 Nov 24;14(1):325.


Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi.

Alzan HF, Knowles DP, Suarez CE.

PLoS Negl Trop Dis. 2016 Nov 10;10(11):e0004983. doi: 10.1371/journal.pntd.0004983. eCollection 2016 Nov. Review.


Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export.

Tsang EK, Abell NS, Li X, Anaya V, Karczewski KJ, Knowles DA, Sierra RG, Smith KS, Montgomery SB.

G3 (Bethesda). 2017 Jan 5;7(1):31-39. doi: 10.1534/g3.116.036137.


Enhancing image quality in cleared tissue with adaptive optics.

Reinig MR, Novak SW, Tao X, Bentolila LA, Roberts DG, MacKenzie-Graham A, Godshalk SE, Raven MA, Knowles DW, Kubby J.

J Biomed Opt. 2016 Dec 1;21(12):121508. doi: 10.1117/1.JBO.21.12.121508.


Expression of 6-Cys Gene Superfamily Defines Babesia bovis Sexual Stage Development within Rhipicephalus microplus.

Alzan HF, Lau AO, Knowles DP, Herndon DR, Ueti MW, Scoles GA, Kappmeyer LS, Suarez CE.

PLoS One. 2016 Sep 26;11(9):e0163791. doi: 10.1371/journal.pone.0163791. eCollection 2016.

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