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Augmenting subnetwork inference with information extracted from the scientific literature.

Kiblawi S, Chasman D, Henning A, Park E, Poon H, Gould M, Ahlquist P, Craven M.

PLoS Comput Biol. 2019 Jun 27;15(6):e1006758. doi: 10.1371/journal.pcbi.1006758. eCollection 2019 Jun.


Cowpea chlorotic mottle bromovirus replication proteins support template-selective RNA replication in Saccharomyces cerevisiae.

Sibert BS, Navine AK, Pennington J, Wang X, Ahlquist P.

PLoS One. 2018 Dec 26;13(12):e0208743. doi: 10.1371/journal.pone.0208743. eCollection 2018.


Predictive value of a multi-biomarker disease activity score for clinical remission and radiographic progression in patients with early rheumatoid arthritis: a post-hoc study of the OPERA trial.

Brahe CH, Østergaard M, Johansen JS, Defranoux N, Wang X, Bolce R, Sasso EH, Ørnbjerg LM, Hørslev-Petersen K, Stengaard-Pedersen K, Junker P, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Schlemmer A, Dam MY, Hansen I, Lottenburger T, Ammitzbøll C, Jørgensen A, Krintel SB, Raun J, Hetland ML.

Scand J Rheumatol. 2019 Jan;48(1):9-16. doi: 10.1080/03009742.2018.1464206. Epub 2018 Jul 9.


Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments.

Garcia-Ruiz H, Diaz A, Ahlquist P.

Viruses. 2018 Mar 15;10(3). pii: E131. doi: 10.3390/v10030131.


Organelle luminal dependence of (+)strand RNA virus replication reveals a hidden druggable target.

Nishikiori M, Ahlquist P.

Sci Adv. 2018 Jan 24;4(1):eaap8258. doi: 10.1126/sciadv.aap8258. eCollection 2018 Jan.


[18F]Sodium fluoride positron emission tomography/computed tomography: a predictor of early rheumatoid arthritis? A case report.

Gram SB, Hess S, Ahlquist P, Høilund-Carlsen PF, Ellingsen T.

Scand J Rheumatol. 2018 Sep;47(5):425-426. doi: 10.1080/03009742.2017.1369153. Epub 2018 Jan 10. No abstract available.


Ultra-high mass multimer analysis of protein-1a capping domains by a silicon nanomembrane detector.

Shin HC, Deterra D, Park J, Kim H, Nishikiori M, Uetrecht C, Ahlquist PG, Arbulu M, Blick RH.

J Proteomics. 2018 Mar 20;175:5-11. doi: 10.1016/j.jprot.2017.11.024. Epub 2017 Dec 1.


Human papillomavirus oncogenes reprogram the cervical cancer microenvironment independently of and synergistically with estrogen.

Spurgeon ME, den Boon JA, Horswill M, Barthakur S, Forouzan O, Rader JS, Beebe DJ, Roopra A, Ahlquist P, Lambert PF.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E9076-E9085. doi: 10.1073/pnas.1712018114. Epub 2017 Oct 9.


Cryo-electron tomography reveals novel features of a viral RNA replication compartment.

Ertel KJ, Benefield D, Castaño-Diez D, Pennington JG, Horswill M, den Boon JA, Otegui MS, Ahlquist P.

Elife. 2017 Jun 27;6. pii: e25940. doi: 10.7554/eLife.25940.


ESCRT-mediated vesicle concatenation in plant endosomes.

Buono RA, Leier A, Paez-Valencia J, Pennington J, Goodman K, Miller N, Ahlquist P, Marquez-Lago TT, Otegui MS.

J Cell Biol. 2017 Jul 3;216(7):2167-2177. doi: 10.1083/jcb.201612040. Epub 2017 Jun 7.


Hand bone loss in early rheumatoid arthritis during a methotrexate-based treat-to-target strategy with or without adalimumab-a substudy of the optimized treatment algorithm in early RA (OPERA) trial.

Ørnbjerg LM, Østergaard M, Jensen T, Hørslev-Petersen K, Stengaard-Pedersen K, Junker P, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Schlemmer A, Dam MY, Hansen I, Lottenburger T, Ammitzbøll CG, Jørgensen A, Krintel SB, Raun J, Hetland ML; OPERA Study Group, Slot O, Nielsen LK, Skjødt H, Majgaard O, Lorenzen T, Horn HC, Kowalski M, Johansen IL, Pedersen PM, Manilo N, Bliddal H.

Clin Rheumatol. 2017 Apr;36(4):781-789. doi: 10.1007/s10067-016-3489-1. Epub 2016 Dec 5.


Diverse activities of viral cis-acting RNA regulatory elements revealed using multicolor, long-term, single-cell imaging.

Pocock GM, Zimdars LL, Yuan M, Eliceiri KW, Ahlquist P, Sherer NM.

Mol Biol Cell. 2017 Feb 1;28(3):476-487. doi: 10.1091/mbc.E16-08-0612. Epub 2016 Nov 30.


Systematic identification of Ctr9 regulome in ERα-positive breast cancer.

Zeng H, Lu L, Chan NT, Horswill M, Ahlquist P, Zhong X, Xu W.

BMC Genomics. 2016 Nov 9;17(1):902.


CARM1 Methylates Chromatin Remodeling Factor BAF155 to Enhance Tumor Progression and Metastasis.

Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W.

Cancer Cell. 2016 Jul 11;30(1):179-180. doi: 10.1016/j.ccell.2016.06.013. Epub 2016 Jul 11. No abstract available.


Multifactorial intervention to prevent cardiovascular disease in patients with early rheumatoid arthritis: protocol for a multicentre randomised controlled trial.

Svensson AL, Christensen R, Persson F, Løgstrup BB, Giraldi A, Graugaard C, Fredberg U, Blegvad J, Thygesen T, Hansen IM, Colic A, Bagdat D, Ahlquist P, Jensen HS, Hørslev-Petersen K, Sheetal E, Christensen TG, Svendsen L, Emmertsen H, Ellingsen T.

BMJ Open. 2016 Apr 20;6(4):e009134. doi: 10.1136/bmjopen-2015-009134.


HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors.

Pocock GM, Becker JT, Swanson CM, Ahlquist P, Sherer NM.

PLoS Pathog. 2016 Apr 12;12(4):e1005565. doi: 10.1371/journal.ppat.1005565. eCollection 2016 Apr.


Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer.

Bodelon C, Vinokurova S, Sampson JN, den Boon JA, Walker JL, Horswill MA, Korthauer K, Schiffman M, Sherman ME, Zuna RE, Mitchell J, Zhang X, Boland JF, Chaturvedi AK, Dunn ST, Newton MA, Ahlquist P, Wang SS, Wentzensen N.

Carcinogenesis. 2016 Feb;37(2):188-196. doi: 10.1093/carcin/bgv171. Epub 2015 Dec 9. No abstract available.


Clinical and radiographic outcome of a treat-to-target strategy using methotrexate and intra-articular glucocorticoids with or without adalimumab induction: a 2-year investigator-initiated, double-blinded, randomised, controlled trial (OPERA).

Hørslev-Petersen K, Hetland ML, Ørnbjerg LM, Junker P, Pødenphant J, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Schlemmer A, Dam MY, Hansen I, Lottenburger T, Ammitzbøll CG, Jørgensen A, Krintel SB, Raun J, Johansen JS, Østergaard M, Stengaard-Pedersen K; OPERA Study-Group.

Ann Rheum Dis. 2016 Sep;75(9):1645-53. doi: 10.1136/annrheumdis-2015-208166. Epub 2015 Oct 21.


Molecular transitions from papillomavirus infection to cervical precancer and cancer: Role of stromal estrogen receptor signaling.

den Boon JA, Pyeon D, Wang SS, Horswill M, Schiffman M, Sherman M, Zuna RE, Wang Z, Hewitt SM, Pearson R, Schott M, Chung L, He Q, Lambert P, Walker J, Newton MA, Wentzensen N, Ahlquist P.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3255-64. doi: 10.1073/pnas.1509322112. Epub 2015 Jun 8.


Prediction of treatment response to adalimumab: a double-blind placebo-controlled study of circulating microRNA in patients with early rheumatoid arthritis.

Krintel SB, Dehlendorff C, Hetland ML, Hørslev-Petersen K, Andersen KK, Junker P, Pødenphant J, Ellingsen T, Ahlquist P, Lindegaard HM, Linauskas A, Schlemmer A, Dam MY, Hansen I, Horn HC, Jørgensen A, Raun J, Ammitzbøll CG, Østergaard M, Stengaard-Pedersen K, Johansen JS.

Pharmacogenomics J. 2016 Apr;16(2):141-6. doi: 10.1038/tpj.2015.30. Epub 2015 May 5.


Correction: Host ESCRT Proteins Are Required for Bromovirus RNA Replication Compartment Assembly and Function.

Diaz A, Zhang J, Ollwerther A, Wang X, Ahlquist P.

PLoS Pathog. 2015 Apr 22;11(4):e1004845. doi: 10.1371/journal.ppat.1004845. eCollection 2015 Apr. No abstract available.


Host ESCRT proteins are required for bromovirus RNA replication compartment assembly and function.

Diaz A, Zhang J, Ollwerther A, Wang X, Ahlquist P.

PLoS Pathog. 2015 Mar 6;11(3):e1004742. doi: 10.1371/journal.ppat.1004742. eCollection 2015 Mar. Erratum in: PLoS Pathog. 2015 Apr;11(4):e1004845.


Sulfonation pathway inhibitors block reactivation of latent HIV-1.

Murry JP, Godoy J, Mukim A, Swann J, Bruce JW, Ahlquist P, Bosque A, Planelles V, Spina CA, Young JA.

Virology. 2014 Dec;471-473:1-12. doi: 10.1016/j.virol.2014.08.016. Epub 2014 Oct 11.


Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism.

Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM.

J Virol. 2014 Dec;88(24):14207-21. doi: 10.1128/JVI.01897-14. Epub 2014 Oct 1.


Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly.

Shen QT, Schuh AL, Zheng Y, Quinney K, Wang L, Hanna M, Mitchell JC, Otegui MS, Ahlquist P, Cui Q, Audhya A.

J Cell Biol. 2014 Sep 15;206(6):763-77. doi: 10.1083/jcb.201403108. Epub 2014 Sep 8.


Inferring host gene subnetworks involved in viral replication.

Chasman D, Gancarz B, Hao L, Ferris M, Ahlquist P, Craven M.

PLoS Comput Biol. 2014 May 29;10(5):e1003626. doi: 10.1371/journal.pcbi.1003626. eCollection 2014 May.


Genome-wide analysis of host factors in nodavirus RNA replication.

Hao L, Lindenbach B, Wang X, Dye B, Kushner D, He Q, Newton M, Ahlquist P.

PLoS One. 2014 Apr 21;9(4):e95799. doi: 10.1371/journal.pone.0095799. eCollection 2014.


CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis.

Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W.

Cancer Cell. 2014 Jan 13;25(1):21-36. doi: 10.1016/j.ccr.2013.12.007. Erratum in: Cancer Cell. 2016 Jul 11;30(1):179-180.


A treat-to-target strategy with methotrexate and intra-articular triamcinolone with or without adalimumab effectively reduces MRI synovitis, osteitis and tenosynovitis and halts structural damage progression in early rheumatoid arthritis: results from the OPERA randomised controlled trial.

Axelsen MB, Eshed I, Hørslev-Petersen K, Stengaard-Pedersen K, Hetland ML, Møller J, Junker P, Pødenphant J, Schlemmer A, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Dam MY, Hansen I, Horn HC, Ammitzbøll CG, Jørgensen A, Krintel SB, Raun J, Krogh NS, Johansen JS, Østergaard M; OPERA study group.

Ann Rheum Dis. 2015 May;74(5):867-75. doi: 10.1136/annrheumdis-2013-204537. Epub 2014 Jan 10.


ZASC1 stimulates HIV-1 transcription elongation by recruiting P-TEFb and TAT to the LTR promoter.

Bruce JW, Reddington R, Mathieu E, Bracken M, Young JA, Ahlquist P.

PLoS Pathog. 2013 Oct;9(10):e1003712. doi: 10.1371/journal.ppat.1003712. Epub 2013 Oct 24.


Limited agreement of independent RNAi screens for virus-required host genes owes more to false-negative than false-positive factors.

Hao L, He Q, Wang Z, Craven M, Newton MA, Ahlquist P.

PLoS Comput Biol. 2013;9(9):e1003235. doi: 10.1371/journal.pcbi.1003235. Epub 2013 Sep 19.


Systematic analyses of the cytotoxic effects of compound 11a, a putative synthetic agonist of photoreceptor-specific nuclear receptor (PNR), in cancer cell lines.

Zhao Z, Wang L, Wen Z, Ayaz-Guner S, Wang Y, Ahlquist P, Xu W.

PLoS One. 2013 Sep 16;8(9):e75198. doi: 10.1371/journal.pone.0075198. eCollection 2013.


ZASC1 knockout mice exhibit an early bone marrow-specific defect in murine leukemia virus replication.

Seidel S, Bruce J, Leblanc M, Lee KF, Fan H, Ahlquist P, Young JA.

Virol J. 2013 Apr 24;10:130. doi: 10.1186/1743-422X-10-130.


The cellular decapping activators LSm1, Pat1, and Dhh1 control the ratio of subgenomic to genomic Flock House virus RNAs.

Giménez-Barcons M, Alves-Rodrigues I, Jungfleisch J, Van Wynsberghe PM, Ahlquist P, Díez J.

J Virol. 2013 Jun;87(11):6192-200. doi: 10.1128/JVI.03327-12. Epub 2013 Mar 27.


Adalimumab added to a treat-to-target strategy with methotrexate and intra-articular triamcinolone in early rheumatoid arthritis increased remission rates, function and quality of life. The OPERA Study: an investigator-initiated, randomised, double-blind, parallel-group, placebo-controlled trial.

Hørslev-Petersen K, Hetland ML, Junker P, Pødenphant J, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Schlemmer A, Dam MY, Hansen I, Horn HC, Ammitzbøll CG, Jørgensen A, Krintel SB, Raun J, Johansen JS, Østergaard M, Stengaard-Pedersen K; OPERA Study-Group.

Ann Rheum Dis. 2014 Apr;73(4):654-61. doi: 10.1136/annrheumdis-2012-202735. Epub 2013 Feb 23.


Role of host reticulon proteins in rearranging membranes for positive-strand RNA virus replication.

Diaz A, Ahlquist P.

Curr Opin Microbiol. 2012 Aug;15(4):519-24. doi: 10.1016/j.mib.2012.04.007. Epub 2012 May 21. Review.


Host acyl coenzyme A binding protein regulates replication complex assembly and activity of a positive-strand RNA virus.

Zhang J, Diaz A, Mao L, Ahlquist P, Wang X.

J Virol. 2012 May;86(9):5110-21. doi: 10.1128/JVI.06701-11. Epub 2012 Feb 15.


Novel antivirals inhibit early steps in HPV infection.

Huang HS, Pyeon D, Pearce SM, Lank SM, Griffin LM, Ahlquist P, Lambert PF.

Antiviral Res. 2012 Feb;93(2):280-287. doi: 10.1016/j.antiviral.2011.12.007. Epub 2011 Dec 16.


Bromovirus RNA replication compartment formation requires concerted action of 1a's self-interacting RNA capping and helicase domains.

Diaz A, Gallei A, Ahlquist P.

J Virol. 2012 Jan;86(2):821-34. doi: 10.1128/JVI.05684-11. Epub 2011 Nov 16.


Orphan nuclear receptor PNR/NR2E3 stimulates p53 functions by enhancing p53 acetylation.

Wen Z, Pyeon D, Wang Y, Lambert P, Xu W, Ahlquist P.

Mol Cell Biol. 2012 Jan;32(1):26-35. doi: 10.1128/MCB.05513-11. Epub 2011 Oct 24.


Top 10 plant viruses in molecular plant pathology.

Scholthof KB, Adkins S, Czosnek H, Palukaitis P, Jacquot E, Hohn T, Hohn B, Saunders K, Candresse T, Ahlquist P, Hemenway C, Foster GD.

Mol Plant Pathol. 2011 Dec;12(9):938-54. doi: 10.1111/j.1364-3703.2011.00752.x. Epub 2011 Oct 21. Review.


Systematic identification of novel, essential host genes affecting bromovirus RNA replication.

Gancarz BL, Hao L, He Q, Newton MA, Ahlquist P.

PLoS One. 2011;6(8):e23988. doi: 10.1371/journal.pone.0023988. Epub 2011 Aug 22.


Intersection of the multivesicular body pathway and lipid homeostasis in RNA replication by a positive-strand RNA virus.

Wang X, Diaz A, Hao L, Gancarz B, den Boon JA, Ahlquist P.

J Virol. 2011 Jun;85(11):5494-503. doi: 10.1128/JVI.02031-10. Epub 2011 Mar 23.


Nodavirus-induced membrane rearrangement in replication complex assembly requires replicase protein a, RNA templates, and polymerase activity.

Kopek BG, Settles EW, Friesen PD, Ahlquist P.

J Virol. 2010 Dec;84(24):12492-503. doi: 10.1128/JVI.01495-10. Epub 2010 Oct 13.


Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories.

den Boon JA, Ahlquist P.

Annu Rev Microbiol. 2010;64:241-56. doi: 10.1146/annurev.micro.112408.134012. Review.


Membrane-shaping host reticulon proteins play crucial roles in viral RNA replication compartment formation and function.

Diaz A, Wang X, Ahlquist P.

Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16291-6. doi: 10.1073/pnas.1011105107. Epub 2010 Aug 30.


Cytoplasmic viral replication complexes.

den Boon JA, Diaz A, Ahlquist P.

Cell Host Microbe. 2010 Jul 22;8(1):77-85. doi: 10.1016/j.chom.2010.06.010. Review.


Cellular transcription factor ZASC1 regulates murine leukemia virus transcription.

Bruce JW, Hierl M, Young JA, Ahlquist P.

J Virol. 2010 Aug;84(15):7473-83. doi: 10.1128/JVI.00299-10. Epub 2010 May 19.


Evaluation of the introduction of an advanced care plan into multiple palliative care settings.

Newton J, Clark R, Ahlquist P.

Int J Palliat Nurs. 2009 Nov;15(11):554-61.


Statistical use of argonaute expression and RISC assembly in microRNA target identification.

Stanhope SA, Sengupta S, den Boon J, Ahlquist P, Newton MA.

PLoS Comput Biol. 2009 Sep;5(9):e1000516. doi: 10.1371/journal.pcbi.1000516. Epub 2009 Sep 25.

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