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Items: 1 to 50 of 144

1.

PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules.

Thody J, Folkes L, Medina-Calzada Z, Xu P, Dalmay T, Moulton V.

Nucleic Acids Res. 2018 Jul 11. doi: 10.1093/nar/gky609. [Epub ahead of print]

PMID:
30007348
2.

Correction: Downregulation of miR-200a-3p, Targeting CtBP2 Complex, Is Involved in the Hypoproduction of IL-2 in Systemic Lupus Erythematosus-Derived T Cells.

Katsuyama E, Yan M, Watanabe KS, Narazaki M, Matsushima S, Yamamura Y, Hiramatsu S, Ohashi K, Watanabe H, Katsuyama T, Zeggar S, Yoshida N, Moulton VR, Tsokos GC, Sada KE, Wada J.

J Immunol. 2018 Aug 1;201(3):1104. doi: 10.4049/jimmunol.1800810. Epub 2018 Jun 25. No abstract available.

PMID:
29941662
3.

Decreased expression of Serine/arginine-rich splicing factor 1 in T cells from patients with active systemic lupus erythematosus accounts for reduced expression of RasGRP1 and DNA methyltransferase 1.

Kono M, Kurita T, Yasuda S, Kono M, Fujieda Y, Bohgaki T, Katsuyama T, Tsokos GC, Moulton VR, Atsumi T.

Arthritis Rheumatol. 2018 Jun 14. doi: 10.1002/art.40585. [Epub ahead of print]

PMID:
29905030
4.

Quarnet Inference Rules for Level-1 Networks.

Huber KT, Moulton V, Semple C, Wu T.

Bull Math Biol. 2018 Aug;80(8):2137-2153. doi: 10.1007/s11538-018-0450-2. Epub 2018 Jun 4.

5.

Aberrant T Cell Signaling and Subsets in Systemic Lupus Erythematosus.

Katsuyama T, Tsokos GC, Moulton VR.

Front Immunol. 2018 May 17;9:1088. doi: 10.3389/fimmu.2018.01088. eCollection 2018. Review.

6.

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.

Stocks MB, Mohorianu I, Beckers M, Paicu C, Moxon S, Thody J, Dalmay T, Moulton V.

Bioinformatics. 2018 May 2. doi: 10.1093/bioinformatics/bty338. [Epub ahead of print]

PMID:
29722807
7.

Downregulation of CD3ζ in NK Cells from Systemic Lupus Erythematosus Patients Confers a Proinflammatory Phenotype.

Suárez-Fueyo A, Bradley SJ, Katsuyama T, Solomon S, Katsuyama E, Kyttaris VC, Moulton VR, Tsokos GC.

J Immunol. 2018 May 1;200(9):3077-3086. doi: 10.4049/jimmunol.1700588. Epub 2018 Mar 30.

PMID:
29602774
8.

Phylogenetic Flexibility via Hall-Type Inequalities and Submodularity.

Huber KT, Moulton V, Steel M.

Bull Math Biol. 2018 Mar 27. doi: 10.1007/s11538-018-0419-1. [Epub ahead of print]

PMID:
29589255
9.

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

Francis A, Moulton V.

J Theor Biol. 2018 Jun 7;446:160-167. doi: 10.1016/j.jtbi.2018.03.011. Epub 2018 Mar 13.

PMID:
29548737
10.

Recovering normal networks from shortest inter-taxa distance information.

Bordewich M, Huber KT, Moulton V, Semple C.

J Math Biol. 2018 Feb 24. doi: 10.1007/s00285-018-1218-x. [Epub ahead of print]

PMID:
29478083
11.

Tree-Based Unrooted Phylogenetic Networks.

Francis A, Huber KT, Moulton V.

Bull Math Biol. 2018 Feb;80(2):404-416. doi: 10.1007/s11538-017-0381-3. Epub 2017 Dec 13.

12.

SPECTRE: a suite of phylogenetic tools for reticulate evolution.

Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.

Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.

13.

Cross-Domain Symptom Development Typologies and Their Antecedents: Results From the UK Millennium Cohort Study.

Patalay P, Moulton V, Goodman A, Ploubidis GB.

J Am Acad Child Adolesc Psychiatry. 2017 Sep;56(9):765-776.e2. doi: 10.1016/j.jaac.2017.06.009. Epub 2017 Jul 4.

PMID:
28838581
14.

Bounds for phylogenetic network space metrics.

Francis A, Huber KT, Moulton V, Wu T.

J Math Biol. 2018 Apr;76(5):1229-1248. doi: 10.1007/s00285-017-1171-0. Epub 2017 Aug 23.

15.

DESNT: A Poor Prognosis Category of Human Prostate Cancer.

Luca BA, Brewer DS, Edwards DR, Edwards S, Whitaker HC, Merson S, Dennis N, Cooper RA, Hazell S, Warren AY; CancerMap Group, Eeles R, Lynch AG, Ross-Adams H, Lamb AD, Neal DE, Sethia K, Mills RD, Ball RY, Curley H, Clark J, Moulton V, Cooper CS.

Eur Urol Focus. 2017 Mar 6. pii: S2405-4569(17)30025-1. doi: 10.1016/j.euf.2017.01.016. [Epub ahead of print]

16.

Pathogenesis of Human Systemic Lupus Erythematosus: A Cellular Perspective.

Moulton VR, Suarez-Fueyo A, Meidan E, Li H, Mizui M, Tsokos GC.

Trends Mol Med. 2017 Jul;23(7):615-635. doi: 10.1016/j.molmed.2017.05.006. Epub 2017 Jun 13. Review.

17.

Minimum triplet covers of binary phylogenetic X-trees.

Huber KT, Moulton V, Steel M.

J Math Biol. 2017 Dec;75(6-7):1827-1840. doi: 10.1007/s00285-017-1117-6. Epub 2017 Jun 12.

18.

The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V.

Methods Mol Biol. 2017;1580:193-224. doi: 10.1007/978-1-4939-6866-4_14.

PMID:
28439835
19.

Downregulation of miR-200a-3p, Targeting CtBP2 Complex, Is Involved in the Hypoproduction of IL-2 in Systemic Lupus Erythematosus-Derived T Cells.

Katsuyama E, Yan M, Watanabe KS, Matsushima S, Yamamura Y, Hiramatsu S, Ohashi K, Watanabe H, Katsuyama T, Zeggar S, Yoshida N, Moulton VR, Tsokos GC, Sada KE, Wada J.

J Immunol. 2017 Jun 1;198(11):4268-4276. doi: 10.4049/jimmunol.1601705. Epub 2017 Apr 24. Erratum in: J Immunol. 2018 Aug 1;201(3):1104.

20.

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.

Paicu C, Mohorianu I, Stocks M, Xu P, Coince A, Billmeier M, Dalmay T, Moulton V, Moxon S.

Bioinformatics. 2017 Aug 15;33(16):2446-2454. doi: 10.1093/bioinformatics/btx210.

21.

Binets: Fundamental Building Blocks for Phylogenetic Networks.

van Iersel L, Moulton V, de Swart E, Wu T.

Bull Math Biol. 2017 May;79(5):1135-1154. doi: 10.1007/s11538-017-0275-4. Epub 2017 Apr 6.

22.

MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect.

Collins DH, Mohorianu I, Beckers M, Moulton V, Dalmay T, Bourke AF.

Sci Rep. 2017 Mar 31;7:45674. doi: 10.1038/srep45674.

23.

Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.

Beckers M, Mohorianu I, Stocks M, Applegate C, Dalmay T, Moulton V.

RNA. 2017 Jun;23(6):823-835. doi: 10.1261/rna.059360.116. Epub 2017 Mar 13.

24.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV.

Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803. Epub 2017 Jan 16.

25.

The role of socio-economic disadvantage in the development of comorbid emotional and conduct problems in children with ADHD.

Flouri E, Midouhas E, Ruddy A, Moulton V.

Eur Child Adolesc Psychiatry. 2017 Jun;26(6):723-732. doi: 10.1007/s00787-017-0940-z. Epub 2017 Jan 7.

26.

Transforming phylogenetic networks: Moving beyond tree space.

Huber KT, Moulton V, Wu T.

J Theor Biol. 2016 Sep 7;404:30-39. doi: 10.1016/j.jtbi.2016.05.030. Epub 2016 May 22.

PMID:
27224010
27.

TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories.

Oldman J, Wu T, van Iersel L, Moulton V.

Mol Biol Evol. 2016 Aug;33(8):2151-62. doi: 10.1093/molbev/msw068. Epub 2016 Apr 15.

PMID:
27189565
28.

INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.

Araujo Granda P, Gras A, Ginovart M, Moulton V.

J Theor Biol. 2016 Aug 21;403:45-58. doi: 10.1016/j.jtbi.2016.05.017. Epub 2016 May 11.

PMID:
27179457
29.

Folding and unfolding phylogenetic trees and networks.

Huber KT, Moulton V, Steel M, Wu T.

J Math Biol. 2016 Dec;73(6-7):1761-1780. Epub 2016 Apr 23.

30.

The minimum evolution problem is hard: a link between tree inference and graph clustering problems.

Bastkowski S, Moulton V, Spillner A, Wu T.

Bioinformatics. 2016 Feb 15;32(4):518-22. doi: 10.1093/bioinformatics/btv623. Epub 2015 Oct 24.

PMID:
26500153
31.

Serine Arginine-Rich Splicing Factor 1 (SRSF1) Contributes to the Transcriptional Activation of CD3ζ in Human T Cells.

Moulton VR, Gillooly AR, Perl MA, Markopoulou A, Tsokos GC.

PLoS One. 2015 Jul 2;10(7):e0131073. doi: 10.1371/journal.pone.0131073. eCollection 2015.

32.

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations.

Huber KT, Linz S, Moulton V, Wu T.

J Math Biol. 2016 Feb;72(3):699-725. doi: 10.1007/s00285-015-0899-7. Epub 2015 Jun 3.

PMID:
26037483
33.

Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes.

Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM.

Glob Chang Biol. 2016 Jan;22(1):61-75. doi: 10.1111/gcb.12983. Epub 2015 Jul 28. Review.

34.

T cell signaling abnormalities contribute to aberrant immune cell function and autoimmunity.

Moulton VR, Tsokos GC.

J Clin Invest. 2015 Jun;125(6):2220-7. doi: 10.1172/JCI78087. Epub 2015 May 11. Review.

35.

Erratum to: Neighborhoods of trees in circular orderings.

Bastkowski S, Moulton V, Spillner A, Wu T.

Bull Math Biol. 2015 Mar;77(3):579. doi: 10.1007/s11538-015-0071-y. No abstract available.

PMID:
25753151
36.

Neighborhoods of trees in circular orderings.

Bastkowski S, Moulton V, Spillner A, Wu T.

Bull Math Biol. 2015 Jan;77(1):46-70. doi: 10.1007/s11538-014-0049-1. Epub 2014 Dec 5. Erratum in: Bull Math Biol. 2015 Mar;77(3):579. Baskowski, Sarah [created to Bastkowski, Sarah].

PMID:
25477080
37.

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation.

Toseland A, Moxon S, Mock T, Moulton V.

BMC Genomics. 2014 Oct 15;15:901. doi: 10.1186/1471-2164-15-901.

38.

How much information is needed to infer reticulate evolutionary histories?

Huber KT, Van Iersel L, Moulton V, Wu T.

Syst Biol. 2015 Jan;64(1):102-11. doi: 10.1093/sysbio/syu076. Epub 2014 Sep 18.

39.

Global discovery and characterization of small non-coding RNAs in marine microalgae.

Lopez-Gomollon S, Beckers M, Rathjen T, Moxon S, Maumus F, Mohorianu I, Moulton V, Dalmay T, Mock T.

BMC Genomics. 2014 Aug 20;15:697. doi: 10.1186/1471-2164-15-697.

40.

Prioritizing populations for conservation using phylogenetic networks.

Volkmann L, Martyn I, Moulton V, Spillner A, Mooers AO.

PLoS One. 2014 Feb 28;9(2):e88945. doi: 10.1371/journal.pone.0088945. eCollection 2014.

41.

FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships.

Balvočūtė M, Spillner A, Moulton V.

Syst Biol. 2014 May;63(3):383-96. doi: 10.1093/sysbio/syu001. Epub 2014 Jan 15.

PMID:
24436254
42.

Ubiquitination regulates expression of the serine/arginine-rich splicing factor 1 (SRSF1) in normal and systemic lupus erythematosus (SLE) T cells.

Moulton VR, Gillooly AR, Tsokos GC.

J Biol Chem. 2014 Feb 14;289(7):4126-34. doi: 10.1074/jbc.M113.518662. Epub 2013 Dec 24.

43.

Modeling the effect of copper availability on bacterial denitrification.

Woolfenden HC, Gates AJ, Bocking C, Blyth MG, Richardson DJ, Moulton V.

Microbiologyopen. 2013 Oct;2(5):756-65. doi: 10.1002/mbo3.111. Epub 2013 Jul 30.

44.

CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

Mohorianu I, Stocks MB, Wood J, Dalmay T, Moulton V.

RNA Biol. 2013 Jul;10(7):1221-30. doi: 10.4161/rna.25538. Epub 2013 Jun 28.

45.

SuperQ: computing supernetworks from quartets.

Grünewald S, Spillner A, Bastkowski S, Bögershausen A, Moulton V.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):151-60. doi: 10.1109/TCBB.2013.8.

PMID:
23702551
46.

Trinets encode tree-child and level-2 phylogenetic networks.

van Iersel L, Moulton V.

J Math Biol. 2014 Jun;68(7):1707-29. doi: 10.1007/s00285-013-0683-5. Epub 2013 May 17.

PMID:
23680992
47.

Splicing factor SF2/ASF rescues IL-2 production in T cells from systemic lupus erythematosus patients by activating IL-2 transcription.

Moulton VR, Grammatikos AP, Fitzgerald LM, Tsokos GC.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1845-50. doi: 10.1073/pnas.1214207110. Epub 2013 Jan 14.

48.

MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome.

Mapleson D, Moxon S, Dalmay T, Moulton V.

J Exp Zool B Mol Dev Evol. 2013 Jan;320(1):47-56. doi: 10.1002/jez.b.22483. Epub 2012 Nov 26.

PMID:
23184675
49.

Generating Functions for Multi-labeled Trees.

Czabarka E, Erdős PL, Johnson V, Moulton V.

Discrete Appl Math. 2013 Jan 1;161(1-2):107-117. Epub 2012 Sep 4.

50.

Computational modeling of the regulatory network organizing the wound response in Arabidopsis thaliana.

Kim JT, Camargo A, Devoto A, Moulton V, Turner J.

Artif Life. 2012 Fall;18(4):445-60. doi: 10.1162/ARTL_a_00076. Epub 2012 Aug 31.

PMID:
22938558

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