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Items: 1 to 50 of 66

1.

liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies.

Aparicio-Puerta E, Jáspez D, Lebrón R, Koppers-Lalic D, Marchal JA, Hackenberg M.

Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky981. [Epub ahead of print]

PMID:
30357370
2.

Putting patients at the center of kidney care transitions: PREPARE NOW, a cluster randomized controlled trial.

Green JA, Ephraim PL, Hill-Briggs FF, Browne T, Strigo TS, Hauer CL, Stametz RA, Darer JD, Patel UD, Lang-Lindsey K, Bankes BL, Bolden SA, Danielson P, Ruff S, Schmidt L, Swoboda A, Woods P, Vinson B, Littlewood D, Jackson G, Pendergast JF, St Clair Russell J, Collins K, Norfolk E, Bucaloiu ID, Kethireddy S, Collins C, Davis D, dePrisco J, Malloy D, Diamantidis CJ, Fulmer S, Martin J, Schatell D, Tangri N, Sees A, Siegrist C, Breed J Jr, Medley A, Graboski E, Billet J, Hackenberg M, Singer D, Stewart S, Alkon A, Bhavsar NA, Lewis-Boyer L, Martz C, Yule C, Greer RC, Saunders M, Cameron B, Boulware LE.

Contemp Clin Trials. 2018 Oct;73:98-110. doi: 10.1016/j.cct.2018.09.004. Epub 2018 Sep 12.

PMID:
30218818
3.

Herpes simplex virus 1 miRNA sequence variations in latently infected human trigeminal ganglia.

Cokarić Brdovčak M, Zubković A, Ferenčić A, Šoša I, Stemberga V, Cuculić D, Rokić F, Vugrek O, Hackenberg M, Jurak I.

Virus Res. 2018 Sep 2;256:90-95. doi: 10.1016/j.virusres.2018.08.002. Epub 2018 Aug 2.

PMID:
30077725
4.

Mesenchymal stem cell's secretome promotes selective enrichment of cancer stem-like cells with specific cytogenetic profile.

Jiménez G, Hackenberg M, Catalina P, Boulaiz H, Griñán-Lisón C, García MÁ, Perán M, López-Ruiz E, Ramírez A, Morata-Tarifa C, Carrasco E, Aguilera M, Marchal JA.

Cancer Lett. 2018 Aug 10;429:78-88. doi: 10.1016/j.canlet.2018.04.042. Epub 2018 May 5.

PMID:
29733965
5.

Exosome-Mediated Pathogen Transmission by Arthropod Vectors.

Hackenberg M, Kotsyfakis M.

Trends Parasitol. 2018 Jul;34(7):549-552. doi: 10.1016/j.pt.2018.04.001. Epub 2018 Apr 24.

PMID:
29703586
6.

Identification and characterisation of a previously unknown drought tolerance-associated microRNA in barley.

Zhou H, Hussain SS, Hackenberg M, Bazanova N, Eini O, Li J, Gustafson P, Shi B.

Plant J. 2018 Jul;95(1):138-149. doi: 10.1111/tpj.13938. Epub 2018 May 23.

PMID:
29681080
7.

Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation.

Gómez-Martín C, Lebrón R, Oliver JL, Hackenberg M.

Methods Mol Biol. 2018;1766:31-47. doi: 10.1007/978-1-4939-7768-0_3.

PMID:
29605846
8.

Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia.

Pentimone I, Lebrón R, Hackenberg M, Rosso LC, Colagiero M, Nigro F, Ciancio A.

Appl Microbiol Biotechnol. 2018 Jan;102(2):907-919. doi: 10.1007/s00253-017-8608-7. Epub 2017 Nov 5.

PMID:
29105020
9.

Viral Ubiquitin Ligase Stimulates Selective Host MicroRNA Expression by Targeting ZEB Transcriptional Repressors.

Lutz G, Jurak I, Kim ET, Kim JY, Hackenberg M, Leader A, Stoller ML, Fekete DM, Weitzman MD, Coen DM, Wilson AC.

Viruses. 2017 Aug 7;9(8). pii: E210. doi: 10.3390/v9080210.

10.

In silico target network analysis of de novo-discovered, tick saliva-specific microRNAs reveals important combinatorial effects in their interference with vertebrate host physiology.

Hackenberg M, Langenberger D, Schwarz A, Erhart J, Kotsyfakis M.

RNA. 2017 Aug;23(8):1259-1269. doi: 10.1261/rna.061168.117. Epub 2017 May 4.

11.

sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine.

Gómez-Martín C, Lebrón R, Rueda A, Oliver JL, Hackenberg M.

Methods Mol Biol. 2017;1580:149-174. doi: 10.1007/978-1-4939-6866-4_12.

PMID:
28439833
12.

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea.

Srivastava AK, Sablok G, Hackenberg M, Deshpande U, Suprasanna P.

Sci Rep. 2017 Apr 6;7:45490. doi: 10.1038/srep45490.

13.

On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica.

Fromm B, Ovchinnikov V, Høye E, Bernal D, Hackenberg M, Marcilla A.

Parasite Immunol. 2017 Feb;39(2). doi: 10.1111/pim.12399. Review.

14.

NGSmethDB 2017: enhanced methylomes and differential methylation.

Lebrón R, Gómez-Martín C, Carpena P, Bernaola-Galván P, Barturen G, Hackenberg M, Oliver JL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D97-D103. doi: 10.1093/nar/gkw996. Epub 2016 Oct 27.

15.

Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent.

Hackenberg M, Rueda A, Gustafson P, Langridge P, Shi BJ.

BMC Genomics. 2016 Sep 15;17(1):735. doi: 10.1186/s12864-016-3023-5.

16.

Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles.

Koppers-Lalic D, Hackenberg M, de Menezes R, Misovic B, Wachalska M, Geldof A, Zini N, de Reijke T, Wurdinger T, Vis A, van Moorselaar J, Pegtel M, Bijnsdorp I.

Oncotarget. 2016 Apr 19;7(16):22566-78. doi: 10.18632/oncotarget.8124.

17.

Sensing of latent EBV infection through exosomal transfer of 5'pppRNA.

Baglio SR, van Eijndhoven MA, Koppers-Lalic D, Berenguer J, Lougheed SM, Gibbs S, Léveillé N, Rinkel RN, Hopmans ES, Swaminathan S, Verkuijlen SA, Scheffer GL, van Kuppeveld FJ, de Gruijl TD, Bultink IE, Jordanova ES, Hackenberg M, Piersma SR, Knol JC, Voskuyl AE, Wurdinger T, Jiménez CR, Middeldorp JM, Pegtel DM.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E587-96. doi: 10.1073/pnas.1518130113. Epub 2016 Jan 14.

18.

The revised microRNA complement of Fasciola hepatica reveals a plethora of overlooked microRNAs and evidence for enrichment of immuno-regulatory microRNAs in extracellular vesicles.

Fromm B, Trelis M, Hackenberg M, Cantalapiedra F, Bernal D, Marcilla A.

Int J Parasitol. 2015 Sep;45(11):697-702. doi: 10.1016/j.ijpara.2015.06.002. Epub 2015 Jul 13.

PMID:
26183562
19.

sRNAtoolbox: an integrated collection of small RNA research tools.

Rueda A, Barturen G, Lebrón R, Gómez-Martín C, Alganza Á, Oliver JL, Hackenberg M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W467-73. doi: 10.1093/nar/gkv555. Epub 2015 May 27.

20.

Integrated microRNA, mRNA, and protein expression profiling reveals microRNA regulatory networks in rat kidney treated with a carcinogenic dose of aristolochic acid.

Li Z, Qin T, Wang K, Hackenberg M, Yan J, Gao Y, Yu LR, Shi L, Su Z, Chen T.

BMC Genomics. 2015 May 8;16:365. doi: 10.1186/s12864-015-1516-2.

21.

Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes.

Koppers-Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Würdinger T, Meijer GA, Pegtel DM.

Cell Rep. 2014 Sep 25;8(6):1649-1658. doi: 10.1016/j.celrep.2014.08.027. Epub 2014 Sep 18.

22.

DNA clustering and genome complexity.

Dios F, Barturen G, Lebrón R, Rueda A, Hackenberg M, Oliver JL.

Comput Biol Chem. 2014 Dec;53 Pt A:71-8. doi: 10.1016/j.compbiolchem.2014.08.011. Epub 2014 Aug 23.

PMID:
25182383
23.

A systems level analysis reveals transcriptomic and proteomic complexity in Ixodes ricinus midgut and salivary glands during early attachment and feeding.

Schwarz A, Tenzer S, Hackenberg M, Erhart J, Gerhold-Ay A, Mazur J, Kuharev J, Ribeiro JM, Kotsyfakis M.

Mol Cell Proteomics. 2014 Oct;13(10):2725-35. doi: 10.1074/mcp.M114.039289. Epub 2014 Jul 21.

24.

Differential expression of microRNAs and other small RNAs in barley between water and drought conditions.

Hackenberg M, Gustafson P, Langridge P, Shi BJ.

Plant Biotechnol J. 2015 Jan;13(1):2-13. doi: 10.1111/pbi.12220. Epub 2014 Jun 29.

25.

Sources of individual variability: miRNAs that predispose to neuropathic pain identified using genome-wide sequencing.

Bali KK, Hackenberg M, Lubin A, Kuner R, Devor M.

Mol Pain. 2014 Mar 19;10:22. doi: 10.1186/1744-8069-10-22.

26.

Surface analysis of Dicrocoelium dendriticum. The molecular characterization of exosomes reveals the presence of miRNAs.

Bernal D, Trelis M, Montaner S, Cantalapiedra F, Galiano A, Hackenberg M, Marcilla A.

J Proteomics. 2014 Jun 13;105:232-41. doi: 10.1016/j.jprot.2014.02.012. Epub 2014 Feb 21.

PMID:
24561797
27.

Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions.

Hackenberg M, Shi BJ, Gustafson P, Langridge P.

BMC Plant Biol. 2013 Dec 13;13:214. doi: 10.1186/1471-2229-13-214.

28.

Expression of herpes simplex virus 1 microRNAs in cell culture models of quiescent and latent infection.

Jurak I, Hackenberg M, Kim JY, Pesola JM, Everett RD, Preston CM, Wilson AC, Coen DM.

J Virol. 2014 Feb;88(4):2337-9. doi: 10.1128/JVI.03486-13. Epub 2013 Dec 4.

29.

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.

Geisen S, Barturen G, Alganza ÁM, Hackenberg M, Oliver JL.

Nucleic Acids Res. 2014 Jan;42(Database issue):D53-9. doi: 10.1093/nar/gkt1202. Epub 2013 Nov 22.

30.

CpGislandEVO: a database and genome browser for comparative evolutionary genomics of CpG islands.

Barturen G, Geisen S, Dios F, Hamberg EJ, Hackenberg M, Oliver JL.

Biomed Res Int. 2013;2013:709042. doi: 10.1155/2013/709042. Epub 2013 Sep 25.

31.

Segmentation of time series with long-range fractal correlations.

Bernaola-Galván P, Oliver JL, Hackenberg M, Coronado AV, Ivanov PC, Carpena P.

Eur Phys J B. 2012 Jun 1;85(6). pii: 211.

32.

Anomalous impurity segregation and local bonding fluctuation in l-Si.

Fisicaro G, Huet K, Negru R, Hackenberg M, Pichler P, Taleb N, La Magna A.

Phys Rev Lett. 2013 Mar 15;110(11):117801. Epub 2013 Mar 13.

PMID:
25166579
33.

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.

Barturen G, Rueda A, Oliver JL, Hackenberg M.

Version 2. F1000Res. 2013 Oct 15 [revised 2014 Jan 1];2:217. doi: 10.12688/f1000research.2-217.v2. eCollection 2013.

34.

A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions.

Hackenberg M, Huang PJ, Huang CY, Shi BJ, Gustafson P, Langridge P.

DNA Res. 2013 Apr;20(2):109-25. doi: 10.1093/dnares/dss037. Epub 2012 Dec 23.

35.

Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes.

Ferreiro MJ, Rodríguez-Ezpeleta N, Pérez C, Hackenberg M, Aransay AM, Barrio R, Cantera R.

BMC Genomics. 2012 Sep 15;13:483. doi: 10.1186/1471-2164-13-483.

36.

A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.

Hackenberg M, Shi BJ, Gustafson P, Langridge P.

PLoS One. 2012;7(8):e42030. doi: 10.1371/journal.pone.0042030. Epub 2012 Aug 1.

37.

Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation.

Meng F, Hackenberg M, Li Z, Yan J, Chen T.

PLoS One. 2012;7(3):e34394. doi: 10.1371/journal.pone.0034394. Epub 2012 Mar 28.

38.

Clustering of DNA words and biological function: a proof of principle.

Hackenberg M, Rueda A, Carpena P, Bernaola-Galván P, Barturen G, Oliver JL.

J Theor Biol. 2012 Mar 21;297:127-36. doi: 10.1016/j.jtbi.2011.12.024. Epub 2011 Dec 30.

PMID:
22226985
39.

ICU nurses' acceptance of electronic health records.

Carayon P, Cartmill R, Blosky MA, Brown R, Hackenberg M, Hoonakker P, Hundt AS, Norfolk E, Wetterneck TB, Walker JM.

J Am Med Inform Assoc. 2011 Nov-Dec;18(6):812-9. doi: 10.1136/amiajnl-2010-000018. Epub 2011 Jun 22.

40.

High-level organization of isochores into gigantic superstructures in the human genome.

Carpena P, Oliver JL, Hackenberg M, Coronado AV, Barturen G, Bernaola-Galván P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Mar;83(3 Pt 1):031908. Epub 2011 Mar 15.

PMID:
21517526
41.

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.

Hackenberg M, Rodríguez-Ezpeleta N, Aransay AM.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W132-8. doi: 10.1093/nar/gkr247. Epub 2011 Apr 22.

42.

WordCluster: detecting clusters of DNA words and genomic elements.

Hackenberg M, Carpena P, Bernaola-Galván P, Barturen G, Alganza AM, Oliver JL.

Algorithms Mol Biol. 2011 Jan 24;6:2. doi: 10.1186/1748-7188-6-2.

43.

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.

Hackenberg M, Barturen G, Oliver JL.

Nucleic Acids Res. 2011 Jan;39(Database issue):D75-9. doi: 10.1093/nar/gkq942. Epub 2010 Oct 21.

44.

TargetSpy: a supervised machine learning approach for microRNA target prediction.

Sturm M, Hackenberg M, Langenberger D, Frishman D.

BMC Bioinformatics. 2010 May 28;11:292. doi: 10.1186/1471-2105-11-292.

45.

Prediction of CpG-island function: CpG clustering vs. sliding-window methods.

Hackenberg M, Barturen G, Carpena P, Luque-Escamilla PL, Previti C, Oliver JL.

BMC Genomics. 2010 May 26;11:327. doi: 10.1186/1471-2164-11-327.

46.

Algorithms and methods for correlating experimental results with annotation databases.

Hackenberg M, Matthiesen R.

Methods Mol Biol. 2010;593:315-40. doi: 10.1007/978-1-60327-194-3_15.

PMID:
19957156
47.

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W68-76. doi: 10.1093/nar/gkp347. Epub 2009 May 11.

48.

Level statistics of words: finding keywords in literary texts and symbolic sequences.

Carpena P, Bernaola-Galván P, Hackenberg M, Coronado AV, Oliver JL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Mar;79(3 Pt 2):035102. Epub 2009 Mar 10.

PMID:
19392005
49.

ContDist: a tool for the analysis of quantitative gene and promoter properties.

Hackenberg M, Lasso G, Matthiesen R.

BMC Bioinformatics. 2009 Jan 7;10:7. doi: 10.1186/1471-2105-10-7.

50.

Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists.

Hackenberg M, Matthiesen R.

Bioinformatics. 2008 Jun 1;24(11):1386-93. doi: 10.1093/bioinformatics/btn178. Epub 2008 Apr 23.

PMID:
18434345

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