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Items: 1 to 50 of 151

1.

The distributions of protein coding genes within chromatin domains in relation to human disease.

Muro EM, Ibn-Salem J, Andrade-Navarro MA.

Epigenetics Chromatin. 2019 Dec 5;12(1):72. doi: 10.1186/s13072-019-0317-2.

2.

Towards identifying drug side effects from social media using active learning and crowd sourcing.

Burkhardt S, Siekiera J, Glodde J, Andrade-Navarro MA, Kramer S.

Pac Symp Biocomput. 2020;25:319-330.

3.

Assessment of computational methods for the analysis of single-cell ATAC-seq data.

Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L.

Genome Biol. 2019 Nov 18;20(1):241. doi: 10.1186/s13059-019-1854-5.

4.

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.

Ibn-Salem J, Andrade-Navarro MA.

BMC Genomics. 2019 Oct 25;20(1):777. doi: 10.1186/s12864-019-6088-0.

5.

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D.

Nucleic Acids Res. 2019 Dec 2;47(21):10994-11006. doi: 10.1093/nar/gkz841.

6.

Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells.

More P, Goedtel-Armbrust U, Shah V, Mathaes M, Kindler T, Andrade-Navarro MA, Wojnowski L.

Oncotarget. 2019 Sep 3;10(51):5298-5312. doi: 10.18632/oncotarget.27112. eCollection 2019 Sep 3.

7.

Repeatability in protein sequences.

Kamel M, Mier P, Tari A, Andrade-Navarro MA.

J Struct Biol. 2019 Nov 1;208(2):86-91. doi: 10.1016/j.jsb.2019.08.003. Epub 2019 Aug 10.

8.

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay.

Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine JF, Andrade-Navarro MA, Silies M, Berger C.

Life Sci Alliance. 2019 Jul 22;2(4). pii: e201900318. doi: 10.26508/lsa.201900318. Print 2019 Aug.

9.

Detection of condition-specific marker genes from RNA-seq data with MGFR.

El Amrani K, Alanis-Lobato G, Mah N, Kurtz A, Andrade-Navarro MA.

PeerJ. 2019 May 27;7:e6970. doi: 10.7717/peerj.6970. eCollection 2019.

10.

AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions.

Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jimenez J, Pérez-Pulido AJ.

Methods Mol Biol. 2019;1962:207-214. doi: 10.1007/978-1-4939-9173-0_12.

PMID:
31020562
11.

Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty.

Scheuermann B, Diem T, Ivics Z, Andrade-Navarro MA.

Sci Rep. 2019 Feb 4;9(1):1171. doi: 10.1038/s41598-018-38061-w.

12.

Disentangling the complexity of low complexity proteins.

Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA.

Brief Bioinform. 2019 Jan 30. doi: 10.1093/bib/bbz007. [Epub ahead of print]

PMID:
30698641
13.

Imidazopyridines as Potent KDM5 Demethylase Inhibitors Promoting Reprogramming Efficiency of Human iPSCs.

Dabiri Y, Gama-Brambila RA, Taškova K, Herold K, Reuter S, Adjaye J, Utikal J, Mrowka R, Wang J, Andrade-Navarro MA, Cheng X.

iScience. 2019 Feb 22;12:168-181. doi: 10.1016/j.isci.2019.01.012. Epub 2019 Jan 11.

14.

Function and Evolution of Nematode RNAi Pathways.

Almeida MV, Andrade-Navarro MA, Ketting RF.

Noncoding RNA. 2019 Jan 15;5(1). pii: E8. doi: 10.3390/ncrna5010008. Review.

15.

Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets.

Taškova K, Fontaine JF, Mrowka R, Andrade-Navarro MA.

PLoS One. 2019 Jan 14;14(1):e0210467. doi: 10.1371/journal.pone.0210467. eCollection 2019.

16.

The Anti-amyloid Compound DO1 Decreases Plaque Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice.

Boeddrich A, Babila JT, Wiglenda T, Diez L, Jacob M, Nietfeld W, Huska MR, Haenig C, Groenke N, Buntru A, Blanc E, Meier JC, Vannoni E, Erck C, Friedrich B, Martens H, Neuendorf N, Schnoegl S, Wolfer DP, Loos M, Beule D, Andrade-Navarro MA, Wanker EE.

Cell Chem Biol. 2019 Jan 17;26(1):109-120.e7. doi: 10.1016/j.chembiol.2018.10.013. Epub 2018 Nov 21.

17.

Automated selection of homologs to track the evolutionary history of proteins.

Mier P, Pérez-Pulido AJ, Andrade-Navarro MA.

BMC Bioinformatics. 2018 Nov 19;19(1):431. doi: 10.1186/s12859-018-2457-y.

18.

Traitpedia: a collaborative effort to gather species traits.

Mier P, Andrade-Navarro MA.

Bioinformatics. 2019 Mar 15;35(6):1079-1081. doi: 10.1093/bioinformatics/bty743.

19.

Evolutionary stability of topologically associating domains is associated with conserved gene regulation.

Krefting J, Andrade-Navarro MA, Ibn-Salem J.

BMC Biol. 2018 Aug 7;16(1):87. doi: 10.1186/s12915-018-0556-x.

20.

Identification of transcribed protein coding sequence remnants within lincRNAs.

Talyan S, Andrade-Navarro MA, Muro EM.

Nucleic Acids Res. 2018 Sep 28;46(17):8720-8729. doi: 10.1093/nar/gky608.

21.

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length.

Mier P, Andrade-Navarro MA.

Genome Biol Evol. 2018 Mar 1;10(3):816-825. doi: 10.1093/gbe/evy046.

22.

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d.

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY.

Genes Dev. 2018 Mar 1;32(5-6):415-429. doi: 10.1101/gad.309146.117. Epub 2018 Mar 13.

23.

CellMap visualizes protein-protein interactions and subcellular localization.

Dallago C, Goldberg T, Andrade-Navarro MA, Alanis-Lobato G, Rost B.

Version 2. F1000Res. 2017 Oct 11 [revised 2018 Jan 1];6:1824. doi: 10.12688/f1000research.12707.2. eCollection 2017.

24.

Proteome-wide comparison between the amino acid composition of domains and linkers.

Brüne D, Andrade-Navarro MA, Mier P.

BMC Res Notes. 2018 Feb 9;11(1):117. doi: 10.1186/s13104-018-3221-0.

25.

Loss-of-function uORF mutations in human malignancies.

Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, Castaños-Vélez E, Fichtner I, Tunn PU, Denkert C, Klaas O, Berdel WE, von Kries JP, Makalowski W, Andrade-Navarro MA, Leutz A, Wethmar K.

Sci Rep. 2018 Feb 5;8(1):2395. doi: 10.1038/s41598-018-19201-8.

26.

Geometric characterisation of disease modules.

Härtner F, Andrade-Navarro MA, Alanis-Lobato G.

Appl Netw Sci. 2018;3(1):10. doi: 10.1007/s41109-018-0066-3. Epub 2018 Jun 18.

27.

Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system.

Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P, König J.

Sci Rep. 2017 Nov 29;7(1):16582. doi: 10.1038/s41598-017-16695-6.

28.

Toward completion of the Earth's proteome: an update a decade later.

Mier P, Andrade-Navarro MA.

Brief Bioinform. 2019 Mar 22;20(2):463-470. doi: 10.1093/bib/bbx127.

PMID:
29040399
29.

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate.

Corwin T, Woodsmith J, Apelt F, Fontaine JF, Meierhofer D, Helmuth J, Grossmann A, Andrade-Navarro MA, Ballif BA, Stelzl U.

Cell Syst. 2017 Aug 23;5(2):128-139.e4. doi: 10.1016/j.cels.2017.08.001.

30.

Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements.

Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC.

Am J Hum Genet. 2017 Aug 3;101(2):206-217. doi: 10.1016/j.ajhg.2017.06.011. Epub 2017 Jul 20.

31.

Evaluation of in vivo and in vitro models of toxicity by comparison of toxicogenomics data with the literature.

Taškova K, Fontaine JF, Mrowka R, Andrade-Navarro MA.

Methods. 2018 Jan 1;132:57-65. doi: 10.1016/j.ymeth.2017.07.010. Epub 2017 Jul 14.

PMID:
28716510
32.

Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data.

Jung S, Angarica VE, Andrade-Navarro MA, Buckley NJ, Del Sol A.

Sci Rep. 2017 Jul 5;7(1):4660. doi: 10.1038/s41598-017-04929-6.

33.

Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2.

Cerdá-Esteban N, Naumann H, Ruzittu S, Mah N, Pongrac IM, Cozzitorto C, Hommel A, Andrade-Navarro MA, Bonifacio E, Spagnoli FM.

Nat Commun. 2017 Feb 13;8:14127. doi: 10.1038/ncomms14127.

34.

The Protein Structure Context of PolyQ Regions.

Totzeck F, Andrade-Navarro MA, Mier P.

PLoS One. 2017 Jan 26;12(1):e0170801. doi: 10.1371/journal.pone.0170801. eCollection 2017.

35.

Context characterization of amino acid homorepeats using evolution, position, and order.

Mier P, Alanis-Lobato G, Andrade-Navarro MA.

Proteins. 2017 Apr;85(4):709-719. doi: 10.1002/prot.25250. Epub 2017 Feb 6.

PMID:
28097686
36.

Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family.

Mier P, Pérez-Pulido AJ, Reynaud EG, Andrade-Navarro MA.

PLoS One. 2017 Jan 10;12(1):e0169750. doi: 10.1371/journal.pone.0169750. eCollection 2017.

37.

dAPE: a web server to detect homorepeats and follow their evolution.

Mier P, Andrade-Navarro MA.

Bioinformatics. 2017 Apr 15;33(8):1221-1223. doi: 10.1093/bioinformatics/btw790.

38.

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.

Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SCE.

Nucleic Acids Res. 2017 Apr 7;45(6):3613. doi: 10.1093/nar/gkw1268. No abstract available.

39.

m6A modulates neuronal functions and sex determination in Drosophila.

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M, Roignant JY.

Nature. 2016 Dec 8;540(7632):242-247. doi: 10.1038/nature20568. Epub 2016 Nov 30.

PMID:
27919077
40.

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.

Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D308-D312. doi: 10.1093/nar/gkw1136. Epub 2016 Nov 29. Erratum in: Nucleic Acids Res. 2017 Apr 7;45(6):3613.

41.

Protein-protein interactions can be predicted using coiled coil co-evolution patterns.

Mier P, Alanis-Lobato G, Andrade-Navarro MA.

J Theor Biol. 2017 Jan 7;412:198-203. doi: 10.1016/j.jtbi.2016.11.001. Epub 2016 Nov 7.

42.

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.

Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985. Epub 2016 Oct 24.

43.

The C-terminal domain of TPX2 is made of alpha-helical tandem repeats.

Sanchez-Pulido L, Perez L, Kuhn S, Vernos I, Andrade-Navarro MA.

BMC Struct Biol. 2016 Oct 26;16(1):17.

44.

Co-regulation of paralog genes in the three-dimensional chromatin architecture.

Ibn-Salem J, Muro EM, Andrade-Navarro MA.

Nucleic Acids Res. 2017 Jan 9;45(1):81-91. doi: 10.1093/nar/gkw813. Epub 2016 Sep 14.

45.

Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors.

Riemke P, Czeh M, Fischer J, Walter C, Ghani S, Zepper M, Agelopoulos K, Lettermann S, Gebhardt ML, Mah N, Weilemann A, Grau M, Gröning V, Haferlach T, Lenze D, Delwel R, Prinz M, Andrade-Navarro MA, Lenz G, Dugas M, Müller-Tidow C, Rosenbauer F.

EMBO J. 2016 Nov 15;35(22):2399-2416. Epub 2016 Aug 29.

46.

Efficient embedding of complex networks to hyperbolic space via their Laplacian.

Alanis-Lobato G, Mier P, Andrade-Navarro MA.

Sci Rep. 2016 Jul 22;6:30108. doi: 10.1038/srep30108.

47.

Editorial: Protein Interaction Networks in Health and Disease.

Petrakis S, Andrade-Navarro MA.

Front Genet. 2016 Jun 14;7:111. doi: 10.3389/fgene.2016.00111. eCollection 2016. No abstract available.

48.

CABRA: Cluster and Annotate Blast Results Algorithm.

Mier P, Andrade-Navarro MA.

BMC Res Notes. 2016 Apr 30;9:253. doi: 10.1186/s13104-016-2062-y.

49.

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C.

Genome Med. 2016 Mar 17;8(1):28. doi: 10.1186/s13073-016-0280-5.

50.

FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases.

Mier P, Andrade-Navarro MA.

J Comput Biol. 2016 Apr;23(4):270-8. doi: 10.1089/cmb.2015.0191. Epub 2016 Feb 1.

PMID:
26828375

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