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51

Mining the literature: new methods to exploit keyword profiles

Miguel A Andrade-Navarro

Journal:

Genome Medicine

Year:

2012

Language:

english

File:

PDF, 121 KB

english, 2012

52

The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo

Christ, Annabel, Terryn, Sara, Schmidt, Vanessa, Christensen, Erik I, Huska, Matthew R, Andrade-Navarro, Miguel A, Hübner, Norbert, Devuyst, Olivier, Hammes, Annette, Willnow, Thomas E

Journal:

Kidney International

Year:

2010

Language:

english

File:

PDF, 410 KB

english, 2010

53

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data

Bollen, S., Leddin, M., Andrade-Navarro, M. A., Mah, N.

Journal:

Year:

2014

Language:

english

File:

PDF, 127 KB

english, 2014

54

Genie: literature-based gene prioritization at multi genomic scale

Fontaine, J.-F., Priller, F., Barbosa-Silva, A., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 2.77 MB

english, 2011

55

Assessment of curated phenotype mining in neuropsychiatric disorder literature

Fontaine, Jean-Fred, Priller, Josef, Spruth, Eike, Perez-Iratxeta, Carol, Andrade-Navarro, Miguel A.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.04 MB

english, 2015

56

Text mining of biomedical literature: Doing well, but we could be doing better

Andrade-Navarro, Miguel, Perez-Iratxeta, Carol

Journal:

Year:

2015

Language:

english

File:

PDF, 242 KB

english, 2015

57

Outer membrane pore protein prediction in mycobacteria using genomic comparison

Mah, N., Perez-Iratxeta, C., Andrade-Navarro, M. A.

Journal:

Microbiology (Society for General Microbiology)

Year:

2010

Language:

english

File:

PDF, 283 KB

english, 2010

58

CellFinder: a cell data repository

Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J.-F., Mah, N., Neves, M., Andrade-Navarro, M. A., Leser, U., Kurtz, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.45 MB

english, 2014

59

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

Muro, E. M., Mah, N., Moreno-Hagelsieb, G., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 2.99 MB

english, 2011

60

The SUMO protease SENP5 is required to maintain mitochondrial morphology and function

Zunino, R., Schauss, A., Rippstein, P., Andrade-Navarro, M., McBride, H. M.

Journal:

Journal of Cell Science

Year:

2007

Language:

english

File:

PDF, 1.10 MB

english, 2007

61

Identification of 2-[4-[(4-Methoxyphenyl)methoxy]-phenyl]acetonitrile and Derivatives as Potent Oct3/4 Inducers

Cheng, Xinlai, Dimou, Eleni, Alborzinia, Hamed, Wenke, Frank, Göhring, Axel, Reuter, Stefanie, Mah, Nancy, Fuchs, Heiko, Andrade-Navarro, Miguel A., Adjaye, James, Gul, Sheraz, Harms, Christoph, Utika

Journal:

Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 497 KB

english, 2015

62

Arabidopsis KCBP interacts with AIR9 but stays in the cortical division zone throughout mitosis via its MyTH4-FERM domain

Buschmann, H., Dols, J., Kopischke, S., Pena, E. J., Andrade-Navarro, M. A., Heinlein, M., Szymanski, D. B., Zachgo, S., Doonan, J. H., Lloyd, C. W.

Journal:

Journal of Cell Science

Year:

2015

Language:

english

File:

PDF, 2.82 MB

english, 2015

63

uORFdb--a comprehensive literature database on eukaryotic uORF biology

Wethmar, K., Barbosa-Silva, A., Andrade-Navarro, M. A., Leutz, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.89 MB

english, 2014

64

Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence

Rodriguez-Seguel, E., Mah, N., Naumann, H., Pongrac, I. M., Cerda-Esteban, N., Fontaine, J.-F., Wang, Y., Chen, W., Andrade-Navarro, M. A., Spagnoli, F. M.

Journal:

Genes & Development

Year:

2013

Language:

english

File:

PDF, 2.36 MB

english, 2013

65

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations

von Eichborn, J., Dunkel, M., Gohlke, B. O., Preissner, S. C., Hoffmann, M. F., Bauer, J. M. J., Armstrong, J. D., Schaefer, M. H., Andrade-Navarro, M. A., Le Novere, N., Croning, M. D. R., Grant, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.85 MB

english, 2013

66

Cardiac Alpha-Myosin (MYH6) Is the Predominant Sarcomeric Disease Gene for Familial Atrial Septal Defects

Posch, Maximilian G., Waldmuller, Stephan, Müller, Melanie, Scheffold, Thomas, Fournier, David, Andrade-Navarro, Miguel A., De Geeter, Bernard, Guillaumont, Sophie, Dauphin, Claire, Yousseff, Dany, Sc

Journal:

Year:

2011

Language:

english

File:

PDF, 517 KB

english, 2011

67

Similarity in targets with REST points to neural and glioblastoma related miRNAs

Gebhardt, M. L., Reuter, S., Mrowka, R., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

68

Identification of gene 3' ends by automated EST cluster analysis

Muro, E. M., Herrington, R., Janmohamed, S., Frelin, C., Andrade-Navarro, M. A., Iscove, N. N.

Journal:

Proceedings of the National Academy of Sciences

Year:

2008

Language:

english

File:

PDF, 465 KB

english, 2008

69

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data

Gebhardt, Marie Luise, Mer, Arvind Singh, Andrade-Navarro, Miguel Angel

Journal:

BMC Research Notes

Year:

2015

Language:

english

File:

PDF, 330 KB

english, 2015

70

MedlineRanker: flexible ranking of biomedical literature

Fontaine, J.-F., Barbosa-Silva, A., Schaefer, M., Huska, M. R., Muro, E. M., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 3.95 MB

english, 2009

71

Update of the G2D tool for prioritization of gene candidates to inherited diseases

Perez-Iratxeta, C., Bork, P., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2007

Language:

english

File:

PDF, 3.28 MB

english, 2007

72

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

Lopes, T. J. S., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.-F., Neumann, G., Andrade-Navarro, M. A., Kawaoka, Y., Kitano, H.

Journal:

Year:

2011

Language:

english

File:

PDF, 393 KB

english, 2011

73

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

Palidwor, Gareth A., Shcherbinin, Sergey, Huska, Matthew R., Rasko, Tamas, Stelzl, Ulrich, Arumughan, Anup, Foulle, Raphaele, Porras, Pablo, Sanchez-Pulido, Luis, Wanker, Erich E., Andrade-Navarro, Mi

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 602 KB

english, 2009

74

Ethyl 2-((4-Chlorophenyl)amino)thiazole-4-carboxylate and Derivatives Are Potent Inducers of Oct3/4

Cheng, Xinlai, Yoshida, Hiroki, Raoofi, Dena, Saleh, Sawsan, Alborzinia, Hamed, Wenke, Frank, Göhring, Axel, Reuter, Stefanie, Mah, Nancy, Fuchs, Heiko, Andrade-Navarro, Miguel A., Adjaye, James, Gul,

Journal:

Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 1.41 MB

english, 2015

75

PDBpaint, a visualization webservice to tag protein structures with sequence annotations

Fournier, D., Andrade-Navarro, M. A.

Journal:

Year:

2011

Language:

english

File:

PDF, 162 KB

english, 2011

76

Prioritization of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypes

Tiffin, N., Okpechi, I., Perez-Iratxeta, C., Andrade-Navarro, M. A., Ramesar, R.

Journal:

Physiological Genomics

Year:

2008

Language:

english

File:

PDF, 499 KB

english, 2008

77

Comprehensive translational control of tyrosine kinase expression by upstream open reading frames

Wethmar, K, Schulz, J, Muro, E M, Talyan, S, Andrade-Navarro, M A, Leutz, A

Journal:

Year:

2015

Language:

english

File:

PDF, 573 KB

english, 2015

78

SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival

Schmid, F, Wang, Q, Huska, M R, Andrade-Navarro, M A, Lemm, M, Fichtner, I, Dahlmann, M, Kobelt, D, Walther, W, Smith, J, Schlag, P M, Stein, U

Journal:

Year:

2015

Language:

english

File:

PDF, 1.61 MB

english, 2015

79

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure

Vlassi, Metaxia, Brauns, Katharina, Andrade-Navarro, Miguel A

Journal:

BMC Structural Biology

Year:

2013

Language:

english

File:

PDF, 2.77 MB

english, 2013

80

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

Mier, Pablo, Andrade-Navarro, Miguel A.

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 248 KB

english, 2016

81

Homologues of Arabidopsis Microtubule-Associated AIR9 in Trypanosomatid Parasites

Buschmann, Henrik, Sanchez-Pulido, Luis, Andrade-Navarro, Miguel A., Lloyd, Clive W.

Journal:

Plant Signaling & Behavior

Year:

2007

Language:

english

File:

PDF, 921 KB

english, 2007

82

A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations

Andrade-Navarro, Miguel A, Kanji, Femina, Palii, Carmen G, Brand, Marjorie, Atkins, Harold, Perez-Iratxeta, Carol

Journal:

BMC Biotechnology

Year:

2013

Language:

english

File:

PDF, 663 KB

english, 2013

83

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

de Oliveira, Kivia A. P., Kaergel, Eva, Heinig, Matthias, Fontaine, Jean-Fred, Patone, Giannino, Muro, Enrique M., Mathas, Stephan, Hummel, Michael, Andrade-Navarro, Miguel A., Hübner, Norbert, Scheid

Journal:

Genome Medicine

Year:

2016

Language:

english

File:

PDF, 4.06 MB

english, 2016

84

CABRA: Cluster and Annotate Blast Results Algorithm

Mier, Pablo, Andrade-Navarro, Miguel A.

Journal:

BMC Research Notes

Year:

2016

Language:

english

File:

PDF, 2.69 MB

english, 2016

85

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

Ibn-Salem, Jonas, Muro, Enrique M., Andrade-Navarro, Miguel A.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.58 MB

english, 2016

86

m6A modulates neuronal functions and sex determination in Drosophila

Lence, Tina, Akhtar, Junaid, Bayer, Marc, Schmid, Katharina, Spindler, Laura, Ho, Cheuk Hei, Kreim, Nastasja, Andrade-Navarro, Miguel A., Poeck, Burkhard, Helm, Mark, Roignant, Jean-Yves

Journal:

Year:

2016

Language:

english

File:

PDF, 3.72 MB

english, 2016

87

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

Mier, Pablo, Alanis-Lobato, Gregorio, Andrade-Navarro, Miguel A.

Journal:

Journal of Theoretical Biology

Year:

2017

Language:

english

File:

PDF, 1.15 MB

english, 2017

88

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

Alanis-Lobato, Gregorio, Andrade-Navarro, Miguel A., Schaefer, Martin H.

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 2.15 MB

english, 2017

89

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

Mier, Pablo, Alanis-Lobato, Gregorio, Andrade-Navarro, Miguel A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

90

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

Cerdá-Esteban, Nuria, Naumann, Heike, Ruzittu, Silvia, Mah, Nancy, Pongrac, Igor M., Cozzitorto, Corinna, Hommel, Angela, Andrade-Navarro, Miguel A., Bonifacio, Ezio, Spagnoli, Francesca M.

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 2.78 MB

english, 2017

91

Efficient embedding of complex networks to hyperbolic space via their Laplacian

Alanis-Lobato, Gregorio, Mier, Pablo, Andrade-Navarro, Miguel A.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.08 MB

english, 2016

92

Manifold learning and maximum likelihood estimation for hyperbolic network embedding

Gregorio Alanis-Lobato,Pablo Mier,Miguel A. Andrade-Navarro

Journal:

Applied Network Science

Year:

2016

Language:

english

File:

PDF, 935 KB

english, 2016

93

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

Jung, Sascha, Angarica, Vladimir Espinosa, Andrade-Navarro, Miguel A., Buckley, Noel J., del Sol, Antonio

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 2.28 MB

english, 2017

94

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

Corwin, Thomas, Woodsmith, Jonathan, Apelt, Federico, Fontaine, Jean-Fred, Meierhofer, David, Helmuth, Johannes, Grossmann, Arndt, Andrade-Navarro, Miguel A., Ballif, Bryan A., Stelzl, Ulrich

Journal:

Year:

2017

Language:

english

File:

PDF, 2.85 MB

english, 2017

95

Liver-kidney-on-chip to study toxicity of drug metabolites

Theobald, Jannick, Ghanem, Ali, Wallisch, Patrick, Banaeiyan, Amin A., Andrade-Navarro, Miguel A., Taskova, Katarina, Haltmeier, Manuela, Kurtz, Andreas, Becker, Holger, Reuter, Stefanie, Mrowka, Ralf

Journal:

ACS Biomaterials Science & Engineering

Year:

2017

Language:

english

File:

PDF, 2.38 MB

english, 2017

96

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

Hildebrandt, Andrea, Alanis-Lobato, Gregorio, Voigt, Andrea, Zarnack, Kathi, Andrade-Navarro, Miguel A., Beli, Petra, König, Julian

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 2.35 MB

english, 2017

97

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6 A machinery component Wtap/Fl(2)d

Knuckles, Philip, Lence, Tina, Haussmann, Irmgard U., Jacob, Dominik, Kreim, Nastasja, Carl, Sarah H., Masiello, Irene, Hares, Tina, Villaseñor, Rodrigo, Hess, Daniel, Andrade-Navarro, Miguel A., Bigg

Journal:

Genes & Development

Year:

2018

Language:

english

File:

PDF, 8.55 MB

english, 2018

98

The latent geometry of the human protein interaction network

Alanis-Lobato, Gregorio, Mier, Pablo, Andrade-Navarro, Miguel

Journal:

Year:

2018

Language:

english

File:

PDF, 2.12 MB

english, 2018

99

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

Mier, Pablo, Andrade-Navarro, Miguel A

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 446 KB

english, 2017

100

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

Brüne, Daniel, Andrade-Navarro, Miguel A., Mier, Pablo

Journal:

BMC Research Notes

Year:

2018

Language:

english

File:

PDF, 2.16 MB

english, 2018