Browse by Research Team

2020

Interactome mapping provides a network of neurodegenerative disease proteins and uncovers widespread protein aggregation in affected brains.
Haenig, C., Atias, N., Taylor, A.K., Mazza, A., Schaefer, M.H., Russ, J., Riechers, S.P., Jain, S., Coughlin, M., Fontaine, J.F., Freibaum, B.D., Brusendorf, L., Zenkner, M., Porras, P., Stroedicke, M., Schnoegl, S., Arnsburg, K., Boeddrich, A., Pigazzini, L., Heutink, P., Taylor, J.P., Kirstein, J., Andrade-Navarro, M.A., Sharan, R. and Wanker, E.E.
Cell Reports 32 (7): 108050. 18 August 2020

2017

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, I.M., Cozzitorto, C., Hommel, A., Andrade-Navarro, M.A., Bonifacio, E. and Spagnoli, F.M.
Nature Communications 8 : 14127. 13 February 2017

2016

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. and Stein, U.
Oncogene 35 (46): 5942-5952. 17 November 2016

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, M.L., Mah, N., Weilemann, A., Grau, M., Groening, V., Haferlach, T., Lenze, D., Delwel, R., Prinz, M., Andrade-Navarro, M.A., Lenz, G., Dugas, M., Mueller-Tidow, C. and Rosenbauer, F.
EMBO Journal 35 (22): 2399-2416. 15 November 2016

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. and Leutz, A.
Oncogene 35 (13): 1736-1742. 31 March 2016

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: dominant roles of p50 and p52 revealed by genome-wide analyses.
de Oliveira, K.A.P., Kaergel, E., Heinig, M., Fontaine, J.F., Patone, G., Muro, E.M., Mathas, S., Hummel, M., Andrade-Navarro, M.A., Hübner, N. and Scheidereit, C.
Genome Medicine 8 (1): 28. 17 March 2016

2015

Ethyl 2-((4-chlorophenyl)amino)thiazole-4-carboxylate and derivatives are potent inducers of Oct3/4.
Cheng, X., Yoshida, H., Raoofi, D., Saleh, S., Alborzinia, H., Wenke, F., Goehring, A., Reuter, S., Mah, N., Fuchs, H.R., Andrade-Navarro, M.A., Adjaye, J., Gul, S., Utikal, J., Mrowka, R. and Woelfl, S.
Journal of Medicinal Chemistry 58 (1): 5742-5750. 13 August 2015

Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers.
Cheng, X., Dimou, E., Alborzinia, H., Wenke, F., Goehring, A., Reuter, S., Mah, N., Fuchs, H., Andrade-Navarro, M.A., Adjaye, J., Gul, S., Harms, C., Utikal, J., Klipp, E., Mrowka, R. and Woelfl, S.
Journal of Medicinal Chemistry 58 (12): 4976-4983. 25 June 2015

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. and Lloyd, C.W.
Journal of Cell Science 28 (11): 2033-2046. 1 June 2015

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity.
Stroedicke, M., Bounab, Y., Strempel, N., Klockmeier, K., Yigit, S., Friedrich, R.P., Chaurasia, G., Li, S., Hesse, F., Riechers, S.P., Russ, J., Nicoletti, C., Boeddrich, A., Wiglenda, T., Haenig, C., Schnoegl, S., Fournier, D., Graham, R.K., Hayden, M.R., Sigrist, S., Bates, G.P., Priller, J., Andrade-Navarro, M.A., Futschik, M.E. and Wanker, E.E.
Genome Research 25 (5): 701-713. May 2015

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data.
Gebhardt, M.L., Mer, A.S. and Andrade-Navarro, M.A.
BMC Research Notes 8 (1): 157. 16 April 2015

Assessment of curated phenotype mining in neuropsychiatric disorder literature.
Fontaine, J.F., Priller, J., Spruth, E., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
Methods 74 : 90-96. March 2015

Comparison of inter- and intraspecies variation in humans and fruit flies.
Shih, J., Hodge, R. and Andrade-Navarro, M.A.
Genomics Data 3 : 49-54. March 2015

2014

PRC1-mediated gene silencing in pluripotent ES cells: function and evolution.
Becker, M., Mah, N., Zdzieblo, D., Li, X., Mer, A.S., Andrade-Navarro, M.A. and Mueller, A.M.
Epigenetics and Human Health 2015 : 141-166. 18 November 2014

Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen.
Suratanee, A., Schaefer, M.H., Betts, M.J., Soons, Z., Mannsperger, H., Harder, N., Oswald, M., Gipp, M., Ramminger, E., Marcus, G., Männer, R., Rohr, K., Wanker, E., Russell, R.B., Andrade-Navarro, M.A., Eils, R. and König, R.
PLoS Computational Biology 10 (9): e1003814. 25 September 2014

Alkemio: association of chemicals with biomedical topics by text and data mining.
Gijon-Correas, J.A., Andrade-Navarro, M.A. and Fontaine, J.F.
Nucleic Acids Research 42 (W1): W422-W429. 1 July 2014

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen, S., Leddin, M., Andrade-Navarro, M.A. and Mah, N.
Bioinformatics 30 (10): 1484-1485. 15 May 2014

Similarity in targets with REST points to neural and glioblastoma related miRNAs.
Gebhardt, M.L., Reuter, S., Mrowka, R. and Andrade-Navarro, M.A.
Nucleic Acids Research 42 (9): 5436-5446. 14 May 2014

Identification of LRRC8 heteromers as an essential component of the volume-regulated anion channel VRAC.
Voss, F.K., Ullrich, F., Muench, J., Lazarow, K., Lutter, D., Mah, N., Andrade-Navarro, M.A., von Kries, J.P., Stauber, T. and Jentsch, T.J.
Science 344 (6184): 634-638. 9 May 2014

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma.
Fehlker, M., Huska, M.R., Joens, T., Andrade-Navarro, M.A. and Kemmner, W.
BMC Cancer 14 (1): 64. 5 February 2014

ROMO1 is an essential redox-dependent regulator of mitochondrial dynamics.
Norton, M., Ng, A.C., Baird, S., Dumoulin, A., Shutt, T., Mah, N., Andrade-Navarro, M.A., McBride, H.M. and Screaton, R.A.
Science Signaling 7 (310): ra10. 28 January 2014

CellFinder: a cell data repository.
Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J.F., Mah, N., Neves, M., Andrade-Navarro, M.A., Leser, U. and Kurtz, A.
Nucleic Acids Research 42 (1): D950-D958. 1 January 2014

uORFdb - a comprehensive literature database on eukaryotic uORF biology.
Wethmar, K., Barbosa-Silva, A., Andrade-Navarro, M.A. and Leutz, A.
Nucleic Acids Research 42 (1): D60-D67. 1 January 2014

2013

A novel approach for protein subcellular location prediction using amino acid exposure.
Mer, A.S. and Andrade-Navarro, M.A.
BMC Bioinformatics 14 (1): 342. 28 November 2013

Functional and genomic analyses of α-solenoid proteins.
Fournier, D., Palidwor, G.A., Shcherbinin, S., Szengel, A., Schaefer, M.H., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
PLoS ONE 8 (11): e79894. 21 November 2013

A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.
Andrade-Navarro, M.A., Kanji, F., Palii, C.G., Brand, M., Atkins, H. and Perez-Iratxeta, C.
BMC Biotechnology 13 (1): 80. 3 October 2013

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure.
Vlassi, M., Brauns, K. and Andrade-Navarro, M.A.
BMC Structural Biology 13 (1): 17. 2 October 2013

Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.
Rodríguez-Seguel, E., Mah, N., Naumann, H., Pongrac, I.M., Cerdá-Esteban, N., Fontaine, J.F., Wang, Y., Chen, W., Andrade-Navarro, M.A. and Spagnoli, F.M.
Genes & Development 27 (17): 1932-1946. 1 September 2013

Bio++: efficient extensible libraries and tools for computational molecular evolution.
Gueguen, L., Gaillard, S., Boussau, B., Gouy, M., Groussin, M., Rochette, N.C., Bigot, T., Fournier, D., Pouyet, F., Cahais, V., Bernard, A., Scornavacca, C., Nabholz, B., Haudry, A., Dachary, L., Galtier, N., Belkhir, K. and Dutheil, J.Y.
Molecular Biology and Evolution 30 (8): 1745-1750. August 2013

Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.
Zhang, G., Hoersch, S., Amsterdam, A., Whittaker, C.A., Beert, E., Catchen, J.M., Farrington, S., Postlethwait, J.H., Legius, E., Hopkins, N. and Lees, J.A.
PLoS Genetics 9 (8): e1003734. August 2013

CELDA - an ontology for the comprehensive representation of cells in complex systems.
Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J.F., Nguyen-Dobinsky, T.N., Leser, U. and Kurtz, A.
BMC Bioinformatics 14 : 228. 17 July 2013

Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners.
Petrakis, S., Schaefer, M.H., Wanker, E.E. and Andrade-Navarro, M.A.
BioEssays 35 (6): 503-507. June 2013

PU.1 level-directed chromatin structure remodeling at the Irf8 gene drives dendritic cell commitment.
Schönheit, J., Kuhl, C., Gebhardt, M.L., Klett, F.F., Riemke, P., Scheller, M., Huang, G., Naumann, R., Leutz, A., Stocking, C., Priller, J., Andrade-Navarro, M.A. and Rosenbauer, F.
Cell Reports 3 (5): 1617-1628. 30 May 2013

DNA microarray and miRNA analyses reinforce the classification of follicular thyroid tumors.
Jacques, C., Guillotin, D., Fontaine, J.F., Franc, B., Mirebeau-Prunier, D., Fleury, A., Malthiery, Y. and Savagner, F.
Journal of Clinical Endocrinology and Metabolism 98 (5): E981-E989. May 2013

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.
Neves, M., Damaschun, A., Mah, N., Lekschas, F., Seltmann, S., Stachelscheid, H., Fontaine, J.F., Kurtz, A. and Leser, U.
Database 2013 (2013): bat020. 18 April 2013

Using cited references to improve the retrieval of related biomedical documents.
Ortuno, F.M., Rojas, I., Andrade-Navarro, M.A. and Fontaine, J.F.
BMC Bioinformatics 14 : 113. 27 March 2013

Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors.
Mirebeau-Prunier, D., Le Pennec, S., Jacques, C., Fontaine, J.F., Gueguen, N., Boutet-Bouzamondo, N., Donnart, A., Malthiery, Y. and Savagner, F.
PLoS ONE 8 (3): e58683. 13 March 2013

CXCL5 limits macrophage foam cell formation in atherosclerosis.
Rousselle, A., Qadri, F., Leukel, L., Yilmaz, R., Fontaine, J.F., Sihn, G., Bader, M., Ahluwalia, A. and Duchene, J.
Journal of Clinical Investigation 123 (3): 1343-1347. 1 March 2013

Development and application of a DNA microarray-based yeast two-hybrid system.
Suter, B., Fontaine, J.F., Yildirimman, R., Raskó, T., Schaefer, M.H., Rasche, A., Porras, P., Vázquez-Álvarez, B.M., Russ, J., Rau, K., Foulle, R., Zenkner, M., Saar, K., Herwig, R., Andrade-Navarro, M.A. and Wanker, E.E.
Nucleic Acids Research 41 (3): 1496-507. 1 February 2013

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.
Schaefer, M.H., Lopes, T.J.S., Mah, N., Shoemaker, J.E., Matsuoka, Y., Fontaine, J.F., Louis-Jeune, C., Eisfeld, A.J., Neumann, G., Perez-Iratxeta, C., Kawaoka, Y., Kitano, H. and Andrade-Navarro, M.A.
PLoS Computational Biology 9 (1): e1002860. 3 January 2013

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.G.N., van Nierop, P., Smit, A.B. and Preissner, R.
Nucleic Acids Research 41 (D1): D834-D840. 1 January 2013

2012

Mining the literature: new methods to exploit keyword profiles.
Andrade-Navarro, M.A.
Genome Medicine 4 (10): 81. 30 October 2012

Peer2ref: a peer-reviewer finding web tool that uses author disambiguation.
Andrade-Navarro, M.A., Palidwor, G.A. and Perez-Iratxeta, C.
BioData Mining 5 (1): 14. 7 September 2012

Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1.
Petrakis, S., Rasko, T., Russ, J., Friedrich, R.P., Stroedicke, M., Riechers, S.P., Muehlenberg, K., Moeller, A., Reinhardt, A., Vinayagam, A., Schaefer, M.H., Boutros, M., Tricoire, H., Andrade-Navarro, M.A. and Wanker, E.E.
PLoS Genetics 8 (8): e1002897. 16 August 2012

Computational approaches to discovering noncoding RNA.
Krzyzanowski, P.M., Muro, E.M. and Andrade-Navarro, M.A.
Wiley Interdisciplinary Reviews: RNA 3 (4): 567-579. July 2012

A role for GPx3 in activity of normal and leukemia stem cells.
Herault, O., Hope, K.J., Deneault, E., Mayotte, N., Chagraoui, J., Wilhelm, B.T., Cellot, S., Sauvageau, M., Andrade-Navarro, M.A., Hebert, J. and Sauvageau, G.
Journal of Experimental Medicine 209 (5): 895-901. 7 May 2012

Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks.
Schaefer, M.H., Wanker, E.E. and Andrade-Navarro, M.A.
Nucleic Acids Research 40 (10): 4273-4287. 1 May 2012

Emergence and evolution of the renin-angiotensin-aldosterone system.
Fournier, D., Luft, F.C., Bader, M., Ganten, D. and Andrade-Navarro, M.A.
Journal of Molecular Medicine 90 (5): 495-508. May 2012

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.
Naba, A., Clauser, K.R., Hoersch, S., Liu, H., Carr, S.A. and Hynes, R.O.
Molecular & Cellular Proteomics 11 (4): M111.014647. 1 April 2012

Comparative genomics identification of a novel set of temporally regulated hedgehog target genes in the retina.
McNeill, B., Perez-Iratxeta, C., Mazerolle, C., Furimsky, M., Mishina, Y., Andrade-Navarro, M.A. and Wallace, V.A.
Molecular and Cellular Neuroscience 49 (3): 333-340. March 2012

HIPPIE: integrating protein interaction networks with experiment based quality scores.
Schaefer, M.H., Fontaine, J.F., Vinayagam, A., Porras, P., Wanker, E.E. and Andrade-Navarro, M.A.
PLoS ONE 7 (2): e31826. 14 February 2012

Caipirini: using gene sets to rank literature.
Soldatos, T.G., O'Donoghue, S.I., Satagopam, V.P., Barbosa-Silva, A., Pavlopoulos, G.A., Wanderley-Nogueira, A.C., Soares-Cavalcanti, N.M. and Schneider, R.
BioData Mining 5 (1): 1. 1 February 2012

Natural antisense transcripts within pseudogenes: an EST survey.
Muro, E.M. and Andrade-Navarro, M.A.
In: Non-coding RNAs and epigenetic regulation of gene expression : drivers of natural selection. Caister Academic Press, Norfolk, 99-108. ISBN 978-1-904455-94-3 February 2012

Prediction of protein secondary structure from circular dichroism using theoretically derived spectra.
Louis-Jeune, C., Andrade-Navarro, M.A. and Perez-Iratxeta, C.
Proteins: Structure, Function, and Bioinformatics 80 (2): 374-381. February 2012

Paired sage-microarray expression data sets reveal antisense transcripts differentially expressed in embryonic stem cell differentiation.
Sandie, R., Porter, C.J., Palidwor, G.A., Price, F., Krzyzanowski, P.M., Muro, E.M., Hoersch, S., Smith, M., Campbell, P.A., Perez-Iratxeta, C., Rudnicki, M.A. and Andrade-Navarro, M.A.
In: Computational Biology of Embryonic Stem Cells. Bentham, Oak Park, 193-215. ISBN 978-1-608-05025-3 2012

2011

Preimplantation development regulatory pathway construction through a text-mining approach.
Donnard, E., Barbosa-Silva, A., Guedes, R.L., Fernandes, G.R., Velloso, H., Kohn, M.J., Andrade-Navarro, M.A. and Ortega, J.M.
BMC Genomics 12 (Suppl 4): S3. 22 December 2011

Cardiac alpha-myosin (MYH6) is the predominant sarcomeric disease gene for familial atrial septal defects.
Posch, M.G., Waldmuller, S., Mueller, M., Scheffold, T., Fournier, D., Andrade-Navarro, M.A., De Geeter, B., Guillaumont, S., Dauphin, C., Yousseff, D., Schmitt, K.R., Perrot, A., Berger, F., Hetzer, R., Bouvagnet, P. and Ozcelik, C.
PLoS ONE 6 (12): e28872. 14 December 2011

In vivo effects on intron retention and exon skipping by the U2AF large subunit and SF1/BBP in the nematode Caenorhabditis elegans.
Ma, L., Tan, Z., Teng, Y., Hoersch, S. and Horvitz, H.R.
RNA 17 (12): 2201-2211. December 2011

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva, A., Fontaine, J.F., Donnard, E.R., Stussi, F., Ortega, J.M. and Andrade-Navarro, M.A.
BMC Bioinformatics 12 (1): 435. 9 November 2011

Functional evidence of post-transcriptional regulation by pseudogenes.
Muro, E.M., Mah, N. and Andrade-Navarro, M.A.
Biochimie 93 (11): 1916-1921. November 2011

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
Krallinger, M., Vazquez, M., Leitner, F., Salgado, D., Chatr-Aryamontri, A., Winter, A., Perfetto, L., Briganti, L., Licata, L., Iannuccelli, M., Castagnoli, L., Cesareni, G., Tyers, M., Schneider, G., Rinaldi, F., Leaman, R., Gonzalez, G., Matos, S., Kim, S., Wilbur, W.J., Rocha, L., Shatkay, H., Tendulkar, A.V., Agarwal, S., Liu, F., Wang, X., Rak, R., Noto, K., Elkan, C., Lu, Z., Dogan, R.I., Fontaine, J.F., Andrade-Navarro, M.A. and Valencia, A.
BMC Bioinformatics 12 (Suppl 8): S3. 3 October 2011

The GNAT library for local and remote gene mention normalization.
Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., Nenadic, G. and Bergman, C.M.
Bioinformatics 27 (19): 2769-2771. 1 October 2011

PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Fournier, D. and Andrade-Navarro, M.A.
Bioinformatics 27 (18): 2605-2606. 15 September 2011

A directed protein interaction network for investigating intracellular signal transduction.
Vinayagam, A., Stelzl, U., Foulle, R., Plassmann, S., Zenkner, M., Timm, J., Assmus, H.E., Andrade-Navarro, M.A. and Wanker, E.E.
Science Signaling 4 (189): rs8. 6 September 2011

Tissue specific subnetworks and characteristics of publicly available human protein interaction databases.
Lopes, T.J., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.F., Neumann, G., Andrade-Navarro, M.A., Kawaoka, Y. and Kitano, H.
Bioinformatics 27 (17): 2414-2421. 1 September 2011

A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in caenorhabditis elegans.
Mansisidor, A.R., Cecere, G., Hoersch, S., Jensen, M.B., Kawli, T., Kennedy, L.M., Chavez, V., Tan, M.W., Lieb, J.D. and Grishok, A.
PLoS Genetics 7 (9): e1002299. September 2011

Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network.
Mah, N., Wang, Y., Liao, M.C., Prigione, A., Jozefczuk, J., Lichtner, B., Wolfrum, K., Haltmeier, M., Floettmann, M., Schaefer, M., Hahn, A., Mrowka, R., Klipp, E., Andrade-Navarro, M.A. and Adjaye, J.
PLoS ONE 6 (8): e24351. 31 August 2011

Genie: literature-based gene prioritization at multi genomic scale.
Fontaine, J.F., Priller, F., Barbosa-Silva, A. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (Suppl 2): W455-W461. July 2011

Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery.
Krzyzanowski, P.M., Price, F.D., Muro, E.M., Rudnicki, M.A. and Andrade-Navarro, M.A.
PLoS ONE 6 (6): e20561. 15 June 2011

Alterations of pre-mRNA splicing in human inflammatory bowel disease.
Haesler, R., Kerick, M., Mah, N., Hultschig, C., Richter, G., Bretz, F., Sina, C., Lehrach, H., Nietfeld, W., Schreiber, S. and Rosenstiel, P.
European Journal of Cell Biology 90 (6-7): 603-611. June 2011

Loss of Lrp2 in zebrafish disrupts pronephric tubular clearance but not forebrain development.
Kur, E., Christa, A., Veth, K.N., Gajera, C.R., Andrade-Navarro, M.A., Zhang, J., Willer, J.R., Gregg, R.G., Abdelilah-Seyfried, S., Bachmann, S., Link, B.A., Hammes, A. and Willnow, T.E.
Developmental Dynamics 240 (6): 1567-1577. June 2011

Aversion to nicotine is regulated by the balanced activity of beta4 and alpha5 nicotinic receptor subunits in the medial habenula.
Frahm, S., Slimak, M.A., Ferrarese, L., Santos-Torres, J., Antolin-Fontes, B., Auer, S., Filkin, S., Pons, S., Fontaine, J.F., Tsetlin, V., Maskos, U. and Ibanez-Tallon, I.
Neuron 70 (3): 522-535. 12 May 2011

QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards.
Fontaine, J.F., Suter, B. and Andrade-Navarro, M.A.
BMC Research Notes 4 (1): 57. 9 March 2011

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons.
Muro, E.M., Mah, N., Moreno-Hagelsieb, G. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (5): 1732-1738. 1 March 2011

Recognition of 2'-O-methylated 3'-end of piRNA by the PAZ domain of a piwi protein.
Simon, B., Kirkpatrick, J.P., Eckhardt, S., Reuter, M., Rocha, E.A., Andrade-Navarro, M.A., Sehr, P., Pillai, R.S. and Carlomagno, T.
Structure 19 (2): 172-180. 9 February 2011

2010

Pseudogenes as an alternative source of natural antisense transcripts.
Muro, E.M. and Andrade-Navarro, M.A.
BMC Evolutionary Biology 10 (1): 338. 3 November 2010

Highly aneuploid zebrafish malignant peripheral nerve sheath tumors have genetic alterations similar to human cancers.
Zhang, G., Hoersch, S., Amsterdam, A., Whittaker, C.A., Lees, J.A. and Hopkins, N.
Proceedings of the National Academy of Sciences of the United States of America 107 (39): 16940-16945. 28 September 2010

The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo.
Christ, A., Terryn, S., Schmidt, V., Christensen, E.I., Huska, M.R., Andrade-Navarro, M.A., Huebner, N., Devuyst, O., Hammes, A. and Willnow, T.E.
Kidney International 78 (5): 473-477. September 2010

Outer membrane pore protein prediction in mycobacteria using genomic comparison.
Mah, N., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
Microbiology 156 (Pt 8): 2506-2515. August 2010

Loss of fish actinotrichia proteins and the fin-to-limb transition.
Zhang, J., Wagh, P., Guay, D., Sanchez-Pulido, L., Padhi, B.K., Korzh, V., Andrade-Navarro, M.A. and Akimenko, M.A.
Nature 466 (7303): 234-237. 8 July 2010

A transcriptional roadmap to the induction of pluripotency in somatic cells.
Wang, Y., Mah, N., Prigione, A., Wolfrum, K., Andrade-Navarro, M.A. and Adjaye, J.
Stem Cell Reviews 6 (2): 282-296. June 2010

A reference guide for tree analysis and visualization.
Pavlopoulos, G.A., Soldatos, T.G., Barbosa-Silva, A. and Schneider, R.
BioData Mining 3 : 1. 22 February 2010

Armadillo motifs involved in vesicular transport.
Striegl, H., Andrade-Navarro, M.A. and Heinemann, U.
PLoS ONE 5 (2): e8991. 1 February 2010

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships.
Barbosa-Silva, A., Soldatos, T.G., Magalhaes, I.L., Pavlopoulos, G.A., Fontaine, J.F., Andrade-Navarro, M.A., Schneider, R. and Ortega, J.M.
BMC Bioinformatics 11 (1): 70. 1 February 2010

Periostin shows increased evolutionary plasticity in its alternatively spliced region.
Hoersch, S. and Andrade-Navarro, M.A.
BMC Evolutionary Biology 10 (1): 30. 28 January 2010

MLTrends: Graphing MEDLINE term usage over time.
Palidwor, G.A. and Andrade-Navarro, M.A.
Journal of Biomedical Discovery and Collaboration 5 : 1-6. 25 January 2010

Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing.
Scime, A., Desrosiers, J., Trensz, F., Palidwor, G.A., Caron, A.Z., Andrade-Navarro, M.A. and Grenier, G.
Mechanisms of Ageing and Development 131 (1): 9-20. January 2010

In silico screening for pathogenesis related-2 gene candidates in Vigna uguiculata transcriptome.
Wanderley-Nogueira, A.C., Da Mota Soares-Cavalcanti, N., Belarmino, L.C., Barbosa-Silva, A., Kido, E.A., Do Monte, S.J.H., Pandolfi, V., Calsa-Junior, T. and Benko-Iseppon, A.M.
Lecture Notes in Computer Science 6160 : 70-81. 2010

2009

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction.
Broeske, A.M., Vockentanz, L., Kharazi, S., Huska, M.R., Mancini, E., Scheller, M., Kuhl, C., Enns, A., Prinz, M., Jaenisch, R., Nerlov, C., Leutz, A., Andrade-Navarro, M.A., Jacobsen, S.E. and Rosenbauer, F.
Nature Genetics 41 (11): 1207-1215. November 2009

Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.
Fontaine, J.F., Mirebeau-Prunier, D., Raharijaona, M., Franc, B., Triau, S., Rodien, P., Goeau-Brissonniere, O., Karayan-Tapon, L., Mello, M., Houlgatte, R., Malthiery, Y. and Savagner, F.
PLoS ONE 4 (10): e7632. 29 October 2009

Linking genes to diseases: it's all in the data.
Tiffin, N., Andrade-Navarro, M.A. and Perez-Iratxeta, C.
Genome Medicine 1 (8): 77. 7 August 2009

Mitochondrial vesicles: an ancient process providing new links to peroxisomes.
Andrade-Navarro, M.A., Sanchez-Pulido, L. and McBride, H.M.
Current Opinion in Cell Biology 21 (4): 560-567. August 2009

Death-associated protein 3 is overexpressed in human thyroid oncocytic tumours.
Jacques, C., Fontaine, J.F., Franc, B., Mirebeau-Prunier, D., Triau, S., Savagner, F. and Malthiery, Y.
British Journal of Cancer 101 (1): 132-138. 7 July 2009

MedlineRanker: flexible ranking of biomedical literature.
Fontaine, J.F., Barbosa-Silva, A., Schaefer, M., Huska, M.R., Muro, E.M. and Andrade-Navarro, M.A.
Nucleic Acids Research 37 (Web Server Issue): W141-W146. 1 July 2009

Detection of alpha-rod protein repeats using a neural network and application to huntingtin.
Palidwor, G.A., Shcherbinin, S., Huska, M.R., Rasko, T., Stelzl, U., Arumughan, A., Foulle, R., Porras, P., Sanchez-Pulido, L., Wanker, E.E. and Andrade-Navarro, M.A.
PLoS Computational Biology 5 (3): e1000304. 13 March 2009

Recent developments in StemBase: a tool to study gene expression in human and murine stem cells.
Sandie, R., Palidwor, G.A., Huska, M.R., Porter, C.J., Krzyzanowski, P.M., Muro, E.M., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
BMC Research Notes 2 (1): 39. 10 March 2009

Use of SNP-arrays for ChIP assays: computational aspects.
Muro, E.M., McCann, J.A., Rudnicki, M.A. and Andrade-Navarro, M.A.
Methods in Molecular Biology 567 : 145-154. 2009

2008

Identification of gene 3' ends by automated EST cluster analysis.
Muro, E.M., Herrington, R., Janmohamed, S., Frelin, C., Andrade-Navarro, M.A. and Iscove, N.N.
Proceedings of the National Academy of Sciences of the United States of America 105 (51): 20286-20290. 23 December 2008

Identification of outer membrane proteins of Mycobacterium tuberculosis.
Song, H., Sandie, R., Wang, Y., Andrade-Navarro, M.A. and Niederweis, M.
Tuberculosis 88 (6): 526-544. November 2008

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. and Ramesar, R.
Physiological Genomics 35 (1): 55-64. 17 September 2008

Genes to diseases (G2D) computational method to identify asthma candidate genes.
Tremblay, K., Lemire, M., Potvin, C., Tremblay, A., Hunninghake, G.M., Raby, B.A., Hudson, T.J., Perez-Iratxeta, C., Andrade-Navarro, M.A. and Laprise, C.
PLoS ONE 3 (8): e2907. 6 August 2008

K2D2: Estimation of protein secondary structure from circular dichroism spectra.
Perez-Iratxeta, C. and Andrade-Navarro, M.A.
BMC Structural Biology 8 (1): 25. 13 May 2008

Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers.
Neuspiel, M., Schauss, A.C., Braschi, E., Zunino, R., Rippstein, P., Rachubinski, R.A., Andrade-Navarro, M.A. and McBride, H.M.
Current Biology 18 (2): 102-108. 22 January 2008

A customized class of functions for modeling and clustering gene expression profiles in embryonic stem cells.
Li, S., Andrade-Navarro, M. and Sankoff, D.
Lecture Notes in Computer Science 5167 : 92-103. 2008

2007

Towards completion of the Earth's proteome.
Perez-Iratxeta, C., Palidwor, G. and Andrade-Navarro, M.A.
EMBO Reports 8 (12): 1135-1141. 1 December 2007

The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily.
Sanchez-Pulido, L. and Andrade-Navarro, M.A.
BMC Biochemistry 8 : 23. 8 November 2007

Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Perez-Iratxeta, C., Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 35 (Web Server Issue): W212-W216. July 2007

StemBase: a resource for the analysis of stem cell gene expression data.
Porter, C.J., Palidwor, G.A., Sandie, R., Krzyzanowski, P.M., Muro, E.M., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
Methods in Molecular Biology 407 : 137-148. 2007

2005

G2D: A tool for mining genes associated with disease.
Perez-Iratxeta, C., Wjst, M., Bork, P. and Andrade, M.A.
BMC Genetics 6 : 45. 22 August 2005

Systematic association of genes to phenotypes by genome and literature mining.
Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A. and Bork, P.
PLoS Biology 3 (5): e134. 5 April 2005

2004

Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J., Perez-Iratxeta, C., Bork, P., Thode, G. and Andrade-Navarro, M.A.
Bioinformatics 20 (13): 2084-2091. 1 January 2004

2003

Update on XplorMed: a web server for exploring scientific literature.
Perez-Iratxeta, C., Perez, A.J., Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 31 (13): 3866-3868. 1 July 2003

Information extraction from full text scientific articles: Where are the keywords?
Shah, P., Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
BMC Bioinformatics 4 (1): 20. 29 May 2003

2002

Association of genes to genetically inherited diseases using data mining.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Nature Genetics 31 (3): 316-319. July 2002

Computing fuzzy associations for the analysis of biological literature.
Perez-Iratxeta, C., Keer, H.S., Bork, P. and Andrade, M.A.
Biotechniques 32 (6): 1380-1385. June 2002

2001

Comparison of ARM and HEAT protein repeats.
Andrade, M.A., Petosa, C., O'Donoghue, S.I., Mueller, C.W. and Bork, P.
Journal of Molecular Biology 309 (1): 1-18. 1 January 2001

XplorMed: a tool for exploring MEDLINE abstracts.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Trends in Biochemical Sciences 26 (9): 573-575. 1 January 2001

2000

NAIL - Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L., Yuan, Y.P., Andrade, M.A. and Bork, P.
Bioinformatics 16 (7): 656-657. 1 July 2000

Automated extraction of information in molecular biology.
Andrade, M.A. and Bork, P.
FEBS Letters 476 (1-2): 12-17. 30 June 2000

1999

Automated genome sequence analysis and annotation.
Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C. and Sander, C.
Bioinformatics 15 (5): 391-412. May 1999

Position-specific annotation of protein function based on multiple homologs.
Andrade, M.A.
In: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) : Heidelberg, Germany, August 6 - 10, 1999. ISMB Conference Series ; 7 . AAAI Press, Menlo Park, Calif., 28-33. ISBN 1-57735-083-9 1 January 1999

1995

Heat repeats in Huntington's disease protein.
Andrade, M.A. and Bork, P.
Nature Genetics 11 (2): 115-116. 1 October 1995

Challenging times for bioinformatics.
Casari, G., Andrade, M.A., Bork, P., Daruvar, A., Ouzounis, C., Schneider, R., Tamames, J., Valencia, A. and Sander, C.
Nature 376 : 647-648. 1 January 1995