Publications by members of our group (2003-)

2017

Cerdá-Esteban N, Naumann H, Ruzittu S, Mah N, Pongrac IM, Cozzitorto C, Hommel A, Andrade-Navarro MA, Bonifacio E, Spagnoli FM. Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2. Nat Commun. 2017 Feb 13;8:14127. doi: 10.1038/ncomms14127.
28193997

Totzeck F, Andrade-Navarro MA, Mier P. The Protein Structure Context of PolyQ Regions. PLoS One. 2017 Jan 26;12(1):e0170801. doi: 10.1371/journal.pone.0170801.
28125688

Mier P, Alanis-Lobato G, Andrade-Navarro MA. Context characterization of amino acid homorepeats using evolution, position and order.
Proteins. 2017 Apr;85(4):709-719. doi: 10.1002/prot.25250. Epub 2017 Feb 6.
28097686

Mier P, Pérez-Pulido AJ, Reynaud EG, Andrade-Navarro MA. Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PLoS One. 2017 Jan 10;12(1):e0169750. doi: 10.1371/journal.pone.0169750.
28072865

Ibn-Salem J, Muro EM, Andrade-Navarro MA. Co-regulation of paralog genes in the three-dimensional chromatin architecture. Nucleic Acids Res. 2017 Jan 9;45(1):81-91. doi: 10.1093/nar/gkw813
27634932

Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH. HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985
27794551

2016

Mier P, Andrade-Navarro MA. dAPE: a web server to detect homorepeats and follow their evolution. Bioinformatics. 2016 Dec 28. pii: btw790. doi: 10.1093/bioinformatics/btw790
28031183

Alanis-Lobato G, Mier P, Andrade-Navarro MA. Manifold learning and maximum likelihood estimation for hyperbolic network embedding. Applied Network Science. 2016 1:10. doi: 10.1007/s41109-016-0013-0.

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M, Roignant JY. m(6)A modulates neuronal functions and sex determination in Drosophila. Nature. 2016 Nov 30. doi:10.1038/nature20568.
27919077

Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SC. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Res. 2016 Nov 29. pii: gkw1136.
27899671

Andrade-Navarro, MA, Fontaine JF. Gene set to Diseases (GS2D): disease enrichment analysis on human gene sets with literature data. Genomics and Computational Biology. 2016. 2(1), 33.

Mier P, Alanis-Lobato G, Andrade-Navarro MA. Protein-protein interactions can be predicted using coiled coil co-evolution patterns. J Theor Biol. 2016 Nov 7;412:198-203. doi: 10.1016/j.jtbi.2016.11.001.
27832945

Sanchez-Pulido L, Perez L, Kuhn S, Vernos I, Andrade-Navarro MA. The C-terminal domain of TPX2 is made of alpha-helical tandem repeats. BMC Struct Biol. 2016 Oct 26;16(1):17.
27782824

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. Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors. EMBO J. 2016 Aug 29. pii: e201693927. [Epub ahead of print]
27572462

Alanis-Lobato G, Mier P, Andrade-Navarro MA. Efficient embedding of complex networks to hyperbolic space via their Laplacian. Sci Rep. 2016 Jul 22;6:30108. doi: 10.1038/srep30108.
27445157

Petrakis S, Andrade-Navarro MA. Front Genet. Editorial: Protein Interaction Networks in Health and Disease. 2016 Jun 14;7:111. doi: 10.3389/fgene.2016.00111. eCollection 2016.
27379161

Mier P, Andrade-Navarro MA. CABRA: Cluster and Annotate Blast Results Algorithm. BMC Res Notes. 2016 Apr 30;9(1):253.
27129717

de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C. A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses. Genome Med. 2016 Mar 17;8(1):28. doi:10.1186/s13073-016-0280-5.
26988706

Mier P, Andrade-Navarro MA. FastaHerder2: four ways to research protein function and evolution with clustering and clustered databases. J Comput Biol. 2016 Apr;23(4):270-8. doi: 10.1089/cmb.2015.0191. Epub 2016 Feb 1.
26828375

Schmid F, Wang Q, Huska MR, Andrade-Navarro MA, Lemm M, Fichtner I, Dahlmann M, Kobelt D, Walther W, Smith J, Schlag PM, Stein U. SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival. Oncogene. 2016 Nov 17;35(46):5942-5952. doi: 10.1038/onc.2015.451. Epub 2015 Dec 21.
26686083

Alanis-Lobato G, Andrade-Navarro MA. Distance distribution between complex network nodes in hyperbolic space. Complex Systems. 2016. 25(3):223-236.

2015

Mier P, Andrade-Navarro MA, Pérez-Pulido AJ. OrthoFind facilitates the discovery of homologous and orthologous proteins. PLoS One. 2015 Dec 1;10(12):e0143906. doi: 10.1371/journal.pone.0143906.
26624019

Amrani KE, Stachelscheid H, Lekschas F, Kurtz A, Andrade-Navarro MA. MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. BMC Genomics. 2015 Aug 28;16:645. doi: 10.1186/s12864-015-1785-9.
26314578

Schaefer MH, Serrano L, Andrade-Navarro MA. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. Front Genet. 2015 Aug 4;6:260. doi: 10.3389/fgene.2015.00260. eCollection 2015.
26300911.

Cheng X, Yoshida H, Raoofi D, Saleh S, Alborzinia H, Wenke F, Goehring A, Reuter S, Mah N, Fuchs HR, Andrade-Navarro MA, Adjaye J, Gul S, Utikal J, Mrowka R, Wölfl S. Ethyl 2-((4-chlorophenyl)amino)thiazole-4-carboxylate and derivatives are potent inducers of Oct3/4. J Med Chem. 2015 Aug 13;58(15):5742-50. doi: 10.1021/acs.jmedchem.5b00226. Epub 2015 Jul 23.
26143659.

Wethmar K, Schulz J, Muro EM, Talyan S, Andrade-Navarro MA, Leutz A. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames. Oncogene. 2016 Mar 31;35(13):1736-42. doi: 10.1038/onc.2015.233. Epub 2015 Jun 22.
26096937.

Stroedicke M, Bounab Y, Strempel N, Klockmeier K, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F, Riechers SP, Russ J, Nicoletti C, Boeddrich A, Wiglenda T, Haenig C, Schnoegl S, Fournier D, Graham RK, Hayden MR, Sigrist S, Bates GP, Priller J, Andrade-Navarro MA, Futschik ME, Wanker EE. Systematic interaction network filtering identifies CRMP-1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Res. 2015 May;25(5):701-13. doi: 10.1101/gr.182444.114.
25908449.

Buschmann H, Dols J, Kopischke S, Peña EJ, Andrade-Navarro MA, Heinlein M, Szymanski DB, Zachgo S, Doonan JH, Lloyd CW. Arabidopsis KCBP interacts with AIR9 but stays in the cortical division zone throughout mitosis via its MyTH4-FERM domain. J Cell Sci. 2015 Jun 1;128(11):2033-46. doi: 10.1242/jcs.156570. Epub 2015 Apr 23.
25908862.

Cheng X, Dimou E, Alborzinia H, Wenke F, Goehring A, Reuter S, Mah N, Fuchs HR, Andrade-Navarro MA, Adjaye J, Gul S, Harms C, Utikal J, Klipp E, Mrowka R, Wölfl S. Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers. J Med Chem. 2015 Apr 21.
25898186.

Gebhardt ML, Mer AS, Andrade-Navarro MA. mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data. BMC Res Notes. 2015 Apr 16;8(1):157.
25889572.

Andrade-Navarro M, Perez-Iratxeta C. Text mining of biomedical literature: Doing well, but we could be doing better. Methods. 2015 Mar;74:1-2. doi:10.1016/j.ymeth.2015.01.014.
25703199.

Fontaine JF, Priller J, Spruth E, Perez-Iratxeta C, Andrade-Navarro MA. Assessment of curated phenotype mining in neuropsychiatric disorder literature. Methods. 2015 Mar;74:90-6. doi: 10.1016/j.ymeth.2014.11.022. Epub 2014 Dec 5.
25484337

Louis-Jeune, C., M.A. Andrade-Navarro and C. Perez-Iratxeta. 2015. FASTA Herder: a web application to trim protein sequence sets. ScienceOpen Research. 7:1-4.

2014

Shih J, Hodge R, Andrade-Navarro MA. Comparison of inter- and intraspecies variation in humans and fruit flies. Genomics Data. 2014 Nov 22;3:49-54. doi:10.1016/j.gdata.2014.11.010. eCollection 2015 Mar. 26484147

Gijón-Correas JA, Andrade-Navarro MA, Fontaine JF. Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W422-9. doi: 10.1093/nar/gku432. Epub 2014 May 16.
24838570

Gijón-Correas JA, Andrade-Navarro MA, Fontaine JF. Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W422-9. doi: 10.1093/nar/gku432. Epub 2014 May 16.
24838570

Voss FK, Ullrich F, Münch J, Lazarow K, Lutter D, Mah N, Andrade-Navarro MA, von Kries JP, Stauber T, Jentsch TJ. Identification of LRRC8 heteromers as an essential component of the Volume-Regulated Anion Channel VRAC. Science. 2014 May 9;344(6184):634-8. doi: 10.1126/science.1252826. Epub 2014 Apr 10.
24790029

Gebhardt ML, Reuter S, Mrowka R, Andrade-Navarro MA. Similarity in targets with REST points to neural and glioblastoma related miRNAs. Nucleic Acids Res. 2014 May 1;42(9):5436-46. doi: 10.1093/nar/gku231. Epub 2014 Apr 11.
24728992

Fehlker M, Huska MR, Jöns T, Andrade-Navarro MA, Kemmner W. Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma. BMC Cancer. 2014 Feb 5;14(1):64.
24495478

Norton, M., A. Cheuk-Him Ng, S. Baird, A. Dumoulin, T. Shutt, N. Mah, M.A. Andrade-Navarro, H.M. McBride, R.A. Screaton. 2014. Genome-wide RNAi screen identifies ROMO1 as an essential redox-dependent regulator of mitochondrial cristae dynamics. Science Signaling. Jan 28;7(310):ra10.
24473195

Bollen S, Leddin M, Andrade-Navarro MA, Mah N. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. Bioinformatics. 2014 May 15;30(10):1484-5. doi: 10.1093/bioinformatics/btu028. Epub 2014 Jan 21.
24451624

Stachelscheid H, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A. CellFinder: a cell data repository. Nucleic Acids Res. 2014 Jan 1;42(1):D950-8. doi: 10.1093/nar/gkt1264. Epub 2013 Dec 3.
24304896

Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A. uORFdb--a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Res. 2014 Jan 1;42(1):D60-7. doi: 10.1093/nar/gkt952. Epub 2013 Oct 24.
24163100

2013

Mer AS, Andrade-Navarro MA. A novel approach for protein subcellular location prediction using amino acid exposure. BMC Bioinformatics. 2013 Nov 28;14(1):342.
24283794

Fournier D, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Perez-Iratxeta C, Andrade-Navarro MA. Functional and genomic analyses of alpha-solenoid proteins. PLoS One. 2013 Nov 21;8(11):e79894. doi: 10.1371/journal.pone.0079894.
24278209

Andrade-Navarro MA, Kanji F, Palii CG, Brand M, Atkins H, Perez-Iratxeta C. A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations. BMC Biotechnol. 2013 Oct 3;13(1):80.
24090206

Vlassi M, Brauns K, Andrade-Navarro MA. Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a beta-solenoid structure. BMC Struct Biol. 2013 Oct 2;13(1):17.
24088384

Rodríguez-Seguel E, Mah N, Naumann H, Pongrac IM, Cerdá-Esteban N, Fontaine JF, Wang Y, Chen W, Andrade-Navarro MA, Spagnoli FM. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence. Genes Dev. 2013 Sep 1;27(17):1932-1946.
24013505

Seltmann S, Stachelscheid H, Damaschun A, Jansen L, Lekschas F, Fontaine JF, Nguyen-Dobinsky TN, Leser U, Kurtz A. CELDA - an ontology for the comprehensive representation of cells in complex systems. BMC Bioinformatics. 2013 Jul 17;14:228.
23865855

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil JY. Bio++: efficient, extensible libraries and tools for computational molecular evolution. Mol Biol Evol. 2013 May 21.
23699471

Schönheit J, Kuhl C, Gebhardt ML, Klett FF, Riemke P, Scheller M, Huang G, Naumann R, Leutz A, Stocking C, Priller J, Andrade-Navarro MA, Rosenbauer F. PU.1 Level-Directed Chromatin Structure Remodeling at the Irf8 Gene Drives Dendritic Cell Commitment. Cell Rep. 2013 May 30;3(5):1617-28. doi: 10.1016/j.celrep.2013.04.007. Epub 2013 Apr 25.
23623495

Neves M, Damaschun A, Mah N, Lekschas F, Seltmann S, Stachelscheid H, Fontaine JF, Kurtz A, Leser U. Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford). 2013 Apr 18;2013(0):bat020. Print 2013.
23599415

Jacques C, Guillotin D, Fontaine JF, Franc B, Mirebeau-Prunier D, Fleury A, Malthiery Y, Savagner F. DNA Microarray and miRNA Analyses Reinforce the Classification of Follicular Thyroid Tumors. J Clin Endocrinol Metab. 2013 May;98(5):E981-9.
23569218

Ortuño FM, Rojas I, Andrade-Navarro MA, Fontaine JF. Using cited references to improve the retrieval of related biomedical documents. BMC Bioinformatics. 2013 Mar 27;14(1):113.
23537461

Petrakis S, Schaefer MH, Wanker EE, Andrade-Navarro MA. Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners. Bioessays. 2013 Jun;35(6):503-7. doi: 10.1002/bies.201300001. Epub 2013 Mar 11.
23483542

Mirebeau-Prunier D, Le Pennec S, Jacques C, Fontaine JF, Gueguen N, Boutet-Bouzamondo N, Donnart A, Malthièry Y, Savagner F. Estrogen-Related Receptor Alpha Modulates Lactate Dehydrogenase Activity in Thyroid Tumors. PLoS ONE. 2013; 8(3):e58683.
doi:10.1371/journal.pone.0058683

Rousselle A, Qadri F, Leukel L, Yilmaz R, Fontaine JF, Sihn G, Bader M, Ahluwalia A, Duchene J. CXCL5 limits macrophage foam cell formation in atherosclerosis. J Clin Invest. 2013 Mar 1;123(3):1343-7.
23376791

Schaefer MH, Lopes TJ, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol. 2013 Jan;9(1):e1002860. doi: 10.1371/journal.pcbi.1002860. Epub 2013 Jan 3.
23300433

von Eichborn J, Dunkel M, Gohlke BO, Preissner SC, Hoffmann MF, Bauer JM, Armstrong JD, Schaefer MH, Andrade-Navarro MA, Le Novere N, Croning MD, Grant SG, van Nierop P, Smit AB, Preissner R. SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Res. 2013 Jan 1;41(D1):D834-D840. Epub 2012 Nov 11. [Epub ahead of print]
23143269

Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE. Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Res. 2013 Feb 1;41(3):1496-507. doi: 10.1093/nar/gks1329. Epub 2012 Dec 28. [Epub ahead of print]
23275563

2012

Andrade-Navarro MA. Mining the literature: new methods to exploit keyword profiles. Genome Med. 2012 Oct 30;4(10):81. [Epub ahead of print]
23114100

Andrade-Navarro MA, Palidwor GA, Perez-Iratxeta C. Peer2ref: a peer-reviewer finding web tool that uses author disambiguation. BioData Min. 2012 Sep 7;5(1):14. [Epub ahead of print]
22958760

Petrakis S, Raskó T, Russ J, Friedrich RP, Stroedicke M, Riechers SP, Muehlenberg K, Möller A, Reinhardt A, Vinayagam A, Schaefer MH, Boutros M, Tricoire H, Andrade-Navarro MA, Wanker EE. Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLoS Genet. 2012 Aug;8(8):e1002897. Epub 2012 Aug 16.
22916034

Krzyzanowski PM, Muro EM, Andrade-Navarro MA. Computational approaches to discovering noncoding RNA. Wiley Interdiscip Rev RNA. 2012 Jul;3(4):567-579. doi: 10.1002/wrna.1121. Epub 2012 May 3.
22555938

Fournier D, Luft FC, Bader M, Ganten D, Andrade-Navarro MA. Emergence and evolution of the renin-angiotensin-aldosterone system. J Mol Med (Berl). 2012 May;90(5):495-508. Epub 2012 Apr 14.
22527880

Herault O, Hope KJ, Deneault E, Mayotte N, Chagraoui J, Wilhelm BT, Cellot S, Sauvageau M, Andrade-Navarro MA, Hébert J, Sauvageau G. A role for GPx3 in activity of normal and leukemia stem cells. J Exp Med. 2012 May 7;209(5):895-901. Epub 2012 Apr 16.
22508837

Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. HIPPIE: integrating protein interaction networks with experiment based quality scores. PLoS One. 2012;7(2):e31826. Epub 2012 Feb 14.
22348130

Schaefer MH, Wanker EE, Andrade-Navarro MA. Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res. 2012 May 1;40(10):4273-87. Epub 2012 Jan 28.
22287626

McNeill B, Perez-Iratxeta C, Mazerolle C, Furimsky M, Mishina Y, Andrade-Navarro MA, Wallace VA. Comparative genomics identification of a novel set of temporally regulated hedgehog target genes in the retina. Mol Cell Neurosci. 2012 Mar;49(3):333-340. Epub 2012 Jan 16.
22281533

Louis-Jeune C, Andrade-Navarro MA, Perez-Iratxeta C. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins. 2012 Feb;80(2):374-381. Epub 2011 Sep 14.
22095872
doi:10.1002/prot.23188

2011

Donnard E, Barbosa-Silva A, Guedes RL, Fernandes GR, Velloso H, Kohn MJ, Andrade-Navarro MA, Ortega JM. Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics. 2011 Dec 22;12 Suppl 4:S3. Epub 2011 Dec 22.
22369103

Dohnt K, Sauer M, Müller M, Atallah K, Weidemann M, Gronemeyer P, Rasch D, Tielen P, Krull R. An in vitro urinary tract catheter system to investigate biofilm development in catheter-associated urinary tract infections. J Microbiol Methods. 2011 Dec;87(3):302-8. Epub 2011 Sep 10.
21939694

Posch MG, Waldmuller S, Müller M, Scheffold T, Fournier D, Andrade-Navarro MA, De Geeter B, Guillaumont S, Dauphin C, Yousseff D, Schmitt KR, Perrot A, Berger F, Hetzer R, Bouvagnet P, Ozcelik C. Cardiac Alpha-Myosin (MYH6) Is the Predominant Sarcomeric Disease Gene for Familial Atrial Septal Defects. PLoS One. 2011;6(12):e28872. Epub 2011 Dec 14.
22194935

Vaz C, Mer AS, Bhattacharya A, Ramaswamy R. MicroRNAs Modulate the Dynamics of the NF-?B Signaling Pathway. PLoS One. 2011;6(11):e27774. Epub 2011 Nov 17.
22114691

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 WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S3.
22151929

Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011 Nov 9;12(1):435
22070195

Muro EM, Mah N, Andrade-Navarro MA. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie. 2011 Nov;93(11):1916-21. Epub 2011 Jul 27.
21816204

Mah N, Wang Y, Liao MC, Prigione A, Jozefczuk J, Lichtner B, Wolfrum K, Haltmeier M, Flöttmann M, Schaefer M, Hahn A, Mrowka R, Klipp E, Andrade-Navarro MA, Adjaye J. Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network. PLoS One. 2011;6(8):e24351. Epub 2011 Aug 31.
21909390

Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE. A directed protein interaction network for investigating intracellular signal transduction. Sci Signal. 2011 Sep 6;4(189):rs8.
21900206

Lopes TJ, Schaefer M, Shoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y, Kitano H. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics. 2011 Sep 1;27(17):2414-2421. Epub 2011 Jul 28.
21798963

Fournier D, Andrade-Navarro MA. PDBpaint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics 2011 Sep 15;27(18):2605-6. Epub 2011 Jul 14.
21757464
doi:10.1093/bioinformatics/btr419

Krzyzanowski PM, Price FD, Muro EM, Rudnicki MA, Andrade-Navarro MA. 2011. Integration of EST data and predicted RNA secondary structures facilitates novel ncRNA discovery. PLoS One. 2011;6(6):e20561. Epub 2011 Jun 15.
21698286

Fontaine JF, Priller F, Barbosa-Silva A and Andrade-Navarro MA. Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res. 2011; 39:W455-W461.
21609954
doi:10.1093/nar/gkr246

Frahm S, Slimak MA, Ferrarese L, Santos-Torres J, Antolin-Fontes B, Auer S, Filkin S, Pons S, Fontaine JF, Tsetlin V, Maskos U, Ibañez-Tallon I. Aversion to Nicotine Is Regulated by the Balanced Activity of ß4 and a5 Nicotinic Receptor Subunits in the Medial Habenula. Neuron. 2011 May 12;70(3):522-535.
21555077

Kur E, Christa A, Veth KN, Gajera CR, Andrade-Navarro MA, Zhang J, Willer JR, Gregg RG, Abdelilah-Seyfried S, Bachmann S, Link BA, Hammes A, Willnow TE. Loss of Lrp2 in zebrafish disrupts pronephric tubular clearance but not forebrain development. Dev Dyn. 2011, 240(6):1567-1577.
21455927

Fontaine JF, Suter B and Andrade-Navarro MA. QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards. BMC Research Notes 2011, 4:57.
21388526

Simon, B., J.P. Kirkpatrick, S. Eckhardt, M. Reuter, E.A. Rocha, M.A. Andrade-Navarro, P. Sehr, R.S. Pillai, T. Carlomagno. 2011. Recognition of 2’-O-methylated 3’-end of piRNA by the PAZ domain of a piwi protein. Structure. 19(2):172-180.
21237665

Muro EM, Mah N, Moreno-Hagelsieb G, Andrade-Navarro MA. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Nucleic Acids Res. 2011, 39:1732-1738.
doi:10.1093/nar/gkq1067
21051341

2010

Muro EM, Andrade-Navarro MA. Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol. 2010 Nov 3;10(1):338.
doi:10.1186/1471-2148-10-338
21047404

Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko MA. Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature. 2010 Jul 8;466(7303):234-237.
20574421

Christ A, Terryn S, Schmidt V, Christensen EI, Huska MR, Andrade-Navarro MA, Hübner N, Devuyst O, Hammes A, Willnow TE. The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo. Kidney Int. 2010 Sep;78(5):473-477.
20531455

Mah N, Perez-Iratxeta C, Andrade-Navarro MA. Outer membrane pore protein prediction in mycobacteria using genomic comparison. Microbiology. 2010 Aug;156(Pt 8):2506-2515.
20466765

Wang Y, Mah N, Prigione A, Wolfrum K, Andrade-Navarro MA, Adjaye J. A Transcriptional Roadmap to the Induction of Pluripotency in Somatic Cells. Stem Cell Rev. 2010 Jun;6(2):282-296.
doi:10.1007/s12015-010-9137-2
20336394

Palidwor GA, Andrade-Navarro MA. MLTrends: Graphing MEDLINE term usage over time. J Biomed Discov Collab. 2010 Jan 25;5:1-6.
20333611

Pavlopoulos, G.A., Soldatos T.G., Barbosa-Silva, A., Schneider, R. (2010) A reference guide for tree analysis and visualization. BioData Mining. 3:1.
doi:10.1186/1756-0381-3-1

Striegl H, Andrade-Navarro MA, Heinemann U. Armadillo motifs involved in vesicular transport. PLoS One. 2010 Feb 1;5(2):e8991.
20126549

Barbosa-Silva, A., Soldatos TG, Magalhães, ILF, Pavlopoulos, GA, Fontaine, J.F., Andrade-Navarro, M.A., Schneider R., Ortega, JM. LAITOR: Literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics. 2010 Feb 1; 11(1):70.
20122157

Hoersch S, Andrade-Navarro MA. Periostin shows increased evolutionary plasticity in its alternatively spliced region. BMC Evol Biol. 2010 Jan 28;10(1):30.
20109226

Scimè, A., J. Desrosiers, F. Trensz, G.A. Palidwor, A.Z. Caron, M.A. Andrade-Navarro, G. Grenier. Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing. Mechanisms of Ageing and Development. 2010 Jan;131(1):9-20.
19913570

2009

Raharijaona M, Le Pennec S, Poirier J, Mirebeau-Prunier D, Rouxel C, Jacques C, Fontaine JF, Malthiery Y, Houlgatte R, Savagner F. PGC-1-Related Coactivator Modulates Mitochondrial-Nuclear Crosstalk through Endogenous Nitric Oxide in a Cellular Model of Oncocytic Thyroid Tumours. PLoS ONE. 2009; 4(11): e7964.
doi:10.1371/journal.pone.0007964

Fontaine JF, Mirebeau-Prunier D, Raharijaona M, Franc B, Triau S, Rodien P, Goëau-Brissonniére O, Karayan-Tapon L, Mello M, Houlgatte R, Malthièry Y and Savagner F. 2009. Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers. PLoS ONE 4(10): e7632. 19893615 doi:10.1371/journal.pone.0007632

Bröske AM, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M, Kuhl C, Enns A, Prinz M, Jaenisch R, Nerlov C, Leutz A, Andrade-Navarro MA, Jacobsen SE, Rosenbauer F. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009 Nov;41(11):1207-1215.
19801979

Tiffin N, Andrade-Navarro M.A., Perez-Iratxeta C. 2009. Linking genes to diseases: it's all in the data. Genome Med. 1:77.
19678910

Muro E.M., McCann J.A., Rudnicki M.A., Andrade-Navarro M.A. 2009. Use of SNP-Arrays for ChIP Assays: Computational Aspects. Methods Mol Biol. 567:145-154.
19588091

Jacques, C., Fontaine, J.-F., Franc, B., Mirebeau, D., Triau, S., Savagner, F., Malthiery, Y. 2009. Death-associated protein 3 is overexpressed in human thyroid oncocytic tumors. British Journal of Cancer. 101:132-138.
19536094 doi:10.1038/sj.bjc.6605111

Palidwor, G.A., S. Shcherbinin, M.R. Huska, T. Rasko, U. Stelzl, A. Arumughan, R. Foulle, P. Porras, L. Sanchez-Pulido, E.E. Wanker, M.A. Andrade-Navarro. 2009. Detection of alpha-rod repeats using a neural network and application to huntingtin. PLoS Comp. Biol. 37:W141-146.
19282972

Häsler R, Begun A, Freitag-Wolf S, Kerick M, Mah N, Zvirbliene A, Spehlmann ME, von Wurmb-Schwark N, Kupcinskas L, Rosenstiel P, Schreiber S. 2009. Genetic control of global gene expression levels in the intestinal mucosa - a human twin study. Physiol Genomics. 38:73-79
19276242

Andrade-Navarro, M.A., L. Sanchez-Pulido and H.M. McBride. 2009. Mitochondrial vesicles: an ancient process providing new links to peroxisomes. Current Opinion in Cell Biology. 21:560-567.
19423315

Fontaine, J.F., A. Barbosa-Silva, M. Schaefer, M.R. Huska, E.M. Muro and M.A. Andrade-Navarro. 2009. MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res. 2009, 37: W141-W146.
19429696 doi:10.1093/nar/gkp353

Sandie, R., G.A. Palidwor, M.R. Huska, C.J. Porter, P.M. Krzyzanowski, E.M. Muro, C. Perez-Iratxeta, M.A. Andrade-Navarro. 2009. Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. BMC Research Notes. 2, 39.
19284540

2008

Fernandes G.R., Barbosa D.V., Prosdocimi F., Pena I.A., Santana-Santos L., Coelho Junior O., Barbosa-Silva A., Velloso H.M., Mudado M.A., Natale D.A., Faria-Campos A.C., Aguiar S.C., Ortega J.M. 2008. A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model. Genet Mol Res. 7:910-924.
18949709 http://www.funpecrp.com.br/gmr/year2008/vol7-3/pdf/X-Meeting008.pdf

Barbosa-Silva, A., Satagopam, V. P., Schneider, R., Ortega, J. M. 2008. Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. BMC Bioinformatics 9:141.
18949709 doi:10.1186/1471-2105-9-141

Muro, E.M., R. Herrington, S. Janmohamed, C. Frelin, M.A. Andrade-Navarro, and N.N. Iscove. 2008. Targeting probes to gene 3’-ends by automated EST cluster analysis. Proc. Natl. Acad. Sci. 150:20286-20290.
19095794 doi:10.1073/pnas.0807813105

Fontaine JF, Mirebeau-Prunier D, Franc B, Triau S, Rodien P, Houlgatte R, Malthièry Y, Savagner F.  Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy. Oncogene. 2008 Apr 3;27(15):2228-36.
17968324 doi:10.1038/sj.onc.1210853

Neuspiel, M., A.C. Schauss, E. Braschi, R. Zunino, P. Rippstein, R.A. Rachubinski, M.A. Andrade-Navarro and H.M. McBride. 2007. Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers. Current Biology. 18, 102-108.
18207745 doi:10.1016/j.cub.2007.12.038

Perez-Iratxeta, C. and M.A. Andrade-Navarro. 2008. K2D2: Estimation of protein secondary structure from CD spectra. BMC Structural Biology. 8:25.
18477405 doi:10.1186/1472-6807-8-25

Song, H., Sandie, R., Y. Wang, S. Sukumaran, M.A. Andrade-Navarro and M. Niederweis. 2008. Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuberculosis. 88:526-544.
18439872 doi:10.1016/j.tube.2008.02.004

Tiffin, N., I. Okpechi, C. Perez-Iratxeta, M.A. Andrade-Navarro, R. Ramesar. 2008. Prioritisation of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypes. Physiological Genomics. 35:55-64.
18612082 doi:10.1152/physiolgenomics.90247.2008

Tremblay, K., M. Lemire, C. Potvin, A. Tremblay, G.M., Hunninghake, B.A. Raby, T.J. Hudson, C. Perez-Iratxeta, M.A. Andrade-Navarro and C. Laprise. 2008. Genes to Diseases (G2D) computational method to identify asthma candidate genes. PLoS ONE. 3:e2907.
18682798 doi:10.1371/journal.pone.0002907

2007

Barbosa-Silva, A., Ortega, J. M., Pafilis, E., Schneider, R. (2007) Development of SRS.php, a SOAP-based library for data acquisition from integrated biological databases. Genetics And Molecular Research 6(4):1142-1150.
18273808 http://www.funpecrp.com.br/gmr/year2007/vol4-6/pdf/gmr387.pdf

Wanderley-Nogueira, A., Soares-Cavalcanti, N. M., Morais, D. A. L., Belarmino, L. C., Barbosa-Silva, A., Benko-Iseppon, A. M. (2007) Abundance and Diversity of Resistance (R) Genes in the Sugarcane Transcriptome Revealed by In Silico Analysis. Genetics And Molecular Research 6 (4): 866-889.
18058709 http://www.funpecrp.com.br/gmr/year2007/vol4-6/pdf/Xm0009.pdf

Grenier G, Scimè A, Le Grand F, Asakura A, Perez-Iratxeta C, Andrade-Navarro MA, Labosky PA, Rudnicki MA. Resident endothelial precursors in muscle, adipose, and dermis contribute to postnatal vasculogenesis. Stem cells (Dayton, Ohio), 2007 Dec 17;25(12):3101-10.
17823241 doi:10.1634/stemcells.2006-0795

Huska MR, Buschmann H, Andrade-Navarro MA. BiasViz: visualization of amino acid biased regions in protein alignments. Bioinformatics (Oxford, England), 2007 Nov 20;23(22):3093-4.
17921493 doi:10.1093/bioinformatics/btm489

Sanchez-Pulido L, Andrade-Navarro MA. The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. BMC biochemistry, 2007 Nov 08;8:23.
17996046 doi:10.1186/1471-2091-8-23

Perez-Iratxeta C, Palidwor G, Andrade-Navarro MA. Towards completion of the Earth's proteome. EMBO reports, 2007 Oct 15;8(12):1135-41.
18059312 doi:10.1038/sj.embor.7401117

Krzyzanowski PM, Andrade-Navarro MA. Identification of novel stem cell markers using gap analysis of gene expression data. Genome biology, 2007 Sep 17;8(9):R193.
17875203 doi:10.1186/gb-2007-8-9-r193

McCann JA, Muro EM, Palmer C, Palidwor G, Porter CJ, Andrade-Navarro MA, Rudnicki MA. ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation. BMC genomics, 2007 Sep 14;8:322.
17868463 doi:10.1186/1471-2164-8-322

Perez-Iratxeta C, Bork P, Andrade-Navarro MA. Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Res. 2007 Jul 16;35(Web Server issue):W212-6.
17478516 doi:10.1093/nar/gkm223

Campbell PA, Perez-Iratxeta C, Andrade-Navarro MA, Rudnicki MA. Oct4 targets regulatory nodes to modulate stem cell function. PLoS ONE, 2007 May 24;2(6):e553.
17579724 doi:10.1371/journal.pone.0000553

Perez-Iratxeta C, Andrade-Navarro MA, Wren JD. Evolving research trends in bioinformatics. Briefings in bioinformatics, 2007 Apr 25;8(2):88-95.
17077138 doi:10.1093/bib/bbl035

Schwarz M, Andrade-Navarro MA, Gross A. Mitochondrial carriers and pores: key regulators of the mitochondrial apoptotic program? Apoptosis : an international journal on programmed cell death, 2007 Apr 24;12(5):869-76.
17453157 doi:10.1007/s10495-007-0748-2

Hailesellasse Sene K, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA. Gene function in early mouse embryonic stem cell differentiation. BMC genomics, 2007 Mar 29;8:85.
17394647 doi:10.1186/1471-2164-8-85

Zunino R, Schauss A, Rippstein P, Andrade-Navarro M, McBride HM. The SUMO protease SENP5 is required to maintain mitochondrial morphology and function. Journal of cell science, 2007 Mar 22;120(Pt 7):1178-88.
17341580 doi:10.1242/jcs.03418

Buschmann H, Sanchez-Pulido L, Andrade-Navarro MA, Lloyd CW. Homologues of Arabidopsis Microtubule-Associated AIR9 in Trypanosomatid Parasites: Hints on Evolution and Function. 2007. Plant Signal Behav. 2:296-299. 19704687

Kulkarni G, Turbin DA, Amiri A, Jeganathan S, Andrade-Navarro MA, Wu TD, Huntsman DG, Lee JM. Expression of protein elongation factor eEF1A2 predicts favorable outcome in breast cancer. Breast cancer research and treatment, 2007 Jun 18;102(1):31-41.
16897428 doi:10.1007/s10549-006-9315-8

2006

Nascimento, D.G., Rates, B., Santos, D.M., Barbosa-Silva, A., Verano-Braga, T., Dutra, A.A.A., Biondi, I., Martin-Eauclaire, M.F., De lima, M.A., Pimenta, A.M.C. (2006) Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones). Toxicon 47(6):628-39.
16551474 doi:10.1016/j.toxicon.2006.01.015

Cestari, I. C., Haver, N. J., Barbosa-Silva, A., Ramirez, M. I. (2006) PROTOGIM: A novel tool to search motifs and domains in hypothetical proteins of protozoan genomes. Parasitology Research 98(4):375-377.
16362340 doi:10.1007/s00436-005-0064-0

Bonnet S, Archer SL, Allalunis-Turner J, Haromy A, Beaulieu C, Thompson R, Lee CT, Lopaschuk GD, Puttagunta L, Bonnet S, Harry G, Hashimoto K, Porter CJ, Andrade MA, Thebaud B, Michelakis ED. A mitochondria-K+ channel axis is suppressed in cancer and its normalization promotes apoptosis and inhibits cancer growth. Cancer cell, 2006 Oct 18;11(1):37-51.
17222789 doi:10.1016/j.ccr.2006.10.020

Buschmann H, Chan J, Sanchez-Pulido L, Andrade-Navarro MA, Doonan JH, Lloyd CW. Microtubule-associated AIR9 recognizes the cortical division site at preprophase and cell-plate insertion. Current biology : CB, 2006 Aug 04;16(19):1938-43.
17027491 doi:10.1016/j.cub.2006.08.028

Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res. 2006 Jun 07;34(10):3067-81.
16757574 doi:10.1093/nar/gkl381

Bonnet S, Michelakis ED, Porter CJ, Andrade-Navarro MA, Thébaud B, Bonnet S, Haromy A, Harry G, Moudgil R, McMurtry MS, Weir EK, Archer SL. An abnormal mitochondrial-hypoxia inducible factor-1alpha-Kv channel pathway disrupts oxygen sensing and triggers pulmonary arterial hypertension in fawn hooded rats: similarities to human pulmonary arterial hypertension. Circulation, 2006 Jun 06;113(22):2630-41.
16735674 doi:10.1161/CIRCULATIONAHA.105.609008

Baldwin RM, Garratt-Lalonde M, Parolin DA, Krzyzanowski PM, Andrade MA, Lorimer IA. Protection of glioblastoma cells from cisplatin cytotoxicity via protein kinase Ciota-mediated attenuation of p38 MAP kinase signaling. Oncogene, 2006 May 11;25(20):2909-19.
16331246 doi:10.1038/sj.onc.1209312

Muro EM, Perez-Iratxeta C, Andrade-Navarro MA. Amplification of the Gene Ontology annotation of Affymetrix probe sets. BMC bioinformatics, 2006 Mar 20;7:159.
16549014 doi:10.1186/1471-2105-7-159

Palidwor G, Reynaud EG, Andrade-Navarro MA. Taxonomic colouring of phylogenetic trees of protein sequences. BMC bioinformatics, 2006 Feb 17;7:79.
16503967 doi:10.1186/1471-2105-7-79

2005

Barbosa-da-Silva, A., Wanderley-Nogueira, A. C., Silva, R. M. R., Berlarmino, L. C., Soares-Cavalcanti, N. M., Benko-Iseppon, A. M. (2005) In silico survey of resistance (R) genes in Eucalyptus transcriptome. Genetics And Molecular Biology 28(3):562-574.
doi:10.1590/S1415-47572005000400011

Reynaud EG, Andrade MA, Bonneau F, Ly TB, Knop M, Scheffzek K, Pepperkok R. Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization. BMC biology, 2005 Oct 07;3:21.
16209721 doi:10.1186/1741-7007-3-21

Perez-Iratxeta C, Wjst M, Bork P, Andrade MA. G2D: a tool for mining genes associated with disease. BMC genetics, 2005 Aug 22;6:45.
16115313 doi:10.1186/1471-2156-6-45

Lambert A, Legendre M, Fontaine JF, Gautheret D. Computing expectation values for RNA motifs using discrete convolutions. BMC Bioinformatics. 2005 May 13;6:118.
15892887 doi:10.1186/1471-2105-6-118

Perez-Iratxeta C, Andrade MA. Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. BMC bioinformatics, 2005 Jul 20;6:183.
16033654 doi:10.1186/1471-2105-6-183

Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sánchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM. The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. The Journal of biological chemistry, 2005 May 09;280(19):19213-20.
15701634 doi:10.1074/jbc.M414421200

Suomela BP, Andrade MA. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC bioinformatics, 2005 Mar 24;6:75.
15790421 doi:10.1186/1471-2105-6-75

Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA, Rudnicki MA, Andrade MA. Study of stem cell function using microarray experiments. FEBS letters, 2005 Feb 10;579(8):1795-801.
15763554 doi:10.1016/j.febslet.2005.02.020

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. PLoS biology, 2005 Feb 02;3(5):e134.
15799710 doi:10.1371/journal.pbio.0030134

Sanchez-Pulido L, Rojas AM, Valencia A, Martinez-A C, Andrade MA. ACRATA: a novel electron transfer domain associated to apoptosis and cancer. BMC cancer, 2005 Jan 28;4:98.
15623366 doi:10.1186/1471-2407-4-98

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. Costello CM, Mah N, Häsler R, Rosenstiel P, Waetzig GH, Hahn A, Lu T, Gurbuz Y, Nikolaus S, Albrecht M, Hampe J, Lucius R, Klöppel G, Eickhoff H, Lehrach H, Lengauer T, Schreiber S. PLoS Med. 2005 Aug;2(8):e199. Epub 2005 Aug 23.
PubMed: 16107186

2004

Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics (Oxford, England), 2004 Aug 31;20(13):2084-91.
15059832 doi:10.1093/bioinformatics/bth207

Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D.  The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W160-5.
15215371 doi:10.1093/nar/gkh418

Doerks T, Andrade MA, Lathe W, von Mering C, Bork P. Global analysis of bacterial transcription factors to predict cellular target processes. Trends in genetics : TIG, 2004 Mar 29;20(3):126-31.
15049306

Mah N, Thelin A, Lu T, Nikolaus S, Kühbacher T, Gurbuz Y, Eickhoff H, Klöppel G, Lehrach H, Mellgård B, Costello CM, Schreiber S. A comparison of oligonucleotide and cDNA-based microarray systems. 2004. Physiol Genomics. 16:361-370.
14645736

2003

Netzel R, Perez-Iratxeta C, Bork P, Andrade MA. The way we write. EMBO reports, 2003 May 02;4(5):446-451.
12728240 doi:10.1038/sj.embor.embor833

Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (Oxford, England), 2003 Apr 14;19(6):717-26.
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