The titles of older publications are linked to Google Scholar. The [>] symbols link to more information about this and related publications. The PubMed numbers link to PubMed. Associated web resources are also linked.
2024
Mac Donagh, J., A. Marchesini, A. Spiga, M.J. Fallico, P.N. Arrías, A.M. Monzon, A.C. Vagiona, M. Gonçalves-Kulik, P. Mier and M.A. Andrade-Navarro. 2024. Structured tandem repeats in protein interactions. Int. J. Mol. Sci. 25, 2994. [>] 38474241
2023
Anyaegbunam, U.A., P. More, J.F. Fontaine, V. ten Cate, K. Bauer, U. Distler, E. Araldi, L. Bindila, P. Wild and M.A. Andrade-Navarro. A systematic review of lipid-focused cardiovascular disease research: trends and opportunities. Curr. Issues Mol. Biol. 45, 9904-9916. [>] 38132464
Gkekas, I., A.C. Vagiona, N. Pechlivanis, G. Kastrinaki, K. Pliatsika, S. Iben, K. Xanthopoulos, F.E. Psomopoulos, M.A. Andrade-Navarro and S. Petrakis. 2023. Intranuclear inclusions of polyQ-expanded ATXN1 sequester RNA molecules. Frontiers in Mol. Neurosci. 16, 1280546. [>] 38125008
Mier, P. and M.A. Andrade-Navarro. 2023. The nucleotide landscape of polyXY regions. Comp. Struct. Biotech. J. 21, 5408-5412. [>] 38022702
Aspromonte, M.C., M.V. Nugnes, F. Quaglia, A. Bouharoua, DisProt Consortium*, S.C.E. Tosatto, D. Piovesan. 2023. DisProt in 2024: improving function annotation of intrinsically disordered proteins. Nucl. Acids Res. gkad928. *Disprot Consortium = V. Sagris, V. Promponas, A. Chasapi, E. Fichó, G.E. Balatti, G. Parisi, M. González Buitrón, G. Erdos, M. Pajkos, Z. Dosztányi, L. Dobson, A. Del Conte, D. Clementel, E. Salladini, E. Leonardi, F. Kordevani, H. Ghafouri, L.G. Tenorio Ku, A.M. Monzon, C. Ferrari, Z. Kálmán, J. Nilsson, J. Santos, C. Pintado-Grima, S. Ventura, V. Ács, R. Pancsa, M.G. Kulik, M.A. Andrade-Navarro, P.J.B. Pereira, S. Longhi, P. Le Mercier, J. Bergier, P. Tompa, T. Lazar. [>] 37904585
Elena Real, C.A., P. Mier, N. Sibille, M.A. Andrade-Navarro and P. Bernadó. 2023. The structure-function relationship in protein homorepeats. Curr. Op. Struct. Biol. 83, 102726. [>] 37924569
Llorián-Salvador, O., J. Akhgar, S. Pigorsch, K. Borm, S. Münch, D. Bernhardt, B. Rost, M.A. Andrade-Navarro, S.E. Combs, J.C. Peeken. 2023. The importance of planning CT-based imaging features for machine learning-based prediction of pain response. Sci. Rep. 13, 17427. [>] 37833283
Zahra N., A.C. Vagiona, R. Uddin and M.A. Andrade-Navarro. 2023. Selection of multi-drug targets against drug-resistant Mycobacterium tuberculosis XDR1219 using the hyperbolic mapping of the protein interaction network. Int. J. Mol. Sci. 24, 14050. [>] 37762354
Monzon, A.M., P.N. Arrías, A. Elofsson, P. Mier, M.A. Andrade-Navarro, M. Bevilacqua, D. Clementel, A. Bateman, L. Hirsh, M.S. Fornasari, G. Parisi, D. Piovesan, A.V. Kajava, S.C.E. Tosatto. 2023. A STRP-ed definition of Structured Tandem Repeats in Proteins. J. Struct. Biol. 215, 108023. [>] 37652396
Gonçalves-Kulik, M., F. Schmid and M.A. Andrade-Navarro. 2023. One step closer to the understanding of the relationship IDR-LCR-structure. Genes. 14, 1711. [>] 37761851
Mier, P. and M.A. Andrade-Navarro. 2023. Evolutionary study of protein short tandem repeats in protein families. Biomolecules. 13, 1116. [>] 37509152
ten Cate, V., S. Rapp, A. Schulz, A. Pallares Robles, K. Jurk, T. Koeck, C. Espinola-Klein, M. Halank, H.J. Seyfarth, M.E. Beutel, A.K. Schuster, F. Marini, L. Hobohm, M. Lankeit, K.J. Lackner, W. Ruf, T. Münzel, M.A. Andrade-Navarro, J.H. Prochaska, S.V. Konstantinides, P.S. Wild. 2023. Circulating microRNAs predict recurrence and death following venous thromboembolism. J. Thromb. Haemost. 21, 2797-2810. [>] 37481073
Schumbera, E., Mier, P. and M.A. Andrade-Navarro. 2023. Phase separating Rho: a widespread regulatory function of disordered regions in proteins revealed in bacteria. Signal Transduct. Target. Ther. 8, 253. [>] 37344523
Kang, H., K. Taškova, N. Wang, L.N. van Oosten, R. Mrowka, J. Utikal, M.A. Andrade-Navarro, J. Wang, S. Wölfl, J. Zhou and X. Cheng. 2023. Development of a next-generation endogenous OCT4 inducer and its anti-aging effect in vivo. Eur. J. Med. Chem. 257, 115513. [>] 37253308
Erdozain, S., E. Barrionuevo, L. Ripoll, P. Mier and M.A. Andrade-Navarro. 2023. Protein repeats evolve and emerge in giant viruses. J. Struct. Biol. 215, 107962. [>] 37031868
Krolevets, M., V. ten Cate, J.H. Prochaska, A. Schulz, S. Rapp, S. Tenzer, M.A. Andrade-Navarro, S. Horvath, C. Niehrs and P.S. Wild. 2023. DNA methylation and cardiovascular disease in humans: a systematic review and database of known CpG methylation sites. Clin. Epigenetics. 15, 56. [>] 36991458
Fan, W., J. Jurado-Arjona, G. Alanis-Lobato, S. Péron, C. Berger, M.A. Andrade-Navarro, S. Falk and B. Berninger. 2023. The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation. EMBO J. 42, e110384. [>] 37083045
Foreman, S.C., O. Llorian-Salvador, D.E. David, V.K.N. Rösner, J.F. Rischewski, G.C. Feuerriegel, D.W. Kramp, I. Luiken, A.K. Lohse, J. Kiefer, C. Mogler, C. Knebel, M. Jung, M.A. Andrade-Navarro, B. Rost, S.E. Combs, M.R. Makowski, K. Woertler, J.C. Peeken, A.S. Gersing. 2023. Development and evaluation of MR-based radiogenomic models to differentiate atypical lipomatous tumors from lipomas. Cancers. 15, 2150. [>] 37046811
Rubio, A., Sprang, M., A. Garzón, A. Moreno-Rodriguez, M.E. Pachón-Ibáñez, J. Pachón, M.A. Andrade-Navarro and A.J. Pérez-Pulido. 2023. Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems. Science Advances. 9, eadd8911. [>] 36961900
Nagel-Wolfrum, K., B.R. Fadl, M.M. Becker, K.A. Wunderlich, J. Schäfer, D. Sturm, J. Fritze, B. Gür, L. Kaplan, T. Andreani, T. Goldmann, M. Brooks, M.R. Starostik, A. Lokhande, M. Apel, K.R. Fath, K. Stingl, S. Kohl, M.M. DeAngelis, U. Schlötzer-Schrehardt, I.K. Kim, L.A. Owen, J.M. Vetter, N. Pfeiffer, M.A. Andrade-Navarro, A. Grosche, A. Swaroop and U. Wolfrum. 2023. Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy. Hum. Mol. Gen. 32, 431-449. [>] 35997788
2022
Kastano, K., P. Mier, Z. Dosztanyi, V.J. Promponas and M.A. Andrade-Navarro. 2022. Functional tuning of intrinsically disordered regions in human proteins by composition bias. Biomolecules. 12, 1486. [>] 36291695
Mier, P. and M.A. Andrade-Navarro. 2022. Regions with two amino acids in protein sequences: a step forward from homorepeats into the low complexity landscape. Comp. Struct. Biotechnol. J. 20, 5516-5523. [>] 36249567
Mier, P., C. Elena-Real, J. Cortés, P. Bernadó and M.A. Andrade-Navarro. 2022. The sequence context in poly-Alanine regions: Structure, function and conservation. Bioinformatics. 38, 4851-4858. [>] 36106994
Gonçalves-Kulik, M., P. Mier, K. Kastano, J. Cortés, P. Bernadó, F. Schmid and M.A. Andrade-Navarro. 2022. Low complexity induces structure in protein regions predicted as intrinsically disordered. Biomolecules. 12, 1098. [>] 36008992
Pallares Robles, A., V. ten Cate, A. Schulz, J.H. Prochaska, S. Rapp, T. Koeck, M. Panova-Noeva, S. Heitmeier, S. Schwers, K. Leineweber, H.J. Seyfarth, C.F. Opitz, H. Spronk, C. Espinola-Klein, K.J. Lackner, T. Münzel, M.A. Andrade-Navarro, S.V. Konstantinides, H. ten Cate and P.S. Wild. 2022. Association of FXI activity with thrombo-inflammation, extracellular matrix, lipid metabolism and apoptosis in venous thrombosis. Sci. Rep. 12, 9761. [>] 35697739
Albrecht, S., T. Andreani, M.A. Andrade-Navarro and J.F. Fontaine. 2022. Single-cell specific and interpretable machine learning models for sparse ChIP-seq data imputation. PLOS ONE. 17, e0270043. [>] 35776722
Cihan, M. and M.A. Andrade-Navarro. 2022. Detection of features predictive of microRNA targets by integration of network data. PLOS ONE. 17, e0269731. [>] 35679295
Vagiona, A.C., P. Mier, S. Petrakis and M.A. Andrade-Navarro. 2022. Analysis of Huntington’s disease modifiers using the hyperbolic mapping of the protein interaction network. Int. J. Mol. Sci. 23, 5853. [>] 35628660
Mier, P., J.F. Fontaine, M. Stoldt, R. Libbrecht, C. Martelli, S. Foitzik and M.A. Andrade-Navarro. 2022. Annotation and analysis of 3,902 odorant receptor protein sequences from 21 insect species provides insights into the evolution of odorant receptor gene families in solitary and social insects. Genes. 13, 919. [>] [iOrME] 35627304
Sprang, M., M.A. Andrade-Navarro and J.F. Fontaine. 2022. Batch effect detection and correction in RNA-Seq data using machine-learning-based automated assessment of quality. BMC Bioinformatics. 23, 279. [>] [seqQscorer] 35836114
Mier, P. and M.A. Andrade-Navarro. 2022. PolyX2: fast detection of homorepeats in large protein datasets. Genes. 13, 758. [PolyX2] [>] 35627143
Czeh, M., S. Stäble, S. Krämer, S. Talyan, J. Carrelha, Y. Meng, B. Heitplatz, M. Schwabenland, L. Tepe, M.D. Milsom, C. Plass, M. Prinz, M. Schlesner, M.A. Andrade-Navarro, C. Nerlov, S.E.W. Jacobsen, D.B. Lipka and F. Rosenbauer. 2022. DNMT1 deficiency impacts on plasmacytoid dendritic cells in homeostasis and autoimmune disease. J. Immunology. 208, 358-370. [>] 34903641
2021
Mier, P. and M.A. Andrade-Navarro. 2021. Between interactions and aggregates: the polyQ balance. Genome Biology and Evolution. 13, evab246. [>] 34791220
Sprang, M., M. Krüger, M.A. Andrade-Navarro, J.F. Fontaine. 2021. Statistical guidelines for quality control of next-generation sequencing techniques. Life Science Alliance. 4, e202101113. [>] 34462322
More, P., L. Bindila, P. Wild, M.A. Andrade-Navarro, J.F. Fontaine. 2021. LipiDisease: associate lipids to diseases using literature mining. Bioinformatics. 6, btab559. [>] [LipiDisease] 34358314
Andrade, M. 2021. Faculty Opinions Recommendation of [Nakanishi M et al., Cell 2019 177(4):910-924.e22]. In Faculty Opinions, 08 Jul 2021; 10.3410/f.735530268.793586598 [>]
Koch, I., M. Andrade-Navarro, M. Schulz and K. Zarnack. 2021. Bioinformatics in Theory and Application – highlights of the 36th German Conference on Bioinformatics. Biol Chem. 402, 869-870. [>] 34192830
Talyan, S., M.A. Andrade-Navarro and E.M. Muro. 2021. A methodology to study pseudogenized lincRNAs. Methods Mol. Biol. 2324, 49-63. [>] 34165708
Ten Cate, V., T. Koeck, J.H. Prochaska, A. Schulz, M. Panova-Noeva, S. Rapp, L. Eggebrecht, M. Lenz, J. Glunz, M. Sauer, R. Ewert, M. Halank, T. Münzel, S. Heitmeier, M.A. Andrade-Navarro, K.J. Lackner, S.V. Konstantinides, K. Leineweber, P.S. Wild. 2021. A targeted proteomics investigation of the obesity paradox in venous thromboembolism. Blood Advances. 402, 945-951 [>] 34309635
More, P., S. Talyan, J.F. Fontaine, E.M. Muro and M.A. Andrade-Navarro. 2021. DiseaseLinc: disease enrichment analysis of sets of differentially expressed lincRNAs. Cells. 10, 751. [>] [DiseaseLinc] 33805436
Mier, P. and M.A. Andrade-Navarro. 2021. The conservation of low complexity regions in bacterial proteins depends on the pathogenicity of the strain and subcellular location of the protein. Genes. 12, 451. [>] 33809982
Kamel, M., K. Kastano, P. Mier and M.A. Andrade-Navarro. 2021. REP2: a web server to detect common tandem repeats in protein sequences. J. Mol. Biol. 433, 166895 [>] [REP2] 33972020
Mier, P. and M.A. Andrade-Navarro. 2021. Avoided Motifs: short amino acid strings missing from protein datasets. Biological Chemistry. 402, 945-951. [>] 33660494
Albrecht, S., M. Sprang, M.A. Andrade-Navarro and J.F. Fontaine. 2021. seqQscorer: automated quality control of next generation sequencing data using machine learning. Genome Biology. 22, 75. [>] 33673854 [seqQscorer]
Kastano, K., P. Mier and M.A. Andrade-Navarro. 2021. The role of low complexity regions in protein interaction modes: an illustration in Huntingtin. Int. J. Mol. Sci. 22, 1727. [>] 33572172
Schulz, J., N. Mah, M. Neuenschwander, T. Kischka, R. Ratei, P.M. Schlag, E. Castaños- Vélez, I. Fichtner, P.U. Tunn, C. Denkert, O. Klaas, W.E. Berdel, J.P. von Kries, W. Makalowski, M.A. Andrade-Navarro, A. Leutz and K. Wethmar. Author Correction: Loss- of-function uORF mutations in human malignancies. Sci Rep. 2021. 11:2917. Erratum for: Sci Rep. 2018. 8, 2395. [>] 33510296
Paladin, L., M. Bevilacqua, S. Errigo, D. Piovesan, I. Mičetić, M. Necci, A.M. Monzon, M.L. Fabre, J.L. Lopez, J.F. Nilsson, J. Rios, P. Lorenzano Menna, M. Cabrera, M. Gonzalez Buitron, M. Gonçalves Kulik, S. Fernandez-Alberti, M.S. Fornasari, G. Parisi, A. Lagares, L. Hirsh, M.A. Andrade-Navarro, A.V. Kajava and S.C.E. Tosatto. 2021. RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. Nucl. Acids Res. 49, D452-D457. [>] 33237313
Ten Cate, V., J.H. Prochaska, A. Schulz, T. Koeck, A. Pallares Robles, M. Lenz, L. Eggebrecht, S. Rapp, M. Panova-Noeva, H.A. Ghofrani, F.J. Meyer, C. Espinola-Klein, K.J. Lackner, M. Michal, A.K. Schuster, K. Strauch, A.M. Zink, V. Laux, S. Heitmeier, S.V. Konstantinides, T. Münzel, M.A. Andrade-Navarro, K. Leineweber and P.S. Wild. 2021. Protein expression profiling suggests relevance of noncanonical pathways in isolated pulmonary embolism. Blood. 137, 2681-2693 [>] 33529319
2020
Andrade, M. 2020. Faculty Opinions Recommendation of [Babu MM, Biochem Soc Trans 2016 44(5):1185-1200]. In Faculty Opinions, 03 Mar 2020; doi:10.3410/f.727061031.793571694 [>]
Lenz, M., A. Schulz, T. Koeck, S. Rapp, M. Nagler, M. Sauer, L. Eggebrecht, V. Ten Cate, M. Panova-Noeva, J.H. Prochaska, K.J. Lackner, T. Münzel, K. Leineweber, P.S. Wild and M.A. Andrade-Navarro. 2020. Missing value imputation in proximity extension assay-based targeted proteomics data. PLOS ONE. 15, e0243487. [>] 33315883
Andrade-Navarro, M.A., K, Muehlenberg, E. Spruth, N. Mah, A. González-López, T. Andreani, J. Russ, M.R. Huska, E.M. Muro, J.F. Fontaine, V. Amstislavskiy, A. Soldatov, W. Nietfeld, E.E. Wanker and J. Priller. 2020. RNA sequencing of human peripheral blood cells indicates upregulation of immune-related genes in Huntington’s disease. Frontiers in Neurology. 11, 573560. [>] 33329316
Kastano, K., G. Erdős, P. Mier, G. Alanis-Lobato, V.J. Promponas, Z. Dosztányi and M.A. Andrade-Navarro. 2020. Evolutionary study of disorder in protein sequences. Biomolecules. 10, 1403. [>] 33036302
Vagiona, A.C., S. Sgardelis, M.A. Andrade-Navarro, F. Psomopoulos and S. Petrakis. 2020. Dynamics of a protein interaction network associated to the aggregation of polyQ-expanded ataxin-1. Genes. 11, E1129. [>] 32992839
Rubio, A., P. Mier, M.A. Andrade-Navarro, A. Garzón, J. Jiménez and A.J. Pérez-Pulido. 2020. CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. Database. 2020, baaa088. [>] 33206958
Mier, P. and M.A. Andrade-Navarro. 2020. Assessing the low complexity of protein sequences via the low complexity triangle. PLOS ONE. 15, e0239154. [>] [LCT] 33378336
Paladin, L., M. Necci, D. Piovesan, P. Mier, M.A. Andrade-Navarro and S.C.E. Tosatto. 2020. A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication. J. Struc Biol. 212, 107608. [>] 32896658
Haenig, C., N. Atias, A.K. Taylor, A. Mazza, M.H. Schaefer, J. Russ, S.P. Riechers, S. Jain, M. Coughlin, J.F. Fontaine, B.D. Freibaum, L. Brusendorf, M. Zenkner, M. Stroedicke, S. Schnoegl, K. Arnsburg, A. Boeddrich, P. Heutink, J.P. Taylor, J. Kirstein, M.A. Andrade-Navarro, R. Sharan, E.E. Wanker. 2020. Interactome mapping provides a network of neurodegenerative disease proteins and uncovers widespread protein aggregation in affected brains. Cell Reports. 32, 108050. [>] 32814053
Mier, P. and M.A. Andrade-Navarro. 2020. The features of polyglutamine regions depend on their evolutionary stability. BMC Evol. Biol. 20, 59. [>] 32448113
Alanis-Lobato, G., J.S. Möllmann, M.H. Schaefer and M.A. Andrade-Navarro. 2020. MIPPIE: the mouse integrated protein-protein interaction reference. Database. 2020, baaa035 [>] [MIPPIE] 32496562
Jarnot, P., J. Ziemska-Legiecka, L. Dobson, M. Merski, P. Mier, M.A. Andrade-Navarro, J.M. Hancock, Z. Dosztányi, L. Paladin, M. Necci, D. Piovesan, S.C.E. Tosatto, V.J. Promponas, M. Grynberg and A. Gruca. 2020. PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Research. 48, W77-W84. [>] [PlaToLoCo] 32421769
Urbanek A., M. Popovic, A. Morató, A. Estaña, C.A. Elena-Real, P. Mier, A. Fournet, F. Allemand, S. Delbecq, M.A. Andrade-Navarro, J. Cortés, N. Sibille and P. Bernadó. 2020. Flanking regions determine the structure of the poly-glutamine homo-repeat in huntingtin through mechanisms common amongst glutamine-rich human proteins. Structure. 28, 733-746.e5. [>] 32402249
Leismann, J., M. Spagnuolo, L. Wacheul, M. Pradhan, M.A. Vu, M. Musheev, P. Mier, M.A. Andrade-Navarro, M. Graille, C. Niehrs, D.L.J. Lafontaine and J.Y. Roignant. 2020. The 18S ribosomal RNA m6A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Reports. 21, e49443. [>] 32350990
Mier, P. and M.A. Andrade-Navarro. 2020. MAGA: a supervised method to detect motifs from annotated groups in alignments. Evolutionary Bioinformatics. 16, 1-4. [>] [MAGA] 32425492
Andreani, T., S. Albrecht, J.F. Fontaine and M.A. Andrade-Navarro. 2020. Computational identification of cell-specific variable regions in ChIP-seq data. Nucleic Acids Research. 48, e53. [>] 32187374
Laidou, S., G. Alanis-Lobato, J. Pribyl, T. Raskó, B. Tichy, K. Mikulasek, M. Tsagiopoulou, J. Oppelt, G. Kastrinaki, M. Lefaki, M. Singh, A. Zink, N. Chondrogianni, F. Psomopoulos, A. Prigione, Z. Ivics, S. Pospisilova, P. Skladal, Z. Izsvak, M.A. Andrade-Navarro and S. Petrakis. 2020. Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biology. 32, 101458. [>] 32145456
Dallago, C., T. Goldberg, M.A. Andrade-Navarro, G. Alanis-Lobato and B. Rost. 2020. Visualizing human protein-protein interactions and subcellular localizations on cell images through CellMap. Current Protocols in Bioinformatics. 69, e97. [>] 32150354
Mier, P., C. Elena-Real, A. Urbanek, P. Bernadó and M.A. Andrade-Navarro. 2020. The importance of definitions in the study of polyQ regions: a tale of thresholds, impurities and sequence context. Comput. Struct. Biotechnol. Journal. 18, 306-313. [>] [sQanner] 32071707
Cheng, X., I.L. Shytaj, S. Haberle, R. Gama-Brambila, J. Theobald, S. Ghaffory, J. Wölker, K. Taškova, A.S. Bauer, J.D. Hoheisel, N. Tsopoulidis, O.T. Fackler, A. Savarino, M.A. Andrade-Navarro, I. Ott, M. Lusic, E. Hadaschik and S. Wölfl. 2020. NHC-gold compounds mediate immune suppression through induction of AHR-TGFβ1 signalling in vitro and in scurfy mice. Communications Biology. 3, 10. [>] 31909202
Burkhardt, S., J. Siekiera, J. Glodde, M.A. Andrade-Navarro and S. Kramer. 2020. Towards identifying drug side effects from social media using active learning and crowd sourcing. Pac. Symp. Biocomput. 25, 319-330. [>] 31797607
Hogan, J.D., J.L. Keenan, L. Luo, J. Ibn-Salem, A. Lamba, D. Schatzberg, M.L. Piacentino, D.T. Zuch, A.B. Core, C. Blumberg, B. Timmermann, J.H. Grau, E. Speranza, M.A. Andrade-Navarro, N. Irie, A.J. Poustka and C.A. Bradham. 2020. The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev. Biol. 460, 139-154. [>] 31816285
Mier, P., L. Paladin, S. Tamana, S. Petrosian, B. Hajdu-Soltész, A. Urbanek, A. Gruca, D. Plewczynski, M. Grynberg, P. Bernadó, Z. Gáspári, C. Ouzounis, V.J. Promponas, A.V. Kajava, J.M. Hancock, S. Tosatto, Z. Dosztanyi, and M.A. Andrade-Navarro. 2020. Disentangling the complexity of low complexity proteins. Briefings in Bioinformatics. 21, 458-472. [>] 30698641
2019
Muro, E.M., J. Ibn-Salem and M.A. Andrade-Navarro. 2019. The distributions of protein coding genes within chromatin domains in relation to human disease. Epigenetics and Chromatin. 12, 72. [>] 31805995
Geiß, C., G. Alanis-Lobato, M.A. Andrade-Navarro and A. Régnier-Vigouroux. 2019. Assessing the reliability of gene expression measurements in very-low-numbers of human monocyte-derived macrophages. Scientific Reports. 9, 17908. [>] 31784632
Chen, H., C. Lareau, T. Andreani, M.E. Vinyard, S.P. Garcia, K. Clement, M.A. Andrade-Navarro, J.D. Buenrostro and L. Pinello. 2019. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biology. 20, 241. [>] 31739806
Tørresen, O.K., B. Star, P. Mier, M.A. Andrade-Navarro, A. Bateman, P. Jarnot, A. Gruca, M. Grynberg, A. Kajava, V. Promponas, M. Asinimova, K.S. Jakobsen and D. Linke. 2019. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res. 47, 10994-11006. [>] 31584084
Ibn-Salem, J. and M.A. Andrade-Navarro. 2019. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. BMC Genomics. 20, 777. [>] 31653198
Kamel, M., P. Mier, A. Tari and M.A. Andrade-Navarro. 2019. Repeatability in protein sequences. Journal of Structural Biology. 208, 86-91. [>] [RES] 31408700
Akhtar, J., P. More, S. Albrecht, F. Marini, W. Kaiser, A. Kulkarni, L. Wojnowski, J.F. Fontaine, M.A. Andrade-Navarro, M. Silies, C. Berger. 2019. TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay. Life Science Alliance. 2, e201900318. [>] 31331983
More, P., U. Goedtel-Armbrust, V. Shah, M. Mathaes, T. Kindler, M.A. Andrade-Navarro and L. Wojnowski. 2019. Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells. Oncotarget. 10, 5298-5312. [>] 31523390
El Amrani, K., G. Alanis-Lobato, N. Mah, A. Kurtz and M.A. Andrade-Navarro. 2019. Detection of condition-specific marker genes from RNA-seq data with MGFR. PeerJ. 7, e6970. [>] [MGFR] 31179178
Mier, P. and M.A. Andrade-Navarro. 2019. Toward completion of the Earth’s proteome: an update a decade later. Briefings in Bioinformatics. 20, 463-470. [>] 29040399
Almeida, M.V., M.A. Andrade-Navarro and R.F. Ketting. 2019. Function and evolution of nematode RNAi pathways. Non-coding RNA. 5, 8. [>] 30650636
Taškova, K., J.F. Fontaine, R. Mrowka and M.A. Andrade-Navarro. 2019. Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets. PLOS ONE. 14, e0210467. [>] 30640953
Dabiri, Y., R.A. Gama-Brambila, K. Taškova, K. Herold, S. Reuter, J. Adjaye, J. Utikal, R. Mrowka, J. Wang, M.A. Andrade-Navarro and X. Cheng. 2019. Imidazopyridines as potent KDM5 demethylase inhibitors promoting reprogramming efficiency of human induced pluripotent stem cells. iScience. 12, 168-181. [>] 30685712
Scheuermann, B., T. Djem, Z. Ivics and M.A. Andrade-Navarro. 2019. Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty. Sci. Reports. 9, 1171. [>] 30718656
Mier, P. and M.A. Andrade-Navarro. 2019. Traitpedia: a collaborative effort to gather species traits. Bioinformatics. 35, 1079-1081. [>] [Traitpedia] 30165582
Rubio, A., C.S. Casimiro-Soriguer, P. Mier, M.A. Andrade-Navarro, A. Garzón, J. Jiménez and A.J. Pérez-Pulido. 2019. AnABlast, re-searching for protein-coding sequences in genomic regions. Methods Mol. Biol. 1962, 207-214. [>] 31020562
Boeddrich A., J.T. Tachu, T. Wiglenda, L. Diez, M. Jacob, W. Nietfeld, M.R. Huska, C. Haenig, N. Groenke, A. Buntru, E. Blanc, J.C. Meier, E. Vannoni, C. Erck, B. Friedrich, H. Martens, N. Neuendorf, S. Schnoegl, D.P. Wolfer, M. Loos, D. Beule, M.A. Andrade-Navarro and E.E. Wanker. 2019. The anti-amyloid compound DO1 decreases plaque pathology and neuroinfammation-related expression changes in 5xFAD transgenic mice. Cell Chem. Biol. 26,109-120 [>] 30472115
2018
Mier, P., A.J. Pérez-Pulido and M.A. Andrade-Navarro. 2018. Automated selection of homologs to track the evolutionary history of proteins. BMC Bioinformatics. 19, 431. [>] [ProteinPathTracker] 30453878
Krefting, J., M.A. Andrade-Navarro and J. Ibn-Salem. 2018. Evolutionary stability of topologically associating domains is associated with conserved gene regulation. BMC Biology. 16, 87. [>] 30086749
Talyan, S, M.A. Andrade-Navarro and E.M. Muro. 2018. Identification of transcribed protein coding sequence remnants within lincRNAs. Nucleic Acids Research. 46, 8720-8729. [>] 29986053
Härtner, F., M.A. Andrade-Navarro and G. Alanis-Lobato. 2018. Geometric characterisation of disease modules. Applied Network Science. 3, 10. [>] 30839777
Alanis-Lobato, G., P. Mier and M.A. Andrade-Navarro. 2018. The latent geometry of the human protein interaction network. Bioinformatics. 34, 2826-2834. [GAPI] [>] 29635317
Dallago, C., T. Goldberg, M.A. Andrade-Navarro, G. Alanis-Lobato and B. Rost. 2018. CellMap visualizes protein-protein interactions and subcellular localization. F1000Research. 6, 1824. [CellMap] [>] 29497493
Mier, P. and M.A. Andrade. 2018. Glutamine codon usage and polyQ evolution in primates depend on the Q stretch length. Genome Biology and Evolution. 10, 816-825. [>] 29608721
Knuckles, P., T. Lence, I. Haussman, D. Jacob, N. Kreim, S.H. Carl, I. Masiello, T. Hares, R. Villaseñor, D. Hess, M.A. Andrade-Navarro, M. Biggiogera, M. Helm, M. Soller, M. Bühler and J.Y. Roignant. 2018. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes and Development. 32, 415-429. [>] 29535189
Brüne, D., M.A. Andrade-Navarro and P. Mier. 2018. Proteome-wide comparison between the amino acid composition of protein domains and linkers. BMC Research Notes. 11, 117. [>] 29426365
Schulz, J., N. Mah, M. Neuenschwander, T. Kischka, R. Ratei, P.M. Schlag, E. Castaños-Vélez, I. Fichtner, P.U. Tunn, C. Denkert, O. Klaas, W.E. Berdel, J.P. von Kries, W. Makalowski, M.A. Andrade-Navarro, A. Leutz and K. Wethmar. 2018. Loss-of-function uORF mutations in human malignancies. Scientific Reports. 8, 2395. [>] 29402903
Theobald, J., A. Ghanem, P. Wallisch, A. Banaeiyan, M.A. Andrade-Navarro, K. Taskova, M. Haltmeier, A. Kurtz, H. Becker, S. Reuter, R. Mrowka, X. Cheng and S. Wölfl. 2018. Liver-kidney-on-chip to study toxicity of drug metabolites. ACS Biomaterials Science & Engineering. 4, 78-89. [>]
Taškova, K., J.F. Fontaine, R. Mrowka and M.A. Andrade-Navarro. 2018. Evaluation of in vivo and in vitro models of toxicity by comparison of toxicogenomics data with the literature. Methods. 132, 57-65. [>] 28716510
2017
Hildebrandt, A., G. Alanis-Lobato, K. Zarnack, M.A. Andrade-Navarro, P. Beli and J. König. 2017. Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Scientific Reports. 7, 16582. [>] 29185492
Corwin, T., J. Woodsmith, F. Apelt, J.F. Fontaine, D. Meierhofer, J. Helmuth, A. Grossmann, M.A. Andrade-Navarro, B.A. Ballif and U. Stelzl. 2017. Defining human tyrosine kinase phosphorylation networks using yeast as an in vivo model substrate. Cell Systems. 5, 128-139. [>] 28837810
Zepeda-Mendoza, C.J., J. Ibn-Salem, T. Kammin, D.J. Harris, C. Redin, H. Brand. D. Rita, K.W. Gripp, J.J. Mackenzie, A. Gropman, B. Graham, R. Shaheen, F.S. Alkuraya, C.K. Brasington, E.J. Spence, D. Masser-Frye, L.M. Bird, E. Spiegel, R.L. Sparkes, Z. Ordulu, M.E. Talkowski, M.A. Andrade-Navarro, P.N. Robinson, C.C. Morton. 2017. Computational prediction of position effects of apparently balanced human chromosome rearrangements. Am. J. Hum. Genetics. 101, 206-217. [>] 28735859
Jung, S., V. Espinosa Angarica, M.A. Andrade-Navarro, N.J. Buckley, A. del Sol. 2017. Prediction of chromatin accessibility in gene-regulatory regions from transcriptomics data. Scientific Reports. 7, 4660 [>] 28680085
Cerdá-Esteban, N., H. Naumann, S. Ruzittu, N. Mah, I.M. Pongrac, C. Cozzicorto, A. Hommel, M.A. Andrade-Navarro, E. Bonifacio, F.M. Spagnoli. 2017. Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2. Nature Communications. 8, 14127. [>] 28193997
Totzeck, F., M.A. Andrade-Navarro and P. Mier. 2017. The protein structure context of polyQ regions. PLOS ONE. 12, e0170801. [>] 28125688
Mier, P., G. Alanis-Lobato and M.A. Andrade-Navarro. 2017. Context characterization of amino acid homorepeats using evolution, position and order. Proteins. 85, 709-719. [>] 28097686
Mier, P., A.J. Pérez-Pulido, E.G. Reynaud and M.A. Andrade-Navarro. 2017. Reading the evolution of compartmentalization in the ribosome assembly toolbox: the YRG protein family. PLOS ONE. 12, e0169750. [>] 28072865
Ibn-Salem, J., E.M. Muro and M.A. Andrade-Navarro. 2017. Co-regulation of paralog genes in the three-dimensional chromatin architecture. Nucleic Acids Research. 45, 81-91. [>] 27634932
Alanis-Lobato, G., M.A. Andrade-Navarro, M. Schaefer. 2017. HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Research. 45, D408-D414. [HIPPIE] [>] 27794551
Mier, P., G. Alanis-Lobato and M.A. Andrade-Navarro. 2017. Protein-protein interactions can be predicted using coiled coil co-evolution patterns. Journal of Theoretical Biology. 412, 198-203. [>] 27832945
Mier, P. and M.A. Andrade-Navarro. 2017. dAPE: a web server to detect homorepeats and follow their evolution. Bioinformatics. 33, 1221-1223. [dAPE] [>] 28031183
Paladin, L., L. Hirsch, D. Piovesan, M.A. Andrade-Navarro, A.V. Kajava and Silvio C.E. Tosatto. 2017. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Research. 45, 3613. [RepeatsDB] [>] 27899671
2016
Alanis-Lobato, G., P. Mier, M.A. Andrade-Navarro. 2016. Manifold learning and maximum likelihood estimation for hyperbolic network embedding. Applied Network Science. 1, 10. [>] 30533502
Lence, T., J. Akhtar, M. Bayer, K. Schmid, L. Spindler, C. Hei Ho, N. Kreim, M.A. Andrade-Navarro, B. Poeck, M. Helm and J.Y. Roignant. 2016. m6A modulates neuronal functions and sex determination in Drosophila. Nature. 540, 242-247. [>] 27919077
Sanchez-Pulido, L., L.H. Perez, S. Kuhn, I. Vernos and M.A. Andrade-Navarro. 2016. The C-terminal domain of TPX2 is made of alpha-helical tandem repeats. BMC Structural Biology. 16, 17. [>] 27782824
Andrade-Navarro, M.A. and J.F. Fontaine. 2016. Gene set to Diseases (GS2D): disease enrichment analysis on human gene sets with literature data. Genomics and Computational Biology. 2, 33. [GeneSet2Diseases] [>]
Riemke, P., M. Czeh, M. Fischer, C. Walter, S. Ghani, M. Zepper, K. Agelopoulos, S. Lettermann, M.L. Gebhardt, N. Mah, A. Weilemann, M. Grau, V. Gröning, T. Haferlach, D. Lenze, R. Delwel, M. Prinz, M.A. Andrade-Navarro, G. Lenz, M. Dugas, C. Müller-Tidow and F. Rosenbauer. 2016. Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors. EMBO Journal. 35, 2399-2416. [>] 27572462
Alanis-Lobato, G.A., P. Mier and M.A. Andrade-Navarro. 2016. Efficient embedding of complex networks to hyperbolic space via the spectral decomposition of their Laplacian. Scientific Reports. 6, 30108. [>] 27445157
Petrakis, S. and M.A. Andrade-Navarro. 2016. Editorial: Protein interaction networks in health and disease. Frontiers in Genetics. 7, 111. [Frontiers eBook] [>] 27379161
Alanis-Lobato, G, and M.A. Andrade-Navarro. 2016. Distance distribution between complex network nodes in hyperbolic space. Complex Systems. 25, 223-236. [>]
Mier, P. and M.A. Andrade-Navarro. 2016. CABRA: cluster and annotate BLAST results algorithm. BMC Research Notes. 9, 253. [CABRA] [>] 27129717
de Oliveira, K.A.P., E. Kaergel, M. Heinig, J.F. Fontaine, G. Patone, E.M. Muro, S. Mathas, M. Hummel, M.A. Andrade-Navarro, N. Hübner, and C. Scheidereit. 2016. A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: dominant roles of p50 and p52 revealed by genome-wide analyses. Genome Medicine. 8, 28. [>] 26988706
Mier, P. and M.A. Andrade-Navarro. 2016. FastaHerder2: four ways to research protein function and evolution with clustering and clustered databases. J. Comp. Biol. 23, 270-278. [FastaHerder2] [>] 26828375
Wethmar, K., J. Schultz, E.M. Muro, S. Talyan, M.A. Andrade-Navarro and A. Leutz. 2016. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames (uORFs). Oncogene. 35, 1736-1742. [>] 26096937
Schmid, F., Q. Wang, M.R. Huska, M.A. Andrade-Navarro, M. Lemm, I. Fichtner, M. Dahlmann, D. Kobelt, W. Walther, J. Smith, P.M. Schlag and U. Stein. 2016. SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival. Oncogene. 35, 5942-5952. [>] 26686083
2015
Mier, P., M.A. Andrade-Navarro and A.J. Pérez-Pulido. 2015. OrthoFind facilitates the discovery of homologous and orthologous proteins. PLOS ONE. 10, e0143906. [orthoFind] [>] 26624019
Schaefer, M.H., L. Serrano and M.A. Andrade-Navarro. 2015. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions in different cancer types. Frontiers in Genetics. 6, 260. [>] 26300911
Cheng, X., H. Yoshida, D. Raoofi, S. Saleh, H. Alborzinia, F. Wenke, A. Göhring, S. Reuter, N. Mah, H. Fuchs, M.A. Andrade-Navarro, J. Adjaye, S. Gul, J. Utikal, R. Mrowka and S. Wölfl. 2015. Ethyl 2-((4-chlorophenyl)amino)thiazole-4-carboxylate and derivatives are potent inducers of Oct3/4. J. Med. Chem. 58, 5742-5750. [>] 26143659
El Amrani, K., H. Stachelscheid, F. Lekschas, A. Kurtz and M.A. Andrade-Navarro. 2015. MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. BMC Genomics. 16, 645. [Marker Tool] [>] 26314578
Stroedicke, M., Y. Bounab, N. Strempel, S. Yigit, R.P. Friedrich, G. Chaurasia, S. Li, F. Hesse, S.P. Riechers, J. Russ, C. Nicoletti, C. Haenig, S. Schnoegl, D. Fournier, R.K. Graham, M.R. Hayden, S. Sigrist, G.P. Bates, J. Priller, M.A. Andrade-Navarro, M.E. Futschik and E.E. Wanker. 2015. Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Research. 25, 701-713. [>] 25908449
Cheng, X., E. Dimou, H. Alborzinia, F. Wenke, A. Göhring, S. Reuter, N. Mah, H.R. Fuchs, M.A. Andrade-Navarro, J. Adjaye, S. Gul, C. Harms, J. Utikal, E. Klipp, R. Mrowka and S. Wölfl. 2015. Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers. J. Med. Chem. 58, 4976-4983. [>] 25898186
Buschmann, H., J. Dols, S. Kopischke, E.J. Peña, M.A. Andrade-Navarro, S. Zachgo, D.B. Szymanski, M. Heinlein, J.H. Doonan and C.W. Lloyd. 2015. Arabidopsis KCBP interacts with AIR9 but stays in the cortical division zone throughout mitosis via its MyTH4-FERM domain. Journal of Cell Science. 128, 2033-2046. [>] 25908862
Gebhardt, M.L., A.S. Mer and M.A. Andrade-Navarro. 2015. mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data. BMC Research Notes. 8, 157. [mBISON] [>] 25889572
Andrade-Navarro, M. and C. Perez-Iratxeta. 2015. Text mining of biomedical literature: doing well, but we could be doing better. Methods. 74, 1-2. [>] 25703199
Fontaine, J.F., J. Priller, E. Spruth, C. Perez-Iratxeta and M.A. Andrade-Navarro. 2015. Assessment of curated phenotype mining in neuropsychiatric disorder literature. Methods. 74, 90-96 [>] 25484337
Shih, J., R. Hodge and M.A. Andrade-Navarro. 2015. Comparison of inter and intraspecies variation in humans and fruit flies. Genomics Data. 3, 49-54 [>] 26484147
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. [FASTA Herder] [>]
2014
Bader, M., N. Alenina, M.A. Andrade-Navarro and R.A. Santos. 2014. Mas and its related G protein-coupled receptors, Mrgprs. Pharmacological Reviews. 66, 1080-1105 [>] 25244929
Suratanee, A., M.H. Schaefer, M.J. Betts, Z. Soons, H. Mannsperger, N. Harder, M. Oswald, M. Gipp, E. Ramminger, G. Marcus, R. Männer, K. Rohr, E.E. Wanker, R.B. Russell, M.A. Andrade-Navarro, R. Eils, R. König. 2014. Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PLOS Comp. Biol. 10, e1003814 [>] 25255318
Gijón-Correas, J.A., M.A. Andrade-Navarro and J.F. Fontaine. 2014. Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Research. 42, W422-W429 [Alkemio] [>] 24838570
Voss, F.K., F. Ullrich, J. Münch, K. Lazarow, D. Lutter, N. Mah, M.A. Andrade-Navarro, J.P. von Kries, T. Stauber, and T.J. Jentsch. 2014. Identification of LRRC8 heteromers as essential component of the volume-regulated anion channel VRAC. Science. 344, 634-638. [>] 24790029
Gebhardt, M.L., S. Reuter, R. Mrowka, and M.A. Andrade-Navarro. 2014. Similarity in targets with REST points to neural and glioblastoma related miRNAs. Nucleic Acids Research. 42, 5436-5446. [>] 24728992
Bollen, S., M. Leddin, M.A. Andrade-Navarro and N. Mah. 2014. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. Bioinformatics. 30, 1484-1485. [>] 24451624
Fehlker, M., M.R. Huska, T. Jöns, M.A. Andrade-Navarro, W. Kemmner. 2014. Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma. BMC Cancer. 14, 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. 7, ra10. [>] 24473195
Stachelscheid, H., S. Seltmann, F. Lekschas, J.F. Fontaine, N. Mah, M. Neves, M.A. Andrade-Navarro, U. Leser and A. Kurtz. 2014. CellFinder: a cell data repository. Nucleic Acids Research. 42, D950-D958. [CellFinder] [>] 24304896
Wethmar, K., A. Barbosa da Silva, M.A. Andrade-Navarro and A. Leutz. 2014. uORFdb a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Research. 42, D60-D67. [uORFdb] [>] 24163100
2013
Mer, A.S. and M.A. Andrade-Navarro. 2013. A novel approach for protein subcellular location prediction using amino acid exposure. BMC Bioinformatics. 14, 342. [NYCE] [>] 24283794
Fournier, D., G.A. Palidwor, S. Shcherbinin, A. Szengel, M.H. Schaefer, C. Perez-Iratxeta and M.A. Andrade-Navarro. 2013. Functional and genomic analyses of alpha-solenoid proteins. PLOS ONE. 8, e79894. [ARD2] [>] 24278209
Vlassi, M., K. Brauns and M.A. Andrade-Navarro. 2013. Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a ß-solenoid structure. BMC Structural Biology. 13, 17. [>] 24088384
Andrade-Navarro, M.A., F. Kanji, C. Palii, M. Brand, H. Atkins and C. Perez-Iratxeta. 2013. A method for cell marker discovery by high-throughput gene expression analysis of mixed cell populations. BMC Biotechnology. 13, 80. [>] 24090206
Rodriguez-Seguel, E., N. Mah, H. Naumann, I.M. Pongrac, N. Cerdá-Esteban, J.F. Fontaine, Y. Wang, W. Chen, M.A. Andrade-Navarro, F.M. Spagnoli. 2013. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineages divergence. Genes and Development. 27, 1932-1946. [>] 24013505
Schönheit, J., C. Kuhl, M.L. Gebhardt, F. Fernández Klett, P. Riemke, M. Scheller, G. Huang, R. Naumann, A. Leutz, C. Stocking, J. Priller, M.A. Andrade-Navarro and F. Rosenbauer. 2013. PU.1 level-directed chromatin structure remodeling at the Irf8 gene drives dendritic cell commitment. Cell Reports. 3, 1617-1628. [>] 23623495
Petrakis, S., M.H. Schaefer, E.E. Wanker, M.A. Andrade-Navarro. 2013. Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled coil partners. Bioessays. 35, 503-507. [>] 23483542
Ortuño, F., I. Rojas, M.A. Andrade-Navarro and J.F. Fontaine. 2013. Using cited references to improve the retrieval of related biomedical documents. BMC Bioinformatics. 14, 113. [>] 23537461
Suter, B., J.F. Fontaine, R. Yildrimann, T. Raskó, M.H. Schaefer, A. Rasche, P. Porras, B.M. Vázquez-Álvarez, J. Russ, K. Rau, R. Foulle, M. Zenkner, K. Saar, R. Herwig, M.A. Andrade-Navarro, E.E. Wanker. 2013. Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Research. 41, 1496-1507. [>] 23275563
Schaefer, M.H., T.J.S. Lopes, N. Mah, J.E. Shoemaker, Y. Matsuoka, J.F. Fontaine, C. Louis-Jeune, A.J. Eisfeld, G. Neumann, C. Perez-Iratxeta, Y. Kawaoka, H. Kitano, M.A. Andrade-Navarro. 2013. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLOS Comp. Biol. 9, e1002860. [HIPPIE] [>] 23300433
von Eichborn, J., M. Dunkel, B. Gohlke, S. Preissner, M. Hoffmann, J. Bauer, J. Armstrong, M.H. Schaefer, M.A. Andrade-Navarro, N. LeNovere, M. Croning, S. Grant, P. van Nierop, A. Smit, R. Preissner. 2013. SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Research. 41,D834-D840. [synsys] [>] 23143269
2012
Sandie, R., Porter, C.J., G.A. Palidwor, F. Price, P.M. Krzyzanowski, E.M. Muro, S. Hoersch, M. Smith, P.A. Campbell, C. Perez-Iratxeta, M.A. Rudnicki, M.A. Andrade-Navarro. 2012. Paired SAGE-microarray expression data sets reveal antisense transcripts differentially expressed in embryonic stem cell differentiation. [Book chapter]. In Computational Biology of Embryonic Stem Cells. M. Zhang (Ed.). Bentham Scientific Publishers. pp. 193-215 [>]
Andrade-Navarro, M.A. 2012. Mining the literature: new methods to exploit keyword profiles. [Research highlight]. Genome Medicine. 8, 41. [>] 23114100
Andrade-Navarro, M.A., G.A. Palidwor and C. Perez-Iratxeta. 2012. Peer2ref: a peer-reviewer finding web tool that uses author disambiguation. BioData Mining. 5, 14. [peer2ref] [>] 22958760
Petrakis, S., T. Rasko, J. Russ, R.P. Friedrich, M. Stroedicke, S.P. Riechers, K. Muehlenberg, A. Moeller, A. Reinhardt, A. Vinayagam, M.H. Schaefer, M. Boutros, H. Tricoire, M.A. Andrade-Navarro and E.E. Wanker. 2012. Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLOS Genetics. 8, e1002897. [>] 22916034
Fournier, D., F.C. Luft, M. Bader, D. Ganten and M.A. Andrade-Navarro. 2012. Emergence and evolution of the renin-angiotensin-aldosterone system. Journal of Molecular Medicine. 90, 495-508. [>] 22527880
Krzyzanowski, P.M., E.M. Muro and M.A. Andrade-Navarro. 2012. Computational approaches to discovering non-coding RNA. Wiley Interdisciplinary Reviews: RNA. 3, 567-579. [>] 22555938
Herault,O., K.J. Hope, E. Deneault, N. Mayotte, J. Chagraoui, B.T. Wilhelm, S. Cellot, A. Faubert, P. Austin, M. Trost, M. Fréchette, L. Voisin, P. Chagnon, E. Soucie, M. Sauvageau, M.A. Andrade-Navarro, G. Sauvageau. 2012. A role for GPx3 in activity of normal and leukemia stem cells. J. Exp. Med. 209, 895-901. [>] 22508837
Schaefer, M.H., J.F. Fontaine, A. Vinayagam, P. Porras, E.E. Wanker and M.A. Andrade-Navarro. 2012. HIPPIE: integrating protein interaction networks with experiment based quality scores. PLOS ONE. 7, e31826. [HIPPIE] [>] 22348130
McNeill, B., C. Perez-Iratxeta, C. Mazerolle, M. Furimsky, Y. Mishina, M.A. Andrade-Navarro, V.A. Wallace. 2012. Comparative genomics identification of a novel set of temporally regulated Hedgehog target genes in the retina. Molecular and Cellular Neuroscience. 49, 333-340. [>] 22281533
Schaefer, M.H., E.E. Wanker and M.A. Andrade-Navarro. 2012. Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Research. 40, 4273-4287. [>] 22287626
Louis-Jeune C., M.A. Andrade-Navarro and C. Perez-Iratxeta. 2012. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins. 80, 374-381. [K2D3] [>] 22095872
2011
Posch, M.G., S. Waldmuller, M. Muller, T. Scheffold, D. Fournier, M.A. Andrade-Navarro, B. De Geeter, S. Giullaumont, C. Dauphin, D. Zousseff, K.R.L. Schmitt, A. Perrot, F. Berger, R. Hetzer, P. Bouvagnet, C. Özcelik. 2011. Cardiac alpha-myosin (MYH6) is the predominant sarcomeric disease gene for familial atrial septal defects. PLOS ONE. 6, e28872. [>] 22194935
Barbosa-Silva, A., J.F. Fontaine, E.R. Donnard, F. Stussi, J. Miguel-Ortega and M.A. Andrade-Navarro. 2011. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 12, 435. [PESCADOR] [>] 22070195
Krallinger, M., M. Vazquez, F. Leitner, D. Salgado, A. Chatr-aryamontri, A. Winter, L. Perfetto, L. Briganti, L. Licata, M. Iannuccelli, L. Castagnoli, G. Cesareni, M. Tyers, G. Schneider, F. Rinaldi, R. Leaman, G. Gonzalez, S. Matos, S. Kim, W.J. Wilbur, L. Rocha, H. Shatkay, A.V. Tendulkar, S. Agarwal, F. Liu, X. Wang, R. Rak, K. Noto, C. Elkan, Z. Lu, R.I. Dogan, J.F. Fontaine, M.A. Andrade-Navarro and A. Valencia. 2011. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 12 Suppl 8, S3. [>] 22151929
Donnard, E., A. Barbosa-Silva, R.M. Guedes, G. Fernandes, H. Velloso, M.J. Kohn, M.A. Andrade-Navarro, J.M. Ortega. 2011. Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics. 12 Suppl 4, S3. [>] 22369103
Mah, N., Y. Wang, M.C. Liao, A. Prigione, J. Jozefczuk, B. Lichtner, K. Wolfrum, M. Haltmeier, M. Flöttmann, M. Schaefer, A. Hahn, R. Mrowka, E. Klipp, M.A. Andrade-Navarro and J. Adjaye. 2011. Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network. PLOS ONE. 6, e24351. [>] 21909390
Muro, E.M., N. Mah and M.A. Andrade-Navarro. 2011. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie. 93, 1916-1921. [>] 21816204
Fournier, D. and M.A. Andrade-Navarro. 2011. PDBpaint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics. 27, 2605-2606. [PDBpaint] [>] 21757464
Lopes, T.J., M. Schaefer, J. Schoemaker, Y. Matsuoka, J.F. Fontaine, G. Neumann, M.A. Andrade-Navarro, Y. Kawaoka and H. Kitano. 2011. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics. 27, 2414-2421. [>] 21798963
Krzyzanowski, P.M., F.D. Price, E.M. Muro, M.A. Rudnicki, M.A. Andrade-Navarro. 2011. Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLOS ONE. 6:e20561. [>] 21698286
Vinayagam, A., U. Stelzl, R. Foulle, S. Plassmann, M. Zenkner, J. Timm, H.E. Assmus, M.A Andrade-Navarro, E.E. Wanker. 2011. A directed protein interaction network for investigating intracellular signal transduction. Science Signaling. 4, rs8. [>] 21900206
Fontaine, J.F., F. Priller, A. Barbosa-Silva, M.A. Andrade-Navarro. 2011. Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Research. 39:W455-W461. [Génie] [>] 21609954
Kur, E., A. Christa, K.N. Veth, C.R. Gajera, M.A. Andrade-Navarro, J. Zhang, J.R. Willer, R.G. Gregg, S. Abdelilah-Seyfried, S. Bachmann, B.A. Link, A. Hammes and T.E. Willnow. 2011. Loss of Lrp2 in zebrafish disrupts pronephric tubular clearance but not forebrain development. Developmental Dynamics. 240, 1567-1577. [>] 21455927
Fontaine, J.F., B. Suter, and M. A. Andrade-Navarro. 2011. QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards. BMC Research Notes. 4, 57. [QiSampler] [>] 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, 172-180 [>] 21237665
Muro, E.M., N. Mah, G. Moreno-Hagelsieb, M.A. Andrade-Navarro. 2011. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Nucleic Acids Research. 39, 1732-1738. [>] 21051341
2010
Muro, E.M., M.A. Andrade-Navarro. 2010. Pseudogenes as an alternative source of natural antisense transcripts. BMC Evolutionary Biology. 10, 338. [>] 21047404
Mah, N., C. Perez-Iratxeta, M.A. Andrade-Navarro. 2010. Outer membrane pore protein prediction in mycobacteria using genomic comparison. Microbiology. 156, 2506-2515. [>] 20466765
Christ, A., S. Terryn, E.I. Christensen, M.R. Huska, M.A. Andrade-Navarro, N. Hübner, O. Devuyst, A. Hammes, and T.E. Willnow. 2010. The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo. Kidney International. 78, 473-477. [>] 20531455
Zhang, J., P. Wagh, D. Guay, L. Sanchez-Pulido, B.K. Padhi, V. Korzh, M.A. Andrade-Navarro and M. Akimenko. 2010. Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature. 466, 234-237. [>] 20574421
Wang, Y., N. Mah, A. Prigione, K. Wolfrum, M.A. Andrade-Navarro and J. Adjaye. 2010. A transcriptional roadmap to the induction of pluripotency in somatic cells. Stem Cell Reviews and Reports. 6, 282-296. [>] 20336394
Barbosa-Silva, A., T.G Soldatos, I.L.F. Magalhães, G.A. Pavlopoulos, J.F. Fontaine, M.A. Andrade-Navarro, R. Schneider, J.M. Ortega. 2010. LAITOR - literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics. 11, 70. [>] 20122157
Striegl, H., M.A. Andrade-Navarro, U. Heinemann. 2010. Armadillo motifs involved in vesicular transport. PLoS ONE. 5, e8991. [>] 20126549
Hoersch, S. and M.A. Andrade-Navarro. 2010. Periostin shows increased evolutionary plasticity in its alternatively spliced region. BMC Evolutionary Biology. 10, 30. [>] 20109226
Palidwor, G., M.A. Andrade-Navarro. 2010. MLTrends: Graphing MEDLINE term usage over time. Journal of Biomedical Discovery and Collaboration. 5, 1-6. [MLTrends]. [>] 20333611
Scimè, A., J. Desrosiers, F. Trensz, G.A. Palidwor, A.Z. Caron, M.A. Andrade-Navarro, G. Grenier. 2010. Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing. Mechanisms of Ageing and Development. 131, 9-20. [>] 19913570
2009
Andrade-Navarro, M.A. 2009. The dictionary of genomics, transcriptomics and proteomics. [Book review]. Bioessays. 31, 13671369. [>]
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
Bröske, A., L. Vockentanz, S. Kharazi, M.R. Huska, E. Mancini, M. Scheller, A. Enns, M. Prinz, R. Jaenisch, C. Nerlov, A. Leutz, M.A. Andrade-Navarro, S.E.W. Jacobsen, F. Rosenbauer. 2009. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nature Genetics. 41, 207-215. [>] 19801979
Fontaine, J., 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 Research. 37, W141-W146. [MedlineRanker] [>] 19429696
Muro, E.M., J.A. McCann, M.A. Rudnicki and M.A. Andrade-Navarro. Use of SNP-Arrays for ChIP assays: computational aspects. Methods Mol Biol. 567, 145-154. [>] 19588091
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. 5, e1000304. [ARD] [>] 19282972
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. [StemBase] [>] 19284540
Tiffin, N., M.A. Andrade-Navarro and C. Perez-Iratxeta. 2009. Linking genes to diseases: it's all in the data. Genome Medicine. 1, 77. [>] 19678910
2008
Muro, E.M., R. Herrington, S. Janmohamed, C. Frelin, M.A. Andrade-Navarro, and N.N. Iscove. 2008. Identification of gene 3' ends by automated EST cluster analysis. Proc. Natl. Acad. Sci. 150, 20286-20290. [Transcriptome Sailor] [>] 19095794
Neuspiel, M., A.C. Schauss, E. Braschi, R. Zunino, P. Rippstein, R.A. Rachubinski, M.A. Andrade-Navarro and H.M. McBride. 2008. Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers. Current Biology.18, 102-108. [>] 18207745
Perez-Iratxeta, C. and M.A. Andrade-Navarro. 2008. K2D2: Estimation of protein secondary structure from CD spectra. BMC Structural Biology. 8, 25. [K2D2] [>] 18477405
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
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.
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
2007
Bonnet, S., S.L. Archer, J. Allalunis-Turner, A. Haromy, C. Beaulieu, R. Thompson, C.T. Lee, G.D. Lopaschuck, L. Puttagunta, S. Bonnet, G. Harry, K. Hashimoto, C.J. Porter, M.A. Andrade, B. Thebaud, E.D. Michelakis. 2007. A mitochondria-K+ channel axis is suppressed in cancer and its normalization promotes apoptosis and inhibits cancer growth. Cancer Cell. 11, 37-51. [>] 17222789
Buschmann, H., L. Sanchez-Pulido, M.A. Andrade-Navarro and C.W. Lloyd. 2007. Homologues of Arabidopsis microtubule-associated AIR9 in trypanosomatid parasites: hints on evolution and function. Plant Signaling & Behavior. 2, 296-299. [>] 19704687
Campbell, P.A., C. Perez-Iratxeta, M.A. Andrade-Navarro, and M.A. Rudnicki. 2007. Oct4 targets regulatory nodes to modulate stem cell function. PLoS ONE. 2, e553. [>] 17579724
Grenier, G., A. Scimè, A. Asakura, C. Perez-Iratxeta, M.A. Andrade-Navarro, P.A. Labosky and M.A. Rudnicki. 2007. Resident endothelial precursors in muscle, adipose and dermis contribute to post-natal vasculogenesis. Stem Cells. 25, 3101-3110. [>] 17823241
Hailesellasse Sene, K., C.J. Porter, G. Palidwor, C. Perez-Iratxeta, E.M. Muro, P.A. Campbell, M.A. Rudnicki, M.A. Andrade-Navarro. 2007. Gene function in early mouse embryonic stem cell differentiation. BMC Genomics. 8, 85. [>] 17394647
Huska, M.R., H. Buschmann and M.A. Andrade-Navarro. 2007. BiasViz: Visualization of amino acid biased regions in protein alignments. Bioinformatics. 23, 3093-3094. [BiasViz] [>] 17921493
Krzyzanowski, P.M. and M.A. Andrade-Navarro. 2007. Identification of novel stem cell markers using gap analysis of gene expression data. Genome Biology. 8, R193.[Marker Server] [>] 17875203
Kulkarni, G., D.A. Turbin, A. Amiri, S. Jeganathan, M.A. Andrade-Navarro, T.D. Wu, D.G. Huntsman and J.M. Lee. 2007. Expression of protein elongation factor eEF1A2 predicts favorable outcome in breast cancer. Breast Cancer Research and Treatment. 102, 31-41. [>] 16897428
McCann, J.A., E.M. Muro, C. Palmer, G. Palidwor, C.J. Porter, M.A. Andrade-Navarro and M.A. Rudnicki. 2007. ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation. BMC Genomics. 8, 322. [>] 17868463
Perez-Iratxeta, C., M.A. Andrade-Navarro and J.D. Wren. 2007. Evolving research trends in bioinformatics. Briefings in Bioinformatics. 8, 88-95. [>] 17077138
Perez-Iratxeta, C., G. Palidwor and M.A. Andrade-Navarro. 2007. Towards completion of the Earth's proteome. EMBO Reports. 8, 1135-1141. [>] 18059312
Perez-Iratxeta, C., P. Bork and M.A. Andrade-Navarro. 2007. Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Research. 35, W212-W216. [>] 17478516
Porter C.J., G.A. Palidwor, R. Sandie, P.M. Krzyzanowski, E.M. Muro, C. Perez-Iratxeta, M.A. Andrade-Navarro. 2007. StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol. Biol. 407, 137-148. [StemBase] [>] 18453254
Sanchez-Pulido, L. and M.A. Andrade-Navarro. 2007. The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. BMC Biochemistry. 8, 23. [>] 17996046
Schwarz, M., M.A. Andrade-Navarro and A. Gross. 2007. Mitochondrial carriers and pores: Key regulators of the mitochondrial apoptotic program? Apoptosis. 12, 869-876. [>] 17453157
Zunino, R., P. Rippstein, M. Andrade-Navarro and H.M. McBride. 2007. The SUMO protease SENP5 is required to maintain mitochondrial morphology and function. J. Cell. Sci. 120, 1178-1188. [>] 17341580
2006
Baldwin, R.M., M. Garratt-Lalonde, D.A.E. Parolin, P.M. Krzyzanowski, M.A. Andrade, and I.A.J. Lorimer. 2006. Protection of glioblastoma cells from cisplatin cytotoxicity via protein kinase Ciota-mediated attenuation of P38 MAP Kinase signaling. Oncogene. 25, 2909-2919. [>] 16331246
Bonnet, S., E.D. Michelakis, C.J. Porter, M.A. Andrade-Navarro, B. Thébaud, S. Bonnet, A. Haromy, G. Harry, R. Moudgil, M.S. McMurtry, E.K. Weir, and S.L. Archer. 2006. 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. 113, 2630-2641. [>] 16735674
Buschmann, H., J. Chan, L. Sanchez-Pulido, M.A. Andrade-Navarro, J.H. Doonan and C.W. Lloyd. 2006. Microtubule-associated AIR9 recognizes the cortical division site at preprophase and cell-plate insertion. Current Biology. 16, 1938-1943. [>] 17027491
Muro, E.M., C. Perez-Iratxeta, and M.A. Andrade-Navarro. 2006. Amplification of the Gene Ontology annotation of Affymetrix probe sets. BMC Bioinformatics. 7, 159. [Probe2GO] [>] 16549014
Palidwor, G., E.G. Reynaud, and M.A. Andrade-Navarro. 2006. Taxonomic colouring of phylogenetic trees of protein sequences. BMC Bioinformatics. 7, 79. [PhyloView] [>] 16503967
Tiffin, N., E. Adie, F. Turner, H.G. Brunner, M.A. van Driel, M. Oti, N. Lopez-Bigas, C. Ouzonis, C. Perez-Iratxeta, M.A. Andrade-Navarro, A. Adeyemo, M.E. Patti, C. Semple and W. Hide. 2006. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Research. 113, 2630-2641. [>] 16757574
2005
Korbel, J.O., T. Doerks, L.J. Jensen, C. Perez-Iratxeta, S. Kaczanowski, S.D. Hooper, M.A. Andrade and P. Bork. 2005. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biology. 3, e134. [>] 15799710
Perez-Iratxeta, C. and M.A. Andrade. 2005. Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. BMC Bioinformatics. 6, 183. [>] 16033654
Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela, E.M. Muro, P. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A. Andrade. 2005. Study of stem cell function using microarray experiments. FEBS Letters. 579, 1795-1801. [StemBase] [>] 15763554
Perez-Iratxeta, C., M. Wjst, P. Bork and M.A. Andrade. 2005. G2D: a tool for mining genes associated with disease. BMC Genetics. 6, 45. [G2D server] [>] 16115313
Reynaud, E.G., M.A. Andrade, F. Bonneau, T.B. Ly, M. Knop, K. Scheffzek and R. Pepperkok. 2005. Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization. BMC Biology. 21, 3. [>] 16209721
Savchenko, A., N. Krogan, J.R. Cort, E. Evdokimova, J.M. Lew, A.A. Yee, L. Sánchez-Pulido, M.A. Andrade, A. Bochkarev, J.D. Watson, M.A. Kennedy, J. Greenblatt, T. Hughes, C.H. Arrowsmith, J.M. Rommens and A.M. Edwards. 2005. The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. Journal of Biological Chemistry. 280, 19213-19220. [>] 15701634
Suomela, B.P. and M.A. Andrade. 2005. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinformatics. 6, 75. [>] 15790421
2004
Doerks, T., M.A. Andrade, W. Lathe 3rd, C. von Mering and P. Bork. 2004. Global analysis of bacterial transcription factors to predict cellular target processes. Trends in Genetics. 20, 126-131. [>] 15049306
Pérez, A.J., C. Perez-Iratxeta, P. Bork, G. Thode and M.A. Andrade. 2004. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics. 20, 2084-2091. [>] 15059832
Sánchez-Pulido, L., A.M. Rojas, A. Valencia, C. Martinez-A and M.A. Andrade. 2004. ACRATA: A novel electron transfer domain associated to apoptosis and cancer. BMC Cancer. 4, 98. [>] 15623366
2003
Andrade, M.A. (Ed.). 2003. Bioinformatics and Genomes: Current Perspectives. Horizon Scientific Press, UK. [Buy the book from Amazon UK]
Iliopoulos, I., S. Tsoka, M.A. Andrade, A.J. Enright, M. Carroll, P. Poullet, V. Promponas, T. Liakopoulos, G. Pahttp://www.horizonpress.com/hsp/books/bgcp.htmllaios, C. Pasquier, S. Hamodrakas, J. Tamames, A.T. Yagnik, A. Tramontano, D. Devos, C. Blaschke, A. Valencia, D. Brett, D. Martin, C. Leroy, I. Rigoutsos, C. Sander and C.A. Ouzounis. 2003. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 19, 717-726 [>] 12691983
Netzel, R., C. Perez-Iratxeta, P. Bork and M.A. Andrade. 2003. The way we write. Country-specific variations of English in the scientific literature. EMBO Reports. 4, 446-451. [>] 12728240
Perez-Iratxeta, C., N. Astola, F.D. Ciccarelli, P.K. Sha, P. Bork and M.A. Andrade. A protocol for the update of references to scientific literature in biological databases. Applied Bioinformatics. 2, 189-191. [>] 15130808
Perez-Iratxeta, C., A.J. Pérez, P. Bork and M.A. Andrade. 2003. Update on XplorMed: a web server for exploring scientific literature. Nucleic Acids Research. 31, 3866-3868. [>] 12824439
Shah, P.K., C. Perez-Iratxeta, P. Bork and M.A. Andrade. 2003. Information extraction from full text scientific articles: where are the keywords? BMC Bioinformatics. 4, 20. [e-version@BMC Bioinformatics] [>] 12775220
2002
Andrade, M.A., F.D. Ciccarelli, C. Perez-Iratxeta and P. Bork. 2002. NEAT: A domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria. Genome Biology. 3, research0047.1-0047.5. [e-version@Genome Biology] [>] 12225586
Muro, E.M., M.A. Andrade and F. Morán. 2002. A self-organizing model for the development of orientation selectivity and ocular dominance patterns in the visual nervous system. Neural Network World. 12, 319-332. [>]
Perez-Iratxeta, C. and M.A. Andrade. 2002. Worldwide scientific publishing activity. Science. 297, 519. [>] 12143877
Perez-Iratxeta, C., P. Bork and M.A. Andrade. 2002. Association of genes to genetically inherited diseases using data mining. Nature Genetics. 31, 316-319. [G2D server] [>] 12006977
Perez-Iratxeta, C., P. Bork and M.A. Andrade. 2002. Exploring MEDLINE abstracts with XplorMed. Drugs of Today. 38, 381-389. [>] 12532176
Perez-Iratxeta, C., H.S. Keer, P. Bork and M.A. Andrade. 2002. Computing fuzzy associations for the analysis of biological literature. Biotechniques. 32, 1380-1385. [>] 12074170
2001
Andrade, M.A. 2001. Tools for automated protein annotation. In Protein Sequence Analysis in the Post-Genomic Era. R. Casadio and L. Masotti (Eds.) Clueb, Bologna, Italy. [web appendix] [HTML version] [>]
Andrade, M.A., M. González-Guzmán, R. Serrano and P.L. Rodríguez. 2001. A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins. Plant Mol. Biol. 46, 603-614. [>] 11516153
Andrade, M.A., E.M. Muro and F. Morán. 2001. Simulation of plasticity in the adult visual cortex. Biological Cybernetics. 84, 445-451. [>] 11417056
Andrade, M.A., C. Perez-Iratxeta, and C.P. Ponting. 2001. Protein repeats: structures, functions and evolution. Journal of Structural Biology. 134, 117-131. [>] 11551174
Andrade, M.A., C. Petosa, S.I. O'Donoghue, C.W. Müller and P. Bork. 2001. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 309, 1-18. [REP server]. [>] 11491282
Iliopoulos, I., S. Tsoka, M.A. Andrade, P. Janssen, B. Audit, A. Tramontano, A. Valencia, C. Leroy, C. Sander and C.A. Ouzounis. 2001. Genome sequences and great expectations. Genome Biology. 2, INTERACTIONS0001. [>] 11178275
Perez-Iratxeta, C., P. Bork and M.A. Andrade. 2001. XplorMed: A tool for exploring MEDLINE abstracts. Trends Biochem Sci. 26, 573-575. [>] 11551795
2000
Andrade, M.A. and P. Bork. 2000. Automated extraction of information in molecular biology. FEBS Letters. 476, 12-17. [web appendix] [>] 10878241
Andrade, M.A., C.P. Ponting, T.J. Gibson and P. Bork. 2000. Homology-based method for identification of protein repeats using statistical significance estimates. J. Mol. Biol. 298, 521-537. [web appendix] [REP server] [>] 10772867
Dandekar, T., M. Huynen, J.T. Regula, C.U. Zimmermann, B. Ueberle, M.A. Andrade, T. Doerks, L. Sánchez-Pulido, B. Snel, M. Suyama, Y.P. Yuan, R. Herrmann and P. Bork. 2000. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Research. 28, 3278-3288. [web appendix] [>] 10954595
Hoersch, S., C. Leroy, N.P. Brown, M.A. Andrade and C. Sander. 2000. The GeneQuiz Web server: protein functional analysis through the Web. Trends in Biochemical Sciences. 25, 33-35. [>] 10637611
Ponting, C.P., J. Schultz, R.R. Copley, M.A. Andrade and P. Bork. 2000. Evolution of domain families. In "Analysis of amino acid sequences". Advances in Protein Chemistry. 54, 185-244. [>] 10829229
Sánchez-Pulido, L., Y.P. Yuan, M.A. Andrade and P. Bork. 2000. NAIL-Network analysis interface for linking HMMER results. Bioinformatics. 16, 656-657. [>] 11038338
1999
Andrade, M.A. 1999. Position-specific annotation of protein function based on multiple homologs. ISMB 99. 7, 28-33. [PostScript version] [>] 10786283
Andrade, M.A., N.P. Brown, C. Leroy, S. Hoersch, A. de Daruvar, C .Reich, A. Franchini, J. Tamames, A. Valencia, C. Ouzounis and C. Sander. 1999. Automated genome sequence analysis and annotation. Bioinformatics. 15, 391-412. [>] 10366660
Andrade, M.A., C. Ouzounis, C. Sander, J. Tamames and A. Valencia. 1999. Functional classes in the three domains of life. J. Mol. Evol. 49, 551-557. [web appendix] [>] 10552036
Blaschke, C., M.A. Andrade, C. Ouzounis and A. Valencia. 1999. Automatic extraction of biological information from Scientific text: protein-protein interactions. ISMB 99. 7, 60-67. [web appendix (C. Blaschke)] [>] 10786287
1998
Andrade, M.A., S.I. O'Donoghue and B. Rost. 1998. Adaptation of protein surfaces to subcellular location. J. Mol. Biol. 276, 517-525. [html version + web appendix (B. Rost)] [>] 9512720
Andrade, M.A., C. Sander and A. Valencia. 1998. Updated catalogue of homologues to human-disease related proteins in the yeast genome. FEBS Letters. 426, 7-16. [web appendix] [>] 9598968
Andrade, M.A. and A. Valencia. 1998. Automatic extraction of keywords from scientific text: Application to the knowledge domain of protein families. Bioinformatics. 14, 600-607. [html version @Bioinformatics] [web appendix] and [>] 9730925
Trelles, O., M.A. Andrade, A. Valencia, E.L. Zapata and J.M. Carazo. 1998. Computational space reduction and parallelization of a new clustering approach for large groups of sequences. Bioinformatics. 14, 439-451. [>] 9682057
1997
Andrade, M.A., G. Casari, A. Daruvar, C. Sander, R. Schneider, J. Tamames, A. Valencia and C. Ouzounis. 1997. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. CABIOS. 13, 481-483. [>] 9283767
Andrade, M.A., G. Casari, C. Sander and A. Valencia. 1997. Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol. Cybern. 76, 441-450. [>] 9263431
Andrade, M.A., A. Daruvar, G. Casari, R. Schneider, M. Termier and C. Sander. 1997. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome. Yeast, 13, 1363-1374. [html version] [>] 9392081
Andrade, M.A. and F. Morán. 1997. Receptive field map development by anti-Hebbian learning. Neural Networks. 10, 1037-1052 [>] 12662497
Andrade, M.A. and C. Sander. 1997. Bioinformatics: from genome data to biological knowledge. Current Opinion in Biotechnology. 8, 675-683. [>] 9425655
Andrade, M.A. and A. Valencia. 1997. Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system. ISMB 97. 5, 25-32. [PostScript version] [>] 9322011
Voss, H., V. Benes, M.A. Andrade, A. Valencia, S. Rechmann, C. Teodoru, C. Schwager, V. Paces, C. Sander and W. Ansorge. 1997. DNA sequencing and analysis of 130 kb from yeast chromosome XV. Yeast. 13, 655-672. [>] 9200815
1996
Andrade, M.A. and F. Morán. 1996. Structural study of the development of ocularity domains using a neural network model. Biol. Cybern., 74, 243-254. [>] 8867470
1995
Andrade, M.A. and P. Bork. 1995. HEAT repeats in the Huntington's disease protein. Nature Genetics, 11, 115-116. [web appendix] [>] 7550332
Casari, G., M.A. Andrade, P. Bork, J. Boyle, A. Daruvar, C. Ouzounis, R. Schneider, R. Tamames, A. Valencia and C. Sander, 1995. Challenging times for bioinformatics. Nature, 376, 647-648. [>] 7651513
1994
Andrade, M.A. Doctoral thesis. March, 1994. Modelizacíon del desarrollo ontogenético del sistema nervioso visual mediante redes neuronales. Universidad Complutense de Madrid. [PDF at UCM] [>]
Merelo, J.J., M.A. Andrade, A. Prieto and F. Morán. 1994. Proteinotopic Feature Maps. Neurocomputing. 6, 443-454. [>]
1993
Andrade, M.A., P. Chacón, J.J. Merelo and F. Morán. 1993. Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised learning neural network. Prot. Eng. 6, 383-390. [>] 8332596
Andrade, M.A., J.C. Nuño, F. Morán, F. Montero and G.J. Mpitsos. 1993. Complex dynamics of a catalytic network having faulty replication into error-species. Physica D. 63, 21-40. [>]
Montero, F., J.C. Nuño and M.A. Andrade. 1993. Evolución Prebiótica: el camino hacia la vida. Colección Eudema Biología. Eudema. [>]
Nuño, J.C., M.A. Andrade, F. Morán and F. Montero. 1993. A model of an autocatalytic network formed by error-prone self-replicative species. Bull. Math. Biol. 55, 385-415. [>]
Nuño, J.C., M.A. Andrade and F. Montero. 1993. Non-uniformities and superimposed competition in a model of autocatalytic network formed by error-prone self-replicative species. Bull. Math. Biol. 55, 417-449. [>]
1992
Montero, F., J.C. Nuño and M.A. Andrade. 1992. Evolución y selección en sistemas biológicos reales. Revista de la Real Academia de Ciencias Exactas, Físicas y Naturales, de Madrid. 86, 315-368. [>]
1991
Andrade, M.A., A.J. García-Tejedor and F. Montero. 1991. Study of an error-prone hypercycle formed from two kinetically distinguishable species. Biophys. Chem. 40, 43-57. [>] 17014773