Publications by members of our group (2003-)


Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Silvina Fornasari M, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol. 2023 Aug 29:108023. doi: 10.1016/j.jsb.2023.108023. Epub ahead of print.

Mier P, Andrade-Navarro MA. Evolutionary Study of Protein Short Tandem Repeats in Protein Families. Biomolecules. 2023 Jul 13;13(7):1116. doi: 10.3390/biom13071116.

Cate VT, Rapp S, Schulz A, Pallares Robles A, Jurk K, Koeck T, Espinola-Klein C, Halank M, Seyfarth HJ, Beutel ME, Schuster AK, Marini F, Hobohm L, Lankeit M, Lackner KJ, Ruf W, Münzel T, Andrade-Navarro MA, Prochaska JH, Konstantinides SV, Wild PS. Circulating microRNAs predict recurrence and death following venous thromboembolism. J Thromb Haemost. 2023 Jul 20:S1538-7836(23)00572-X. doi: 10.1016/j.jtha.2023.07.010.

Schumbera E, Mier P, Andrade-Navarro MA. Phase separating Rho: a widespread regulatory function of disordered regions in proteins revealed in bacteria. Signal Transduct Target Ther. 2023 Jun 21;8(1):253. doi: 10.1038/s41392-023-01505-5.

Kang H, Hasselbeck S, Taškova K, Wang N, Oosten LNV, Mrowka R, Utikal J, Andrade-Navarro MA, Wang J, Wölfl S, Cheng X. Development of a next-generation endogenous OCT4 inducer and its anti-aging effect in vivo. Eur J Med Chem. 2023 May 24;257:115513. doi: 10.1016/j.ejmech.2023.115513. Epub ahead of print.

Fan W, Jurado-Arjona J, Alanis-Lobato G, Péron S, Berger C, Andrade-Navarro MA, Falk S, Berninger B. The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation. EMBO J. 2023 Apr 21:e110384. doi: 10.15252/embj.2021110384.

Foreman SC, Llorián-Salvador O, David DE, Rösner VKN, Rischewski JF, Feuerriegel GC, Kramp DW, Luiken I, Lohse AK, Kiefer J, Mogler C, Knebel C, Jung M, Andrade-Navarro MA, Rost B, Combs SE, Makowski MR, Woertler K, Peeken JC, Gersing AS. Development and Evaluation of MR-Based Radiogenomic Models to Differentiate Atypical Lipomatous Tumors from Lipomas. Cancers (Basel). 2023 Apr 5;15(7):2150. doi: 10.3390/cancers15072150.

Erdozain S, Barrionuevo E, Ripoll L, Mier P, Andrade-Navarro MA. Protein repeats evolve and emerge in giant viruses. J Struct Biol. 2023 Apr 7:107962. doi: 10.1016/j.jsb.2023.107962.

Krolevets M, Cate VT, Prochaska JH, Schulz A, Rapp S, Tenzer S, Andrade- Navarro MA, Horvath S, Niehrs C, Wild PS. DNA methylation and cardiovascular disease in humans: a systematic review and database of known CpG methylation sites. Clin Epigenetics. 2023 Mar 30;15(1):56. doi: 10.1186/s13148-023-01468-y.

Rubio A, Sprang M, Garzón A, Moreno-Rodriguez A, Pachón-Ibáñez ME, Pachón J, Andrade-Navarro MA, Pérez-Pulido AJ. Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems. Sci Adv. 2023 Mar 24;9(12):eadd8911. doi: 10.1126/sciadv.add8911.

Nagel-Wolfrum K, Fadl BR, Becker MM, Wunderlich KA, Schäfer J, Sturm D, Fritze J, Gür B, Kaplan L, Andreani T, Goldmann T, Brooks M, Starostik MR, Lokhande A, Apel M, Fath KR, Stingl K, Kohl S, DeAngelis MM, Schlötzer- Schrehardt U, Kim IK, Owen LA, Vetter JM, Pfeiffer N, Andrade-Navarro MA, Grosche A, Swaroop A, Wolfrum U. Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy. Hum Mol Genet. 2023 Jan 13;32(3):431-449. doi: 10.1093/hmg/ddac211.


Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA. Functional Tuning of Intrinsically Disordered Regions in Human Proteins by Composition Bias. Biomolecules. 2022 Oct 15;12(10):1486. doi: 10.3390/biom12101486.

Mier P, Andrade-Navarro MA. Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape. Comput Struct Biotechnol J. 2022 Sep 18;20:5516-5523. doi: 10.1016/j.csbj.2022.09.011.

Mier P, Elena-Real CA, Cortés J, Bernadó P, Andrade-Navarro MA. The sequence context in poly-alanine regions: structure, function and conservation. Bioinformatics. 2022 Oct 31;38(21):4851-4858. doi: 10.1093/bioinformatics/btac610.

Gonçalves-Kulik M, Mier P, Kastano K, Cortés J, Bernadó P, Schmid F, Andrade- Navarro MA. Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered. Biomolecules. 2022 Aug 10;12(8):1098. doi: 10.3390/biom12081098.

Sprang M, Andrade-Navarro MA, Fontaine JF. Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. BMC Bioinformatics. 2022 Jul 14;23(Suppl 6):279. doi: 10.1186/s12859-022-04775-y.

Albrecht S, Andreani T, Andrade-Navarro MA, Fontaine JF. Single-cell specific and interpretable machine learning models for sparse scChIP-seq data imputation. PLoS One. 2022 Jul 1;17(7):e0270043. doi: 10.1371/journal.pone.0270043.

Pallares Robles A, Ten Cate V, Schulz A, Prochaska JH, Rapp S, Koeck T, Panova-Noeva M, Heitmeier S, Schwers S, Leineweber K, Seyfarth HJ, Opitz CF, Spronk H, Espinola-Klein C, Lackner KJ, Münzel T, Andrade-Navarro MA, Konstantinides SV, Ten Cate H, Wild PS. Association of FXI activity with thrombo-inflammation, extracellular matrix, lipid metabolism and apoptosis in venous thrombosis. Sci Rep. 2022 Jun 13;12(1):9761. doi: 10.1038/s41598-022-13174-5.

Cihan M, Andrade-Navarro MA. Detection of features predictive of microRNA targets by integration of network data. PLoS One. 2022 Jun 9;17(6):e0269731. doi: 10.1371/journal.pone.0269731.

Vagiona AC, Mier P, Petrakis S, Andrade-Navarro MA. Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network. Int J Mol Sci. 2022 May 23;23(10):5853. doi: 10.3390/ijms23105853.

Mier P, Fontaine JF, Stoldt M, Libbrecht R, Martelli C, Foitzik S, Andrade- Navarro MA. Annotation and Analysis of 3902 Odorant Receptor Protein Sequences from 21 Insect Species Provide Insights into the Evolution of Odorant Receptor Gene Families in Solitary and Social Insects. Genes. 2022 May 20;13(5):919. doi: 10.3390/genes13050919.

Mier P, Andrade-Navarro MA. PolyX2: Fast Detection of Homorepeats in Large Protein Datasets. Genes. 2022 Apr 25;13(5):758. doi: 10.3390/genes13050758.

Czeh M, Stäble S, Krämer S, Tepe L, Talyan S, Carrelha J, Meng Y, Heitplatz B, Schwabenland M, Milsom MD, Plass C, Prinz M, Schlesner M, Andrade-Navarro MA, Nerlov C, Jacobsen SEW, Lipka DB, Rosenbauer F. DNMT1 Deficiency Impacts on Plasmacytoid Dendritic Cells in Homeostasis and Autoimmune Disease. J Immunol. 2022 Jan 15;208(2):358-370. doi: 10.4049/jimmunol.2100624.


Mier P, Andrade-Navarro MA. Between interactions and aggregates: the polyQ balance. Genome Biol Evol. 2021 Nov 13:evab246. doi: 10.1093/gbe/evab246.

Diener N, Fontaine JF, Klein M, Hieronymus T, Wanke F, Kurschus FC, Ludwig A, Ware C, Saftig P, Bopp T, Clausen BE, Backer RA. Posttranslational modifications by ADAM10 shape myeloid antigen-presenting cell homeostasis in the splenic marginal zone. Proc Natl Acad Sci U S A. 2021 Sep 21;118(38):e2111234118. doi: 10.1073/pnas.2111234118.

Sprang M, Krüger M, Andrade-Navarro MA, Fontaine JF. Statistical NGS quality control guidelines. Life Science Alliance. Aug 2021;4(11):e202101113. doi: 10.26508/lsa.202101113

More P, Bindila L, Wild P, Andrade-Navarro M, Fontaine JF. LipiDisease: associate lipids to diseases using literature mining. Bioinformatics. 2021 Aug 6:btab559. doi: 10.1093/bioinformatics/btab559.

Ten Cate V, Koeck T, Prochaska J, Schulz A, Panova-Noeva M, Rapp S, Eggebrecht L, Lenz M, Glunz J, Sauer M, Ewert R, Halank M, Münzel T, Heitmeier S, Andrade-Navarro MA, Lackner KJ, Konstantinides SV, Leineweber K, Wild PS. A targeted proteomics investigation of the obesity paradox in venous thromboembolism. Blood Adv. 2021 Jul 27;5(14):2909-2918. doi: 10.1182/bloodadvances.2020003800.

Koch I, Andrade-Navarro M, Schulz MH, Zarnack K. Bioinformatics in theory and application - highlights of the 36th German Conference on Bioinformatics. Biol Chem. 2021 Jun 30;402(8):869-870. doi: 10.1515/hsz-2021-0298.

Talyan S, Andrade-Navarro MA, Muro EM. A Methodology to Study Pseudogenized lincRNAs. Methods Mol Biol. 2021;2324:49-63. doi: 10.1007/978-1-0716-1503-4_4.

Kamel M, Kastano K, Mier P, Andrade-Navarro MA. REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences. J Mol Biol. 2021 May 28;433(11):166895. doi: 10.1016/j.jmb.2021.166895. Epub 2021 Feb 24.

Mier P, Andrade-Navarro MA. The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein. Genes (Basel). 2021 Mar 22;12(3):451. doi: 10.3390/genes12030451.

More P, Talyan S, Fontaine JF, Muro EM, Andrade-Navarro MA. DiseaseLinc: Disease Enrichment Analysis of Sets of Differentially Expressed LincRNAs. Cells. 2021 Mar 29;10(4):751. doi: 10.3390/cells10040751.

Albrecht S, Sprang M, Andrade-Navarro MA, Fontaine JF. seqQscorer: automated quality control of next-generation sequencing data using machine learning. Genome Biol. 2021 Mar 5;22(1):75. doi: 10.1186/s13059-021-02294-2.

Mier P, Andrade-Navarro MA. Avoided motifs: short amino acid strings missing from protein datasets. Biol Chem. 2021 Mar 2. doi: 10.1515/hsz-2020-0383.

Kastano K, Mier P, Andrade-Navarro MA. The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. Int J Mol Sci. 2021 Feb 9;22(4):1727. doi: 10.3390/ijms22041727.

Ten Cate V, Prochaska JH, Schulz A, Koeck T, Pallares Robles A, Lenz M, Eggebrecht L, Rapp S, Panova-Noeva M, Ghofrani HA, Meyer FJ, Espinola-Klein C, Lackner KJ, Michal M, Schuster AK, Strauch K, Zink AM, Laux V, Heitmeier S, Konstantinides SV, Münzel T, Andrade-Navarro MA, Leineweber K, Wild PS. Protein expression profiling suggests relevance of noncanonical pathways in isolated pulmonary embolism. Blood. 2021 May 13;137(19):2681-2693. doi: 10.1182/blood.2019004571.

Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, Castaños-Vélez E, Fichtner I, Tunn PU, Denkert C, Klaas O, Berdel WE, von Kries JP, Makalowski W, Andrade-Navarro MA, Leutz A, Wethmar K. Author Correction: Loss-of-function uORF mutations in human malignancies. Sci Rep. 2021 Jan 28;11(1):2917. doi: 10.1038/s41598-021-82176-6. Erratum for: Sci Rep. 2018 Feb 5;8(1):2395.

Paladin L, Bevilacqua M, Errigo S, Piovesan D, Mičetić I, Necci M, Monzon AM, Fabre ML, Lopez JL, Nilsson JF, Rios J, Menna PL, Cabrera M, Buitron MG, Kulik MG, Fernandez-Alberti S, Fornasari MS, Parisi G, Lagares A, Hirsh L, Andrade-Navarro MA, Kajava AV, Tosatto SCE. RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. Nucleic Acids Res. 2021 Jan 8;49(D1):D452-D457. doi: 10.1093/nar/gkaa1097.


Mier P, Andrade-Navarro MA. Assessing the low complexity of protein sequences via the low complexity triangle. PLoS One. 2020 Dec 30;15(12):e0239154. doi: 10.1371/journal.pone.0239154.

Andrade-Navarro MA, Mühlenberg K, Spruth EJ, Mah N, González-López A, Andreani T, Russ J, Huska MR, Muro EM, Fontaine JF, Amstislavskiy V, Soldatov A, Nietfeld W, Wanker EE, Priller J. RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's Disease. Front Neurol. 2020 Nov 27;11:573560. doi: 10.3389/fneur.2020.573560.

Lenz M, Schulz A, Koeck T, Rapp S, Nagler M, Sauer M, Eggebrecht L, Ten Cate V, Panova-Noeva M, Prochaska JH, Lackner KJ, Münzel T, Leineweber K, Wild PS, Andrade-Navarro MA. Missing value imputation in proximity extension assay-based targeted proteomics data. PLoS One. 2020 Dec 14;15(12):e0243487. doi: 10.1371/journal.pone.0243487.

Rubio A, Mier P, Andrade-Navarro MA, Garzón A, Jiménez J, Pérez-Pulido AJ. CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. Database (Oxford). 2020 Jan 1;2020:baaa088. doi: 10.1093/database/baaa088.

Sloun BV, Goossens GH, Erdos B, Lenz M, Riel NV, Arts ICW. The Impact of Amino Acids on Postprandial Glucose and Insulin Kinetics in Humans: A Quantitative Overview. Nutrients. 2020 Oct 21;12(10):3211. doi: 10.3390/nu12103211.

Kastano K, Erdős G, Mier P, Alanis-Lobato G, Promponas VJ, Dosztányi Z, Andrade-Navarro MA. Evolutionary Study of Disorder in Protein Sequences. Biomolecules. 2020 Oct 6;10(10):E1413. doi: 10.3390/biom10101413.

Vagiona AC, Andrade-Navarro MA, Psomopoulos F, Petrakis S. Dynamics of a Protein Interaction Network Associated to the Aggregation of polyQ-Expanded Ataxin-1. Genes (Basel). 2020 Sep 25;11(10):E1129. doi: 10.3390/genes11101129.

Paladin L, Necci M, Piovesan D, Mier P, Andrade-Navarro MA, Tosatto SCE. A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication. J Struct Biol. 2020 Nov 1;212(2):107608. doi: 10.1016/j.jsb.2020.107608. Epub 2020 Sep 5.

Haenig C, Atias N, Taylor AK, Mazza A, Schaefer MH, Russ J, Riechers SP, Jain S, Coughlin M, Fontaine JF, Freibaum BD, Brusendorf L, Zenkner M, Porras P, Stroedicke M, Schnoegl S, Arnsburg K, Boeddrich A, Pigazzini L, Heutink P, Taylor JP, Kirstein J, Andrade-Navarro MA, Sharan R, Wanker EE. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell Rep. 2020 Aug 18;32(7):108050. doi: 10.1016/j.celrep.2020.108050.

O'Donovan SD, Driessens K, Lopatta D, Wimmenauer F, Lukas A, Neeven J, Stumm T, Smirnov E, Lenz M, Ertaylan G, Jennen DGJ, van Riel NAW, Cavill R, Peeters RLM, de Kok TMCM. Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes. PLoS One. 2020 Aug 11;15(8):e0236392. doi: 10.1371/journal.pone.0236392.

Lenz M, Arts ICW, Peeters RLM, de Kok TM, Ertaylan G. Adipose tissue in health and disease through the lens of its building blocks. Sci Rep. 2020 Jun 26;10(1):10433. doi: 10.1038/s41598-020-67177-1.

Alanis-Lobato G, Möllmann JS, Schaefer MH, Andrade-Navarro MA. MIPPIE: the mouse integrated protein-protein interaction reference. Database (Oxford). 2020 Jan 1;2020:baaa035. doi: 10.1093/database/baaa035. PMID: 32496562; PMCID: PMC7271249.

Mier P, Andrade-Navarro MA. The features of polyglutamine regions depend on their evolutionary stability. BMC Evol Biol. 2020 May 24;20(1):59. doi: 10.1186/s12862-020-01626-3.

Mier P, Andrade-Navarro MA. MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments. Evol Bioinform Online. 2020 Apr 29;16:1176934320916199. doi: 10.1177/1176934320916199. eCollection 2020.

Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D, Tosatto SCE, Promponas VJ, Grynberg M, Gruca A. PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Res. 2020 Jul 2;48(W1):W77-W84. doi: 10.1093/nar/gkaa339.

Urbanek A, Popovic M, Morató A, Estaña A, Elena-Real CA, Mier P, Fournet A, Allemand F, Delbecq S, Andrade-Navarro MA, Cortés J, Sibille N, Bernadó P. Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins. Structure. 2020; 28(7):733-746.e5. doi:10.1016/j.str.2020.04.008.

Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m6A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep. 2020;21(7):e49443. doi:10.15252/embr.201949443.

Ten Cate V, Eggebrecht L, Schulz A, Panova-Noeva M, Lenz M, Koeck T, Rapp S, Arnold N, Lackner KJ, Konstantinides S, Espinola-Klein C, Münzel T, Prochaska JH, Wild PS. Isolated Pulmonary Embolism Is Associated With a High Risk of Arterial Thrombotic Disease: Results From the VTEval Study. Chest. 2020 Jul;158(1):341-349. doi: 10.1016/j.chest.2020.01.055. Epub 2020 Mar 23.

Andreani T, Albrecht S, Fontaine JF, Andrade-Navarro MA. Computational identification of cell-specific variable regions in ChIP-seq data. Nucleic Acids Res. 2020; 48(9):e53. doi:10.1093/nar/gkaa180

Dallago C, Goldberg T, Andrade-Navarro MA, Alanis-Lobato G, Rost B. Visualizing Human Protein-Protein Interactions and Subcellular Localizations on Cell Images Through CellMap. Curr Protoc Bioinformatics. 2020 Mar;69(1):e97. doi: 10.1002/cpbi.97.

Laidou S, Alanis-Lobato G, Pribyl J, Raskó T, Tichy B, Mikulasek K, Tsagiopoulou M, Oppelt J, Kastrinaki G, Lefaki M, Singh M, Zink A, Chondrogianni N, Psomopoulos F, Prigione A, Ivics Z, Pospisilova S, Skladal P, Izsvák Z, Andrade-Navarro MA, Petrakis S. Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biol. 2020 Feb 11;32:101458. doi: 10.1016/j.redox.2020.101458.

Mier P, Elena-Real C, Urbanek A, Bernadó P, Andrade-Navarro MA. The importance of definitions in the study of polyQ regions: A tale of thresholds, impurities and sequence context. Comput Struct Biotechnol J. 2020 Feb 4;18:306-313. doi:10.1016/j.csbj.2020.01.012.

Sarathy C, Kutmon M, Lenz M, Adriaens ME, Evelo CT, Arts ICW. EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models. Metabolites. 2020 Feb 12;10(2):66. doi: 10.3390/metabo10020066.

Cheng X, Haeberle S, Luca Shytaj I, Gama-Brambila RA, Theobald J, Ghafoory S, Wölker J, Basu U, Schmidt C, Timm A, Taškova K, Bauer AS, Hoheisel J, Tsopoulidis N, Fackler OT, Savarino A, Andrade-Navarro MA, Ott I, Lusic M, Hadaschik EN, Wölfl S. NHC-gold compounds mediate immune suppression through induction of AHR-TGFβ1 signalling in vitro and in scurfy mice. Commun Biol. 2020 Jan 3;3:10. doi: 10.1038/s42003-019-0716-8.

Burkhardt S, Siekiera J, Glodde J, Andrade-Navarro MA, Kramer S. Towards identifying drug side effects from social media using active learning and crowd sourcing. Pac Symp Biocomput. 2020;25:319-330.

Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA. The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev Biol. 2020 Apr 15;460(2):139-154. doi: 10.1016/j.ydbio.2019.12.002. Epub 2019 Dec 6.

Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform. 2020 Mar 23;21(2):458-472. doi: 10.1093/bib/bbz007.


Muro EM, Ibn-Salem J, Andrade-Navarro MA. The distributions of protein coding genes within chromatin domains in relation to human disease. Epigenetics Chromatin. 2019 Dec 5;12(1):72. doi: 10.1186/s13072-019-0317-2.

Geiß C, Alanis-Lobato G, Andrade-Navarro M, Régnier-Vigouroux A. Assessing the reliability of gene expression measurements in very-low-numbers of human monocyte-derived macrophages. Sci Rep. 2019 Nov 29;9(1):17908. doi: 10.1038/s41598-019-54500-8.

Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol. 2019 Nov 18;20(1):241. doi: 10.1186/s13059-019-1854-5.

Ibn-Salem J, Andrade-Navarro MA. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. BMC Genomics. 2019 Oct 25;20(1):777. doi: 10.1186/s12864-019-6088-0.

Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res. 2019 Dec 2;47(21):10994-11006. doi: 10.1093/nar/gkz841.

O'Donovan SD, Lenz M, Vink RG, Roumans NJT, de Kok TMCM, Mariman ECM, Peeters RLM, van Riel NAW, van Baak MA, Arts ICW. A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data. PLoS Comput Biol. 2019 Oct 3;15(10):e1007400. doi: 10.1371/journal.pcbi.1007400. eCollection 2019 Oct.

More P, Goedtel-Armbrust U, Shah V, Mathaes M, Kindler T, Andrade-Navarro MA, Wojnowski L. Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells. Oncotarget. 2019 Sep 3;10(51):5298-5312. doi:10.18632/oncotarget.27112. eCollection 2019 Sep 3.

Félix Garza ZC, Lenz M, Liebmann J, Ertaylan G, Born M, Arts ICW, Hilbers PAJ, van Riel NAW. Characterization of disease-specific cellular abundance profiles of chronic inflammatory skin conditions from deconvolution of biopsy samples. BMC Med Genomics. 2019 Aug 17;12(1):121. doi: 10.1186/s12920-019-0567-7.

Kamel M, Mier P, Tari A, Andrade-Navarro MA. Repeatability in protein sequences. J Struct Biol. 2019 Aug 10. pii: S1047-8477(19)30173-X. doi:10.1016/j.jsb.2019.08.003.

Ten Cate V, Koeck T, Panova-Noeva M, Rapp S, Prochaska JH, Lenz M, Schulz A, Eggebrecht L, Hermanns MI, Heitmeier S, Krahn T, Laux V, Münzel T, Leineweber K, Konstantinides SV, Wild PS; Collaborators: Investigators FOCUS BioSeq Study and VTEval Study. A prospective cohort study to identify and evaluate endotypes of venous thromboembolism: Rationale and design of the Genotyping and Molecular Phenotyping in Venous ThromboEmbolism project (GMP-VTE). Thromb Res. 2019 Sep;181:84-91. doi:10.1016/j.thromres.2019.07.019.

Akhtar J, More P, Albrecht S, Marini F, Kaiser W, Kulkarni A, Wojnowski L, Fontaine JF, Andrade-Navarro MA, Silies M, Berger C. TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life Sci Alliance. 2019 Jul 22;2(4). pii: e201900318. doi: 10.26508/lsa.201900318.

El Amrani K, Alanis-Lobato G, Mah N, Kurtz A, Andrade-Navarro MA. Detection of condition-specific marker genes from RNA-seq data with MGFR. PeerJ. 2019 May 27;7:e6970. doi: 10.7717/peerj.6970. eCollection 2019.

Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jimenez J, Pérez-Pulido AJ. AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions. Methods Mol Biol. 2019;1962:207-214. doi: 10.1007/978-1-4939-9173-0_12.

Mier P, Andrade-Navarro MA. Toward completion of the Earth's proteome: an update a decade later. Brief Bioinform. 2019 Mar 22;20(2):463-470. doi: 10.1093/bib/bbx127.

Scheuermann B, Diem T, Ivics Z, Andrade-Navarro MA. Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty. Sci Rep. 2019 Feb 4;9(1):1171. doi: 10.1038/s41598-018-38061-w.

Dabiri Y, Gama-Brambila RA, Taškova K, Herold K, Reuter S, Adjaye J, Utikal J, Mrowka R, Wang J, Andrade-Navarro MA, Cheng X. Imidazopyridines as Potent KDM5 Demethylase Inhibitors Promoting Reprogramming Efficiency of Human iPSCs. iScience. 2019 Jan 11;12:168-181. doi: 10.1016/j.isci.2019.01.012.

Almeida MV, Andrade-Navarro MA, Ketting RF. Function and Evolution of Nematode RNAi Pathways. Noncoding RNA. 2019 Jan 15;5(1). pii: E8. doi:10.3390/ncrna5010008.

Taškova K, Fontaine JF, Mrowka R, Andrade-Navarro MA. Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets. PLoS One. 2019 Jan 14;14(1):e0210467.

Mier P, Andrade-Navarro MA. Traitpedia: a collaborative effort to gather species traits. Bioinformatics. 2019. Mar 15;35(6):1079-1081. doi: 10.1093/bioinformatics/bty743.

Boeddrich A, Babila JT, Wiglenda T, Diez L, Jacob M, Nietfeld W, Huska MR, Haenig C, Groenke N, Buntru A, Blanc E, Meier JC, Vannoni E, Erck C, Friedrich B, Martens H, Neuendorf N, Schnoegl S, Wolfer DP, Loos M, Beule D, Andrade-Navarro MA, Wanker EE. The Anti-amyloid Compound DO1 Decreases Plaque Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice. Cell Chem Biol. 2019 Jan 17;26(1):109-120.e7. doi:10.1016/j.chembiol.2018.10.013.


Härtner F, Andrade-Navarro MA, Alanis-Lobato G. Geometric characterisation of disease modules. Appl Netw Sci. 2018;3(1):10. doi: 10.1007/s41109-018-0066-3. Epub 2018 Jun 18.

Mier P, Pérez-Pulido AJ, Andrade-Navarro MA. Automated selection of homologs to track the evolutionary history of proteins. BMC Bioinformatics. 2018 Nov 19;19(1):431. doi: 10.1186/s12859-018-2457-y.

Krefting J, Andrade-Navarro MA, Ibn-Salem J. Evolutionary stability of topologically associating domains is associated with conserved gene regulation. BMC Biol. 2018 Aug 7;16(1):87. doi: 10.1186/s12915-018-0556-x.

Talyan S, Andrade-Navarro MA, Muro EM. Identification of transcribed protein coding sequence remnants within lincRNAs. Nucleic Acids Res. 2018 Sep 28;46(17):8720-8729. doi: 10.1093/nar/gky608

Mier P, Andrade-Navarro MA. Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length. Genome Biol Evol. 2018 Mar 1;10(3):816-825. doi: 10.1093/gbe/evy046.

Alanis-Lobato G, Mier P, Andrade-Navarro M. The latent geometry of the human protein interaction network. Bioinformatics. 2018 Apr 4. doi: 10.1093/bioinformatics/bty206.

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m(6)A machinery component Wtap/Fl(2)d. Genes Dev. 2018 Mar 1;32(5-6):415-429. doi: 10.1101/gad.309146.117. Epub 2018 Mar 13.

Dallago C, Goldberg T, Andrade-Navarro MA, Alanis-Lobato G, Rost B. CellMap visualizes protein-protein interactions and subcellular localization. F1000Res. 2017 Oct 11;6:1824. doi: 10.12688/f1000research.12707.1. eCollection 2017.

Brüne D, Andrade-Navarro MA, Mier P. Proteome-wide comparison between the amino acid composition of domains and linkers. BMC Res Notes. 2018 Feb 9;11(1):117. doi: 10.1186/s13104-018-3221-0.

Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, Castaños-Vélez E, Fichtner I, Tunn PU, Denkert C, Klaas O, Berdel WE, von Kries JP, Makalowski W, Andrade-Navarro MA, Leutz A, Wethmar K. Loss-of-function uORF mutations in human malignancies. Sci Rep. 2018 Feb 5;8(1):2395. doi: 10.1038/s41598-018-19201-8.

Taškova K, Fontaine JF, Mrowka R, Andrade-Navarro MA. Evaluation of in vivo and in vitro models of toxicity by comparison of toxicogenomics data with the literature. Methods. 2018 Jan 1;132:57-65. doi: 10.1016/j.ymeth.2017.07.010.


Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P, König J. Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Sci Rep. 2017 Nov 29;7(1):16582. doi: 10.1038/s41598-017-16695-6.

Ibn-Salem J, Meiers S, Eigenbrod O, Sehlke R, Talyan S, Schwahn K, Otto R, Pataskar A, Metge F, Angerer P. Highlights of the 1st Student Symposium on Computational Genomics. Genomics Comput Biol. 2017;2(1):e59. doi:10.18547/gcb.2016.vol2.iss1.e59.

Corwin T, Woodsmith J, Apelt F, Fontaine JF, Meierhofer D, Helmuth J, Grossmann A, Andrade-Navarro MA, Ballif BA, Stelzl U. Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate. Cell Syst. 2017 Aug 23;5(2):128-139.e4. doi: 10.1016/j.cels.2017.08.001.

Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC. Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. Am J Hum Genet. 2017 Jul 13. pii: S0002-9297(17)30246-X. doi:10.1016/j.ajhg.2017.06.011.

Jung S, Angarica VE, Andrade-Navarro MA, Buckley NJ, Del Sol A. Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data. Sci Rep. 2017 Jul 5;7(1):4660. doi: 10.1038/s41598-017-04929-6. 28680085

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.

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.

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.

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.

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

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

Mier P, Alanis-Lobato G, Andrade-Navarro MA. Protein-protein interactions can be predicted using coiled coil co-evolution patterns. J Theor Biol. 2017 Jan 7;412:198-203. doi: 10.1016/j.jtbi.2016.11.001. Epub 2016 Nov 7.


Hansen P, Hecht J, Ibn-Salem J, Menkuec BS, Roskosch S, Truss M, Robinson PN. Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus. BMC Genomics. 2016 Nov 4;17(1):873.

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

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

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.

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.

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.

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

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.

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.

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

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.

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.

Piacentino ML, Zuch DT, Fishman J, Rose S, Speranza EE, Li C, Yu J, Chung O, Ramachandran J, Ferrell P, Patel V, Reyna A, Hameeduddin H, Chaves J, Hewitt FB, Bardot E, Lee D, Core AB, Hogan JD, Keenan JL, Luo L, Coulombe-Huntington J, Blute TA, Oleinik E, Ibn-Salem J, Poustka AJ, Bradham CA. RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins. Development. 2016 Feb 15;143(4):703-14. doi: 10.1242/dev.129312. Epub 2016 Jan 11.

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.

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


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.

El Amrani K, 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.

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.

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.

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.

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.

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.

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.

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.

Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Res. 2015 Jun;25(6):825-35. doi:10.1101/gr.185157.114. Epub 2015 Feb 26.

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.

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.

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.


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.

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.

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.

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.

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.

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.

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.

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.


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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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


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.

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.

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.

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.

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.

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.

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.

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


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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.


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

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.

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.

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.

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.

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

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

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

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.

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

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.


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. 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.

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

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.

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.

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

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.

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.


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.

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/

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


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.

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.

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


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


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.

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


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.

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.


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.