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

Alanis-Lobato G, Mier P and Andrade-Navarro MA (2016). Efficient embedding of complex networks to hyperbolic space via their Laplacian. Sci Rep, 6, 30108

Alanis-Lobato G, Mier P and Andrade-Navarro MA (2016). Manifold learning and maximum likelihood estimation for hyperbolic network embedding. Applied Network Science, 1, 10

Andrade-Navarro MA and Fontaine JF (2016). Gene set to diseases (GS2D): Disease enrichment analysis on human gene sets with literature data. Genomics and Computational Biology, 2, e33

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Hei Ho C, Kreim N, Andrade-Navarro MA, Poeck B, Helm M and Roignant JY (2016). m6A modulates neuronal functions and sex determination in Drosophila. Nature, 540, 242–247

Mier P and Andrade-Navarro MA (2016). CABRA: Cluster and annotate blast results algorithm. BMC Res Notes, 9, 253

Mier P and Andrade-Navarro MA (2016). FastaHerder2: Four ways to research protein function and evolution with clustering and clustered databases. J Comput Biol, 23, 270-278

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

Petrakis S and Andrade-Navarro MA (2016). Editorial: Protein interaction networks in health and disease. Front Genet, 7, 111

Riemke P, Walter C, Ghani S, Fischer J, Zepper M, Agelopoulos K, Lettermann S, Gebhardt ML, Mah N, Weilemann A, Grau M, Haferlach T, Delwel R, Prinz M, Andrade-Navarro MA, Lenz G, Dugas M, Müller-Tidow C and Rosenbauer F (2016). Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors. EMBO J, 35, 2399-2416

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

Schmid F, Wang Q, Huska MR, Andrade-Navarro MA, Lemm M, Fichtner I, Dahlmann M, Kobelt D, Walther W, Smith J, Schlag PM and Stein U (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

Wethmar K, Schulz J, Muro EM, Talyan S, Andrade-Navarro MA and Leutz A (2016). Comprehensive translational control of tyrosine kinase expression by upstream open reading frames. Oncogene, 35, 1736-1742

Andrade-Navarro MA and Perez-Iratxeta C (2015). Text mining of biomedical literature: Doing well, but we could be doing better. Methods, 1-2

Buschmann H, Dols J, Kopischke S, Peña EJ, Andrade-Navarro MA, Heinlein M, Szymanski DB, Zachgo S, Doonan JH and Lloyd CW (2015). Arabidopsis KCBP interacts with AIR9 but stays in the cortical division zone throughout mitosis via its MyTH4-FERM domain. J Cell Sci, jcs-156570

Cheng X, Dimou E, Alborzinia H, Wenke F, Goehring A, Reuter S, Mah N, Fuchs HR, Andrade-Navarro MA and Adjaye J (2015). Identification of 2-[4-[(4-methoxyphenyl) methoxy]-phenyl] acetonitrile and derivatives as potent Oct3/4 inducers. J Medic Chem, 58, 4976-4983

Cheng X, Yoshida H, Raoofi D, Alborzinia H, Wenke F, Göhring A, Reuter S, Mah N, Fuchs H, Andrade-Navarro MA, Adjaye J, Gul S, Utikal J, Mrowka R and Wölfl S (2015). Ethyl 2-((4 chlorophenyl)amino) thiazole-4-carboxylate and derivatives are potent inducers of Oct3/4. J Med Chem, 58, 5742-5750

El Amrani K, Stachelscheid H, Lekschas F, Kurtz A and Andrade-Navarro MA (2015). MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. BMC Genomics, 28, 645

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

Gebhardt ML, Mer AS and Andrade-Navarro MA (2015). mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data. BMC Research Notes, 8, 157

Louis-Jeune C, Andrade-Navarro MA and Perez-Iratxeta C (2015). FASTA Herder: a web application to trim protein sequence sets. ScienceOpen Research, doi:10.14293/A2199-1006.01.SOR-LIFE.67837.v2

Mier P, Andrade-Navarro MA and Pérez-Pulido AJ (2015). orthoFind facilitates the discovery of homologous and orthologous proteins. PloS One, 10, e0143906

Schaefer MH, Serrano L and Andrade-Navarro MA (2015). Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions in different cancer types. Front Genet, 4, 260

Shih J, Hodge R and Andrade-Navarro MA (2015). Comparison of inter-and intraspecies variation in humans and fruit flies. Genomics Data, 3, 49-54

Stroedicke M, Bounab Y, Strempel N, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F,  Riechers SP, Russ J, Nicoletti C, Haenig C, Schnoegl S, Fournier D, Graham RK, Hayden MR, Sigrist S, Bates GP, Priller J, Andrade-Navarro MA, Futschik ME and Wanker EE (2015). Systematic interaction network filtering identifies CRMP-1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Res, 25, 701-713

Bader M, Alenina N, Andrade-Navarro MA and Santos RA (2014). Mas and its related G protein-coupled receptors, Mrgprs. Pharmacol Rev, 66, 1080-1105

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

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

Gebhardt ML, Reuter S, Mrowka R, and Andrade-Navarro MA (2014). Similarity in targets with REST points to neural and glioblastoma related miRNAs. Nucleic Acids Res, 42, 5436-5446

Gijón-Correas JA, Andrade-Navarro MA and Fontaine JF (2014). Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Res, 42, W422-429

Norton M, Cheuk-Him Ng A, Baird S, Dumoulin A, Shutt T, Mah N, Andrade-Navarro MA, McBride HM, Screaton RA (2014). Genome-wide RNAi screen identifies ROMO1 as an essential redox-dependent regulator of mitochondrial cristae dynamics. Sci Signal, 7, ra10

Suratanee A, Schaefer MH, Betts MJ, Soons Z, Mannsperger H, Harder N, Oswald M, Gipp M, Ramminger E, Marcus G, Männer R, Rohr K, Wanker E, Russell RB, Andrade-Navarro MA, Eils R, König R (2014). Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PLoS Comp Biol, 10, e1003814

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

Voss F, Ullrich F, Münch J, Lazarow K, Lutter D, Mah N, Andrade-Navarro MA, von Kries JP, Stauber T, and Jentsch TJ (2014). Identification of LRRC8 heteromers as essential component of the volume-regulated anion channel VRAC. Science, 344, 634-638

Wethmar K, Barbosa da Silva A, Andrade-Navarro A and Leutz A (2014). uORFdb – a comprehensive literature database on eukaryotic uORF biology. Nucleic Acids Res, 42, D60-D67

Andrade-Navarro MA, Kanji F, Palii C, Brand M, Atkins H and Perez-Iratxeta C (2013). Cell marker discovery by high-throughput gene expression analysis of mixed cell populations. BMC Biotechnol, 13, 80

Fournier D, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Perez-Iratxeta C and Andrade-Navarro MA (2013). Functional and genomic analyses of alpha-solenoid proteins. PLOS ONE, 8, e79894

Mer AS and Andrade-Navarro MA (2013). A novel approach for protein subcellular location prediction using amino acid exposure. BMC Bioinformatics, 14, 342

Ortuño F, Rojas I, Andrade-Navarro MA and Fontaine JF (2013). Using cited references to improve the retrieval of related biomedical documents. BMC Bioinformatics, 14, 113

Petrakis S, Schaefer MH, Wanker E, Andrade-Navarro MA (2013). Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled coil partners. Bioessays, 35, 503-507

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

Schaefer MH, Lopes TJS, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Amie Eisfeld C, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA (2013). Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLOS Comp Biol, 9, e1002860

Schmid F, Wang Q, Huska MR, Andrade-Navarro MA, Lemm M, Fichtner I, Walther W, Schlag PM and Stein US (2013). S100P, a target gene of MACC1, contributes to colorectal cancer metastasis. Cancer Res, 73, 416

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

Suter B, Fontaine JF, Yildrimann 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 (2013). Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Res, 41, 1496-1507

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

von Eichborn J, Dunkel M, Gohlke B, Preissner S, Hoffmann M, Bauer J, Armstrong J, Schaefer MH, Andrade-Navarro MA, LeNovere N, Croning M, Grant S, van Nierop P, Smit A, Preissner R (2013). SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Res, 41, D834-D840

Andrade-Navarro MA (2012). Mining the literature: new methods to exploit keyword profiles. [Research highlight]. Genome Med, 8, 41

Andrade-Navarro MA, Palidwor GA and Perez-Iratxeta CA (2012). Peer2ref: a peer-reviewer finding web tool that uses author disambiguation. BioData Min, 5, 14

Fournier D, Luft FC, Bader M, Ganten D and Andrade-Navarro MA (2012). Emergence and evolution of the renin-angiotensin-aldosterone system. J Mol Med, 90, 495-508

Herault O, Hope KJ, Deneault E, Mayotte N, Chagraoui J, Wilhelm BT, Cellot S, Faubert A, Austin P, Trost M, Fréchette M, Voisin L, Chagnon P, Soucie E, Sauvageau M, Andrade-Navarro MA, Sauvageau G (2012). A role for GPx3 in activity of normal and leukemia stem cells. J Exp Med, 209, 895-901

Krzyzanowski PM, Muro EM and Andrade-Navarro MA (2012). Computational approaches to discovering non-coding RNA. Wiley Interdiscip Rev: RNA, 3, 567-579

Louis-Jeune C, Andrade-Navarro MA and Perez-Iratxeta C (2012). Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins, 80, 374-381

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

Muro EM and Andrade-Navarro MA (2012). Natural Antisense Transcripts within pseudogenes: an EST survey. In Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection. (Ed. K Morris). Horizon Scientific Press. 99-108

Petrakis S, Rasko T, Russ J, Friedrich RP, Stroedicke M, Riechers SP, Muehlenberg K, Moeller A, Reinhardt A, Vinayagam A, Schaefer MH, Boutros M, Tricoire H, Andrade-Navarro MA and Wanker EE (2012). Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1. PLOS Genet, 8, e1002897

Sandie R, Porter CJ, Palidwor GA, Price F, Krzyzanowski PM, Muro EM, Hoersch S, Smith M, Campbell PA, Perez-Iratxeta C, Rudnicki MA, Andrade-Navarro MA (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

Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE and Andrade-Navarro MA (2012). HIPPIE: integrating protein interaction networks with experiment based quality scores. PLOS One, 7, e31826

Schaefer MH, Wanker EE and Andrade-Navarro MA (2012). Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res, 40, 4273-4287

Wethmar K, Schulz J, Muro E, Andrade-Navarro M and Leutz A (2012). Translational control of tyrosine kinase expression by upstream open reading frames (uORFs). Oncologie, 35, 80-81

Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Miguel-Ortega J and Andrade-Navarro MA (2011). PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics, 12, 435

Donnard E, Barbosa-Silva A, Guedes RM, Fernandes G, Velloso H, Kohn MJ, Andrade-Navarro MA, Ortega JM (2011). Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics, 12 Suppl 4, S3

Fontaine JF, Priller F, Barbosa-Silva A and Andrade-Navarro MA (2011). Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res, 39:W455-W461

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

Fournier D and Andrade-Navarro MA (2011). PDBpaint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics, 27, 2605-2606

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 and Valencia A (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

Krzyzanowski PM, Price FD, Muro EM, Rudnicki MA and Andrade-Navarro MA (2011). Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLoS One, 6, e20561

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

Lopes TJ, Schaefer M, Schoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y and Kitano H (2011). Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics, 27, 2414-2421

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 and Adjaye J (2011). Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network. PLoS One, 6, e24351

Muro EM, Mah N and Andrade-Navarro MA (2011). Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie, 93, 1916-1921

Muro EM, Mah N, Moreno-Hagelsieb G and Andrade-Navarro MA (2011). The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Nucleic Acids Res, 39, 1732-1738

Posch MG, Waldmuller S, Muller M, Scheffold T, Fournier D, Andrade-Navarro MA, De Geeter B, Giullaumont S, Dauphin C, Zousseff D, Schmitt KRL, Perrot A, Berger F, Hetzer R, Bouvagnet P and Özcelik C (2011). Cardiac alpha-myosin (MYH6) is the predominant sarcomeric disease gene for familial atrial septal defects. PLOS One, 6, e28872

Simon B, Kirkpatrick JP, Eckhardt S, Reuter M, Rocha EA, Andrade-Navarro MA, Sehr P, Pillai RS and Carlomagno T (2011). Recognition of 2’-O-methylated 3’-end of piRNA by the PAZ domain of a piwi protein. Structure, 19, 172-180

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

Wanker EE, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Vinayagam A, Stelzl U, Foulle R and Plassmann S (2011). A Directed Protein Interaction Network for Investigating Intracellular Signal. Sci Signal, 4, rs8

Barbosa-Silva A, Soldatos TG, Magalhães ILF, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R and Ortega JM (2010). LAITOR – literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics, 11, 70

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

Fontaine J-F and Andrade-Navarro MA (2010). Fast classification of scientific abstracts related to protein-protein interaction using a naïve Bayesian linear classifier. Proceedings of BioCreative III, Maryland, USA, 62-66

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

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

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

Palidwor G and Andrade-Navarro MA (2010). MLTrends: Graphing MEDLINE term usage over time. J Biomed Discov Collab, 5, 1-6

Scimè A, Desrosiers J, Trensz F, Palidwor GA, Caron AZ, Andrade-Navarro MA and Grenier G (2010). Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing. Mech Ageing Dev,131, 9-20

Striegl H, Andrade-Navarro MA and Heinemann U (2010). Armadillo motifs involved in vesicular transport. PLoS One, 5, e8991

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

Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA and Akimenko M (2010). Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature, 466, 234-7

Andrade-Navarro MA (2009). The dictionary of genomics, transcriptomics and proteomics. [Book review]. Bioessays, 31, 1367–1369

Andrade-Navarro MA, Sanchez-Pulido L and McBride HM (2009). Mitochondrial vesicles: an ancient process providing new links to peroxisomes. Curr Opin Cell Biol, 21, 560-567

Bröske A, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M, Enns A, Prinz M, Jaenisch R, Nerlov C, Leutz A, Andrade-Navarro MA, Jacobsen SEW and Rosenbauer F (2009). DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nature Genet, 41, 207-215

Fontaine J, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM and Andrade-Navarro MA (2009). MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res, 37, W141-W146

Muro EM, McCann JA, Rudnicki MA and Andrade-Navarro MA. Use of SNP-Arrays for ChIP assays: computational aspects. Methods Mol Biol, 567, 145-154

Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, Arumughan A, Foulle R, Porras P, Sanchez-Pulido L, Wanker EE and Andrade-Navarro MA (2009). Detection of alpha-rod repeats using a neural network and application to huntingtin. PLOS Comp Biol, 5, e1000304

Sandie R, Palidwor GA, Huska MR, Porter CJ, Krzyzanowski PM, Muro EM, Perez-Iratxeta C and Andrade-Navarro MA (2009). Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. BMC Res Notes, 2, 39

Schaefer M and Andrade-Navarro MA (2009). Evidence for a functional role of CAG/glutamine repeats. German Conference on Bioinformatics, 159

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