Publications - RG3: Molecular Networks in Medical Bioinformatics

Publications ( PubMed | Google Scholar | ResearchGATE | ResearcherID | Microsoft Academic Search )

  1. Malek, M., Ibragimov, R., Albrecht, M., Baumbach, J.
    CytoGEDEVO - global alignment of biological networks with Cytoscape.
    Bioinformatics, 32(9):1259-1261, 2016. (10.1093/bioinformatics/btv732) (pmid:26669930)
    (Abstract) (Supplement)

  2. Poenisch, M., Metz, P., Blankenburg, H., Ruggieri, A., Lee, J.Y., Rupp, D., Rebhan, I., Diederich, K., Kaderali, L., Domingues, F.S., Albrecht, M., Lohmann, V., Erfle, H., Bartenschlager, R.
    Identification of HNRNPK as regulator of hepatitis C virus particle production.
    PLoS Pathogens, 11(1):e1004573.1-21, 2015. (doi:10.1371/journal.ppat.1004573) (pmid:25569684)
    (Abstract) (Supplement)

  3. Pohlmann, T., Baumann, S., Haag, C., Albrecht, M., Feldbrügge, M.
    A FYVE domain protein specifically links mRNA transport to endosome trafficking.
    eLIFE, 4:e06041.1-27, 2015. (doi:10.7554/eLife.06041) (pmid:25985087)
    (Abstract)

  4. Andreassen, O.A., Desikan, R.S., Wang, Y., Thompson, W.K., Schork, A.J., Zuber, V., Doncheva, N.T., Ellinghaus, E., Albrecht, M., Mattingsdal, M., Franke, A., Lie, B.A., Mills, I., Aukrust, P., McEvoy, L.K., Djurovic, S., Karlsen, T.H., Dale, A.M.
    Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms.
    PLoS ONE, 10(4):e0123057.1-17, 2015. (doi:10.1371/journal.pone.0123057) (pmid:25853426)
    (Abstract) (Supplement)

  5. Doncheva, N.T., Klein, K., Morris, J.H., Wybrow, M., Domingues, F.S., Albrecht, M.
    Integrative visual analysis of protein sequence mutations.
    BMC Proceedings, 8(Suppl 2):S2.1-11, 2014. (doi:10.1186/1753-6561-8-S2-S2) (pmid:25237389)
    (Abstract) (First presented as Data Contest Overall Favorite at the 3rd IEEE Symposium on Biological Data Visualization (BioVis), Atlanta, GA, USA, 2013.)

  6. Morris, J.H., Wu, A., Doncheva, N.T., Albrecht, M., Ferrin, T.E.
    setsApp: Set operations for Cytoscape nodes and edges.
    F1000Research, 3:149.1-10, 2014. (doi:10.12688/f1000research.4392.1) (pmid:25352980)
    (Abstract)

  7. Bouter, Y., Kacprowski, T., Weissmann, R., Dietrich, K., Borgers, H., Brauß, A., Sperling, C., Wirths, O., Albrecht, M., Jensen, L.R., Kuss, A.W., Bayer, T.A.
    Deciphering the molecular profile of plaques, memory decline and neuron loss in two mouse models for Alzheimer’s disease by deep sequencing.
    Frontiers in Aging Neuroscience, 6(4):75.1-28, 2014. (doi:10.3389/fnagi.2014.00075) (pmid:24795628)
    (Abstract)

  8. Zanon, A., Rakovic, A., Blankenburg, H., Doncheva, N.T., Schwienbacher, C., Serafin, A., Alexa, A., Weichenberger, C.X., Albrecht, M., Klein, C., Hicks, A.A., Pramstaller, P.P., Domingues, F.S., Pichler, I.
    Profiling of parkin-binding partners using tandem affinity purification.
    PLoS ONE, 8(11):e78648.1-17, 2013. (doi:10.1371/journal.pone.0078648) (pmid:24244333)
    (Abstract) (Supplement)

  9. Kacprowski, T., Doncheva, N.T., Albrecht, M.
    NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules.
    Bioinformatics, 29(11):1471-1473, 2013. (doi:10.1093/bioinformatics/btt164) (pmid:23595661)
    (Abstract) (First presented as Highlight Paper at the German Conference on Bioinformatics (GCB), Göttingen, Germany, 2013.)

  10. Foerster, S., Kacprowski, T., Dhople, V.M., Hammer, E., Herzog, S., Saafan, H., Bien-Möller, S., Albrecht, M., Völker, U., Ritter, C.A.
    Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics.
    Proteomics, 13(21):3131-3144, 2013. (doi:10.1002/pmic.201300154) (pmid:23956138)
    (Abstract) (Supplement)

  11. Liu, J.Z., Hov, J.R., Folseraas, T., Ellinghaus, E., Rushbrook, S.M., Doncheva, N.T., Andreassen, O.A., Weersma, R.K., Weismüller, T.J., Eksteen, B., Invernizzi, P., Hirschfield, G.M., Gotthardt, D.N, Pares, A., Ellinghaus, D., Shah, T., Juran, B.D., Milkiewicz, P., Rust, C., Schramm, C., Müller, T., Srivastava, B., Dalekos, G., Nöthen, M.M., Herms, S., Winkelmann, J., Mitrovic, M., Braun, F., Ponsioen, C.Y., Croucher, P.J., Sterneck, M., Teufel, A., Mason, A.L., Saarela, J., Leppa, V., Dorfman, R., Alvaro, D., Floreani, A., Onengut-Gumuscu, S., Rich, S.S., Thompson, W.K., Schork, A.J., Næss, S., Thomsen, I., Mayr, G., König, I.R., Hveem, K., Cleynen, I., Gutierrez-Achury, J., Ricaño-Ponce, I., van Heel, D., Björnsson, E., Sandford, R.N., Durie, P.R., Melum, E., Vatn, M.H., Silverberg, M.S., Duerr, R.H., Padyukov, L., Brand, S., Sans, M., Annese, V., Achkar, J.P., Boberg, K.M., Marschall, H.U., Chazouillères, O., Bowlus, C.L., Wijmenga, C., Schrumpf, E., Vermeire, S., Albrecht, M.; The UK-PSCSC Consortium; The International IBD Genetics Consortium, Rioux, J.D., Alexander, G., Bergquist, A., Cho, J., Schreiber, S., Manns, M.P, Färkkilä, M., Dale, A.M., Chapman, R.W., Lazaridis, K.N.; The International PSC Study Group, Franke, A., Anderson, C.A., Karlsen, T.H.
    Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.
    Nature Genetics, 45(6):670-677, 2013. (doi:10.1038/ng.2616) (pmid:23603763)
    (Abstract) (Supplement) (Press release 1) (Press release 2 in English) (Press release 2 in German)

  12. Ellinghaus, D., Zhang, H., Zeissig, S., Lipinski, S., Till, A., Jiang, T., Stade, B., Bromberg, Y., Ellinghaus, E., Keller, A., Rivas, M.A., Skieceviciene, J., Doncheva, N.T., Liu, X., Liu, Q., Jiang, F., Forster, M., Mayr, G., Albrecht, M., Häsler, R., Boehm, B.O., Goodall, J., Berzuini, C.R., Lee, J., Andersen, V., Vogel, U., Kupcinskas, L., Kayser, M., Krawczak, M., Nikolaus, S., Weersma, R.K., Ponsioen, C.Y., Sans, M., Wijmenga, C., Strachan, D.P., McArdle, W.L., Vermeire, S., Rutgeerts, P., Sanderson, J.D., Mathew, C.G., Vatn, M.H., Wang, J., Nöthen, M.M., Duerr, R.H., Büning, C., Brand, S., Glas, J., Winkelmann, J., Illig, T., Latiano, A., Annese, V., Halfvarson, J., D'Amato, M., Daly, M.J., Nothnagel, M., Karlsen, T.H., Subramani, S., Rosenstiel, P., Schreiber, S., Parkes, M., Franke, A.
    Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies.
    Gastroenterology, 145(2):339-347, 2013. (doi:10.1053/j.gastro.2013.04.040) (pmid:23624108)
    (Abstract) (Supplement)

  13. Blankenburg, H., Albrecht, M.
    PSISCORE.
    In Encyclopedia of Systems Biology, Springer-Verlag, Heidelberg, Germany, ISBN 978-1-4419-9862-0, 1801-1802, 2013. (doi:10.1007/978-1-4419-9863-7_1464)
    (Abstract)

  14. Doncheva, N.T., Kacprowski, T., Albrecht, M.
    Recent approaches to the prioritization of candidate disease genes.
    Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 4(5):429-442, 2012. (doi:10.1002/wsbm.1177) (pmid:22689539)
    (Abstract)

  15. Garai, A., Zeke, A., Gógl, G., Törő, I., Fördő, F., Blankenburg, H., Bárkai, T., Varga, J., Alexa, A., Emig, D., Albrecht, M., Reményi, A.
    Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove.
    Science Signaling, 5(245), ra74.1-14, 2012. (doi:10.1126/scisignal.2003004) (pmid:23047924)
    (Abstract) (Supplement) (Summary)

  16. Ramírez, F., Lawyer, G., Albrecht, M.
    Novel search method for the discovery of functional relationships.
    Bioinformatics, 28(2):269-276, 2012. (doi:10.1093/bioinformatics/btr631) (pmid:22180409)
    (Abstract) (Supplement)

  17. Faria, D., Schlicker, A., Pesquita, C., Bastos, H., Ferreira, A.E., Albrecht, M., Falcão, A.O.
    Mining GO annotations for improving annotation consistency.
    PLoS ONE, 7(7):e40519.1-7, 2012. (doi:10.1371/journal.pone.0040519) (pmid:22848383)
    (Abstract) (Supplement)

  18. Emig, D., Blankenburg, H., Ramírez, F., Albrecht, M.
    Functional characterization of human genes from exon expression and RNA interference results.
    In Bioinformatics and Drug Discovery (2nd Edition), Methods in Molecular Biology, Springer Protocols, Humana Press, New York, NY, USA, ISBN 978-1-61779-964-8, 910:33-53, 2012. (doi:10.1007/978-1-61779-965-5_3) (pmid:22821591)
    (Abstract)

  19. Lengauer, T., Albrecht, M., Domingues, F.S.
    Computational Biology.
    In Encyclopedia of Molecular Cell Biology and Molecular Medicine (2nd Edition), Wiley-VCH Verlag, Weinheim, Germany, ISBN 978-3-527-60090-8, 1-71, 2012. Also in Systems Biology: Advances in Molecular Biology and Medicine (Current Topics from the Encyclopedia of Molecular Cell Biology and Molecular Medicine), Wiley-VCH Verlag, Weinheim, Germany, ISBN 978-3-527-32607-5, 277-348, 2012. (doi:10.1002/3527600906.mcb.200400023.pub2)
    (Abstract)

  20. Doncheva, N.T., Assenov, Y., Domingues, F.S., Albrecht, M.
    Topological analysis and interactive visualization of biological networks and protein structures.
    Nature Protocols, 7(4):670-685, 2012. (doi:10.1038/nprot.2012.004) (pmid:22422314)
    (Abstract) (Press article in English) (Press article in German)

  21. Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M.
    Analyzing and visualizing residue networks of protein structures.
    Trends in Biochemical Sciences, 36(4):179-182, 2011. (doi:10.1016/j.tibs.2011.01.002) (pmid:21345680)
    (Abstract) (Press release) (Press article in English) (Press article in German)

  22. Aranda, B., Blankenburg, H., Kerrien, S., Brinkman, F.S., Ceol, A., Chautard, E., Dana, J.M., De Las Rivas, J., Dumousseau, M., Galeota, E., Gaulton, A., Goll, J., Hancock, R.E., Isserlin, R., Jimenez, R.C., Kerssemakers, J., Khadake, J., Lynn, D.J., Michaut, M., OKelly, G., Ono, K., Orchard, S., Prieto, C., Razick, S., Rigina, O., Salwinski, L., Simonovic, M., Velankar, S., Winter, A., Wu, G., Bader, G.D., Cesareni, G., Donaldson, I.M., Eisenberg, D., Kleywegt, G.J., Overington, J., Ricard-Blum, S., Tyers, M., Albrecht, M., Hermjakob, H.
    PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
    Nature Methods, 8(7):528-529, 2011. (doi:10.1038/nmeth.1637) (pmid:21716279)
    (Abstract) (Supplement)

  23. Schelhorn, S.E., Mestre, J., Albrecht, M., Zotenko, E.
    Inferring physical protein contacts from large-scale purification data of protein complexes.
    Molecular & Cellular Proteomics, 10(6):M110.004929.1-15, 2011. (doi:10.1074/mcp.M110.004929) (pmid:21451165)
    (Abstract) (Supplement)

  24. Emig, D., Albrecht, M.
    Tissue-specific proteins and functional implications.
    Journal of Proteome Research, 10(4):18931903, 2011. (doi:10.1021/pr101132h) (pmid:21341747)
    (Abstract) (Supplement)

  25. Emig, D., Kacprowski, T., Albrecht, M.
    Measuring and analyzing tissue specificity of human genes and protein complexes.
    EURASIP Journal on Bioinformatics and Systems Biology, 2011(1):5.1-6, 2011. (doi:10.1186/1687-4153-2011-5) (pmid:21970702)
    (Abstract) (First presented and published in Proceedings of the 7th International Workshop on Computational Systems Biology (WCSB), Luxembourg, 2010, in
    Tampere International Center for Signal Processing (TICSP series), Tampere University of Technology, Tampere, Finland, ISBN 978-952-15-2384-7, 51:27-30, 2010.)

  26. Emig, D., Sander, O., Mayr, G., Albrecht, M.
    Structure collisions between interacting proteins.
    PLoS ONE, 6(6):e19581.1-7, 2011. (doi:10.1371/journal.pone.0019581) (pmid:21655095)
    (Abstract) (Supplement)

  27. Nebot, V., Min, Y., Albrecht, M., Eom, J.H., Weikum, G.
    DIDO: a disease-determinants ontology from web sources.
    In Proceedings of the 20th International Conference on World Wide Web (WWW 2011), ACM, New York, NY, USA, ISBN 978-1-4503-0637-9, 237-240, 2011. (doi:10.1145/1963192.1963298)
    (Abstract) (First presented and published at the 20th International World Wide Web Conference (WWW), Hyderabad, India, 2011.)

  28. Wittkop, T., Emig, D., Truss, A., Albrecht, M., Böcker, S., Baumbach, J.
    Comprehensive cluster analysis with Transitivity Clustering.
    Nature Protocols, 6(3):285-295, 2011. (doi:10.1038/nprot.2010.197) (pmid:21372810)
    (Abstract)

  29. Reiss, S., Rebhan, I., Backes, P., Romero-Brey, I., Erfle, H., Matula, P., Kaderali, L., Poenisch, M., Blankenburg, H., Hiet, M.S., Longerich, T., Diehl, S., Ramírez, F., Balla, T., Rohr, K., Kaul, A., Bühler, S., Pepperkok, R., Lengauer, T., Albrecht, M., Eils, R., Schirmacher, P., Lohmann, V., Bartenschlager, R.
    Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.
    Cell Host & Microbe, 9(1):32-45, 2011. (doi:10.1016/j.chom.2010.12.002) (pmid:21238945)
    (Abstract) (Supplement) (Preview) (Press release) (Press article in English) (Press article in German)

  30. Ellinghaus, E., Ellinghaus, D., Stuart, P.E., Nair, R.P., Debrus, S., Raelson, J.V., Belouchi, M., Fournier, H., Reinhard, C., Ding, J., Li, Y., Tejasvi, T., Gudjonsson, J., Stoll, S.W., Voorhees, J.J., Lambert, S., Weidinger, S., Eberlein, B., Kunz, M., Rahman, P., Gladman, D.D., Gieger, C., Wichmann, H.E., Karlsen, T.H., Mayr, G., Albrecht, M., Kabelitz, D., Mrowietz, U., Abecasis, G.R., Elder, J.T., Schreiber, S., Weichenthal, M., Franke, A.
    Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2.
    Nature Genetics, 42(11):991-995, 2010. (doi:10.1038/ng.689) (pmid:20953188)
    (Abstract) (Supplement) (Press release)

  31. Albrecht, M.
    Color blindness.
    Nature Methods, 7(10):775, 2010. (doi:10.1038/nmeth1010-775a) (pmid:20885436)
    (Abstract)

  32. Schlicker, A., Lengauer, T., Albrecht, M.
    Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
    Bioinformatics, 26(18):i561-i567, 2010. (doi:10.1093/bioinformatics/btq384) (pmid:20823322)
    (Abstract) (Supplement) (First presented and published at the 9th European Conference on Computational Biology (ECCB), Ghent, Belgium, 2010.)

  33. Brunner, S., Hurni, S., Streckeisen, P., Mayr, G., Albrecht, M., Yahiaoui, N., Keller, B.
    Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles.
    The Plant Journal, 64(3):433-445, 2010. (doi:10.1111/j.1365-313X.2010.04342.x) (pmid:20804457)
    (Abstract) (Supplement)

  34. Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B.R., Albrecht, M.
    AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
    Nucleic Acids Research, 38(Web Server issue):W755-W762, 2010. (doi:10.1093/nar/gkq405) (pmid:20513647)
    (Abstract) (Press release) (Newsletter)

  35. Welker, M.W., Welsch, C., Meyer, A., Antes, I., Albrecht, M., Forestier, N., Kronenberger, B., Lengauer, T., Piiper, A., Zeuzem, S., Sarrazin, C.
    Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper.
    Protein Science, 19(7):1327-1336, 2010. (doi:10.1002/pro.409) (pmid:20506268)
    (Abstract)

  36. Wittkop, T., Emig, D., Lange, S., Rahmann, S., Albrecht, M., Morris, J.H., Böcker, S., Stoye, J., Baumbach, J.
    Partitioning biological data with transitivity clustering.
    Nature Methods, 7(6):419-420, 2010. (doi:10.1038/nmeth0610-419) (pmid:20508635)
    (Abstract) (Supplement)

  37. Franke, A., Balschun, T., Sina, C., Ellinghaus, D., Hsler, R., Mayr, G., Albrecht, M., Wittig, M., Buchert, E., Nikolaus, S., Gieger, C., Wichmann, H.E., Sventoraityte, J., Kupcinskas, L., Onnie, C.M., Gazouli, M., Anagnou, N.P., Strachan, D., McArdle, W.L., Mathew, C.G., Rutgeerts, P., Vermeire, S., Vatn, M.H., the IBSEN study group, Krawczak, M., Rosenstiel, P., Karlsen, T.H., Schreiber, S.
    Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL).
    Nature Genetics, 42(4):292-294, 2010. (doi:10.1038/ng.553) (pmid:20228798)
    (Abstract) (Supplement) (Press release)

  38. Ramírez, F., Albrecht, M.
    Finding scaffold proteins in interactomes.
    Trends in Cell Biology, 20(1):2-4, 2010. (doi:10.1016/j.tcb.2009.11.003) (pmid:20005715)
    (Abstract) (Supplement)

  39. Schlicker, A., Albrecht, M.
    FunSimMat update: new features for exploring functional similarity.
    Nucleic Acids Research, 38(Database issue):D244-248, 2010. (doi:10.1093/nar/gkp979) (pmid:19923227)
    (Abstract)

  40. Albrecht, M., Kerren, A., Klein, K., Kohlbacher, O., Mutzel, P., Paul, W., Schreiber, F., Wybrow, M.
    On open problems in biological network visualization.
    Lecture Notes in Computer Science, Springer-Verlag, Berlin, Germany, ISBN 978-3-642-11804-3, 5849:256-267, 2010. (doi:10.1007/978-3-642-11805-0_25)
    (Abstract) (First presented and published at the 17th International Symposium on Graph Drawing (GD), Chicago, IL, USA, 2009.)

  41. Blankenburg, H., Finn, R.D., Prlić, A., Jenkinson, A.M., Ramírez, F., Emig, D., Schelhorn, S.E., Büch, J., Lengauer, T., Albrecht, M.
    DASMI: exchanging, annotating and assessing molecular interaction data.
    Bioinformatics, 25(10):1321-1328, 2009. (doi:10.1093/bioinformatics/btp142) (pmid:19420069)
    (Abstract) (Supplement) (Press release)

  42. Blankenburg, H., Ramírez, F., Büch, J., Albrecht, M.
    DASMIweb: online integration, analysis and assessment of distributed protein interaction data.
    Nucleic Acids Research, 37(Web Server issue):W122-W128, 2009. (doi:10.1093/nar/gkp438) (pmid:19502495)
    (Abstract) (Press release)

  43. Frishman, D., Albrecht, M., Blankenburg, H., Bork, P., Harrington, E.D., Hermjakob, H., Jensen, L.J., Juan, D.A., Lengauer, T., Pagel, P., Schachter, V., Valencia, A.
    Protein-protein interactions: analysis and prediction.
    In Modern Genome Annotation: The Biosapiens Network, Springer-Verlag, Wien, Austria, ISBN 978-3-211-75122-0, 353-410, 2008. (doi:10.1007/978-3-211-75123-7_17)
    (Abstract)

  44. Schelhorn, S.E., Lengauer, T., Albrecht, M.
    An integrative approach for predicting interactions of protein regions.
    Bioinformatics, 24(16):i35-i41, 2008. (doi:10.1093/bioinformatics/btn290) (pmid:18689837)
    (Abstract) (Supplement) (First presented and published at the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 2008.)

  45. Emig, D., Cline, M.S., Lengauer, T., Albrecht, M.
    Integrating expression data with domain interaction networks.
    Bioinformatics, 24(21):2546-2548, 2008. (doi:10.1093/bioinformatics/btn437) (pmid:18710874)
    (Abstract) (First presented at the 6th Annual Cytoscape Retreat, Toronto, Canada, 2008.)

  46. Franke, A., Balschun, T., Karlsen, T.H., Sventoraityte, J., Nikolaus, S., Mayr, G., Domingues, F.S., Albrecht, M., Nothnagel, M., Ellinghaus, D., Sina, C., Onnie, C.M., Weersma, R.K., Stokkers, P.C.F., Wijmenga, C., Gazouli, M., Strachan, D., McArdle, W.L., Vermeire, S., Rutgeerts, P., Rosenstiel, P., Krawczak, M., Vatn, M.H., the IBSEN study group, Mathew, C.G., Schreiber, S.
    Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis susceptibility.
    Nature Genetics, 40(11):1319-1323, 2008. (doi:10.1038/ng.221) (pmid:18836448)
    (Abstract) (Supplement) (Press release 1) (Press release 2)

  47. Emig, D., Cline, M.S., Klein, K., Kunert, A., Mutzel, P., Lengauer, T., Albrecht, M.
    Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.
    Journal of Integrative Bioinformatics, 5(2):101.1-15, 2008. (doi:10.2390/biecoll-jib-2008-101) (pmid:20134061)
    (Abstract) (First presented and published at the 5th Annual Meeting of the International Symposium on Integrative Bioinformatics (IB08), Lutherstadt Wittenberg, Germany, 2008.)

  48. Emig, D., Klein, K., Kunert, A., Mutzel, P., Albrecht, M.
    Visualizing domain interaction networks and the impact of alternative splicing events.
    In Proceedings of the 5th International Conference on BioMedical Visualization (MediVis): Information Visualization in Medical and Biomedical Informatics, IEEE Computer Society, Los Alamitos, CA, USA, ISBN 978-0-7695-3284-4, 36-43, 2008. (doi:10.1109/MediVis.2008.16)
    (Abstract) (First presented and published at the 2nd International Symposium of Information Visualization in Biomedical Informatics (IVBi) as part of MediVis, London, United Kingdom, 2008.)

  49. Jenkinson, A.M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R.D., Hermjakob, H., Hubbard, T.J., Jimenez, R.C., Jones, P., Kähäri, A., Kulesha, E., Macías, J.R., Reeves, G.A., Prlić, A.
    Integrating biological data - the Distributed Annotation System.
    BMC Bioinformatics, 9(Suppl. 8):S3.1-7, 2008. (doi:10.1186/1471-2105-9-S8-S3) (pmid:18673527)
    (Abstract) (First presented and published at the 5th International Workshop on Data Integration in the Life Sciences (DILS), Evry, France, 2008.)

  50. Welsch, C., Domingues, F.S., Susser, S., Antes, I., Hartmann, C., Mayr, G., Schlicker, A., Sarrazin, C., Albrecht, M., Zeuzem, S., Lengauer, T.
    Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV.
    Genome Biology, 9(1):R16.1-18, 2008. (doi:10.1186/gb-2008-9-1-r16) (pmid:18215275)
    (Abstract) (Supplement)

  51. Assenov, Y., Ramírez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M.
    Computing topological parameters of biological networks.
    Bioinformatics, 24(2):282-284, 2008. (doi:10.1093/bioinformatics/btm554) (pmid:18006545)
    (Abstract) (Supplement) (First presented at the 5th Annual Cytoscape Retreat, Amsterdam, The Netherlands, 2007.)

  52. Schlicker, A., Albrecht, M.
    FunSimMat: a comprehensive functional similarity database.
    Nucleic Acids Research, 36(Database issue):D434-D439, 2008. (doi:10.1093/nar/gkm806) (pmid:17932054)
    (Abstract)

  53. Van Ooijen, G., Mayr, G., Kasiem, M.M., Albrecht, M., Cornelissen, B.J., Takken, F.L.
    Structure-function analysis of the NB-ARC domain of plant disease resistance proteins.
    Journal of Experimental Botany, 59(6):1383-1397, 2008. (doi:10.1093/jxb/ern045) (pmid:18390848)
    (Abstract) (Supplement)

  54. Van Ooijen, G., Mayr, G., Albrecht, M., Cornelissen, B.J., Takken, F.L.
    Transcomplementation, but not physical association of the CC-NB-ARC and LRR domains of tomato R protein Mi-1.2 is altered by mutations in the ARC2 subdomain.
    Molecular Plant, 1(3):401-410, 2008. (doi:10.1093/mp/ssn009) (pmid:19825549)
    (Abstract)

  55. Scheller, N., Resa-Infante, P., De la Luna, S., Galao, R.P., Albrecht, M., Kaestner, L., Lipp, P., Lengauer, T., Meyerhans, A., Díez, J.
    Identification of PatL1, a human homolog to yeast P body component Pat1.
    Biochimica et Biophysica Acta - Molecular Cell Research, 1773(12):1786-1792, 2007. (doi:10.1016/j.bbamcr.2007.08.009) (pmid:17936923)
    (Abstract) (Supplement)

  56. Ramírez, F., Schlicker, A., Assenov, Y., Lengauer, T., Albrecht, M.
    Computational analysis of human protein interaction networks.
    Proteomics, 7(15):2541-2552, 2007. (doi:10.1002/pmic.200600924) (pmid:17647236)
    (Abstract) (Supplement) (In this issue) (Press release)

  57. Schlicker, A., Huthmacher, C., Ramírez, F., Lengauer, T., Albrecht, M.
    Functional evaluation of domain-domain interactions and human protein interaction networks.
    Bioinformatics, 23(7):859-865, 2007. (doi:10.1093/bioinformatics/btm012) (pmid:17456608)
    (Abstract) (Supplement) (First presented and published in Proceedings of the German Conference on Bioinformatics (GCB), Tübingen, Germany, 2006, in
    GI-Edition - Lecture Notes in Informatics (LNI), Köllen Verlag, Bonn, Germany, ISBN 978-3-88579-177-5, P-83:115-126, 2006.)

  58. Schlicker, A., Rahnenführer, J., Albrecht, M., Lengauer, T., Domingues, F.S.
    GOTax: investigating biological processes and biochemical activities along the taxonomic tree.
    Genome Biology, 8(3):R33.1-10, 2007. (doi:10.1186/gb-2007-8-3-r33) (pmid:17346342)
    (Abstract) (Supplement)

  59. Salamat-Miller, N., Fang, J., Seidel, C.W., Assenov, Y., Albrecht, M., Middaugh, C.R.
    A network-based analysis of polyanion-binding proteins utilizing human protein arrays.
    The Journal of Biological Chemistry, 282(14):10153-10163, 2007. (doi:10.1074/jbc.M610957200) (pmid:17276992)
    (Abstract) (Supplement)

  60. Hampe, J., Franke, A., Rosenstiel, P., Till, A., Teuber, M., Huse, K., Albrecht, M., Mayr, G., De La Vega, F.M., Briggs, J., Günther, S., Prescott, N.J., Onnie, C.M., Häsler, R., Sipos, B., Fölsch, U.R., Lengauer, T., Platzer, M., Mathew, C.G., Krawczak, M., Schreiber, S.
    A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.
    Nature Genetics, 39(2):207-211, 2007. (doi:10.1038/ng1954) (pmid:17200669)
    (Abstract) (Supplement)

  61. Franke, A., Hampe, J., Rosenstiel, P., Becker, C., Wagner, F., Häsler, R., Little, R.D., Huse, K., Ruether, A., Balschun, T., Wittig, M., ElSharawy, A., Mayr, G., Albrecht, M., Prescott, N.J., Onnie, C.M., Fournier, H., Keith, T., Radelof, U., Platzer, M., Mathew, C.G., Stoll, M., Krawczak, M., Nürnberg, P., Schreiber, S.
    Systematic association mapping identifies NELL1 as a novel IBD disease gene.
    PLoS ONE, 2(8):e691.1-13, 2007. (doi:10.1371/journal.pone.0000691) (pmid:17684544)
    (Abstract) (Supplement)

  62. Söderhäll, C., Marenholz, I., Kerscher, T., Rüschendorf, F., Esparza-Gordillo, J., Worm, M., Gruber, C., Mayr, G., Albrecht, M., Rohde, K., Schulz, H., Wahn, U., Hubner, N., Lee, Y.A.
    Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis.
    PLoS Biology, 5(9):e242.1952-1961, 2007. (doi:10.1371/journal.pbio.0050242) (pmid:17850181)
    (Abstract) (Supplement) (Press release)

  63. Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J., Yeats, C., Ólason, P.Í., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., López, G., Sadowski, M.I., Watson, J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Størling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher, C., Ramírez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigó, R., Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M., Tramontano, A., Valencia, A.
    The implications of alternative splicing in the ENCODE protein complement.
    PNAS, 104(13):5495-5500, 2007. (doi:10.1073/pnas.0700800104) (pmid:17372197)
    (Abstract) (Supplement)

  64. Welsch, C., Albrecht, M., Maydt, J., Herrmann, E., Welker, M.W., Sarrazin, C., Scheidig, A., Lengauer, T., Zeuzem, S.
    Structural and functional comparison of the non-structural protein 4B in flaviviridae.
    Journal of Molecular Graphics and Modelling, 26(2):546-557, 2007. (doi:10.1016/j.jmgm.2007.03.012) (pmid:17507273)
    (Abstract)

  65. Salamat-Miller, N., Fang, J., Seidel, C.W., Smalter, A.M., Assenov, Y., Albrecht, M., Middaugh, C.R.
    A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays.
    Molecular & Cellular Proteomics, 5(12):2263-2278, 2006. (doi:10.1074/mcp.M600240-MCP200) (pmid:1698267)
    (Abstract) (Supplement)

  66. Boeddrich, A., Gaumer, S., Haacke, A., Tzvetkov, N., Albrecht, M., Evert, B.O., Müller, E.C., Lurz, R., Breuer, P., Schugardt, N., Plaßmann, S., Xu, K., Warrick, J.M., Suopanki, J., Wüllner, U., Frank, R., Hartl, U.F., Bonini, N.M., Wanker, E.E.
    An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis.
    The EMBO Journal, 25(7):1547-1558, 2006. (doi:10.1038/sj.emboj.7601043) (pmid:16525503)
    (Abstract) (Supplement) (Press release)

  67. Plotz, G., Welsch, C., Giron-Monzon, L., Friedhoff, P., Albrecht, M., Piiper, A., Biondi, R.M., Lengauer, T., Zeuzem, S., Raedle, J.
    Mutations in the MutSα interaction interface of MLH1 can abolish DNA mismatch repair.
    Nucleic Acids Research, 34(22):6574-6586, 2006. (doi:10.1093/nar/gkl944) (pmid:17135187)
    (Abstract) (Supplement)

  68. Mihm, U., Grigorian, N., Welsch, C., Herrmann, E., Kronenberger, B., Teuber, G., von Wagner, M., Hofmann, W.P., Albrecht, M., Lengauer, T., Zeuzem, S., Sarrazin, C.
    Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C.
    Antiviral Therapy, 11(4):507-519, 2006. (pmid:16856625)
    (Abstract)

  69. Takken, F.L., Albrecht, M., Tameling, W.I.
    Resistance proteins: molecular switches of plant defence.
    Current Opinion in Plant Biology, 9(4):383-390, 2006. (doi:10.1016/j.pbi.2006.05.009) (pmid:16713729)
    (Abstract) (Supplement)

  70. Tameling, W.I., Vossen, J.H., Albrecht, M., Lengauer, T., Berden, J.A., Haring, M.A., Cornelissen, B.J., Takken, F.L.
    Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation.
    Plant Physiology, 140(4):1233-1245, 2006. (doi:10.1104/pp.105.073510) (pmid:16489136)
    (Abstract) (First presented and published at the 12th International Congress on Molecular Plant-Microbe Interactions (MPMI), Mrida, Mexico, 2005, in
    Biology of Plant-Microbe Interactions, APS Press, Saint Paul, MN, USA, ISBN 0-9654625-4-9, 5:225-230, 2006.)

  71. Albrecht, M., Takken, F.L.
    Update on the domain architectures of NLRs and R proteins.
    Biochemical and Biophysical Research Communications, 339(2):459-462, 2006. (doi:10.1016/j.bbrc.2005.10.074) (pmid:16271351)
    (Abstract)

  72. Albrecht, M., Huthmacher, C., Tosatto, S.C., Lengauer, T.
    Decomposing protein networks into domain-domain interactions.
    Bioinformatics, 21(Suppl. 2):ii220-ii221, 2005. (doi:10.1093/bioinformatics/bti1135) (pmid:16204107)
    (Abstract) (Supplement) (First presented and published at the 4th European Conference on Computational Biology (ECCB), Madrid, Spain, 2005.)

  73. Castellano, S., Lobanov, A.V., Chapple, C., Novoselov, S.V., Albrecht, M., Hua, D., Lescure, A., Lengauer, T., Krol, A., Gladyshev, V.N., Guigo, R.
    Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family.
    PNAS, 102(45):16188-16193, 2005. (doi:10.1073/pnas.0505146102) (pmid:16260744)
    (Abstract) (Supplement) (Commentary) (In this issue)

  74. Ralser, M., Nonhoff, U., Albrecht, M., Lengauer, T., Wanker, E.E., Lehrach, H., Krobitsch, S.
    Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways.
    Human Molecular Genetics, 14(19):2893-2909, 2005. (doi:10.1093/hmg/ddi321) (pmid:16115810)
    (Abstract) (Supplement)

  75. Ralser, M., Albrecht, M., Nonhoff, U., Lengauer, T., Lehrach, H., Krobitsch, S.
    An integrative approach to gain insights into the cellular function of human ataxin-2.
    Journal of Molecular Biology, 346(1):203-214, 2005. (doi:10.1016/j.jmb.2004.11.024) (pmid:15663938)
    (Abstract) (Supplement)

  76. Albrecht, M.
    LRRK2 mutations and parkinsonism.
    The Lancet, 365(9466):1230, 2005. (doi:10.1016/S0140-6736(05)74810-8) (pmid:15811455)
    (Abstract)

  77. Schreiber, S., Rosenstiel, P., Albrecht, M., Hampe, J., Krawczak, M.
    Genetics of Crohn disease, an archetypal inflammatory barrier disease.
    Nature Reviews Genetics, 6(5):376-388, 2005. (doi:10.1038/nrg1607) (pmid:15861209)
    (Abstract)

  78. Valentonyte, R., Hampe, J., Huse, K., Rosenstiel, P., Albrecht, M., Stenzel, A., Nagy, M., Gaede, K.I., Franke, A., Haesler, R., Koch, A., Lengauer, T., Seegert, D., Reiling, N., Ehlers, S., Schwinger, E., Platzer, M., Krawczak, M., Muller-Quernheim, J., Schurmann, M., Schreiber, S.
    Sarcoidosis is associated with a truncating splice site mutation in BTNL2.
    Nature Genetics, 37(4):357-364, 2005. (doi:10.1038/ng1519) (pmid:15735647)
    (Abstract) (Supplement) (Press release 1) (Press release 2)

  79. Costello, C.M., Mah, N., Häsler, R., Rosenstiel, P., Waetzig, G.H., Hahn, A., Lu, T., Gurbuz, Y., Nikolaus, S., Albrecht, M., Hampe, J., Lucius, R., Klöppel, G., Eickhoff, H., Lehrach, H., Lengauer, T., Schreiber, S.
    Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes.
    PLoS Medicine, 2(8):e199.1-17, 2005. (doi:10.1371/journal.pmed.0020199) (pmid:16107186)
    (Abstract) (Synopsis) (Press release)

  80. Van Duist, M.M., Albrecht, M., Podswiadek, M., Giachino, D., Lengauer, T., Punzi, L., De Marchi, M.
    A new CARD15 mutation in Blau syndrome.
    European Journal of Human Genetics, 13(6):742-747, 2005. (doi:10.1038/sj.ejhg.5201404) (pmid:15812565)
    (Abstract)

  81. Sarrazin, C., Mihm, U., Herrmann, E., Welsch, C., Albrecht, M., Sarrazin, U., Traver, S., Lengauer, T., Zeuzem, S.
    Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
    The Journal of Infectious Diseases, 192(10):1710-1719, 2005. (doi:10.1086/497142) (pmid:16235168)
    (Abstract)

  82. Bojunga, J., Welsch, C., Antes, I., Albrecht, M., Lengauer, T., Zeuzem, S.
    Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency.
    Human Genetics, 117(6):558-564, 2005. (doi:10.1007/s00439-005-1339-3) (pmid:16028060)
    (Abstract)

  83. Albrecht, M., Choubey, D., Lengauer, T.
    The HIN domain of IFI-200 proteins consists of two OB folds.
    Biochemical and Biophysical Research Communications, 327(3):679-687, 2005. (doi:10.1016/j.bbrc.2004.12.056) (pmid:15649401)
    (Abstract)

  84. Stoll, M., Corneliussen, B., Costello, C.M., Waetzig, G.H., Mellgard, B., Koch, W.A., Rosenstiel, P., Albrecht, M., Croucher, P.J., Seegert, D., Nikolaus, S., Hampe, J., Lengauer, T., Pierrou, S., Foelsch, U.R., Mathew, C.G., Lagerstrom-Fermer, M., Schreiber, S.
    Genetic variation in DLG5 is associated with inflammatory bowel disease.
    Nature Genetics, 36(5):476-480, 2004. (/doi:10.1038/ng1345) (pmid:15107852)
    (Abstract) (Supplement) (Press release)

  85. Albrecht, M., Golatta, M., Wüllner, U., Lengauer, T.
    Structural and functional analysis of ataxin-2 and ataxin-3.
    European Journal of Biochemistry, 271(15):3155-3170, 2004. (doi:10.1111/j.1432-1033.2004.04245.x) (pmid:15265035)
    (Abstract) (Supplement)

  86. Albrecht, M., Lengauer, T.
    Novel Sm-like proteins with long C-terminal tails and associated methyltransferases.
    FEBS Letters, 569(1-3):18-26, 2004. (doi:10.1016/j.febslet.2004.03.126) (pmid:15225602)
    (Abstract) (Supplement)

  87. Albrecht, M., Lengauer, T.
    Survey on the PABC recognition motif PAM2.
    Biochemical and Biophysical Research Communications, 316(1):129-138, 2004. (doi:10.1016/j.bbrc.2004.02.024) (pmid:15003521)
    (Abstract)

  88. Albrecht, M., Lengauer, T., Schreiber, S.
    Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence.
    Bioinformatics, 19(17):2171-2175, 2003. (doi:10.1093/bioinformatics/btg370) (pmid:14630645)
    (Abstract)

  89. Albrecht, M., Domingues, F.S., Schreiber, S., Lengauer, T.
    Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2.
    FEBS Letters, 554(3):520-528, 2003. (doi:10.1016/S0014-5793(03)01222-5) (pmid:14623123)
    (Abstract) (Supplement)

  90. Albrecht, M., Domingues, F.S., Schreiber, S., Lengauer, T.
    Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.
    FEBS Letters, 538(1-3):173-177, 2003. (doi:10.1016/S0014-5793(03)00161-3) (pmid:12633874)
    (Abstract) (Supplement)

  91. Albrecht, M., Tosatto, S.C., Lengauer, T., Valle, G.
    Simple consensus procedures are effective and sufficient in secondary structure prediction.
    Protein Engineering, 16(7):459-462, 2003. (doi:10.1093/protein/gzg063) (pmid:12915722)
    (Abstract) (Supplement)

  92. Albrecht, M., Lengauer, T.
    Pyranose oxidase identified as a member of the GMC oxidoreductase family.
    Bioinformatics, 19(10):1216-1220, 2003. (doi:10.1093/bioinformatics/btg140) (pmid:12835264)
    (Abstract)

  93. Albrecht, M., Hoffmann, D., Evert, B.O., Schmitt, I., Wüllner, U., Lengauer, T.
    Structural modeling of ataxin-3 reveals distant homology to adaptins.
    Proteins: Structure, Function, and Genetics, 50(2):355-370, 2003. (doi:10.1002/prot.10280) (pmid:12486728)
    (Abstract)

  94. Albrecht, M., Hanisch, D., Zimmer, R., Lengauer, T.
    Improving fold recognition of protein threading by experimental distance constraints.
    In Silico Biology, 2(3):325-337, 2002. (pmid:12542417)
    (Abstract) (First presented and published in Proceedings of the German Conference on Bioinformatics (GCB), Braunschweig, Germany, ISBN 3-00-008114-3, 68-77, October 7-10, 2001.)

  95. Hoffmann, D., Schnaible, V., Wefing, S., Albrecht, M., Hanisch, D., Zimmer, R.
    A new method for the fast solution of protein-3D-structures, combining experiments and bioinformatics.
    In Coupling of Biological and Electronic Systems: Proceedings of the 2nd Caesarium, Bonn, 2000, Springer-Verlag, Berlin, Germany, ISBN 978-3-540-43699-7, 59-78, 2002.
    (Abstract)