The Kaderali Lab

Publications

Older Publications (before 2015)

Journal and Conference Proceedings

2014

  1. F. Hentzschel, C. Hammerschmidt-Kamper, K. Börner, K. Heiss, B. Knapp, J. M. Sattler, L. Kaderali, M. Castoldi, J. G. Bindman, Y. Malato, H. Willenbring, A.-K. Mueller, D. Grimm (2014). AAV8-mediated in vivo overexpression of miR-155 enhances the protective capacity of genetically-attenuated malaral parasites, Moleculer Therapy 22(12):2130-41.
  2. D. Bankwitz, G. Vieyres, K. Hueging, J. Bitzegeio, M. Doepke, P. Chhatwal, S. Haid, M. Catanese, M. Zeisel, A. Nicosia, T. Baumert, L. Kaderali, T. Pietschmann (2014). Role of the hypervariable region 1 (HVR1) for the interplay of hepatitis C virus with entry factors and lipoproteins.Journal of Virology 88(21):12644-55.
  3. N. A. Kiani, L. Kaderali (2014). Dynamic Probabilistic Threshold Networks to Infer Signaling Pathways from Time-Course Perturbation Data.BMC Bioinformatics 15:250.
  4. C. Stephan, H.-M. Baldauf, J. Barry, F. Giordano, C. Bartholomä, A. Haberl, M. Bickel, M. Schmidt, S. Laufs, L. Kaderali, O. Keppler (2014). Impact of raltegravir on HIV-1 RNA and DNA species following initiation of antiretroviral therapy in treatment-naïve patients.J of Antimicrob Chemother 69(10):2809-18.
  5. C. Engeland, N. Brown, K. Boerner, M. Schümann, E. Krause, L. Kaderali, G. Müller, H.-G. Kraeusslich (2014). Proteome Analysis of the HIV-1 Gag Interactome.Virology 460-461:194-206.
  6. J. Doerrbecker, M. Friesland, N. Riebesehl, C. Ginkel, P. Behrendt, R. Brown, S. Ciesek, H. Wedemeyer, C. Sarrazin, L. Kaderali, T. Pietschmann, E. Steinmann (2014). Incorporation of primary patient-derived glycoproteins into authentic infectious hepatitis C virus particles.Hepatology 60(2):508-20.
  7. A. Eskova, B. Knapp, D. Matelska, S. Reusing, A. Arjonen, T. Lisauskas, R. Pepperkok, R. Russell, R. Eils, J. Ivaska, L. Kaderali, H. Erfle, V. Starkuviene (2014). RNAi Screen Identifies KIF15 as a Novel Regulator of Integrin Endocytic Trafficking.J. Cell Science 127(Pt11):2433-47.
  8. N. V. Ivanisenko, E. L. Mishchenko, I. R. Akberdin, P. S. Demenkov, V. A. Likhoshvai, K. Kozlov, D. Todorov, V. V. Gursky, M. G. Samsonova, A. M. Samsonov, D. Clausznitzer, L. Kaderali, N. A. Kolchanov, V. A. Ivanisenko (2014). A new stochastic model for subgenomic hepatitis C virus replication considers drug resistant mutants.PLoS One 9(3):e91502.
  9. K. Hueging, M. Doepke, G. Vieyres, D. Bankwitz, A. Frentzen, J. Doerrbecker, F. Gumz, S. Haid, B. Wölk, L. Kaderali, T. Pietschmann (2013). Apolipoprotein E co-determines tissue-tropism of hepatitis C virus and it is crucial for viral cell-to-cell transmission by contributing to a post-envelopment step of assembly.Journal of Virology 88(3):1433-46.
  10. N. Levtov, S. Amberkar, Z. Frenkel, L. Kaderali, Z. Volkovich (2014). Detecting Non-Uniform Clusters in Large-Scale Interaction Graphs.J Comput Biol 21(2):173-83, doi: 10.1089/cmb.2013.0095.
  11. A. Frentzen, A. Kusuma, E. Guerlevik, K. Hueging, S. Knocke, C. Ginkel, R. J. Brown, M. Heim, M. T. Dill, A. Kröger, U. Kalinke, L. Kaderali, F. Kuehnel, T. Pietschmann (2014). Cell entry, efficient RNA replication, and production of infectious hepatitis C virus progeny in mouse liver-derived cells.Hepatology 59(1):78-88, doi: 10.1002/hep.26626.
  12. S. Haid, C. Grethe, M. Dill, M. Heim, L. Kaderali, T. Pietschmann (2014). Isolate-dependent use of Claudins for cell entry by hepatitis C virus.Hepatology 59(1):24-34, doi: 10.1002/hep.26567.

2013

  1. G. Raddatz, S. Hagemann, D. Aran, J. Söhle, P. Kulkarni, L. Kaderali, A. Hellmann, M. Winnefeld, F. Lyko (2013). Aging is associated with highly defined epigenetic changes in the human epidermis.Epigenetics & Chromatin 6(1):36, doi: 10.1186/1756-8935-6-36.
  2. E. Steinemann, J. Doerrbecker, M. Friesland, N. Riebesehl, C. Ginkel, J. Gentzsch, C. Lauber, R. Brown, A. Frentzen, T. Pietschmann (2013). Characterization of hepatitis C virus intra- and inter-genotypic chimeras reveals a role of the glycoproteins in virus envelopment. Journal of Virology 87(24):13297-306, doi: 10.1128/JVI.01708-13.
  3. S. Eisenreich, K. Abou-El-Ardat, K. Szafranski, J.A. Campos-Valenzuela, A. Rump, J.M. Nigro, R. Bjerkvig, E.M. Gerlach, K. Hackmann, E. Schröck, D. Krex, L. Kaderali, G. Schackert, M. Platzer, B. Klink (2013). Novel CIC Point Mutations and an Exon-Spanning, Homozygous Deletion Identified in Oligodendroglial Tumors by a Comprehensive Genomic Approach Including Transcriptome Sequencing.PLoS One 8(9):e76623, doi:10.1371/journal.pone.0076623.
  4. M. Binder*, N. Sulaimanov*, D. Clausznitzer, M. Schulze, C. M. Hueber, S. Lenz, J. Schloeder, M. Trippler, R. Bartenschlager, V. Lohmann, L. Kaderali (2013). Replication Vesicles are Load- and Choke-Points in the Hepatitis C Virus Lifecycle. PLoS Pathogens 9(8):e1003561, doi:10.1371/journal.ppat.1003561.
  5. B. Knapp, L. Kaderali (2013). Reconstruction of Cellular Signal Transduction Networks using Perturbation Assays and Linear Programming.PLoS One 8(7):e69220, doi:10.1371/journal.pone.0069220.
  6. S. Amberkar, N. Kiani, R. Bartenschlager, G. Alvisi, L. Kaderali (2013). High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.World J Virol. 2(2):18-31, doi: 10.5501/wjv.v2.i2.18.
  7. J. Gentzsch, C. Brohm, E. Steinmann, M. Friesland, N. Menzel, G. Vieyres, P. Perin, A. Frentzen, L. Kaderali, T. Pietschmann (2013). Hepatitis C Virus p7 is Critical for Capsid Assembly and Envelopment.PLoS Pathogens 9(5):e1003355, doi:10.1371/journal.ppat.1003355.
  8. B. Klink, H. Miletic, D. Stieber, P. C. Huszthy, J. A. Campos Valenzuela, J. Balss, J. Wang, M. Schubert, P. O. Sakariassen, T. Sundstrom, A. Torsvik, M. Aarhus, R. Mahesparan, A. von Deimling, L. Kaderali, S. P. Niclou, E. Schröck, R. Bjerkvig, J. M. Nigro (2013). A novel, diffusely infilrative xenograft model of human anaplastic oligodendroglioma with mutations in FUBP1, CIC, and IDH1.PLoS One 8(3):e59773, doi:10.1371/journal.pone.0059773.
  9. Z. M. Frenkel, S. Amberkar, L. Kaderali, Z. Volkovich (2013). Repeated Bisections approach for local clustering of PPINs. Journal of Modern Mathematics Frontier (JMMF) 2(1):19-24.
  10. U. Maulik, A. Mukhopadhyay, M. Bhattacharyya, L. Kaderali, B. Brors, S. Bandyopadhyay, R. Eils (2013). Mining Quasi-Bicliques from HIV-1–Human Protein Interaction Network: A Multiobjective Biclustering Approach. IEEE/ACM Trans Comput Biol Bioinform 10(2):423-35, http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.139.

2012

  1. A. Serva, B. Knapp, Y.-T. Tsai, C. Claas, T. Lisauskas, P. Matula, N. Harder, L. Kaderali, K. Rohr, H. Erfle, R. Eils, V. Braga, V. Starkuviene (2012). miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus.PLoS One 7(12):e52555, doi:10.1371/journal.pone.0052555.
  2. H. Poschke, M. Dees, M. Chang, S. Amberkar, L. Kaderali, R. Rothstein and B. Luke (2012). Rif2 promotes a telomere fold-back structure through Rpd3L recruitment in budding yeast.PLoS Genetics 8(9):e1002960.
  3. A. Ruggieri, E. Dazert, P. Metz, S. Hofmann, J. P. Bergeest, J. Mazur, P. Bankhead, M. S. Hiet, S. Kallis S, G. Alvisi, C. E. Samuel, V. Lohmann, L. Kaderali, K. Rohr, M. Frese, G. Stoecklin, R. Bartenschlager (2012). Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection.Cell Host & Microbe 12:71-85.
  4. N. Menzel, W. Fischl, K. Hueging, D. Bankwitz, A. Frentzen, S. Haid, J. Gentzsch, L. Kaderali, R. Bartenschlager, T. Pietschmann (2012). MAP-kinase regulated cytosolic phospholipase A2 activity is essential for production of infectious hepatitis C virus particles.PLoS Pathogens 8(7):e1002829.
  5. P. Metz, E. Dazert, A. Ruggieri, J. Mazur, L. Kaderali, A. Kaul, U. Zeuge, M. Trippler, V. Lohmann, M. Binder, M. Freese, R. Bartenschlager (2012). Identification of type I and type II interferon-induced effectors controlling hepatitis C virus replication.Hepatology 56(6):2082-93, doi:10.1002/hep.25908.
  6. M. Böck, S. Ogishima, H. Tanaka, S. Kramer, L. Kaderali (2012). Hub-Centered Gene Network Reconstruction using Automatic Relevance Determination.PLoS ONE 7(5): e35077. doi:10.1371/journal.pone.0035077.
  7. N. Naseabadi, A. Dehnokhalaji, N. A. Kiani, P. J. Korhonen, J. Wallenius (2011). Resource allocation for performance improvement. Ann Oper Res 196(1), 459-468, doi:10.1007/s10479-011-1016-y.

2011

  1. B. Knapp, I. Rebhan, A. Kumar, P. Matula, N. A. Kiani, M. Binder, H. Erfle, K. Rohr, R. Eils, R. Bartenschlager, L. Kaderali (2011). Normalizing for Individual Cell Population Context in the Analysis of high-content Cellular Screens.BMC Bioinformatics 12:485.
  2. D. Clausznitzer, N. Sulaimanov, M. Binder, V. Lohmann, R. Bartenschlager, L. Kaderali (2011). Systembiologie der Hepatitis C-Virus-Wirts-Interaktionen. Laborwelt 6:13-15.
  3. J. Mazur, L. Kaderali (2011). Bayesian Experimental Design for the Inference of Gene Regulatory Networks. In: Proceedings of the Fifth International Workshop on Machine Learning in Systems Biology, Vienna, Austria, July 20-21, 2011. Stefan Kramer and Neil Lawrence (Eds.), 54-58.
  4. M. Binder, F. Eberle, S. Seitz, N. Mücke, C. M. Hüber, N. Kiani, L. Kaderali, V. Lohmann, A. Dalpke, R. Bartenschlager (2011). Molecular mechanism of signal perception and integration by the innate immune sensor retinoic acid inducible gene-I (RIG-I).J Biol Chem. 286:27278-87.
  5. J. Gentzsch, B. Hinkelmann, L. Kaderali, H. Irschik, R. Jansen, F. Sasse, R. Frank, T. Pietschmann (2011). Hepatitis C virus complete life cycle screen for identification of small molecules with pro- or antiviral activity.Antiviral Research 89(2):136-48.
  6. S. Reiss, I. Rebhan, P. Backes, I. Romero-Brey, H. Erfle, P. Matula, L. Kaderali, M. Pönisch, H. Blankenburg, M.-S. Hiet, T. Longerich, S. Diehl, F. Ramirez, T. Balla, K. Rohr, A. Kaul, S. Bühler, R. Pepperkok, T. Lengauer, M. Albrecht, R. Eils, P. Schirmacher, V. Lohmann, R. Bartenschlager (2011) Recruitment and activation of a lipid kinase by NS5A of the hepatitis C virus is essential for integrity of the membranous replication compartment.Cell Host & Microbe 9(1):32-45.

2010

  1. A, Suratanee, I. Rebhan, P. Matula, A. Kumar, L. Kaderali, K. Rohr, R. Bartenschlager, R. Eils, R. König (2010). Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images.Bioinformatics 26:i653-i658, doi:10.1093/bioinformatics/btq398.
  2. J.-M. Löhr, R. Faissner, D. Koczan, P. Bewerunge, C. Bassi, B. Brors, R. Eils, L. Frulloni, A. Funk, W. Halangk, R. Jesenofsky, L. Kaderali, J. Kleef, B. Krüger, M. M. Lerch, R. Lösel, M. Magnani, M. Neumaier, S. Nittka, M. Sahin-Toth, J. Sänger, S. Serafini, M. Schnölzer, H.-J. Thierse, S. Wandschneider, G. Zamboni, G. Klöppel (2010). Autoantibodies Against the Exocrine Pancreas in Autoimmune Pancreatitis: Gene and Protein Expression Profiling and Immunoassays Identify Pancreatic Enzymes as a Major Target of the Inflammatory Process.Am. J. Gastroenerology 105(9):2060-71.
  3. J. H. Schulte, B. Schowe, P. Mestdagh, L. Kaderali, P. Kalaghatgi, S. Schlierf, B. Brockmeyer, K. Pajtler, T. Thor, K. de Preter, F. Spelemen, K. Morik, A. Eggert, J. Vandesompele, A. Schramm (2010). Accurate Prediction of Neuroblastoma Outcome based on miRNA Expression Profiles.International Journal of Cancer, 127(10):2374-85.
  4. A. Oberthuer, B. Hero, F. Berthold, D. Juraeva, A. Faldum, Y. Kahlert, S. Asgharzadeh, R. Seeger, P. Scaruffi, G. P. Tonini, I. Janoueix-Lerosey, O. Delattre, G. Schleiermacher, J. Vandesompele, J. Vermeulen, F. Speleman, R. Noguera, M. Piqueras, J. Benard, A. Valent, S. Avigad, I. Yaniv, A. Weber, H. Christiansen, R. Grundy, K. Schardt, M. Schwab, R. Eils, P. Warnat, L. Kaderali, T. Simon, B. DeCarolis, J. Theissen, F. Westermann, B. Brors, M. Fischer (2010). The Prognostic Impact of Gene Expression-Based Classification for Low and Intermediate Risk Neuroblastoma.Journal of Clinical Oncology 28(21):3506-15.
  5. A. D. Ebert, M. Laussmann, S. Wegehingel, L. Kaderali, H. Erfle, J. Reichert, J. Lechner, H.-D. Beer, R. Pepperkok, W. Nickel (2010). Tec-Kinase-mediated Phosphorylation of Fibroblast Growth Factor 2 is Essential for Unconventional Secretion. Traffic, 11(6):813-26.
  6. K. Börner, J. Hermle, C. Sommer, N. P. Brown, B. Knapp, B. Glass, J. Kunkel, G. Torralba, J. Reymann, N. Beil, J. Beneke, R. Pepperkok, R. Schneider, T. Ludwig, M. Hausmann, F. Hamprecht, H. Erfle, L. Kaderali, H.-G. Kräusslich, M. J. Lehmann (2010) From experimental setup to bioinformatics: An RNAi screening platform to identify host factors and potential cellular networks involved in HIV-1 replication, Biotechnology Journal, 5(1), 39-49.

2009

  1. J. Mazur, D. Ritter, G. Reinelt, L. Kaderali (2009). Reconstructing Nonlinear Dynamic Models of Gene Regulation using Stochastic Sampling.BMC Bioinformatics 10:448.
  2. S. Geuenich, L. Kaderali, I. Allespach, S. Sertel, O. T. Keppler (2009). Biological Signature Characterisitics of Primary Isolates from HIV-1 Group O in the ex vivo Human Tonsil Histoculture.Journal of Virology, 83(20), 10494-10503, doi:10.1128/JVI.00928-09.
  3. L. Kaderali, E. Dazert, U. Zeuge, M. Frese, R. Bartenschlager (2009). Recontructing Signaling Pathways from RNAi Data using Probabilistic Boolean Threshold Networks.Bioinformatics, 25(17), 2229-2235, doi:10.1093/bioinformatics/btp375.
  4. A. Schramm, I. Mierswa, L. Kaderali, K. Morik, A. Eggert, J. H. Schulte (2009). Reanalysis of Neuroblastoma Expression Profiling Data using improved Methodology and extended Follow-Up increases Validity of Outcome Prediction.Cancer Letters, 282(1):55-62, doi:10.1016/j.canlet.2009.02.052.
  5. N. Rieber, B. Knapp, R. Eils, L. Kaderali (2009). RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.Bioinformatics, 25, 678-679, doi:10.1093/bioinformatics/btp014.
  6. N. Radde, L. Kaderali (2009). Inference of an Oscillating Model for the Yeast Cell Cylce.Discrete Applied Mathematics 157, 2285-2295, doi:10.1016/j.dam.2008.06.036.

2008 and before

  1. A. Oberthür*, L. Kaderali*, Y. Kahlert, B. Hero, F. Westermann, F. Berthold, B. Brors, R. Eils, M. Fischer (2008). Sub-classification and individual survival time prediction from gene-expression data of neuroblastoma patients using CASPAR.Clinical Cancer Research, 14(20):6590-6601.
  2. M. Zapatka, L. Kaderali (2007). Statistische Analyse von Daten klinischer Studien.GynSpectrum 3, 18-19.
  3. L. Kaderali (2007). Individualized Predictions of Survival Time Distributions from Gene Expression Data using a Bayesian MCMC Approach. S. Hochreiter and R. Wagner (Eds.): BIRD 2007, LNBI Lecture Notes in Bioinformatics 4414, 77-89.
  4. N. Radde, L. Kaderali (2007). Bayesian Inference of Gene Regulatory Networks using Gene Expression Time Series Data. S. Hochreiter and R. Wagner (EDS): BIRD 2007, LNBI Lecture Notes in Bioinformatics, 4414, 1-15.
  5. A. Schramm, J. Vandesompele, J. H. Schulte, S. Dreesmann, L. Kaderali, B. Brors, R. Eils, F. Speleman, A. Eggert (2007). Translating Expression Profiling into a Clinically Feasible Test to Predict Neuroblastoma Outcome.Clinical Cancer Research 13(5), 1459-1465.
  6. L. Kaderali, T. Zander, U. Faigle, J. Wolf, J. L. Schultze, R. Schrader (2006). CASPAR: A Hierarchical Bayesian Approach to predict Survival Times in Cancer from Gene Expression Data.Bioinformatics 22, 1495-1502.
  7. M. Leber, L. Kaderali, A. Schönhuth, R. Schrader (2005). A fractional programming approach to efficient DNA melting temperature calculation. Bioinformatics 21, 2375-2382.
  8. L. Kaderali, A. Deshpande, J. P. Nolan, P. S. White (2003). Primer-design for multiplexed genotyping.Nucleic Acids Research 31, 1796-1802.
  9. L. D. Green, H. Cai, D. C. Torney, D. J. Wood, F. J. Uribe-Romeo, L. Kaderali, J. P. Nolan, P. S. White (2002). High-throughput SNP scoring with GAMMArrays: genomic analysis using multiplexed microsphere assays. In: Bornshop, Darryl and others (editors), Proc. SPIE, Volume 4626, 308-315.
  10. L. Kaderali, A. Schliep (2002). Selecting signature oligonucleotides to identify organisms using DNA arrays.Bioinformatics 18, 1340-1349.
  11. L. Kaderali, A. Schliep (2001). A new Algorithm for accelerating Pair-Wise Computations of Melting Temperature.Electronic Notes in Discrete Mathematics, 8, 46-49.

Books and Book Contributions

  1. N. Kiani, L. Kaderali (2013). Systems Virology. In: Encyclopedia of Systems Biology, Edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota. Springer Verlag, 2013.
  2. J. Mazur, L. Kaderali (2013). The Importance and Challenges of Bayesian Parameter Learning in Systems Biology. In: Model Based Parameter Estimation: Theory and Applications, H. G. Bock, T. Carraro, W. Jäger, S. Körkel, R. Rannacher, J. P. Schlöder (Eds.), Contributions in Mathematical and Computational Sciences, Vol. 4, Springer Verlag, Heidelberg.
  3. J. Mazur, L. Kaderali (2012). The Relevance of Bayesian Experimental Design for Modeling in Systems Biology. In: Computational Intelligence. Alexandru Floares (Ed.), Computer Science, Technology and Applications, Nova, pp. 69-74.
  4. B. Knapp, L. Kaderali (2012). Single-Cell Analysis of High-Content, High-Throughput Cellular Assays. In: Introduction to sequence and genome analysis, iConcept Press.
  5. N. Radde, L. Kaderali (2010). A Bayes regularized ODE Model for the Inference of Gene Regulatory Networks. In: Das, Carayea, Hsu, Welch, Handbook of Research: Computation Methodologies in Gene Regulatory Networks. IGI-Global.
  6. L. Kaderali, N. Radde (2008). Inferring Gene Regulatory Networks from Expression Data. In: A. Kelemen, A. Abraham, Y. Chen (Editors), Computational Intelligence in Bioinformatics. Studies in Computational Intelligence 94, Springer-Verlag, Heidelberg.
  7. L. Kaderali (2007). Primer Design for Multiplexed Genotyping. In: A. Yuryev (Editor), PCR Primer Design. Methods in Molecular Biology, Humana Press, Totowa.
  8. L. Kaderali (2006). A Hierarchical Bayesian Approach to Regression and its Application to Predicting Survival Times in Cancer. Shaker Verlag, Aachen.

Other Publications

  1. A. Oberthuer, B. Hero B, D. Juraeva, A. Faldum, Y. Kahlert, S. Asgharzadeh, R. Seeger, P. Scaruffi, G. P. Tonini, I. Janoueix-Lerosey, O. Delattre, G. Schleiermacher, J. Vandesompele,J. Vermeulen, F. Speleman, R. Noguera, M. Piqueras M, J. Benard, A. Valent, S. Avigad, I. Yaniv, A. Weber, H. Christiansen, R. G. Grundy, K. Schardt, M. Schwab, R. Eils, P. Warnat, L. Kaderali, T. Simon, B. DeCarolis, J. Theissen, F. Westermann, B. Brors, F. Berthold, M. Fischer (2010). Gene expression-based classification improves risk estimation of neuroblastoma patients. Klinische Pädiatrie 222(3):221-221.
  2. B. Knapp, P. Matula, L. Kaderali, K. Rohr, H. Erfle, V. Starkuviene, C. Claas C (2009). Regulatory elements specific for the secretion of procollagen I. European Journal of Cell Biology 88 Suppl. 59, p. 12.
  3. L. Kaderali, A. Gösling, P. S. White, R. Schrader (2007). Automated Design of Multiplexed Polymerase Chain Reaction Experiments with MPXprimer. Technical Report, Cologne University Bioinformatics Center, University of Cologne (pdf).
  4. L. Kaderali (2005). Vorhersage des Überlebens bei Tumorpatienten. Jahresbericht “Kooperative Informationsverarbeitung an der Universität zu Köln” für das Jahr 2005.
  5. L. Kaderali (2003). Neural Network Feature Selection in Complex Trait Analysis. Technical Report, ZAIK, University of Cologne.
  6. L. Kaderali (2001). Selecting target specific Probes for DNA Arrays. Diploma Thesis, University of Cologne.