Publications
Journal Publications and Conference Proceedings
2021
- L Schönborn, T Thiele, L Kaderali, A Greinacher (2021). Decline in Pathogenic Antibodies over Time in VITT. N Engl J Med, in press.
- A Osterman, M Iglhaut, A Lehner, P Späth, M Stern, H Autenrieth, M Muenchhoff, A Graf, S Krebs, H Blum, A Baiker, N Grzimek-Koschewa, U Protzer, L Kaderali, HM Baldauf, OT Keppler (2021). Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern. Med Microbiol Immunol, in press.
- PR Wratil, NA Schmacke, A Osterman, T Weinberger, J Rech, B Karakoc, M Zeilberger, J Steffen, TT Mueller, PM Spaeth, M Stern, M Albanese, H Thun, J Reinbold, B Sandmeyer, P Kressirer, B Grabein, P Falkai, K Adorjan, V Hornung, L Kaderali, M Klein, OT Keppler (2021). In-depth profiling of COVID-19 risk factors and preventive measures in healthcare workers. Infection, in press.
- J. Gamain, T. Herr, R. Fleischmann, A. Stenner, M. Vollmer, C. Willert, B. Veit, B. Lehnert, J.-U. Mueller, F. Steigerwald, F. Tost, M. Kronenbuerger (2021). Smell and taste in idiopathic blepharospasm. J Neural Transmission, in press.
- N. Holzscheck, C. Falckenhayn, J. Söhle, B. Kristof, R. Siegner, A. Werner, J. Schössow, C. Jürgens, H. Völzke, H. Wenck, M. Winnefeld, E. Grönniger, L. Kaderali (2021). Modeling transcriptomic age using knowledge-primed artificial neural networks. NPJ Aging Mech Dis 7(1):15.
- C. Metelmann, B. Metelmann, L. Schuffert, K. Hahnenkamp, M. Vollmer, P. Brinkrolf (2021). Smartphone apps to support laypersons in bystander CPR are of ambivalent benefit: a controlled trial using medical simulation. Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine 29:76.
- S. Römer, M.J. Meyer, K. Klein, L.V. Schneider, J. Matthaei, A. Tzvetkova, J. Lapczuk-Romanska, J. Gaedcke, M. Drozdzik, J. Brockmöller, A.T. Nies, M.V. Tzvetkov (2021). Effects of a Common Eight Base Pairs Duplication at the Exon 7-Intron 7 Junction on Splicing, Expression, and Function of OCT1. Frontiers in Pharmacology 12:986.
- W. Goettsch, N. Beerenwinkel, L. Deng, L. Dölken, B. E. Dutilh, F. Erhard, L. Kaderali, M. von Kleist, R. Marquet, J. Matthijnssens, S. McCallin, D. McMahon, T. Rattei, R. Van Rij, D. L. Robertson, M. Schwemmle, N. Stern-Ginossar, M. Marz (2021). ITN - ViroInf: Understanding (harmful) virus-host interactions by linking virology and bioinformatics. Viruses 13(5), 766.
- M. Sironi, L. Kaderali (2021). Bioinformatics Algorithms and Predictive Models: The Grand Challenge in Computational Virology. Front Virol 1:684608.
- A.K. Becker, M. Dörr, S.B. Felix, F. Frost, H.J. Grabe, M.M. Lerch, M. Nauck, U. Völker, H. Völzke, L. Kaderali (2021). From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach. PLoS Comput Biol. 17(2):e1008735.
- A. Osterman, H.-M. Baldauf, M. Eletreby, J.M. Wettengel, S.Q. Afridi, T. Fuchs, E. Holzmann, A. Maier, J. Döring, N. Grzimek-Koschewa, M. Muenchhoff, U. Protzer, L. Kaderali, O.T. Keppler (2021). Evaluation of two rapid antigen tests to detect SARS-CoV-2 in a hospital setting. Medical Microbiology and Immunology 210(1):65-72.
- F. Hufsky, K. Lamkiewicz, A.Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C. Brandt, M. Cacciabue, S. Chuguransky, O. Drechsel, R.D. Finn, A. Fritz, S. Fuchs, G. Hattab, A.-C. Hauschild, D. Heider, M. Hoffmann, M. Holzer, S. Hoops, L. Kaderali, I. Kalvari, M. von Kleist, R. Kmiecinski, D. Kuhnert, G. Lasso, P. Libin, M. List, H.F. Lochel, M.J. Martin, R. Martin, J. Matschinske, A.C. McHardy, P. Mendes , J. Mistry, V. Navratil, E.P. Nawrocki, A.N. O'Toole, N. Palacios-Ontiveros, A.I. Petrov, G. Rangel-Pineros, N. Redaschi, S. Reimering, K. Reinert, A. Reyes, L. Richardson, D.L. Robertson, S. Sadegh, J.B. Singer, K. Theys, C. Upton , M. Welzel, L. Williams, M. Marz (2021). Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and Coronavirus research. Briefings in Bioinformatics 22(2):642-663
- B. Metelmann, P. Brinkrolf, M. Kliche, M. Vollmer, K. Hahnenkamp, C. Metelmann (2021). Rettungsdienst, kassenärztlicher Notdienst oder Notaufnahme. Med Klin Intensivmed Notfmed, in press.
2020
- S. Trump, S. Lukassen, M.S. Anker, R.L. Chua, J. Liebig, L. Thürmann, V.M. Corman, M. Binder, J. Loske, C. Klasa, T. Krieger, B.P. Hennig, M. Messingschlager, F. Pott, J. Kazmierski, S. Twardziok, J.P. Albrecht, J. Eils, S. Hadzibegovic, A. Lena, B. Heidecker, T. Bürgel, J. Steinfeldt, C. Goffinet, F. Kurth, M. Witzenrath, M.T. Völker, S.D. Müller, U.G. Liebert, N. Ishaque, L. Kaderali, L.E. Sander, C. Drosten, S. Laudi, R. Eils, C. Conrad, U. Landmesser, I. Lehmann (2020). Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nat Biotechnol., in press.
- J. Rüdebusch, A. Benkner, N. Nath, L. Fleuch, L. Kaderali, K. Grube, K. Klingel, G. Eckstein, T. Meitinger, J. Fielitz, S. Felix (2020). Stimulation of soluble guanylate cyclase by riociguat attenuates heart failure and pathological cardiac remodelling, Brit J Pharmacology, in press.
- H. Müller, S.P. Godehard, G.J. Palm, L. Berndt, C.P.S. Badenhorst, A.-K. Becker, M. Lammers, U. Bornscheuer (2020). Discovery and Design of Family VIII Carboxylesterases as Highly Efficient Acyltransferases. Angew. Chemie, in press.
- M. Franz, L. Hagenau, R. Koch, S. Neubauer, B. Nowack, A. Tzvetkova, L.R. Jensen, A.W. Kuss (2020). Generation of an iPSC line (UMGWi001-B) from a patient with Floating-Harbor Syndrome (FLHS) carrying a heterozygous SRCAP mutation (p.Arg2444). Stem Cell Res 49:102028.
- C. Zitzmann, L. Kaderali, A.S. Perelson (2020). Mathematical Modeling of Hepatitis C RNA Replication, Exosome Secretion and Virus Release. PLOS Comp Biol, in press.
- M. Gholizadeh, S. Szelag-Pieniek, M. Post, M. Kurzawski, J. Prieto, J. Argemi, M. Drozdzik, L. Kaderali (2020). Identifying Differentially Expressed MicroRNAs, Target Genes, and Key Pathways Deregulated in Patients with Liver Diseases. Int. J. Mol. Sci. 21(19):7368.
- T. Herr, J. Gamain, R. Fleischmann, B. Lehnert, M. Vollmer, C. Willert, B. Veit, A. Stenner, J.-U. Müller, B. Caspers, M. Kronbürger (2020). Olfaction as a Marker for Dystonia: Background, Current State and Directions. Brain Sciences 10(10), 727.
- A. El Damaty, S. Marx, G. Cohrs, M. Vollmer, A. Eltanahy, E. El Refaee, J. Baldauf, S. Fleck, H. Baechli, A. Zohdi, M. Synowitz, A. Unterberg, H.W.S. Schroeder (2020). ETV in infancy and childhood below 2 years of age for treatment of hydrocephalus. Child's Nervous System, in press.
- N. Holzscheck, J. Söhle, T. Schläger, C. Falckenhayn, E. Grönninger, L. Kolbe, H. Wenck, L. Terstegen, L. Kaderali, M. Winnefeld, K. Gorges (2020). Concomitant DNA methylation and transcripome signatures define epidermal responses to acute solar UV radiation. Sci Rep, in press.
- D. Streit, T. Shanmugam, A. Garbelyanski, S. Simm, E. Schleiff (2020). The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. Plants (Basel) 9(8):2016.
- N. Nath, L. Hagenau, S. Weiss, A. Tzvetkova, L.R. Jensen, L. Kaderali, M. Port, H. Scherthan, A.W. Kuss (2020). Genome-Wide DNA alterations in X-Irradiated Human Gingiva Fibroblasts. Int J Mol Sci, in press.
- L. Haralambiev, A. Bandyophadyay, B. Suchy, M. Weiss, A. Kramer, S. Bekeschus, A. Ekkernkamp, A. Mustea, L. Kaderali, M.B. Stope (2020). Determination of Immediate vs. Kinetic Growth Retardation in Physically Plasma-treated Cells by Experimental and Modelling Data. Anticancer Res 40(7):3743-3749.
- Y. Hu, S. Fragkostefanakis, E. Schleiff, S. Simm (2020). Transcriptional Basis for Differential Thermosensitivity of Seedlings of Various Tomato Genotypes. Genes (Basel) 11(6):655.
- L. Palma Medina, A.-K. Becker, S. Michalik, K. Surmann, P. Hildebrandt, M. Gesell Salazar, S.A. Mekonnen, L. Kaderali, U. Völker, J.M. van Dijl (2020). Interaction of Staphylococcus aureus and host cells upon infection of bronchial epithelium during different stages of regeneration, ACS Infectious Diseases, in press.
- N. Holzscheck, J. Söhle, B. Kristof, E. Grönninger, S. Gallinat, H. Wenck, M. Winnefeld, C. Falckenhayn*, L. Kaderali* (2020). Mulit-omics networks analysis reveals distinct stages in the human aging progression in epidermal tissue.Aging, in press.
- D. Schweinoch, P. Bachmann, D. Clausznitzer, M. Binder, L. Kaderali (2020). Mechanistic modeling explains the dsRNA length-dependent activation of the RIG-I mediated immune response, J Theor Biol, in press.
- C. Zitzmann, B. Schmid, A. Ruggieri, A.S. Perelson, M. Binder, R. Bartenschlager, L. Kaderali (2020). A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection. Front. Microbiol., in press.
- H. Müller, A.-K. Becker, G. Palm, L. Berndt, C.P.S. Badenhorst, S.P. Godehard, L. Reisky, M. Lammers, U. Bornscheuer (2020). Sequence-Based Prediction of Promiscuous Acyltransferase Activity in Hydrolases. Angew Chem, in press.
- M. Gholizadeh, J. Fayazi, Y- Asgari, H. Zali, L. Kaderali (2020). Reconstruction and analysis of cattle metabolic networks in normal and acidosis rumen tissue. Animals, in press.
- L.E. Gross, N. Spies, S. Simm, E. Schleiff (2020). Toc75-V/OEP80 is processed during translocation into chloroplasts, and the membrane-embedded form exposes its POTRA domain to the intermembrane space. FEBS Open Bio 10(3):444-454.
- M. Keller, E. Schleiff, S. Simm (2020). miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum. Sci Rep 10(1):10694.
- C. Luz, M. Vollmer, J. Decruyenaere, M. Nijsten, C. Glasner, B. Sinha (2020). Machine learning in infection management using routine electronic health records: tools, techniques, and reporting of future technologies. Clinical Microbiology and Infection, in press.
- T. Herr, T. Hummel, M. Vollmer, C. Willert, B. Veit, J. Gamain, R. Fleischmann, B. Lehnert, J.-U. Müller, A. Stenner, M. Kronenbürger (2020). Smell and taste in cervical dystonia. Journal of Neural Transmission, in press.
- S. Dirmeier, C. Dächert, M. van Hemert, A. Tas, N.S. Ogando, F. van Kuppeveld, R. Bartenschlager, L. Kaderali, M. Binder, N. Beerenwinkel (2020). Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLOS Comp Biol 16(2):e1007587.
- F. Kriesel, L. Stegmann, S. Ciesek, L. Kaderali, H.-M. Baldauf (2020). Efficient inactivation of pseudotyped HIV-based lentiviral vectors and infectious HIV. J Virol Methods, 276:113768.
2019
- J. Schwarzenbacher, S.-O. Kuhn, M. Vollmer, C. Scheer, C. Fuchs, S. Rehberg, V. Balau, K. Hahnenkamp, J.A. Bohnert, M. Gründling (2019). On-site blood culture incubation shortens the time to knowledge of positivity and microbiological results in septic patients. PLOS One 14(12):e0225999.
- B. Metelmann, C. Metemann, L. Schneider, M. Vollmer, M. Fischer, A. Bohn, J. Wnent, K. Hahnenkamp, P. Brinkrolf (2019). Anstieg der Laienreanimationsrate in Deutschland geht mit vermehrter Telefonreanomation einher. Der Notarzt 35(06), 232-328.
- N. Nath, L. Hagenau, S. Weiss, A. Tzvetkova, L.R. Jensen, L. Kaderali, M. Port, H. Scherthan, A.W. Kuss (2019). Ionizing Radiation alters the transition/transversion ratio in the exome of human gingiva fibroblasts. Health Physics Journal, in press.
- G. Köhler*, M. Vollmer*, N. Nath, P.-A. Hessler, K. Dennis, A. Lehr, M. Köller, C. Riechmann, H. Bralo, D. Trojnarska, H. Lehnhoff, J. Krichbaum, M. Krichbaum, K. Evert, M. Evert, M. Zygmunt*, L. Kaderali* (2019). Benign uterine mass - Discrimination from leiomyosarcoma by a preoperative risk score: a multicenter cohort study. Archives of Gynecology and Obstetrics 300(6):1719-1727.
- A.-K. Becker, H. Holzmann (2019). Nonparametric identification in the dynamic stochastic block model. IEEE Transactions on Information Theory 56(7):4335-44.
- T. Westphal, W. Konschake, H. Haase, M. Vollmer, M. Jünger, H. Riebe (2019). Medical compression stockings on the skin moisture in patients with chronic venous disease. Vasa, in press.
- T. Oellerich, C. Schneider, D. Thomas, K. Knecht, O. Buzovetsky, L. Kaderali, C. Schliemann, H. Bohnenberger, L. Angenendt, W. Hartmann, E. Wardelmann, T. Rothenburger, S. Mohr, S. Scheich, F. Comoglio, A. Wilke, P. Ströbel, H. Serve, M. Michaelis, N. Ferreiros, G. Geisslinger, Y. Xiong, O. Keppler, J. Cinatl (2019). Selective Inactivation of Hypomethylating Agents by SAMHD1 Provides a Rationale for Therapeutic Stratification in AML. Nature Comm. 10(1):3475.
- M. Cortese, A. Kumar, P. Matula, L. Kaderali, P. Scaturro, H. Erfle,
E.G. Acosta, S. Buehler, A. Ruggieri, L. Chatel-Chaix, K. Rohr, R. Bartenschlager (2019).
Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus
Replication and Virion Production. Cell Rep. 27(9):2579-92.
- N. Exner, J.A. Valenzuela-Campos, K. Abou-El-Ardat, H. Miletic,
P. Huszthy, P. Radehaus, E. Schröck, R. Bjerkvig, L. Kaderali,
B. Klink, J. Nigro (2019) Deep sequencing of a recurrent oligodentroglioma
and the derived xenografts reveals new insights into the evolution of human
oligodendroglioma and candidate driver genes. Oncotarget 10(38):3641-3653.
- L.M. Palma Medina, A.K. Becker, S. Michalik, H.
Yedavally, E.J.M. Raineri, P. Hildebrandt, M. Gesell Salazar, K.
Surmann, H. Pförtner, S.A. Nekonnen, A. Salvati, L. Kaderali,
J.M. van Dijl, U. Völker (2019). Metabolic cross-talk between
human bronchial epithelial cells and internalized Staphylococcus aureus
as a driver for infection. Mol Cell Proteomics 18(5):892-908.
- L. Kaderali, F. Theis, V.V. Ganusov, S.M. Ciupe, R. Mehr,
R.M. Ribeiro, E.A. Hernandez-Vargas (2019). Editorial: Integrative
Computational Systems Biology Approaches in Immunology and Medicine.
Front
Microbiol 9:3338.
- P. Jansen, A. Sümnig, M. Esefeld, K. Greffin, L. Kaderali,
A. Greinacher (2019). Well-being and return rate of first-time
whole blood donors. Vox
Sanguinis 114(2):154-161.
- A. E-Shershaby, S. Ullrich, S. Simm, K.D. Scharf, E. Schleiff, S. Fragkostefanakis (2019).
Functional diversification of tomato HsfA1 factors is based on DNA binding domain properties.
Gene. 714:143985.
- U.S. Bodensohn, S. Simm, K. Fischer, M. Jaeschke, L.E. Gross, K. Kramer, C. Ehmann, S.A. Rensing, R. Ladig, E. Schleiff (2019).
The intracellular distribution of the components of the GET system in vascular plants.
Biochim Biophys Acta Mol Cell Res. 1866(10):1650-1662.
- J. Berz, S. Simm, S. Schuster, K.D. Scharf, E. Schleiff, I. Ebersberger (2019).
HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants.
Bioinform. Biol. Insights eCollection: 13:1177932218821365.
- S. Fragkostefanakis, S. Simm, A. El-Shershaby, Y. Hu, D. Bublak, A. Mesihovic, K. Darm, S.K. Mishra, B. Tschiersch, K. Theres, C. Scharf, E. Schleiff, K.D. Scharf (2019).
The repressor and co-activator HsfB1 regulates the major heat stress transcription factors in tomato.
Plant Cell Environ. 42(3):874-890.
- J. Kovacevic, D. Palm, D. Jooss, D. Bublak, S. Simm, E. Schleiff (2019). Co-orthologues of ribosome biogenesis factors in A. thaliana are differentially regulated by transcription factors. Plant Cell Rep., in press.
- D. Palm, D. Streit, T. Shanmugam, B.L. Weis, M. Ruprecht, S. Simm, E. Schleiff (2019). Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. Nucleic Acids Res. 47(4):1880-1895.
- K. Wiesemann, S. Simm, O. Mirus, R. Ladig, E. Schleiff (2019). Regulation of two GTPases Toc159 and Toc34 in the translocon of the outer envelope of chloroplasts.
Biochim. Biophys. Acta Proteins Proteom 1867(6):627-636.
2018
- K.M. Knecht, O. Buzovetsky, C. Schneider. D. Thomas, V. Srikanth,
L. Kaderali, F. Tofoleanu, K. Reiss, N. Ferreiros, G.
Geisslinger, V.S. Batista, X. Ji,. J Jr Cinatl, O.T. Keppler, Y. Xiong
(2018). The structural basis for cancer drug interactions with the
catalytic and allosteric sites of SAMHD1. Proc
Natl Acad SCI USA 115(43):E10022-E10031.
- P. Sodmann, M. Vollmer, N. Nath, L.
Kaderali (2018). A Convolutional Neural Network for ECG
Annotation as the Basis for Classification of Cardiac Rythms. Physiological
Measurements 39(10):104005.
- C.S. Scheer, C. Fuchs, M. Gründling, M. Vollmer, J. Bast,
J.A. Bohnert, K. Zimmermann, K. Hahnenkamp, S. Rehberg, S.-O. Kuhn
(2018). Impact of antibiotic administration on blood culture
positivity at the beginning of sepsis: a prospective clinical cohort
study. Clin
Microb Inf 25(3):326-331.
- C.S. Scheer, S.-O. Kuhn, C. Fuch, M. Vollmer, A. Modler,
F. Brunkhorst, M. Shankar-Hari, K. Hahnenkamp, M. Gründling, S. Rehberg
(2018). Do Sepsis-3 criteria facilitate earlier recognition of
sepsis and septic shock? A retrospective cohort study. SHOCK
51(3):306-311.
- M. Gast, B.H. Rauch, S. Nakagawa, A. Haghikia, A. Jasina, J.
Haas, N. Nath, L. Jensen, A. Stroux, A. Böhm, J. Friebel, U.
Rauch, C. Skurk, S. Blankenberg, T. Zeller, K.V. Prasanth, B. Meder, A.
Kuss, U. Landmesser, W. Poller (2018). Immune system-mediated
atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in
ApoE-/- mice, Cardiovascular
Research 115(2):302-314.
- H. Bohnenberger*, L. Kaderali*, P. Ströbel, D. Yepes, U.
Plessmann, S. Yao, C. Heydt, S. Merkelbach-Bruse, A. Emmert, J.
Hoffmann, J. Bodemeyer, K. Reuter-Jessen, A.-M. Lois, L.H. Dröge, P.
Baumeister, C. Walz, L. Biggemann, R. Walter, B. Häupl, F. Comoglio,
K.-T. Pan, S. Scheich, C. Lenz, S. Küffer, F. Bremmer, J. Kitz, M.
Sitte, T. Beissbarth, M. Hinterthaner, M. Sebastian, J. Lotz, H.-U.
Schildhaus, H. Wolff, B.C. Danner, C. Brandts, R. Büttner, M. Canis, H.
Serve, H. Urlaub, T. Oellerich (2018). Comparative proteomics
reveals a diagnostic signature for pulmonary head-and-neck cancer
metastasis. EMBO Mol.
Med. 10(9), pii: e8428.
- J. Bruening, L. Lasswitz, P. Banse, S. Kahl, C. Marinach, F.W.
Vondran, L. Kaderali, O. Silvie, T. Pietschmann, F. Meissner,
G. Gerold (2018). Hepatitis C virus enters liver cells using the
CD81 receptor complex proteins calpain-5 and CBLB. PLOS Pathogens
14(7):e1007111.
- N. Endlich, T. Lange, J. Kuhn, P. Klemm, A.M. Kotb, F. Siegerist,
F. Kindt, M.T. Lindenmeyer, C.D.Cohen, A.W. Kuss, N. Nath, R.
Rettig, U. Lendeckel, U. Zimmermann, K. Amann, S. Stracke, K. Endlich
(2018) BDNF: mRNA expression in urine cells of patients with
chronic kidney disease and its role in kidney function. J Cell Mol Med
22(11):5265-5277.
- C. Zitzmann, L. Kaderali (2018). Mathematical
Analysis of Viral Replication Dynamics and Antiviral Treatment
Strategies: From Basic Models to Age-based Multiscale Modeling. Frontiers in Microbiology 9:1546.
- M. del Mar Saez-Freire, A. Blanco-Gomez, S. Castillo-Lluva, A.
Gomez-Vecino, J.M. Galvis-Jimenez, C. Martin-Seisdedos, M.
Isidoro-Garcia, L. Hontecillas-Prieto, M.B. Garcia-Cenador, F.J.
Garcia-Criado, M.C. Patino-Alonso, P. Galindo-Villardon, J.-H. Mao, C.
Prieto, A. Castellanos-Martin, L. Kaderali, J. Perez-Losada
(2018). Supplementary data for the biological age linked to
oxidative stress modifies breast cancer aggressiveness. Data Brief
18:1172-84.
- S. Noack, M. Raab, Y. Matthess, M. Sanhaji, A. Krämer, B.
Gyorffy, L. Kaderali, A. El-Balat, S. Becker, K. Strebhardt
(2019). Synthetic lethality in CCNE1-amplified high grade serous
ovarian cancer through combined inhibition of Polo-like kinase 1 and
microtubule dynamics. Oncotarget
9(40):25842-59.
- N. Nath, J. Esche, L.R. Jensen, M- Port, M. Stanke, L.
Kaderali, H. Scherthan, A.W.Kuss (2018). Exome Sequencing
Discloses Ionizing-radiation-induced DNA Variants in the Genome of
Human Gingiva Fibroblasts. Health Phys
115(1):151-160.
- A.-K. Becker, H. Erfle, M. Gunkel, N. Beil, L. Kaderali*,
V. Starkuviene* (2018). Comparison of cell arrays and multi-well
plates in microscopy-based screening. High Throughput
7(2) pii:E13..
- M. del Mar Saez-Freir, A. Blanco-Gomez, S. Castillo-Lluva, A.
Gomez-Vecino, J.M. Galvis-Jimenez, C. Martin-Seisdedos, M.
Isidoro-Garcia, L. Hontecillas-Prieto, M.B. Garcia-Cenador, F.J.
Garcia-Criado, M.C. Patino-Alonso, P. Galindo-Villardon, J.-H. Mao, C.
Prieto, A. Castellanos-Martin, L. Kaderali, J. Perez-Losada
(2018). The biological age linked to oxidative stress modifies
breast cancer aggressiveness. Free Radical
Biology & Medicine 120:133-146, doi:
10.1016/j.freeradbiomed.2018.03.012..
- R. Appweiler, T. Beissbarth, M.R. Berthold, N. Blüthgen, Y.
Burmeister, O. Dammann, A. Deutsch, F. Feuerhake, A. Franke, J.
Hasenauer, S. Hoffmann, T. Höfer, P.L. JansenL, L. Kaderali, U.
Klingmüller, I. Koch, O. Kohlbacher, L. Kuepfer, F. Lammert, D. Maier,
N. Pfeifer, N. Radde, M. Rehm, I. Roeder, J. Saez-Rodriguez, U. Sax, B.
Schmeck, A. Schuppert, B. Seilheimer, F.J. Theis, J. Vera, O.
Wolkenhauer (2018). Whither systems medicine? Exp Mol Med.
50(3):e453, doi: 10.1038/emm.2017.290.
- D. Palm, D. Streit, M. Ruprecht, S. Simm, C. Scharf, E. Schleiff (2018).
Late ribosomal protein localization in Arabidopsis thaliana differs to that in Saccharomyces cerevisiae.
FEBS Open Bio. 8(9):1437-1444.
- M. Keller, SPOT-ITN Consortium, S. Simm (2018). The coupling of transcriptome and proteome adaptation
during development and heat stress response of tomato pollen.
BMC Genomics 19(1):447.
- S. Lampe, M. Kunze, A. Scholz, T.F. Brauss, S. Winslow, S. Simm, M. Keller, J. Heidler, I. Wittig, B. Brüne, T. Schmid (2018).
Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors.
Biochim. Biophys. Acta Gene Regul. Mech. 1861(2):147-157.
2017
- C. Scheer, C. Fuchs, S. Kuhn, M. Vollmer, S. Rehberg, S.
Friesecke, P. Abel, V. Balau, C. Bandt, K. Meissner, K. Hahnenkamp, M.
Gründling (2017). Qualitys improvement initiative for severe
sepsis and septic shock reduced 90-day mortality: A 7.5-year
observational study.. Crit Care Med
45(2):241-252.
- C. Yang, U. Bork, S. Schölch, Y. Kulu, L. Kaderali, U.L.
Bolstorff, C. Kahlert, J. Weitz, N.N. Rahbari, C. Reissfelder (2017). Postoperative
course and prognostic value of circulating angiogenic cytokines after
pancreatic cancer resection. Oncotarget
8(42):72315-72323.
- I.K. Stoeck, J.Y. Lee, K. Tabata, I. Romero-Brey, D. Paul, P.
Schult, V. Lohmann, L. Kaderali, R. Bartenschlager (2017). Hepatitis
C virus replication depends on endosomal cholesterol homeostasis. J. Virol.
92(1). pii: e01196-17.
- C. Lauber, S. Seitz, S. Mattei, A. Suh, J. Beck, J.
Herstein, J. Bärold, W. Salzburger, L. Kaderali, J.A.G Briggs,
R. Bartenschlager (2017). Deciphering the Origin and Evolution of
Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.
Cell Host
& Microbe 22(3):387-399.e6.
- C. Fuchs, S. Wauschkuhn, C. Scheer, M. Vollmer, K.
Meissner, S.-O. Kuhn, K. Hahnenkamp, A. Morelli, M. Gründling, S.
Rehberg (2017). Continuing chronic beta-blockade in the acute
phase of severe sepsis and septic shock is associated with decreased
mortality rates up to 90 days. Brit J Anaesthes
119(4):616-25.
- M. Rath, S.E. Jenssen, K. Schwefel, D. Kleimeier, C.
Sperling, L. Kaderali, U. Felbor (2017). High-throughput
sequencing of the entire genomic regions of CCM1/KRIT1, CCM2 and
CCM3/PDCD10 to search for pathogenic deep-intronic splice mutations in
cerebral cavernous malformations. Eur J Med Genet
60(9):479-84.
- J. Willemsen, O. Wicht, J.C. Wolanski, N. Baur, S. Bastian, D.A.
Haas, P. Matula, B. Knapp, L. Meyniel-Schicklin, C. Wang, R.
Bartenschlager, V. Lohmann, K. Rohr, H. Erfle, L. Kaderali, J.
Marcotriagiano, A. Pichlmair, M. Binder (2017). Phosphorylation-Dependent
Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA
Screening. Mol
Cell 65(3):403-15.
- C. Schneider, T. Oellerich, H.M. Baldauf, S.M. Schwarz, D.
Thomas, R. Flick, H. Bohnenberger, L. Kaderali, L. Stegmann, A.
Cremer, M. Martin, J. Lohmeier, M. Michaelis, V. Hornung, C.
Schliemann, W.E. Berdel, W. Hartmann, E. Wardelmann, F. Comoglio, M.L.
Hansmann, A.F. Yakunin, G. Geisslinger, P. Ströbel, N. Ferreiros, H.
Serve, O.T. Keppler, J. Cinatl Jr. (2017). SAMHD1 is a biomarker
for cytarabine response and a therapeutic target in acute myeloid
leukemia. Nat.
Med. 23(2):250-255.
- M. Keller, Y. Hu, A. Mesihovic, S. Fragkostefanakis, E. Schleiff, S. Simm (2017).
Alternative splicing in tomato pollen in response to heat stress. DNA Res.
24(2):205-217.
2016
- K. Skoskiewicz-Malinowska, B. Noack, L. Kaderali, B.
Malicka, K. Lorenz, K. Walczak, M.-T. Weber, M. Mendak-Ziolko, T.
Hoffmann, M. Zietek, M. Walter, U. Kaczmarek, C. Hannig, M.
Radwan-Oczko, M. Raedel (2016). Oral Health and Quality of Life in
Old Age: A Cross-Sectional Pilot Project in Germany and Poland. Adv Clin Exp Med
25(5):951-59.
- M. Rath, S. Spiegler, N. Nath, K. Schwefel, N. Di Donato,
J. Gerber, G.C. Korenke, Y. Hellenbroich, U. Hehr, S. Gross, U. Sure,
B. Zoll, E. Gilberg, L. Kaderali, U. Felbor (2016). Constitutional
de novo and postcygotic mutations in isolated cases of cerebral
cavernous malformations. Mol Genet Genomic
Med 5(1):21-27.
- S.C. Hamer, A. Becker, K. Rateitschak, A. Mohr, F.L.
Ripoli, S. Hennecke, J. Junginger, M. Hewicker-Trautwein, B. Brenig, A.
Ngezahoy, I. Nolte, H.M. Escobar (2016). Longitudinal Claudin Gene
Expression Analyses in Canine Mammary Tissues and Thereof Derived
Primary Cultures and Cell Lines. Int J Mol Sci17(10) pii:E1655.
- L. Kaderali, V. Thiel (2016). Systems biology of
viral infection. Virus Res.
218:1.
- F. Bormann, M. Rodriguez-Paredes, S. Hagemann, H. Manchanda,
B. Kristof, J. Gutekunst, G. Raddatz, R. Haas, L. Terstegen, H. Wenck, L.
Kaderali, M. Winnefeld, F. Lyko (2016). Reduced DNA
methylation patterning and transcriptional connectivity define human
skin aging. Aging
Cell 15(3):563-71.
- G. Vieyres, K. Welsch, G. Gerold, J. Gentzsch, S. Kahl, F. W. R.
Vondran, L. Kaderali, T. Pietschmann (2016). ABHD5/CGI-58,
the Chanarin-Dorfman syndrome protein, mobilises lipid stores for
hepatitis C virus production. PLOS Pathogens
12(4):e1005568.
- SM Hill, LM Heiser, T Cokelaer, M Unger, NK Nesser, DE Carlin, Y
Zhang, A Sokolov, EO Paull, CK Wong, K Graim, A Bivol, H Wang, F Zhu, B
Afsar, LV Danilova, AV Favorov, WS Lee, D Taylor, CW Hu, BL Long, DP
Noren, AJ Bisberg, HPN-DRESAM Consortium (B Afsari, R Al-Ouran, B
Anton, T Arodz, OA Sichani, N Bagheri, N Berlow, AJ Bisberg, A Bivol, A
Bohler, J Bonet, R Bonneau, G Budak, R Bunescu, M Cagla, B Cai, C Cai,
DE Carlin, A Carlon, L Chen, MF Ciaccio, T Cokelaer, G Cooper, CJ
Creighton, SM Daneshmand, A de la Fuente, B Di Camillo, LV Danilova, J
Dutta-Moscato, K Emmett, C Evelo, MK Fassia, AV Favorov, EJ Fertig, JD
Finkle, F Finotello, S Friend, X Gao, J Gao, J Garcia-Garcia, S Ghosh,
A Giaretta, K Graim, JW Gray, R Großeholz, Y Guan, J Guinney, C
Hafemeister, O Hahn, S Haider, T Hase, LM Heiser, SM Hill, J Hodgson, B
Hoff, CH Hsu, CW Hu, Y Hu, X Huang, M Jalili, X Jiang, T Kacprowski, L
Kaderali, M Kang, V Kannan, M Kellen, K Kikuchi, DC Kim, H Kitano, B
Knapp, G Komatsoulis, H Koeppl, A Krämer, MB Kursa, M Kutmon, WS
Lee, Y Li, X Liang, Z Liu, Y Liu, BL LongL, S Lu, X Lu, M Manfrini, MR
Matos, D Meerzaman, GB Mills, W Min, S Mukherjee, CL Müller, RE
Neapolitan, NK Nesser, DP Noren, T Norman, B Oliva, SO Opiyo, R Pal, A
Palinkas, EO Paull, J Planas-Iglesias, D Poglayen, AA Qutub, J
Saez-Rodriguez, F Sambo, T Sanavia, A Sharifi-Zarchi, J Slawek, A
Sokolov, M Song, PT Spellman, A Streck, G Stolovitzky, S Strunz, JM
Stuart, D Taylor, J Tegnér, K Thobe, GM Toffolo, E Trifoglio, M Unger,
Q Wan, H Wang, L Welch, CK Wong, JJ Wu, AY Xue, R Yamanaka, C Yan, S
Zairis, M Zengerling, H Zenil, S Zhang, Y Zhang, F Zhu, Z Zi.), GB
Mills, JW Gray, M Kellen, T Norman, S Friend, AA Qutub, EJ Fertig, Y
Guan, M Song, JM Stuart, PT Spellman, H Koeppl, G Stolovitzky, J
Saez-Rodriguez, S Mukherjee. (2016). Inferring causal molecular
networks: empirical assessment through a community-based effort. Nature Methods
13(4):310-8.
- K. Rateitschak, L. Kaderali, O. Wolkenhauer, R.
Jaster (2016). Autocrine TGF-ß/ZEB/microRNA-200 signal
transduction drives epithelial-mesenchymal transition: Kinetic models
predict minimal drug dose to inhibit metastasis. Cell Signal
28(8):861-70.
- P. M. Perin, S. Haid, J. Doerrbecker, K. Schulze, C. Zeilinger,
M. von Schaewen, B. Heller, K. Vercauteren, E. Luxenburger, Y. M.
Baktash, F. W. Vondran, S. Speerstra, F. Mukhtarov, L. M. Schang, A.
Kirschning, R. Müller, C. A. Guzman, L. Kaderali, G. Randall,
P. Meuleman, A. Ploss, T. Pietschmann (2016). Flunarizine prevents
hepatitis C virus membrane fusion in a genotype-dependent manner by
targeting the potential fusion petptide within E1. Hepatology
36(1):49-62 doi: 10.1002/hep.28111.
2015
- C. Hölscher, F. Sonntag, K. Henrich, Q. Chen, J. Beneke, P.
Matula, K. Rohr, L. Kaderali, N. Beil, H. Erfle, J.
Kleinschmidt, M. Müller (2015). The SUMOylation pathway restricts
gene transduction by adeno-associated viruses. PLOS Pathogens
11(12):e1005281.
- D. Clausznitzer, J. Harnisch, L. Kaderali (2015). Multi-scale
model for hepatitis C viral load kinetics under treatment with direct
acting antivirals. Virus Res
63(1):49-62.
- K. Hueging, R. Weller, M. Doepke, G. Vieyres, D. Todt, B. Wölk,
F. Vondran, R. Geffers, C. Lauber, L. Kaderali, F.
Penin, T. Pietschmann (2015). Several Human Liver Cell Expressed
Apolipoproteins Complement HCV Virus Production with Varying Efficacy
Conferring Differential Specific Infectivity to Released Viruses. PLoS One
10(7):e0134529.
- G. Gerold, F. Meissner, J. Brüning, K. Welsch, P. Perin, T. F.
Baumert, F. W. Vondran, L. Kaderali, M. Mann, C. M. Rice, T.
Pietschmann (2014). Quantitative proteomics identifies serum
response factor binding protein 1 as host factor for hepatitis C virus
entry. Cell
reports 2(5):864-78.
- M. Matos, B. Knapp, L. Kaderali (2015). lpNet:
a linear programming approach to reconstruct signal transduction
networks. Bioinformatics
31(19):3231-3.
- C. Lauber, G. Vieyres, E. Terczynska-Dyla, A. Kusuma, R.
Dijkman, H. H. Gad, H. Akthar, R. Geffers, F. Vondran. V. Thiel, L.
Kaderali, T. Pietschmann, R. Hartmann (2015). Transcriptome
analysis reveals a classical interferon signature induced by IFNL4 in
primary cells. Genes and Immunity
16(6):414-21.
- B. Baier, A. Kern, L. Kaderali, B. Bis, D. Koschel, A.
Rolle (2015). Retrospective survival analysis of 237 consecutive
patients with multiple metastases from advanced renal cell carcinoma
exclusively resected by 1318 nm laser. European Journal
of Cardio-thoracic Surgery 21(2):211-7.
- C. Lauber, S. Kazem, A. Kravchenko, M. Feltkamp, A.
Gorbalenya (2015). Interspecific adaptation by binary choice at de
novo polyomavirus T antigen site through accelerated codon-constrained
Val-Ala toggling within an intrinsically disordered region,
Nucleic Acids Research 43(10):4800-13.
- S. Amberkar, L. Kaderali (2015). An
integrative approach for a network based meta-analysis of viral RNAi
screens. BMC
Algorithms for Molecular Biology 10:6.
- L. Mailly, F. Xiao, J. Lupberger, G. K. Wilson, P. Aubert, F. H.
T. Duong, D. Calabrese, C. Leboeuf, I. Fofana, C. Thumann, S. Bandiera,
M. Lütgehetmann, T. Volz, C. Davis, H. J. Harris, C. Mee, E. Girardi,
B. Chane-Woon-Ming, M. Ericsson, N. Fletcher, R. Bartenschlager, P.
Pessaux, K. Vercauteren, P. Meuleman, P. Villa, L. Kaderali, S.
Pfeffer, M. H. Heim, M. Neunlist, M. B. Zeisel, M. Dandri, J. A.
McKeating, E. Robinet, T. F. Baumert (2015). Clearance of
persistent hepatitis C virus infection using a monochlonal antibody
specific for thight junction protein claudin-1. Nature
Biotechnology 33(5):549-54.
- S. Boutin, Y. Graeber, M. Weitnauer, M. Stahl, D. Clausnitzer,
L. Kaderali, G. Einarsson, M. M. Tunney, J. S. Elborn, M.
Mall, A. Dalpke (2015). Comparison of microbiomes from different
niches of upper and lower airways in children and adolescents with
cystic fibrosis, PLoS One
10(1):e0116029.
- M. Poenisch, H. Blankenburg, A. Ruggieri, I. Rebhan, P. Metz, D.
Rupp, K. Diederich, L. Kaderali, F. Domingues, M. Albrecht, V.
Lohmann, H. Erfle, R. Bartenschlager (2014). Identification of
HNRNPK as regulator of hepatitis C virus particle production. PLoS Pathogens
11(1):e1004578.
2014
- 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.
- 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.
- N. A. Kiani, L. Kaderali (2014). Dynamic
Probabilistic Threshold Networks to Infer Signaling Pathways from
Time-Course Perturbation Data. BMC Bioinformatics
15:250.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- D. Clausznitzer, N. Sulaimanov, M. Binder, V.
Lohmann, R. Bartenschlager, L. Kaderali (2011). Systembiologie
der Hepatitis C-Virus-Wirts-Interaktionen. Laborwelt 6:13-15.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- J. Mazur, D. Ritter, G. Reinelt, L. Kaderali
(2009). Reconstructing Nonlinear Dynamic Models of Gene Regulation
using Stochastic Sampling. BMC Bioinformatics
10:448.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- M. Zapatka, L. Kaderali (2007). Statistische Analyse
von Daten klinischer Studien. GynSpectrum
3, 18-19.
- 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.
- 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.
- 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.
- 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.
- M. Leber, L. Kaderali, A. Schönhuth, R. Schrader (2005).
A fractional programming approach to efficient DNA melting temperature
calculation. Bioinformatics 21, 2375-2382.
- L. Kaderali, A. Deshpande, J. P. Nolan, P. S. White
(2003). Primer-design for multiplexed genotyping. Nucleic Acids Research 31, 1796-1802.
- 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.
- L. Kaderali, A. Schliep (2002). Selecting signature
oligonucleotides to identify organisms using DNA arrays. Bioinformatics 18, 1340-1349.
- L. Kaderali, A. Schliep (2001). A new Algorithm for
accelerating Pair-Wise Computations of Melting Temperature. Electronic Notes in Discrete Mathematics, 8, 46-49.
*) Joint first or joint last authorship.
Books and Book contributions
- 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.
- 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.
- 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.
- B. Knapp, L. Kaderali (2012). Single-Cell
Analysis of High-Content, High-Throughput Cellular Assays. In:
Introduction to sequence and genome analysis, iConcept Press.
- 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.
- 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.
- L. Kaderali (2007). Primer Design for Multiplexed
Genotyping. In: A. Yuryev (Editor), PCR Primer Design.
Methods in Molecular Biology, Humana Press, Totowa.
- L. Kaderali (2006). A Hierarchical Bayesian Approach
to Regression and its Application to Predicting Survival Times in Cancer.
Shaker Verlag, Aachen.
Other Publications
- P. Sodmann, M. Vollmer (2020). ECG Segmentation Using a Neural Network as the Basis for Detection of Cardiac Pathologies. Computing in Cardiology 47
- M. Vollmer, D. Bläsing, J.E. Reiser, M. Nisser, A. Buder (2020). Simultaneous physiological measurements with five devices at different cognitive and physical loads (version 1.0.0). *PhysioNet*, https://doi.org/10.13026/chd5-t946.
- M. Vollmer, D. Bläsing, L. Kaderali (2019). Alignment of Multi-Sensored Data: Adjustment of Sampling Frequencies and Time Shifts. Computing in Cardiology (CinC), Vol 46.
- M. Vollmer, C.F. Luz, P. Sodmann, B. Sinha, S.-O. Kuhn (2019). Time-specific Metalearners for the Early Prediction of Sepsis. Computing in Cardiology (CinC) Vol 46.
- M. Vollmer (2019). HRVTool - an Open-Source Matlab Toolbox for Analyzing Heart Rate Variability. Computing in Cardiology (CinC), Vol 46.
- W. Poller. M. Gast, S. Nakagawa, J. Haas, N. Nath, C.
Mueller, T. Hirose, U. Rauch, C. Skurk, B. Rauch, S. Blankenberg, A.
Kuss, B. Meder, U. Landmesser, T. Zeller (2018) Long noncoding RNA
NEAT1 controls ROS production in macrophages and is suppressed in
post-myocardial infarction patients. European
Heart Journal 39, Issue suppl_1, ehy563.P3198.
- M. Vollmer M, P. Sodmann, L. Caanitz, N.
Nath, L. Kaderali (2017). Can supervised learning be
used to classify cardiac rhythms? Computing in
Cardiology 44:347-176.
- M. Vollmer (2017). Noise resistance of several
top-scored heart beat detectors. Computing in
Cardiology 44:182-178
- M. Vollmer (2017), Arrhythmia classification in
long-term data using relative RR intervals. Computing in
Cardiology 44:213-185
- 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.
- 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.
- 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).
- L. Kaderali (2005). Vorhersage des Überlebens bei
Tumorpatienten. Jahresbericht "Kooperative
Informationsverarbeitung an der Universität zu Köln" für das Jahr 2005.
- L. Kaderali (2003). Neural Network Feature Selection
in Complex Trait Analysis. Technical Report, ZAIK, University of
Cologne.
- L. Kaderali (2001). Selecting target specific Probes
for DNA Arrays. Diploma Thesis, University of Cologne.
Software
Available on request: lars.kaderali{at}uni-greifswald.de.
- MCMCpbtn - Network reconstruction from intervention data
using probabilistic Boolean threshold networks
- RNAither - Statistical Analysis of High-Throughput RNAi
screens
- CASPAR - Survival Time Prediction in Cancer from
Microarray Gene Expression Data
- MPXprimer - Multiplex PCR Primer Design
- SBEprimer - Primer Design for Multiplexed Genotyping
- FracTherm - Melting Temperature Calculation for
Oligonucleotides
- ProbeSel - Probe Design for DNA Microarrays
Dissertations / PhD Theses
- J. K. Barry (2017), Mathematical Modeling of the HIV
Lifecycle: Identifying optimal treatment strategies. PhD thesis,
Medical Faculty, University of Greifswald.
- J. Campos Valenzuela (2017), Classification of Glioblastoma
Multiforme Patients based on an integrative multi-layer finite mixture
model system. PhD Thesis, Medical Faculty, TU Dresden.
- S. Amberkar (2014), Integrative bioinformatics analysis of
genome-wide RNAi screens. PhD Thesis, Faculty of Biology,
University of Heidelberg.
- N. Sulaimanov (2012), Mathematical Modeling of Hepatitis C
Virus Replication, PhD Thesis, Faculty of Mathematics and Natural
Sciences, University of Heidelberg
- G. Suryavanshi (2012), Mathematical model to uncover the
role of receptor ubiquitination in dose dependent EGFR trafficking.,
PhD Thesis, Faculty of Biology, University of Heidelberg.
- J. Mazur (2012), Bayesian Inference of Gene Regulatory
Networks: From Paramneter Estimation to Experimental Design., PhD
Thesis, Faculty of Mathematics and Natural Sciences, University of
Heidelberg.
- B. Knapp (2011), RNA Interference Data: From a Statistical
Analysis to Network Inference. PhD Thesis, Faculty of Mathematica
and Natural Sciences, University of Heidelberg
Diploma / Bachelor / Master Theses
- J. Oldenburg (2019), Optimierung eines künstlichen neuronalen Netzes zur Vorhersage einer nichtalkoholischen Fettleber mit Hilfe von KEGG-Pathways, Master Thesis, Biomathematics, University of Greifswald.
- E. Brammen (2019), Integration von KEGG Daten in neuronale Netze zur Identifikation relevanter KEGG Pathways für die Blutdruckvorhersage, Master Thesis, Biomathematics, University of Greifswald.
- D. Ovtchinnikov (2019), Gehirngewebeklassifikation mmithilfe von maschinellem Lernen und intraoperativer Infrarotspektroskopie, Bachelor Thesis, Biomathematics, University of Greifswald.
- A. Wilsdorf (2019), Anwendung Bayes'scher Netze zur Identifikation von Risikofaktoren in epidemiologischen Studien, Master thesis, Biomathematics, University of Greifswald.
- A. Haack (2018), Vergleich von bioinformatischen Methoden zur Vorhersage von B-Zell-Epitopen am Beispiel von Staphylococcus Aureus-Proteinen, Bachelor Thesis, Biomathematics, University of Greifswald.
- A.-M. Schuknecht (2018), Anwendung maschineller Lernverfahren zur Diagnostik der Parodontitis mit Mulit-OMICs-Daten, Bachelor Thesis, Biomathematics, University of Greifswald.
- M.-C. Cwikla (2018), Classification of Thyroid dysfunction using Multinomial Probit Bayesian Additive Regression Trees, Bachelor Thesis, Biomathematics, University of Greifswald.
- C. Bruckmann (2017), Eine Analyse von Genexpressionsdaten mittels maschinellen Lernens zur Untersuchung der Krankheit Fettleber unter Ausschluss von alkoholbedingten Ursachen. Bachelor Thesis, Biomathematics, University of Greifswald.
- R. Wagner (2017), Multilevel weightes support vector machine for high dimensional data sets, Bachelor Thesis, Biomathematics, University of Greifswald.
- A. Weihs (2017), Automated recognition of inherited platelet disorders from digital pictures of blood smears, Bachelor Thesis, Biomathematics, University of Greifswald.
- P. Bachmann (2017), Lipidom-Daten als Biomarker für Alzheimer, Multiple Sklerose und leichte kognitive Beeinträchtigung, Bachelor Thesis, Biomathematics, University of Greifswald.
- J. Harnisch (2015), Multi-scale model for hepatitis C viral load kinetics under treatment with direct acting antivirals, Master Thesis, Biomathematics, University of Greifswald.
- L. Heinrich (2013), Kopplung des Replikationsmodells des Hepatitis-C-Virus mit der Immunantwort. Diploma Thesis (FH), Hochschule Zittau-Görlitz.
- S. Neumann (2013), Modeling of EGFR trafficking. Diploma Thesis, University of Heidelberg.
- C. Gallo-Lopez (2012), Mathematical Model of Ligand-Dose-Dependent Epidermal Growth Factor Receptor Trafficking and Signaling. Master Thesis, University of Evry-Val-d'Essonne.
- S. Faassen (2012), Image-processing pipeline for RNAi microscopy data. Diploma Thesis (FH).
- B. Yadav (2011), Modeling the IL-6 stimulated Jak/Stat pathway in Fibroblasts and Keratinocytes. Master thesis.
- D. Mugahid (2010), Predicting Cancer Survival from aCGH and Gene Expression Data. Master Thesis, Faculty of Biosciences, University of Heideleberg (with Prof. Dr. U. Kummer).
- T. Stumpf (2009), Considerations on Clustering RNAi high throughput screening data assuming a Gamma Distribution. Diploma Thesis, Biology, University of Heidelberg (with Prof. Dr. R. Eils).
- M. Böck (2008), Bayesian learning of Boolean regulatory networks derived from expression data. Diploma Thesis, Bioinformatics, Technical University of Munich (with Prof. Dr. S. Kramer).
- D. Ritter (2008), Machine Network Learning - Bayesian Inference of Gene Regulatory Networks with Differential Equations using Stochastic Simulation. Master Thesis, Faculty of Mathematics and Computer Science, University of Heidelberg (with Prof. Dr. G. Reinelt).
- N. Rieber (2008), An automated pipeline for the statistical analysis of high-throughput RNAi screens. Master Thesis, Faculty of Biosciences, University of Heidelberg (with Prof. Dr. R. Eils).
- B. Heinzel (2008), Ein Markov-Chain-Monte-Carlo Ansatz zur Klassifikation und Überlebenszeitvorhersage von Krebspatienten auf Basis von Genexpressionsdaten. Diplomarbeit, FB Bioinformatik, Fachhochschule Weihenstephan (with Prof. Haubold and Prof. Lesske).
- G. Klingbeil (2007), Inference of Biochemical Networks using a Hybrid Approach. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- C. Giesselbach (2005), Ein Färbungsproblem in partitionierten Graphen. Diplomarbeit, Mathematisches Institut, Universität zu Köln (with Prof. Dr. R. Schrader).
- M. Endriga (2004), Analysis of Complex Genetic Traits. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- C. Kolarik (2004), Development of Clustering Software for SNP Genotyping Data Analysis. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- T.-C. Deng (2004), Development of Clustering Software for SNP Genotyping Data Analysis. Comparison of two clustering methods. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- M. Leber (2003), Design of a Fractional Programming Algorithm for DNA Melting Temperature Determination. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- V. Singh (2003), Probeprep: A Graphical User Interface for the Software for Microarray Probe Design. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.
- A. Gösling (2003), MPCR-Primer. Ein Programm zum selektiven Primer-Design für Multiplex-Polymerase-Kettenreaktionen. Thesis, CUBIC Graduate Course in Bioinformatics, University of Cologne.