Publications

2018

  • Ankerst, Donna P.; Goros, Martin; Tomlins, Scott A.; Patil, Dattatraya; Feng, Ziding; Wei, John T.; Sanda, Martin G.; Gelfond, Jonathan; Thompson, Ian M.; Leach, Robin J.; Liss, Michael A.: Incorporation of Urinary Prostate Cancer Antigen 3 and TMPRSS2:ERG into Prostate Cancer Prevention Trial Risk Calculator. European Urology Focus, 2018 more… BibTeX
  • Ankerst, Donna P.; Straubinger, Johanna; Selig, Katharina; Guerrios, Lourdes; De Hoedt, Amanda; Hernandez, Javier; Liss, Michael A.; Leach, Robin J.; Freedland, Stephen J.; Kattan, Michael W.; Nam, Robert; Haese, Alexander; Montorsi, Francesco; Boorjian, Stephen A.; Cooperberg, Matthew R.; Poyet, Cedric; Vertosick, Emily; Vickers, Andrew J.: A Contemporary Prostate Biopsy Risk Calculator Based on Multiple Heterogeneous Cohorts. European Urology 74 (2), 2018, 197-203 more… BibTeX
  • Castañeda-Tamez, Paulina; Ramírez-Peris, Jimena; Pérez-Velázquez, Judith; Kuttler, Christina; Jalalimanesh, Ammar; Saucedo-Mora, Miguel Á.; Jiménez-Cortés, J. Guillermo; Maeda, Toshinari; González, Yael; Tomás, María; Wood, Thomas K.; García-Contreras, Rodolfo: Pyocyanin Restricts Social Cheating in Pseudomonas aeruginosa. Frontiers in Microbiology 9, 2018, 1348 more… BibTeX
  • Castañeda-Tamez, Paulina; Ramírez-Peris, Jimena; Pérez-Velázquez, Judith; Kuttler, Christina; Jalalimanesh, Ammar; Saucedo-Mora, Miguel Á.; Jiménez-Cortés, J. Guillermo; Maeda, Toshinari; González, Yael; Tomás, María; Wood, Thomas K.; García-Contreras, Rodolfo: Pyocyanin Restricts Social Cheating in Pseudomonas aeruginosa. Frontiers in Microbiology 9, 2018, 1348 more… BibTeX
  • Hernandez, Javier; Gelfond, Jonathan; Goros, Martin; Liss, Michael A.; Liang, Yuanyuan; Ankerst, Donna; Thompson, Ian M.; Leach, Robin J.: The effect of 3-month finasteride challenge on biomarkers for predicting cancer outcome on biopsy: Results of a randomized trial. PLOS ONE 13 (10), 2018, e0204823 more… BibTeX
  • Liss, Michael A.; White, James Robert; Goros, Martin; Gelfond, Jonathan; Leach, Robin; Johnson-Pais, Teresa; Lai, Zhao; Rourke, Elizabeth; Basler, Joseph; Ankerst, Donna; Shah, Dimpy P.: Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer. European Urology 74 (5), 2018, 575-582 more… BibTeX

2017

  • Adam, Jonathan; Brandmaier, Stefan; Troll, Martina; Rotter, Markus; Mohney, Robert P.; Heier, Margit; Adamski, Jerzy; Li, Yixue; Neschen, Susanne; Kastenmüller, Gabi; Suhre, Karsten; Ankerst, Donna; Meitinger, Thomas; Wang-Sattler, Rui: Response to Comment on Adam et al. Metformin Effect on Nontargeted Metabolite Profiles in Patients With Type 2 Diabetes and in Multiple Murine Tissues. Diabetes 2016;65:3776–3785. Diabetes 66 (5), 2017, e3-e4 more… BibTeX
  • Ballnus, Benjamin; Hug, Sabine; Hatz, Kathrin; Görlitz, Linus; Hasenauer, Jan; Theis, Fabian J.: Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. BMC Systems Biology 11 (1), 2017 more… BibTeX
  • Bartel, Sabine; Schulz, Nikola; Alessandrini, Francesca; Schamberger, Andrea C.; Pagel, Philipp; Theis, Fabian J.; Milger, Katrin; Noessner, Elfriede; Stick, Stephen M.; Kicic, Anthony; Eickelberg, Oliver; Freishtat, Robert J.; Krauss-Etschmann, Susanne: Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma. Scientific Reports 7, 2017, 46026 more… BibTeX
  • Beyerlein, Andreas; Strobl, Andreas N.; Winkler, Christiane; Carpus, Michaela; Knopff, Annette; Donnachie, Ewan; Ankerst, Donna P.; Ziegler, Anette-G.: Vaccinations in early life are not associated with development of islet autoimmunity in type 1 diabetes high-risk children: Results from prospective cohort data. Vaccine 35 (14), 2017, 1735-1741 more… BibTeX
  • Blasi, Thomas; Buettner, Florian; Strasser, Michael K; Marr, Carsten; Theis, Fabian J: cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics. Physical Biology 14 (3), 2017, 036001 more… BibTeX
  • Buggenthin, Felix; Buettner, Florian; Hoppe, Philipp S; Endele, Max; Kroiss, Manuel; Strasser, Michael; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hilsenbeck, Oliver; Schroeder, Timm; Theis, Fabian J; Marr, Carsten: Prospective identification of hematopoietic lineage choice by deep learning. Nature Methods 14 (4), 2017, 403-406 more… BibTeX
  • Chen, Rui; Sjoberg, Daniel D.; Huang, Yiran; Xie, Liping; Zhou, Liqun; He, Dalin; Vickers, Andrew J.; Sun, Yinghao; Sun, Yinghao; Huang, Yiran; Xie, Liping; Zhou, Liqun; He, Dalin; Ding, Qiang; Wei, Qiang; Shao, Pengfei; Tian, Ye; Sun, Zhongquan; Fu, Qiang; Ma, Lulin; Zheng, Junhua; Ye, Zhangqun; Ye, Dingwei; Xu, Danfeng; Hou, Jianquan; Xu, Kexin; Yuan, Jianlin; Gao, Xin; Liu, Chunxiao; Pan, Tiejun; Gao, Xu; Ren, Shancheng; Xu, Chuanliang; Vickers, Andrew J.; Roobol, Monique J.; Hugosson, Jonas; Jones, J. Stephen; Kattan, Michael W.; Klein, Eric; Hamdy, Freddie; Neal, David; Donovan, Jenny; Parekh, Dipen J.; Ankerst, Donna; Bartsch, George; Klocker, Helmut; Horninger, Wolfgang; Benchikh, Amine; Salama, Gilles; Villers, Arnauld et al.: Prostate Specific Antigen and Prostate Cancer in Chinese Men Undergoing Initial Prostate Biopsies Compared with Western Cohorts. The Journal of Urology 197 (1), 2017, 90-96 more… BibTeX
  • Chlis, Nikolaos K.; Wolf, F. Alexander; Theis, Fabian J.: Model-based branching point detection in single-cell data by K-branches clustering. Bioinformatics, 2017 more… BibTeX
  • Florea, Ana-Maria; Varghese, Elizabeth; McCallum, Jennifer E.; Mahgoub, Safa; Helmy, Irfan; Varghese, Sharon; Gopinath, Neha; Sass, Steffen; Theis, Fabian J.; Reifenberger, Guido; Büsselberg, Dietrich: Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma. Oncotarget, 2017 more… BibTeX
  • Frohnert, Brigitte I; Laimighofer, Michael; Krumsiek, Jan; Theis, Fabian J; Winkler, Christiane; Norris, Jill M; Ziegler, Anette-Gabriele; Rewers, Marian J; Steck, Andrea K: Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young. Pediatric Diabetes, 2017 more… BibTeX
  • Fröhlich, Fabian; Kaltenbacher, Barbara; Theis, Fabian J.; Hasenauer, Jan: Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLOS Computational Biology 13 (1), 2017, e1005331 more… BibTeX
  • Guinney, Justin; Wang, Tao; Laajala, Teemu D; Winner, Kimberly Kanigel; Bare, J Christopher; Neto, Elias Chaibub; Khan, Suleiman A; Peddinti, Gopal; Airola, Antti; Pahikkala, Tapio; Mirtti, Tuomas; Yu, Thomas; Bot, Brian M; Shen, Liji; Abdallah, Kald; Norman, Thea; Friend, Stephen; Stolovitzky, Gustavo; Soule, Howard; Sweeney, Christopher J; Ryan, Charles J; Scher, Howard I; Sartor, Oliver; Xie, Yang; Aittokallio, Tero; Zhou, Fang Liz; Costello, James C; Abdallah, Kald; Aittokallio, Tero; Airola, Antti; Anghe, Catalina; Azima, Helia; Baertsch, Robert; Ballester, Pedro J; Bare, Chris; Bhandari, Vinayak; Bot, Brian M; Dang, Cuong C; Dunbar, Maria Bekker-Nielsen; Buchardt, Ann-Sophie; Buturovic, Ljubomir; Cao, Da; Chalise, Prabhakar; Cho, Junwoo; Chu, Tzu-Ming; Coley, R Yates; Conjeti, Sailesh; Correia, Sara; Costello, James C; Dai, Ziwei et al.: Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. The Lancet Oncology 18 (1), 2017, 132-142 more… BibTeX
  • Hilsenbeck, Oliver; Schwarzfischer, Michael; Loeffler, Dirk; Dimopoulos, Sotiris; Hastreiter, Simon; Marr, Carsten; Theis, Fabian J.; Schroeder, Timm: fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinformatics 33 (13), 2017, 2020-2028 more… BibTeX
  • Inoue, Lurdes Y.T.; Lin, Daniel W.; Newcomb, Lisa F.; Leonardson, Amy S.; Ankerst, Donna; Gulati, Roman; Carter, H. Ballentine; Trock, Bruce J.; Carroll, Peter R.; Cooperberg, Matthew R.; Cowan, Janet E.; Klotz, Laurence H.; Mamedov, Alexandre; Penson, David F.; Etzioni, Ruth: Comparative Analysis of Biopsy Upgrading in Four Prostate Cancer Active Surveillance Cohorts. Annals of Internal Medicine 168 (1), 2017, 1 more… BibTeX
  • Jagiella, Nick; Rickert, Dennis; Theis, Fabian J.; Hasenauer, Jan: Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models. Cell Systems 4 (2), 2017, 194-206.e9 more… BibTeX
  • Koopmann, Bendix; Müller, Johannes; Tellier, Aurélien; Živković, Daniel: Fisher–Wright model with deterministic seed bank and selection. Theoretical Population Biology 114, 2017, 29-39 more… BibTeX
  • Matiu, Michael; Ankerst, Donna P.; Menzel, Annette: Interactions between temperature and drought in global and regional crop yield variability during 1961-2014. PLOS ONE 12 (5), 2017, e0178339 more… BibTeX
  • Milger, K.; Götschke, J.; Krause, L.; Nathan, P.; Alessandrini, F.; Tufman, A.; Fischer, R.; Bartel, S.; Theis, F. J.; Behr, J.; Dehmel, S.; Mueller, N. S.; Kneidinger, N.; Krauss-Etschmann, S.: Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach. Allergy, 2017 more… BibTeX
  • Peng, Tingying; Thorn, Kurt; Schroeder, Timm; Wang, Lichao; Theis, Fabian J.; Marr, Carsten; Navab, Nassir: A BaSiC tool for background and shading correction of optical microscopy images. Nature Communications 8, 2017, 14836 more… BibTeX
  • Pruthi, Deepak K.; Ankerst, Donna P.; Liss, Michael A.: Novel Definitions of Low-risk and High-risk Prostate Cancer: Implications for the European Randomized Study of Screening for Prostate Cancer Risk Assessment Tool. European Urology 72 (1), 2017, 52-53 more… BibTeX
  • Sadim, Maureen; Xu, Yanfei; Selig, Katharina; Paulus, Julie; Uthe, Regina; Agarwl, Surbhi; Dubin, Iram; Oikonomopoulou, Panagiota; Zaichenko, Lesya; McCandlish, Silvia Aki; Van Horn, Linda; Mantzoros, Christos; Ankerst, Donna Pauler; Kaklamani, Virginia G.: A prospective evaluation of clinical and genetic predictors of weight changes in breast cancer survivors. Cancer 123 (13), 2017, 2413-2421 more… BibTeX
  • Saucedo-Mora, Miguel A.; Castañeda-Tamez, Paulina; Cazares, Adrián; Pérez-Velázquez, Judith; Hense, Burkhard A.; Cazares, Daniel; Figueroa, Wendy; Carballo, Marco; Guarneros, Gabriel; Pérez-Eretza, Berenice; Cruz, Nelby; Nishiyama, Yoshito; Maeda, Toshinari; Belmont-Díaz, Javier A.; Wood, Thomas K.; García-Contreras, Rodolfo: Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa. Frontiers in Microbiology 8, 2017, 1669 more… BibTeX
  • Saucedo-Mora, Miguel A.; Castañeda-Tamez, Paulina; Cazares, Adrián; Pérez-Velázquez, Judith; Hense, Burkhard A.; Cazares, Daniel; Figueroa, Wendy; Carballo, Marco; Guarneros, Gabriel; Pérez-Eretza, Berenice; Cruz, Nelby; Nishiyama, Yoshito; Maeda, Toshinari; Belmont-Díaz, Javier A.; Wood, Thomas K.; García-Contreras, Rodolfo: Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa. Frontiers in Microbiology 8, 2017, 1669 more… BibTeX
  • Schneider, Marc; Christopoulos, Petros; Muley, Thomas; Warth, Arne; Klingmueller, Ursula; Thomas, Michael; Herth, Felix; Dienemann, Hendrik; Mueller, Nikola; Theis, Fabian; Meister, Michael: AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients. International Journal of Oncology, 2017 more… BibTeX
  • Stoecker, Katharina; Sass, Steffen; Theis, Fabian J.; Hauner, Hans; Pfaffl, Michael W.: Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data. Biomolecular Detection and Quantification 11, 2017, 31-44 more… BibTeX
  • Thalgott, Mark; Kron, Martina; Brath, Johannes M.; Ankerst, Donna P.; Thompson, Ian M.; Gschwend, Juergen E.; Herkommer, Kathleen: Men with family history of prostate cancer have a higher risk of disease recurrence after radical prostatectomy. World Journal of Urology 36 (2), 2017, 177-185 more… BibTeX
  • Thalgott, Mark; Kron, Martina; Brath, Johannes M.; Ankerst, Donna P.; Thompson, Ian M.; Gschwend, Juergen E.; Herkommer, Kathleen: Men with family history of prostate cancer have a higher risk of disease recurrence after radical prostatectomy. World Journal of Urology 36 (2), 2017, 177-185 more… BibTeX

2016

  • What Is the Key Best Practice for Collaborating with a Computational Biologist? Cell Systems 3 (1), 2016, 7-11 more… BibTeX
  • Adam, Jonathan; Brandmaier, Stefan; Leonhardt, Jörn; Scheerer, Markus F.; Mohney, Robert P.; Xu, Tao; Bi, Jie; Rotter, Markus; Troll, Martina; Chi, Shen; Heier, Margit; Herder, Christian; Rathmann, Wolfgang; Giani, Guido; Adamski, Jerzy; Illig, Thomas; Strauch, Konstantin; Li, Yixue; Gieger, Christian; Peters, Annette; Suhre, Karsten; Ankerst, Donna; Meitinger, Thomas; Hrabĕ de Angelis, Martin; Roden, Michael; Neschen, Susanne; Kastenmüller, Gabi; Wang-Sattler, Rui: Metformin Effect on Nontargeted Metabolite Profiles in Patients With Type 2 Diabetes and in Multiple Murine Tissues. Diabetes 65 (12), 2016, 3776-3785 more… BibTeX
  • Ankerst, Donna Pauler: GARRETT M. FITZMAURICE, NAN M. LAIRD, AND JAMES H. WARE, Applied Longitudinal Analysis. Hoboken: Wiley. Biometrics 72 (3), 2016, 1009-1009 more… BibTeX
  • Ankerst, Donna Pauler: KATIE HARRON, HARVEY GOLDSTEIN, AND CHRIS DIBBEN, eds, Methodological Developments in Data Linkage. New York: Wiley. Biometrics 72 (2), 2016, 661-662 more… BibTeX
  • Ankerst, Donna Pauler; Gelfond, Jonathan; Goros, Martin; Herrera, Jesus; Strobl, Andreas; Thompson, Ian M., Jr.; Hernandez, Javier; Leach, Robin J.: Serial Percent Free Prostate Specific Antigen in Combination with Prostate Specific Antigen for Population Based Early Detection of Prostate Cancer. The Journal of Urology 196, 2016, 355-360 more… BibTeX
  • Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J.; Becker, Peter B.; Marr, Carsten: Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions. Cell Systems, 2016, 49-58 more… BibTeX
  • Blasi, Thomas; Hennig, Holger; Summers, Huw D.; Theis, Fabian J.; Cerveira, Joana; Patterson, James O.; Davies, Derek; Filby, Andrew; Carpenter, Anne E.; Rees, Paul: Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications 7, 2016, 10256 more… BibTeX
  • Brath, Johannes M.S.; Grill, Sonja; Ankerst, Donna P.; Thompson, Ian M., Jr.; Gschwend, Juergen E.; Herkommer, Kathleen: No Detrimental Effect of a Positive Family History on Long-Term Outcomes Following Radical Prostatectomy. The Journal of Urology 195, 2016, 343-348 more… BibTeX
  • Chen, Haitao; Liu, Xu; Brendler, Charles B.; Ankerst, Donna P.; Leach, Robin J.; Goodman, Phyllis J.; Lucia, M. Scott; Tangen, Catherine M.; Wang, Li; Hsu, Fang-Chi; Sun, Jielin; Kader, A. Karim; Isaacs, William B.; Helfand, Brian T.; Zheng, S.Lilly; Thompson, Ian M.; Platz, Elizabeth A.; Xu, Jianfeng: Adding genetic risk score to family history identifies twice as many high-risk men for prostate cancer: Results from the prostate cancer prevention trial. The Prostate 76 (12), 2016, 1120-1129 more… BibTeX
  • Feigelman, Justin; Ganscha, Stefan; Hastreiter, Simon; Schwarzfischer, Michael; Filipczyk, Adam; Schroeder, Timm; Theis, Fabian J.; Marr, Carsten; Claassen, Manfred: Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells. Cell Systems 3 (5), 2016, 480-490.e13 more… BibTeX
  • Fiedler, Anna; Raeth, Sebastian; Theis, Fabian J.; Hausser, Angelika; Hasenauer, Jan: Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. BMC Systems Biology 10 (1), 2016 more… BibTeX
  • Fröhlich, Fabian; Theis, Fabian J.; Rädler, Joachim O.; Hasenauer, Jan: Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 2016, btw764 more… BibTeX
  • Fröhlich, Fabian; Thomas, Philipp; Kazeroonian, Atefeh; Theis, Fabian J.; Grima, Ramon; Hasenauer, Jan: Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLOS Computational Biology 12 (7), 2016, e1005030 more… BibTeX
  • Garzorz-Stark, Natalie; Krause, Linda; Lauffer, Felix; Atenhan, Anne; Thomas, Jenny; Stark, Sebastian P.; Franz, Regina; Weidinger, Stephan; Balato, Anna; Mueller, Nikola S.; Theis, Fabian J.; Ring, Johannes; Schmidt-Weber, Carsten B.; Biedermann, Tilo; Eyerich, Stefanie; Eyerich, Kilian: A novel molecular disease classifier for psoriasis and eczema. Experimental Dermatology 25 (10), 2016, 767-774 more… BibTeX
  • Geissen, Eva-Maria; Hasenauer, Jan; Heinrich, Stephanie; Hauf, Silke; Theis, Fabian J.; Radde, Nicole E.: MEMO: multi-experiment mixture model analysis of censored data. Bioinformatics 32 (16), 2016, 2464-2472 more… BibTeX
  • Grill, Sonja; Ankerst, Donna P.; Gail, Mitchell H.; Chatterjee, Nilanjan; Pfeiffer, Ruth M.: Comparison of approaches for incorporating new information into existing risk prediction models. Statistics in Medicine 36 (7), 2016, 1134-1156 more… BibTeX
  • Grill, Sonja; Ankerst, Donna P.; Gail, Mitchell H.; Chatterjee, Nilanjan; Pfeiffer, Ruth M.: Comparison of approaches for incorporating new information into existing risk prediction models. Statistics in Medicine 36 (7), 2016, 1134-1156 more… BibTeX
  • Haghverdi, Laleh; Büttner, Maren; Wolf, F Alexander; Buettner, Florian; Theis, Fabian J: Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods 13 (10), 2016, 845-848 more… BibTeX
  • Hilsenbeck, Oliver; Schwarzfischer, Michael; Skylaki, Stavroula; Schauberger, Bernhard; Hoppe, Philipp S; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hastreiter, Simon; Skylaki, Eleni; Filipczyk, Adam; Strasser, Michael; Buggenthin, Felix; Feigelman, Justin S; Krumsiek, Jan; van den Berg, Adrianus J J; Endele, Max; Etzrodt, Martin; Marr, Carsten; Theis, Fabian J; Schroeder, Timm: Software tools for single-cell tracking and quantification of cellular and molecular properties. Nature Biotechnology 34 (7), 2016, 703-706 more… BibTeX
  • Hoppe, Philipp S.; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D.; Hilsenbeck, Oliver; Moritz, Nadine; Endele, Max; Filipczyk, Adam; Gambardella, Adriana; Ahmed, Nouraiz; Etzrodt, Martin; Coutu, Daniel L.; Rieger, Michael A.; Marr, Carsten; Strasser, Michael K.; Schauberger, Bernhard; Burtscher, Ingo; Ermakova, Olga; Bürger, Antje; Lickert, Heiko; Nerlov, Claus; Theis, Fabian J.; Schroeder, Timm: Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature 535 (7611), 2016, 299-302 more… BibTeX
  • Huypens, Peter; Sass, Steffen; Wu, Moya; Dyckhoff, Daniela; Tschöp, Matthias; Theis, Fabian; Marschall, Susan; de Angelis, Martin Hrabě; Beckers, Johannes: Epigenetic germline inheritance of diet-induced obesity and insulin resistance. Nature Genetics 48 (5), 2016, 497-499 more… BibTeX
  • Jung, Bomi; Padula, Daniela; Burtscher, Ingo; Landerer, Cedric; Lutter, Dominik; Theis, Fabian; Messias, Ana C.; Geerlof, Arie; Sattler, Michael; Kremmer, Elisabeth; Boldt, Karsten; Ueffing, Marius; Lickert, Heiko: Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation. PLOS ONE 11, 2016, e0149477 more… BibTeX
  • Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan: CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PLOS ONE 11, 2016, e0146732 more… BibTeX
  • Kondofersky, Ivan; Theis, Fabian J.; Fuchs, Christiane: Inferring catalysis in biological systems. IET Systems Biology 10 (6), 2016, 210-218 more… BibTeX
  • Kong, Bo; Bruns, Philipp; Behler, Nora A; Chang, Ligong; Schlitter, Anna Melissa; Cao, Jing; Gewies, Andreas; Ruland, Jürgen; Fritzsche, Sina; Valkovskaya, Nataliya; Jian, Ziying; Regel, Ivonne; Raulefs, Susanne; Irmler, Martin; Beckers, Johannes; Friess, Helmut; Erkan, Mert; Mueller, Nikola S; Roth, Susanne; Hackert, Thilo; Esposito, Irene; Theis, Fabian J; Kleeff, Jörg; Michalski, Christoph W: Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy. Gut, 2016, gutjnl-2015-310913 more… BibTeX
  • Krause, Linda; Mourantchanian, Vagkan; Brockow, Knut; Theis, Fabian J.; Schmidt-Weber, Carsten B.; Knapp, Bettina; Mueller, Nikola S.; Eyerich, Stefanie: A computational model to predict severity of atopic eczema from 30 serum proteins. Journal of Allergy and Clinical Immunology 138 (4), 2016, 1207-1210.e2 more… BibTeX
  • Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J: Computational approaches for systems metabolomics. Current Opinion in Biotechnology 39, 2016, 198-206 more… BibTeX
  • Laimighofer, Michael; Krumsiek, Jan; Buettner, Florian; Theis, Fabian J.: Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. Journal of Computational Biology 23, 2016, 279-290 more… BibTeX
  • Morales, Edwin E.; Grill, Sonja; Svatek, Robert S.; Kaushik, Dharam; Thompson, Ian M., Jr.; Ankerst, Donna P.; Liss, Michael A.: Finasteride Reduces Risk of Bladder Cancer in a Large Prospective Screening Study. European Urology 69, 2016, 407-410 more… BibTeX
  • Much, Daniela; Beyerlein, Andreas; Kindt, Alida; Krumsiek, Jan; Stückler, Ferdinand; Rossbauer, Michaela; Hofelich, Anna; Wiesenäcker, David; Hivner, Susanne; Herbst, Melanie; Römisch-Margl, Werner; Prehn, Cornelia; Adamski, Jerzy; Kastenmüller, Gabi; Theis, Fabian; Ziegler, Anette-G.; Hummel, Sandra: Lactation is associated with altered metabolomic signatures in women with gestational diabetes. Diabetologia 59 (10), 2016, 2193-2202 more… BibTeX
  • Mund, A.; Kuttler, C.; Pérez-Velázquez, J.; Hense, B.A.: An age-dependent model to analyse the evolutionary stability of bacterial quorum sensing. Journal of Theoretical Biology 405, 2016, 104-115 more… BibTeX
  • Müller, Johannes; Koopmann, Bendix: The effect of delay on contact tracing. Mathematical Biosciences 282, 2016, 204-214 more… BibTeX
  • Nieboer, D.; Vergouwe, Y.; Ankerst, Danna P.; Roobol, Monique J.; Steyerberg, Ewout W.: Improving prediction models with new markers: a comparison of updating strategies. BMC Medical Research Methodology 16 (1), 2016, 128 (10 pages) more… BibTeX
  • Nuss, Aaron Mischa; Schuster, Franziska; Roselius, Louisa; Klein, Johannes; Bücker, René; Herbst, Katharina; Heroven, Ann Kathrin; Pisano, Fabio; Wittmann, Christoph; Münch, Richard; Müller, Johannes; Jahn, Dieter; Dersch, Petra: A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence. PLOS Pathogens 12 (12), 2016, e1006091 more… BibTeX
  • Patel, Tejal A.; Puppala, Mamta; Ogunti, Richard O.; Ensor, Joe E.; He, Tiancheng; Shewale, Jitesh B.; Ankerst, Donna P.; Kaklamani, Virginia G.; Rodriguez, Angel A.; Wong, Stephen T. C.; Chang, Jenny C.: Correlating mammographic and pathologic findings in clinical decision support using natural language processing and data mining methods. Cancer 123 (1), 2016, 114-121 more… BibTeX
  • Preusse, Martin; Theis, Fabian J.; Mueller, Nikola S.: miTALOS v2: Analyzing Tissue Specific microRNA Function. PLOS ONE 11, 2016, e0151771 more… BibTeX
  • Pérez-Velázquez, Judith; Gölgeli, Meltem; García-Contreras, Rodolfo: Mathematical Modelling of Bacterial Quorum Sensing: A Review. Bulletin of Mathematical Biology, 2016 more… BibTeX
  • Reim, Daniel; Strobl, Andreas N.; Buchner, Christian; Schirren, Rebekka; Mueller, Werner; Luppa, Peter; Ankerst, Donna Pauler; Friess, Helmut; Novotny, Alexander: Perioperative transfusion of leukocyte depleted blood products in gastric cancer patients negatively influences oncologic outcome. Medicine 95 (29), 2016, e4322 more… BibTeX
  • Rolle-Kampczyk, Ulrike E.; Krumsiek, Jan; Otto, Wolfgang; Röder, Stefan W.; Kohajda, Tibor; Borte, Michael; Theis, Fabian; Lehmann, Irina; von Bergen, M.: Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns. Metabolomics 12, 2016 more… BibTeX
  • Sacher, A.; Theis. F. J.: Von lernfähigen Maschinen lernen. Laborjournal (7-8), 2016, 59-61 more… BibTeX
  • Senís, Elena; Mockenhaupt, Stefan; Rupp, Daniel; Bauer, Tobias; Paramasivam, Nagarajan; Knapp, Bettina; Gronych, Jan; Grosse, Stefanie; Windisch, Marc P.; Schmidt, Florian; Theis, Fabian J.; Eils, Roland; Lichter, Peter; Schlesner, Matthias; Bartenschlager, Ralf; Grimm, Dirk: TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus. Nucleic Acids Research 45 (1), 2016, e3-e3 more… BibTeX
  • Stojcheva, Nina; Schechtmann, Gennadi; Sass, Steffen; Roth, Patrick; Florea, Ana-Maria; Stefanski, Anja; Stühler, Kai; Wolter, Marietta; Müller, Nikola S.; Theis, Fabian J.; Weller, Michael; Reifenberger, Guido; Happold, Caroline: MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM. Oncotarget 7 (11), 2016, 12937-12950 more… BibTeX
  • Styczynski, Mark P; Theis, Fabian J: Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology. Current Opinion in Biotechnology 39, 2016, iv-vi more… BibTeX
  • Sánchez-Garduño, Faustino; Pérez-Velázquez, Judith: Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations. The Scientific World Journal 2016, 2016, 1-21 more… BibTeX
  • Theis, F; Corbacioglu, A; Gaidzik, V I; Paschka, P; Weber, D; Bullinger, L; Heuser, M; Ganser, A; Thol, F; Schlegelberger, B; Göhring, G; Köhne, C-H; Germing, U; Brossart, P; Horst, H-A; Haase, D; Götze, K; Ringhoffer, M; Fiedler, W; Nachbaur, D; Kindler, T; Held, G; Lübbert, M; Wattad, M; Salih, H R; Krauter, J; Döhner, H; Schlenk, R F; Döhner, K: Clinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group. Leukemia 30 (11), 2016, 2248-2250 more… BibTeX
  • Thompson, Ian M., Jr.; Ankerst, Donna P.: The Role of Magnetic Resonance Imaging in Prostate Cancer: Focusing on What Really Matters. European Urology 70 (4), 2016, 574-575 more… BibTeX
  • Thompson, Ian M., Jr.; Ankerst, Donna P.: The Role of Magnetic Resonance Imaging in Prostate Cancer: Focusing on What Really Matters. European Urology 70 (4), 2016, 574-575 more… BibTeX
  • Willmann, Stefanie J.; Mueller, Nikola S.; Engert, Silvia; Sterr, Michael; Burtscher, Ingo; Raducanu, Aurelia; Irmler, Martin; Beckers, Johannes; Sass, Steffen; Theis, Fabian J.; Lickert, Heiko: The global gene expression profile of the secondary transition during pancreatic development. Mechanisms of Development 139, 2016, 51-64 more… BibTeX
  • von Toerne, Christine; Laimighofer, Michael; Achenbach, Peter; Beyerlein, Andreas; de las Heras Gala, Tonia; Krumsiek, Jan; Theis, Fabian J.; Ziegler, Anette G.; Hauck, Stefanie M.: Peptide serum markers in islet autoantibody-positive children. Diabetologia 60 (2), 2016, 287-295 more… BibTeX

2015

  • Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J.; Marr, Carsten; Buettner, Florian: destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32 (8), 2015, 1241-1243 more… BibTeX
  • Ankerst, Donna P.; Liss, Michael; Zapata, David; Hoefler, Josef; Thompson, Ian M.; Leach, Robin J.: A case control study of sarcosine as an early prostate cancer detection biomarker. BMC Urology 15 (1), 2015 more… BibTeX
  • Ankerst, Donna P.; Xia, Jing; Thompson, Ian M., Jr.; Hoefler, Josef; Newcomb, Lisa F.; Brooks, James D.; Carroll, Peter R.; Ellis, William J.; Gleave, Martin E.; Lance, Raymond S.; Nelson, Peter S.; Wagner, Andrew A.; Wei, John T.; Etzioni, Ruth; Lin, Daniel W.: Precision Medicine in Active Surveillance for Prostate Cancer: Development of the Canary–Early Detection Research Network Active Surveillance Biopsy Risk Calculator. European Urology 68, 2015, 1083-1088 more… BibTeX
  • Barbosa, J. S.; Sanchez-Gonzalez, R.; Di Giaimo, R.; Baumgart, E. V.; Theis, F. J.; Gotz, M.; Ninkovic, J.: Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain. Science 348 (6236), 2015, 789-793 more… BibTeX
  • Bartel, Jörg; Krumsiek, Jan; Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.: The Human Blood Metabolome-Transcriptome Interface. PLoS Genet 11, 2015, e1005274 more… BibTeX
  • Buettner, Florian; Natarajan, Kedar N; Casale, F Paolo; Proserpio, Valentina; Scialdone, Antonio; Theis, Fabian J; Teichmann, Sarah A; Marioni, John C; Stegle, Oliver: Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33, 2015, 155-160 more… BibTeX
  • Calzolari, Filippo; Michel, Julia; Baumgart, Emily Violette; Theis, Fabian; Götz, Magdalena; Ninkovic, Jovica: Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone. Nature Neuroscience 18, 2015, 490-492 more… BibTeX
  • Conlon, T. M.; Bartel, J.; Ballweg, K.; Gunter, S.; Prehn, C.; Krumsiek, J.; Meiners, S.; Theis, F. J.; Adamski, J.; Eickelberg, O.; Yildirim, A. O.: Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema. Clinical Science 130, 2015, 273-287 more… BibTeX
  • Cui, H.; Hense, B.A.; Müller, J.; Schröder, P.: Short term uptake and transport process for metformin in roots of Phragmites australis and Typha latifolia. Chemosphere 134, 2015, 307-312 more… BibTeX
  • Filipczyk, Adam; Marr, Carsten; Hastreiter, Simon; Feigelman, Justin; Schwarzfischer, Michael; Hoppe, Philipp S.; Loeffler, Dirk; Kokkaliaris, Konstantinos D.; Endele, Max; Schauberger, Bernhard; Hilsenbeck, Oliver; Skylaki, Stavroula; Hasenauer, Jan; Anastassiadis, Konstantinos; Theis, Fabian J.; Schroeder, Timm: Network plasticity of pluripotency transcription factors in embryonic stem cells. Nature Cell Biology 17 (10), 2015, 1235-1246 more… BibTeX
  • Gelfond, Jonathan; Choate, Kara; Ankerst, Donna P.; Hernandez, Javier; Leach, Robin J.; Thompson, Ian M., Jr.: Intermediate-Term Risk of Prostate Cancer is Directly Related to Baseline Prostate Specific Antigen: Implications for Reducing the Burden of Prostate Specific Antigen Screening. The Journal of Urology 194, 2015, 46-51 more… BibTeX
  • Grill, Sonja; Fallah, Mahdi; Leach, Robin J.; Thompson, Ian M.; Freedland, Stephen; Hemminki, Kari; Ankerst, Donna P.: Incorporation of Detailed Family History from the Swedish Family Cancer Database into the PCPT Risk Calculator. The Journal of Urology 193 (2), 2015, 460-465 more… BibTeX
  • Grill, Sonja; Fallah, Mahdi; Leach, Robin J.; Thompson, Ian M.; Hemminki, Kari; Ankerst, Donna P.: A simple-to-use method incorporating genomic markers into prostate cancer risk prediction tools facilitated future validation. Journal of Clinical Epidemiology 68, 2015, 563-573 more… BibTeX
  • Haghverdi, L.; Buettner, F.; Theis, F. J.: Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics, 2015 more… BibTeX
  • Hasenauer, J.; Jagiella, N.; Hross, S.; Theis, F. J.: Data-driven modelling of biological multi-scale processes. Journal of Coupled Systems and Multiscale Dynamics, 2015 more… BibTeX
  • Helmbrecht, Michaela S.; Soellner, Heidi; Castiblanco-Urbina, Maria A.; Winzeck, Stefan; Sundermeier, Julia; Theis, Fabian J.; Fouad, Karim; Huber, Andrea B.: A Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring. PLOS ONE 10, 2015, e0123643 more… BibTeX
  • Hug, Sabine; Schwarzfischer, Michael; Hasenauer, Jan; Marr, Carsten; Theis, Fabian J.: An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule. Statistics and Computing, 2015 more… BibTeX
  • Illner, Katrin; Miettinen, Jari; Fuchs, Christiane; Taskinen, Sara; Nordhausen, Klaus; Oja, Hannu; Theis, Fabian J.: Model selection using limiting distributions of second-order blind source separation algorithms. Signal Processing 113, 2015, 95-103 more… BibTeX
  • Kohler, D.; Müller, J.; Wever, U.: Cellular non-deterministic automata and partial differential equations. Physica D: Nonlinear Phenomena 311-312, 2015, 1-16 more… BibTeX
  • Kohler, Dominic; Marzouk, Youssef M.; Müller, Johannes; Wever, Utz: A new network approach to Bayesian inference in partial differential equations. International Journal for Numerical Methods in Engineering 104, 2015, 313-329 more… BibTeX
  • Kondofersky, Ivan; Fuchs, Christiane; Theis, Fabian J.: Identifying latent dynamic components in biological systems. IET Systems Biology, 2015 more… BibTeX
  • Kong, B.; Wu, W.; Cheng, T.; Schlitter, A. M.; Qian, C.; Bruns, P.; Jian, Z.; Jager, C.; Regel, I.; Raulefs, S.; Behler, N.; Irmler, M.; Beckers, J.; Friess, H.; Erkan, M.; Siveke, J. T.; Tannapfel, A.; Hahn, S. A.; Theis, F. J.; Esposito, I.; Kleeff, J.; Michalski, C. W.: A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling. Gut, 2015 more… BibTeX
  • Kong, Bo; Bruns, Philipp; Raulefs, Susanne; Rieder, Simon; Paul, Laura; Prazeresda Costa, Olivia; Buch, Thorsten; Theis, Fabian J.; Michalski, Christoph W.; Kleeff, Jörg: Metabolism gene signatures and surgical site infections in abdominal surgery. International Journal of Surgery 14, 2015, 67-74 more… BibTeX
  • Krumsiek, Jan; Mittelstrass, Kirstin; Do, Kieu Trinh; Stückler, Ferdinand; Ried, Janina; Adamski, Jerzy; Peters, Annette; Illig, Thomas; Kronenberg, Florian; Friedrich, Nele; Nauck, Matthias; Pietzner, Maik; Mook-Kanamori, Dennis O.; Suhre, Karsten; Gieger, Christian; Grallert, Harald; Theis, Fabian J.; Kastenmüller, Gabi: Gender-specific pathway differences in the human serum metabolome. Metabolomics, 2015 more… BibTeX
  • Kühn, Angelika R.; Grill, Sonja; Baumgarten, Manuela; Ankerst, Donna P.; Matyssek, Rainer: Daily growth of European beech (Fagus sylvatica L.) on moist sites is affected by short-term drought rather than ozone uptake. Trees 29, 2015, 1501-1519 more… BibTeX
  • Linnemann, J. R.; Miura, H.; Meixner, L. K.; Irmler, M.; Kloos, U. J.; Hirschi, B.; Bartsch, H. S.; Sass, S.; Beckers, J.; Theis, F. J.; Gabka, C.; Sotlar, K.; Scheel, C. H.: Quantification of regenerative potential in primary human mammary epithelial cells. Development, 2015 more… BibTeX
  • Masserdotti, Giacomo; Gillotin, Sébastien; Sutor, Bernd; Drechsel, Daniela; Irmler, Martin; Jørgensen, Helle F.; Sass, Steffen; Theis, Fabian J.; Beckers, Johannes; Berninger, Benedikt; Guillemot, François; Götz, Magdalena: Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes. Cell Stem Cell 17, 2015, 74-88 more… BibTeX
  • Matiu, Michael; Ankerst, Donna P.; Menzel, Annette: Asymmetric trends in seasonal temperature variability in instrumental records from ten stations in Switzerland, Germany and the UK from 1864 to 2012. International Journal of Climatology 36, 2015, 13-27 more… BibTeX
  • Matiu, Michael; Ankerst, Donna P.; Menzel, Annette: Asymmetric trends in seasonal temperature variability in instrumental records from ten stations in Switzerland, Germany and the UK from 1864 to 2012. International Journal of Climatology 36 (1), 2015, 13-27 more… BibTeX
  • Matur, Meltem Gölgeli; Müller, Johannes; Kuttler, Christina; Hense, Burkhard A.: An Approximative Approach for Single Cell Spatial Modeling of Quorum Sensing. Journal of Computational Biology 22 (3), 2015, 227-235 more… BibTeX
  • Meyer, Swanhild U.; Sass, Steffen; Mueller, Nikola S.; Krebs, Stefan; Bauersachs, Stefan; Kaiser, Sebastian; Blum, Helmut; Thirion, Christian; Krause, Sabine; Theis, Fabian J.; Pfaffl, Michael W.: Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1. PLOS ONE 10, 2015, e0135284 more… BibTeX
  • Miettinen, Jari; Illner, Katrin; Nordhausen, Klaus; Oja, Hannu; Taskinen, Sara; Theis, Fabian J.: Separation of Uncorrelated Stationary time series using Autocovariance Matrices. Journal of Time Series Analysis, 2015, n/a-n/a more… BibTeX
  • Moignard, Victoria; Woodhouse, Steven; Haghverdi, Laleh; Lilly, Andrew J; Tanaka, Yosuke; Wilkinson, Adam C; Buettner, Florian; Macaulay, Iain C; Jawaid, Wajid; Diamanti, Evangelia; Nishikawa, Shin-Ichi; Piterman, Nir; Kouskoff, Valerie; Theis, Fabian J; Fisher, Jasmin; Göttgens, Berthold: Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 33, 2015, 269-276 more… BibTeX
  • Müller, Johannes; Jiang, Hengrui: Graphical limit sets for general cellular automata. Theoretical Computer Science 580, 2015, 14-27 more… BibTeX
  • Müller, Sören; Raulefs, Susanne; Bruns, Philipp; Afonso-Grunz, Fabian; Plötner, Anne; Thermann, Rolf; Jäger, Carsten; Schlitter, Anna Melissa; Kong, Bo; Regel, Ivonne; Roth, W Kurt; Rotter, Björn; Hoffmeier, Klaus; Kahl, Günter; Koch, Ina; Theis, Fabian J; Kleeff, Jörg; Winter, Peter; Michalski, Christoph W: Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer. Molecular Cancer 14, 2015 more… BibTeX
  • Müller, Sören; Raulefs, Susanne; Bruns, Philipp; Afonso-Grunz, Fabian; Plötner, Anne; Thermann, Rolf; Jäger, Carsten; Schlitter, Anna Melissa; Kong, Bo; Regel, Ivonne; Roth, W Kurt; Rotter, Björn; Hoffmeier, Klaus; Kahl, Günter; Koch, Ina; Theis, Fabian J; Kleeff, Jörg; Winter, Peter; Michalski, Christoph W: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer. Molecular Cancer 14, 2015 more… BibTeX
  • Münch, Karin M.; Müller, Johannes; Wienecke, Sarah; Bergmann, Simone; Heyber, Steffi; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter: Polar Fixation of Plasmids during Recombinant Protein Production in Bacillus megaterium Results in Population Heterogeneity. Applied and Environmental Microbiology 81 (17), 2015, 5976-5986 more… BibTeX
  • Nieboer, Daan; Vergouwe, Yvonne; Roobol, Monique J.; Ankerst, Donna P.; Kattan, Michael W.; Vickers, Andrew J.; Steyerberg, Ewout W.: Nonlinear modeling was applied thoughtfully for risk prediction: the Prostate Biopsy Collaborative Group. Journal of Clinical Epidemiology 68 (4), 2015, 426-434 more… BibTeX
  • Ocone, A.; Haghverdi, L.; Mueller, N. S.; Theis, F. J.: Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinformatics 31 (12), 2015, i89-i96 more… BibTeX
  • Preusse, Martin; Marr, Carsten; Saunders, Sita; Maticzka, Daniel; Lickert, Heiko; Backofen, Rolf; Theis, Fabian: SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biology 12, 2015, 998-1009 more… BibTeX
  • Pérez-Velázquez, Judith; Quiñones, Beatriz; Hense, Burkhard A.; Kuttler, Christina: A mathematical model to investigate quorum sensing regulation and its heterogeneity in Pseudomonas syringae on leaves. Ecological Complexity 21, 2015, 128-141 more… BibTeX
  • Raue, A.; Steiert, B.; Schelker, M.; Kreutz, C.; Maiwald, T.; Hass, H.; Vanlier, J.; Tönsing, C.; Adlung, L.; Engesser, R.; Mader, W.; Heinemann, T.; Hasenauer, J.; Schilling, M.; Höfer, T.; Klipp, E.; Theis, F.; Klingmüller, U.; Schöberl, B.; Timmer, J.: Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1. Bioinformatics, 2015, btv405 more… BibTeX
  • Sadic, D.; Schmidt, K.; Groh, S.; Kondofersky, I.; Ellwart, J.; Fuchs, C.; Theis, F. J.; Schotta, G.: Atrx promotes heterochromatin formation at retrotransposons. EMBO reports 16, 2015, 836-850 more… BibTeX
  • Sass, Steffen; Pitea, Adriana; Unger, Kristian; Hess, Julia; Mueller, Nikola; Theis, Fabian: MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma. IJMS 16 (12), 2015, 30204-30222 more… BibTeX
  • Schmidt, Johanna M.; Panzilius, Elena; Bartsch, Harald S.; Irmler, Martin; Beckers, Johannes; Kari, Vijayalakshmi; Linnemann, Jelena R.; Dragoi, Diana; Hirschi, Benjamin; Kloos, Uwe J.; Sass, Steffen; Theis, Fabian; Kahlert, Steffen; Johnsen, Steven A.; Sotlar, Karl; Scheel, Christina H.: Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation. Cell Reports 10, 2015, 131-139 more… BibTeX
  • Stavropoulou, Faidra; Müller, Johannes: Parametrization of Random Vectors in Polynomial Chaos Expansions via Optimal Transportation. SIAM Journal on Scientific Computing 37, 2015, A2535-A2557 more… BibTeX
  • Strasser, Michael K.; Feigelman, Justin; Theis, Fabian J.; Marr, Carsten: Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. BMC Systems Biology, 2015 more… BibTeX
  • Strobl, Andreas N.; Thompson, Ian M.; Vickers, Andrew J.; Ankerst, Donna P.: The Next Generation of Clinical Decision Making Tools: Development of a Real-Time Prediction Tool for Outcome of Prostate Biopsy in Response to a Continuously Evolving Prostate Cancer Landscape. The Journal of Urology 194, 2015, 58-64 more… BibTeX
  • Strobl, Andreas N.; Vickers, Andrew J.; Van Calster, Ben; Steyerberg, Ewout; Leach, Robin J.; Thompson, Ian M.; Ankerst, Donna P.: Improving patient prostate cancer risk assessment: Moving from static, globally-applied to dynamic, practice-specific risk calculators. Journal of Biomedical Informatics 56, 2015, 87-93 more… BibTeX
  • Theis, F. J.; Ugelvig, L. V.; Marr, C.; Cremer, S.: Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society B: Biological Sciences 370 (1669), 2015, 20140108-20140108 more… BibTeX
  • Wahl, Simone; Vogt, Susanne; Stückler, Ferdinand; Krumsiek, Jan; Bartel, Jörg; Kacprowski, Tim; Schramm, Katharina; Carstensen, Maren; Rathmann, Wolfgang; Roden, Michael; Jourdan, Carolin; Kangas, Antti J; Soininen, Pasi; Ala-Korpela, Mika; Nöthlings, Ute; Boeing, Heiner; Theis, Fabian J; Meisinger, Christa; Waldenberger, Melanie; Suhre, Karsten; Homuth, Georg; Gieger, Christian; Kastenmüller, Gabi; Illig, Thomas; Linseisen, Jakob; Peters, Annette; Prokisch, Holger; Herder, Christian; Thorand, Barbara; Grallert, Harald: Multi-omic signature of body weight change: results from a population-based cohort study. BMC Medicine 13, 2015 more… BibTeX
  • Wilson, Nicola K.; Kent, David G.; Buettner, Florian; Shehata, Mona; Macaulay, Iain C.; Calero-Nieto, Fernando J.; Sánchez Castillo, Manuel; Oedekoven, Caroline A.; Diamanti, Evangelia; Schulte, Reiner; Ponting, Chris P.; Voet, Thierry; Caldas, Carlos; Stingl, John; Green, Anthony R.; Theis, Fabian J.; Göttgens, Berthold: Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell 16, 2015, 712-724 more… BibTeX
  • Zissler, U M; Chaker, A M; Effner, R; Ulrich, M; Guerth, F; Piontek, G; Dietz, K; Regn, M; Knapp, B; Theis, F J; Heine, H; Suttner, K; Schmidt-Weber, C B: Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways. Mucosal Immunology 9 (4), 2015, 917-926 more… BibTeX

2014

  • Acevedo-Cabra, Ricardo; Wiersma, Yolanda; Ankerst, Donna; Knoke, Thomas: Assessment of Wildfire Hazards with a Semiparametric Spatial Approach. Environmental Modeling & Assessment 19, 2014, 533-546 more… BibTeX
  • Ankerst, Donna P.; Boeck, Andreas; Freedland, Stephen J.; Stephen Jones, J.; Cronin, Angel M.; Roobol, Monique J.; Hugosson, Jonas; Kattan, Michael W.; Klein, Eric A.; Hamdy, Freddie; Neal, David; Donovan, Jenny; Parekh, Dipen J.; Klocker, Helmut; Horninger, Wolfgang; Benchikh, Amine; Salama, Gilles; Villers, Arnauld; Moreira, Daniel M.; Schroeder, Fritz H.; Lilja, Hans; Vickers, Andrew J.; Thompson, Ian M.: Evaluating the Prostate Cancer Prevention Trial High Grade prostate cancer risk calculator in 10 international biopsy cohorts: results from the prostate biopsy collaborative group. World Journal of Urology 32 (1), 2014, 185-191 more… BibTeX
  • Ankerst, Donna P.; Hoefler, Josef; Bock, Sebastian; Goodman, Phyllis J.; Vickers, Andrew; Hernandez, Javier; Sokoll, Lori J.; Sanda, Martin G.; Wei, John T.; Leach, Robin J.; Thompson, Ian M.: Prostate Cancer Prevention Trial Risk Calculator 2.0 for the Prediction of Low- vs High-grade Prostate Cancer. Urology 83 (6), 2014, 1362-1368 more… BibTeX
  • Bajikar, S. S.; Fuchs, C.; Roller, A.; Theis, F. J.; Janes, K. A.: Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proceedings of the National Academy of Sciences 111, 2014, E626-E635 more… BibTeX
  • Baumann, S.; Rockstroh, M.; Bartel, J.; Krumsiek, J.; Otto, W.; Jungnickel, H.; Potratz, S.; Luch, A.; Willscher, E.; Theis, F.; von Bergen, M.; Tomm, J.: Subtoxic concentrations of benzo[a]pyrene induce metabolic changes and oxidative stress in non-activated and affect the mTOR pathway in activated Jurkat T cells. Journal of Integrated OMICS 4 (1), 2014, 11-20 more… BibTeX
  • Boeck, Andreas; Dieler, Jochen; Biber, Peter; Pretzsch, Hans; Ankerst, Donna P.: Predicting Tree Mortality for European Beech in Southern Germany Using Spatially Explicit Competition Indices. Forest Science 60 (4), 2014, 613-622 more… BibTeX
  • Buettner, F.; Moignard, V.; Gottgens, B.; Theis, F. J.: Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. Bioinformatics 30 (13), 2014, 1867-1875 more… BibTeX
  • Do, Kieu Trinh; Kastenmüller, Gabi; Mook-Kanamori, Dennis O.; Yousri, Noha A.; Theis, Fabian J.; Suhre, Karsten; Krumsiek, Jan: Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva. J. Proteome Res., 2014, 141209141645008 more… BibTeX
  • Feigelman, Justin; Theis, Fabian J; Marr, Carsten: MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. BMC Bioinformatics 15, 2014, 240 more… BibTeX
  • Giessen, C.; Laubender, R. P.; Ankerst, D. P.; Stintizing, S.; Modest, D. P.; Schulz, C.; Mansmann, U.; Heinemann, V.: Surrogate endpoints in second-line treatment for mCRC: A systematic literature-based analysis from 23 randomized trials. Acta Oncologica 14, 2014, 1-7 more… BibTeX
  • Grote, J.; Krysciak, D.; Schorn, A.; Dahlke, R. I.; Soonvald, L.; Muller, J.; Hense, B. A.; Schwarzfischer, M.; Sauter, M.; Schmeisser, C.; Streit, W. R.: Evidence of Autoinducer-Dependent and -Independent Heterogeneous Gene Expression in Sinorhizobium fredii NGR234. Applied and Environmental Microbiology 80 (18), 2014, 5572-5582 more… BibTeX
  • Hasenauer, Jan; Hasenauer, Christine; Hucho, Tim; Theis, Fabian J.: ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. PLoS Computational Biology 10, 2014, e1003686 more… BibTeX
  • Illner, K.; Fuchs, C.; Theis, F. J.: Single-cell analysis: Biology at high resolution. Separation - Science & Applications (34), 2014, 24-26 more… BibTeX
  • Illner, K.; Fuchs, C.; Theis, F. J.: Einzelzellanalysen: Biologie in Hochauflösung. GIT Labor-Fachzeitschrift (9), 2014, 28-30 more… BibTeX
  • Illner, Katrin; Fuchs, Christiane; Theis, Fabian J.: Bayesian Blind Source Separation for Data with Network Structure. Journal of Computational Biology 21 (11), 2014, 855-865 more… BibTeX
  • Kohler, Dominic; Müller, Johannes; Wever, Utz: Cellular Probabilistic Automata---A Novel Method for Uncertainty Propagation. SIAM/ASA Journal on Uncertainty Quantification 2 (1), 2014, 29-54 more… BibTeX
  • Laube, J.; Sparks, T. H.; Estrella, N.; Höfler, J.; Ankerst, D. P.; Menzel, A.: Chilling outwights photoperiod in preventing precocious spring development. Global Change Biology 20 (1), 2014, 170-182 more… BibTeX
  • Matthes, M.; Preusse, M.; Zhang, J.; Schechter, J.; Mayer, D.; Lentes, B.; Theis, F.; Prakash, N.; Wurst, W.; Trumbach, D.: Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. Database 2014, 2014, bau083-bau083 more… BibTeX
  • Medina, E. A.; Shi, X.; Grayson, M. H.; Ankerst, D. P.; Livi, C. B.; Medina, M. V.; Thompson Jr., I. M.; Leach, R. J.: The diagnostic value of adiponectin multimers in healthy men undergoing screening for prostate cancer. Cancer Epidemiology, Biomarkers and Prevention 23 (2), 2014, 309-315 more… BibTeX
  • Müller, J.; Hense, B.A.; Marozava, S.; Kuttler, Ch.; Meckenstock, R.U.: Model selection for microbial nutrient uptake using a cost-benefit approach. Mathematical Biosciences 255, 2014, 52-70 more… BibTeX
  • Onyango, Nelson Owuor; Müller, Johannes: Determination of optimal vaccination strategies using an orbital stability threshold from periodically driven systems. Journal of Mathematical Biology 68 (3), 2014, 763-784 more… BibTeX
  • Quaranta, M.; Knapp, B.; Garzorz, N.; Mattii, M.; Pullabhatla, V.; Pennino, D.; Andres, C.; Traidl-Hoffmann, C.; Cavani, A.; Theis, F. J.; Ring, J.; Schmidt-Weber, C. B.; Eyerich, S.; Eyerich, K.: Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema. Science Translational Medicine (244), 2014, 244ra90-244ra90 more… BibTeX
  • Quaranta, Maria; Eyerich, Stefanie; Knapp, Bettina; Nasorri, Francesca; Scarponi, Claudia; Mattii, Martina; Garzorz, Natalie; Harlfinger, Anna T.; Jaeger, Teresa; Grosber, Martine; Pennino, Davide; Mempel, Martin; Schnopp, Christina; Theis, Fabian J.; Albanesi, Cristina; Cavani, Andrea; Schmidt-Weber, Carsten B.; Ring, Johannes; Eyerich, Kilian: Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting. PLoS ONE, 2014, e101814 more… BibTeX
  • Ried, J. S.; Shin, S.-Y.; Krumsiek, J.; Illig, T.; Theis, F. J.; Spector, T. D.; Adamski, J.; Wichmann, H.- E.; Strauch, K.; Soranzo, N.; Suhre, K.; Gieger, C.: Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses. Human Molecular Genetics 23 (21), 2014, 5847-5857 more… BibTeX
  • Roselius, Louisa; Langemann, Dirk; Müller, Johannes; Hense, Burkhard A.; Filges, Stefan; Jahn, Dieter; Münch, Richard: Modelling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator. Journal of Theoretical Biology 363, 2014, 290-299 more… BibTeX
  • Röck, Katharina; Tigges, Julia; Sass, Steffen; Schütze, Alexandra; Florea, Ana-Maria; Fender, Anke C; Theis, Florian J; Krutmann, Jean; Boege, Fritz; Fritsche, Ellen; Reifenberger, Guido; Fischer, Jens W: miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging. J Investig Dermatol 135, 2014, 369-377 more… BibTeX
  • Sass, S.; Buettner, F.; Mueller, N. S.; Theis, F. J.: RAMONA: a Web application for gene set analysis on multilevel omics data. Bioinformatics 31, 2014, 128-130 more… BibTeX
  • Shin, So-Youn; Fauman, Eric B; Petersen, Ann-Kristin; Krumsiek, Jan; Santos, Rita; Huang, Jie; Arnold, Matthias; Erte, Idil; Forgetta, Vincenzo; Yang, Tsun-Po; Walter, Klaudia; Menni, Cristina; Chen, Lu; Vasquez, Louella; Valdes, Ana M; Hyde, Craig L; Wang, Vicky; Ziemek, Daniel; Roberts, Phoebe; Xi, Li; Grundberg, Elin; Waldenberger, Melanie; Richards, J Brent; Mohney, Robert P; Milburn, Michael V; John, Sally L; Trimmer, Jeff; Theis, Fabian J; Overington, John P; Suhre, Karsten; Brosnan, M Julia; Gieger, Christian; Kastenmüller, Gabi; Spector, Tim D; Soranzo, Nicole: An atlas of genetic influences on human blood metabolites. Nat Genet 46, 2014, 543-550 more… BibTeX
  • Thalheimer, Frederic B.; Wingert, Susanne; De Giacomo, Pangrazio; Haetscher, Nadine; Rehage, Maike; Brill, Boris; Theis, Fabian J.; Hennighausen, Lothar; Schroeder, Timm; Rieger, Michael A.: Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells. Stem Cell Reports, 2014, 34-43 more… BibTeX
  • Thompson, Ian M., Jr; Leach, Robin J.; Ankerst, Donna P.: Focusing PSA Testing on Detection of High-Risk Prostate Cancers by Incorporating Patient Preferences Into Decision Making. Journal of the American Medical Association 312 (10), 2014, 995 more… BibTeX
  • Uecke, Hannes; Müller, Johannes; Hense, Burkhard A.: Individual-Based Model for Quorum Sensing with Background Flow. Bulletin of Mathematical Biology 76, 2014, 1727-1746 more… BibTeX
  • Vinnikov, I. A.; Hajdukiewicz, K.; Reymann, J.; Beneke, J.; Czajkowski, R.; Roth, L. C.; Novak, M.; Roller, A.; Dorner, N.; Starkuviene, V.; Theis, F. J.; Erfle, H.; Schutz, G.; Grinevich, V.; Konopka, W.: Hypothalamic miR-103 Protects from Hyperphagic Obesity in Mice. Journal of Neuroscience 34 (32), 2014, 10659-10674 more… BibTeX
  • Waldera-Lupa, D. M.; Kalfalah, F.; Florea, A. M.; Sass, S.; Kruse, F. E.; Rieder, V.; Tigges, J.; Fritsche, E.; Krutmann, J.; Busch, H.; Boerries, M.; Meyer, H. E.; Boege, F.; Theis, F. J.; Reifenberger, G.; Stühler, K.: Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging-US (6), 2014, 856-878 more… BibTeX
  • Winkler, Christiane; Krumsiek, Jan; Buettner, Florian; Angermüller, Christof; Giannopoulou, Eleni Z.; Theis, Fabian J.; Ziegler, Anette-Gabriele; Bonifacio, Ezio: Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia 58, 2014, 206-206 more… BibTeX
  • Winkler, Christiane; Krumsiek, Jan; Buettner, Florian; Angermüller, Christof; Giannopoulou, Eleni Z.; Theis, Fabian J.; Ziegler, Anette-Gabriele; Bonifacio, Ezio: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia 57 (12), 2014, 2521-2529 more… BibTeX
  • Winter, Susanne; Höfler, Josef; Michel, Alexa K.; Böck, Andreas; Ankerst, Donna P.: Association of tree and plot characteristics with microhabitat formation in European beech and Douglas-fir forests. European Journal of Forest Research 134, 2014, 335-347 more… BibTeX
  • Yang, D.; Lutter, D.; Burtscher, I.; Uetzmann, L.; Theis, F. J.; Lickert, H.: miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm. Development 141, 2014, 514-525 more… BibTeX

2013

  • Albrecht, Eva; Waldenberger, Melanie; Krumsiek, Jan; Evans, Anne M.; Jeratsch, Ulli; Breier, Michaela; Adamski, Jerzy; Koenig, Wolfgang; Zeilinger, Sonja; Fuchs, Christiane; Klopp, Norman; Theis, Fabian J.; Wichmann, H.-Erich; Suhre, Karsten; Illig, Thomas; Strauch, Konstantin; Peters, Annette; Gieger, Christian; Kastenmüller, Gabi; Doering, Angela; Meisinger, Christa: Metabolite profiling reveals new insights into the regulation of serum urate in humans. Metabolomics 10, 2013, 141-151 more… BibTeX
  • Altmaier, E.; Emeny, R. T.; Krumsiek, J.; Lacruz, M. E.; Lukaschek, K.; Häfner, S.; Kastenmüller, G.; Römisch-Margl, W.; Prehn, C.; Mohney, R. P.; Evans, A. M.; Milburn, M. V.; Illig, T.; Adamski, J.; Theis, F. J.; Suhre, K.; Ladwig, K. H.: Metabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality. Psychoneuroendocrinology 38 (8), 2013, 1299-1309 more… BibTeX
  • Andres, C.; Hasenauer, J.; Ahn, H. S.; Joseph, E. K.; Isensee, J.; Theis, F. J.; Allgöwer, F.; Levine, J. D.; Dib-Hajj, S. D.; Waxman, S. G.; Hucho, T.: Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia. Pain 154 (10), 2013, 2216-2226 more… BibTeX
  • Ankerst, D. P.; Till, C.; Boeck, A.; Goodman, P. J.; Tangen, C. M.; Thompson, I. M.: Predicting risk of prostate cancer in men receiving finasteride: effect of prostate volume, number of biopsy cores, and american urological association symptom score. Urology 82 (5), 2013, 1076--1082 more… BibTeX
  • Ankerst, D. P.; Till, C.; Boeck, A.; Goodman, P.; Tangen, C. M.; Feng, Z.; Partin, A. W.; Chan, D. W.; Sokoll, L.; Kagan, J.; Wei, J. T.; Thompson, I. M.: The impact of prostate volume, number of biopsy cores and American Urological Association symptom score on the sensitivity of cancer detection using the Prostate Cancer Prevention Trial risk calculator. Journal of Urology 190 (1), 2013, 70--76 more… BibTeX
  • Bardehle, S.; Krüger, M.; Buggenthin, F.; Schwausch, J.; Ninkovic, J.; Clevers, H.; Snippert, H. J.; Theis, F. J.; Meyer-Luehmann, M.; Bechmann, I.; Dimou, L.; Götz, M.: Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation. Nat. Neurosci. 16 (5), 2013, 580-586 more… BibTeX
  • Bartel, J.; Krumsiek, J.; Theis, F. J.: Statistical methods for the analysis of high-throughput metabolomics data. Comp. Struc. Biotech. J. 4 (5), 2013 more… BibTeX
  • Bonifacio, E.; Krumsiek, J.; Winkler, C.; Theis, F. J.; Ziegler, A. G.: A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion. Acta Diabetol., 2013, 10.1007/s00592-013-0526-2 more… BibTeX
  • Buggenthin, F.; Marr, C.; Schwarzfischer, M.; Hoppe, P. S.; Hilsenbeck, O.; Schroeder, T.; Theis, F. J.: An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics 14 (1), 2013 more… BibTeX
  • Dräxl, Stephan; Müller, Johannes; Li, Wei B.; Michalke, Bernhard; Scherb, Hagen; Hense, Burkhard A.; Tschiersch, Jochen; Kanter, Ulrike; Schäffner, Anton R.: Caesium accumulation in yeast and plants is selectively repressed by loss of the SNARE Sec22p/SEC22. Nature Communications 4, 2013, 2092 more… BibTeX
  • Giessen, C.; Laubender, R. P.; Ankerst, D. P.; Stintzing, S.; Modest, D. P.; Mansmann, U.; Heinemann, V.: Progression-free survival as a surrogate endpoint for median overall survival in metastatic colorectal cancer: literature-based analysis from 50 randomized first-line trials. Clinical Cancer Research 19 (1), 2013, 225--235 more… BibTeX
  • Hasenauer, J.; Wolf, V.; Kazeroonian, A.; Theis, F. J.: Method of conditional moments (MCM) for the Chemical Master Equation. Journal of Mathematical Biology 69, 2013, 687-735 more… BibTeX
  • Hemminki, K.; Ankerst, D. P.; Sundquist, J.; Mousavi, S. M.: Prostate cancer incidence and survival in immigrants to Sweden. World Journal of Urology 31 (6), 2013, 1483--1488 more… BibTeX
  • Hock, S.; Ng, Y. K.; Hasenauer, J.; Wittmann, D. M.; Lutter, D.; Trümbach, D.; Wurst, W.; Prakash, N.; Theis, F. J.: Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. BMC Syst. Biol. 7, 2013 more… BibTeX
  • Hug, S.; Raue, A.; Hasenauer, J.; Bachmann, J.; Klingmüller, U.; Timmer, J.; Theis, F. J.: High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling. Math. Biosci. 246 (2), 2013, 293-304 more… BibTeX
  • Jochner, S.; Hoefler, J.; Beck, I.; Goettlein, A.; Ankerst, D. P.; Traidl-Hoffmann, C.; Menzel, A.: Nutrient status: a missing factor in phenological and pollen research. Journal of Experimental Botany 64 (7), 2013, 2081--2092 more… BibTeX
  • Köttgen, A.; Albrecht, E.; Teumer, A.; Vitart, V.; Krumsiek, J.; Hundertmark, C.; Pistis, G.; Ruggiero, D.; O'Seaghdha, C. M.; Haller, T.; Yang, Q.; Tanaka, T.; Johnson, A. D.; Kutalik, Z.; Smith, A. V.; Shi, J.; Struchalin, M.; Middelberg, R. P.; Brown, M. J.; Gaffo, A. L.; Pirastu, N.; Li, G.; Hayward, C.; Zemunik, T.; Huffman, J.; Yengo, L.; Zhao, J. H.; Demirkan, A.; Feitosa, M. F.; Liu, X.; Malerba, G.; Lopez, L. M.; van der Harst, P.; Li, X.; Kleber, M. E.; Hicks, A. A.; Nolte, I. M.; Johansson, A.; Murgia, F.; Wild, S. H.; Bakker, S. J.; Peden, J. F.; Dehghan, A.; Steri, M.; Tenesa, A.; Lagou, V.; Salo, P.; Mangino, M.; Rose, L. M.; Lehtimäki, T. et al.: Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. Nat. Genet. 45 (2), 2013, 145-154 more… BibTeX
  • Liang, Y.; Ankerst, D. P.; Feng, Z.; Fu, R.; Stanford, J. L.; Thompson, I. M.: The risk of biopsy-detectable prostate cancer using the prostate cancer prevention Trial Risk Calculator in a community setting. Urologic Oncology 31 (8), 2013, 1464--1469 more… BibTeX
  • Moignard, V.; Macaulay, I. C.; Swiers, G.; Buettner, F.; Schütte, J.; Calero-Nieto, F. J.; Kinston, S.; Joshi, A.; Hannah, R.; Theis, F. J.; Jacobsen, S. E.; de Bruijn, M. F.; Gottgens, B.: Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat. Cell Biol. 15 (4), 2013, 363-372 more… BibTeX
  • Müller, J.; Hense, B.A.; Fuchs, T.M.; Utz, M.; Pötzsche, Ch.: Bet-hedging in stochastically switching environments. Journal of Theoretical Biology 336, 2013, 144-157 more… BibTeX
  • Müller, Johannes; Uecker, Hannes: Approximating the dynamics of communicating cells in a diffusive medium by ODEs—homogenization with localization. Journal of Mathematical Biology 67 (5), 2013, 1023-1065 more… BibTeX
  • Raue, A.; Kreutz, C.; Theis, F. J.; Timmer, J.: Joining forces of Bayesian and frequentist methodology: A study for inference in the presence of non-identiability. Philos. Transact. R. Soc. A - Math. Phys. Eng. Sci. 371 (1984), 2013 more… BibTeX
  • Raue, A.; Schilling, M.; Bachmann, J.; Matteson, A.; Schelke, M.; Kaschek, D.; Hug, S.; Kreutz, C.; Harms, B. D.; Theis, F. J.; Klingmüller, U.; Timmer, J.: Lessons learned from quantitative dynamical modeling in systems biology. PLoS One 8 (9), 2013 more… BibTeX
  • Ried, J. S.; Baurecht, H.; Stückler, F.; Krumsiek, J.; Gieger, C.; Heinrich, J.; Kabesch, M.; Prehn, C.; Peters, A.; Rodriguez, E.; Schulz, H.; Strauch, K.; Suhre, K.; Wang-Sattler, R.; Wichmann, H. E.; Theis, F. J.; Illig, T.; Adamski, J.; Weidinger, S.: Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma. Allergy 68 (5), 2013, 629-636 more… BibTeX
  • Rinck, A.; Preusse, M.; Laggerbauer, B.; Lickert, H.; Engelhardt, S.; Theis, F. J.: The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance. RNA Biol. 10 (7), 2013, 1125-1135 more… BibTeX
  • Sass, S.; Büttner, F.; Müller, N. S.; Theis, F. J.: A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res. 41 (21), 2013, 9622-9633 more… BibTeX
  • Schmidl, D.; Czado, C.; Hug, S.; Theis, F. J.: Rejoinder on 'A vine-copula based adaptive MCMC sampler for efficient inference of dynamical systems&quot. Bayesian Anal. 8 (1), 2013, 33-42 more… BibTeX
  • Schmidl, D.; Czado, C.; Hug, S.; Theis, F. J.: A vine-copula based adaptive MCMC sampler for efficient inference of dynamical systems. Bayesian Anal. 8 (1), 2013, 1-22 more… BibTeX
  • Taylor, J. M.; Park, Y.; Ankerst, D. P.; Proust-Lima, C.; Williams, S.; Kestin, L.; Bae, K.; Pickles, T.; Sandler, H.: Real-time individual predictions of prostate cancer recurrence using joint models. Biometrics 69 (1), 2013, 206--213 more… BibTeX
  • Vehlow, C.; Hasenauer, J.; Theis, F. J.; Weiskopf, D.: Visualizing edge-edge relations in graphs. , 2013, 201-208 more… BibTeX
  • Vickers, A. J.; Sjoberg, D. D.; Ankerst, D. P.; Tangen, C. M.; Goodman, P. J.; Thompson, I. M.: The Prostate Cancer Prevention Trial risk calculator and the relationship between prostate-specific antigen and biopsy outcome. Cancer 119 (16), 2013, 3007--3011 more… BibTeX
  • Wittmann, D. M.; Hock, S.; Theis, F. J.: Truth-content and phase transitions of random boolean networks with generic logics. SIAM J. Appl. Dyn. Syst. 12 (1), 2013, 315-351 more… BibTeX
  • Xu, T.; Holzapfel, C.; Dong, X.; Bader, E.; Yu, Z.; Prehn, C.; Perstorfer, K.; Jaremek, M.; Römisch-Margl, W.; Rathmann, W.; Li, Y.; Wichmann, H. E.; Wallaschofski, H.; Ladwig, K. H.; Theis, F. J.; Suhre, K.; Adamski, J.; Illig, T.; Peters, A.; Wang-Sattler, R.: Effects of smoking and smoking cessation on human serum metabolite profile: Results from the KORA cohort study. BMC Med. 11 (1), 2013 more… BibTeX

2012

  • Ankerst, D. P.; Boeck, A.; Freedland, S. J.; Jones, J. S.; Cronin, A. M.; Roobol, M. J.; Hugosson, J.; Kattan, M. W.; Klein, E. A.; Hamdy, F.; Neal, D.; Donovan, J.; Parekh, D. J.; Klocker, H.; Horninger, W.; Benchikh, A.; Salama, G.; Villers, A.; Moreira, D. M.; Schroeder, F. H.; Lilja, H.; Vickers, A. J.; Thompson, I. M.: Evaluating the Prostate Cancer Prevention Trial High Grade prostate cancer risk calculator in 10 international biopsy cohorts: results from the prostate biopsy collaborative group. World Journal of Urology, 2012 more… BibTeX
  • Ankerst, D. P.; Boeck, A.; Freedland, S. J.; Thompson, I. M.; Cronin, A. M.; Roobol, M. J.; Hugosson, J.; Jones, J. S..; Kattan, M. W.; Klein, E. A.; Hamdy, F.; Neal, D.; Donovan, J.; Parekh, D. J.; Klocker, H.; Horninger, W.; Benchikh, A.; Salama, G.; Villers, A.; Moreira, D. M.; Schroeder, F. H.; Lilja, H.; Vickers, A. J.: Evaluating the PCPT risk calculator in ten international biopsy cohorts: results from the Prostate Biopsy Collaborative Group. World Journal of Urology 30 (2), 2012, 181--187 more… BibTeX
  • Ankerst, D. P.; Koniarski, T.; Liang, Y.; Leach, R. J.; Feng, Z.; Sanda, M. G.; Partin, A. W.; Chan, D. W.; Kagan, J.; Sokoll, L.; Wei, J. T.; Thompson, I. M.: Updating risk prediction tools: a case study in prostate cancer. Biometrical Journal 54 (1), 2012, 127-142 more… BibTeX
  • Ankerst, DP; Thompson, IM: Re: Combining 33 genetic variants with prostate-specific antigen for the prediction of prostate cancer: longitudinal study. European Urology 62 (1), 2012, 180 more… BibTeX
  • Burtscher, I.; Barkey, W.; Schwarzfischer, M.; Theis, F. J.; Lickert, H.: The Sox17-mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development. Genesis 50 (6), 2012, 496-505 more… BibTeX
  • Büttner, F.; Theis, F. J.: A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics 28 (18), 2012, i626-i632 more… BibTeX
  • Chursov, A.; Kopetzky, S. J.; Leshchiner, I.; Kondofersky, I.; Theis, F. J.; Frishman, D.; Shneider, A.: Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus. RNA Biol. 9 (10), 2012, 1266-1274 more… BibTeX
  • Cichocki, A.; Theis, F. J.; Yeredor, A.; Zibulevsky, M.: Preface. Lecture Notes Comp. Sci. 7191, 2012, V-VII more… BibTeX
  • Falkinger, Marita; Schell, Stefan; Müller, Johannes; Wilkens, Jan J.: Prioritized optimization in intensity modulated proton therapy. Zeitschrift für Medizinische Physik 22 (1), 2012, 21-28 more… BibTeX
  • Gutch, H. W.; Gruber, P.; Yeredor, A.; Theis, F. J.: ICA over finite fields - separability and algorithms. Signal Process. 92 (8), 2012, 1796-1808 more… BibTeX
  • Gutch, H. W.; Theis, F. J.: Uniqueness of linear factorizations into independent subspaces. J. Multivar. Anal. 112, 2012, 48-62 more… BibTeX
  • Henkel, A.; Müller, J.; Pötzsche, C.: Modeling the spread of Phytophthora. Journal of Mathematical Biology 65 (6-7), 2012, 1359-1385 more… BibTeX
  • Hense, Burkhard A.; Müller, Johannes; Kuttler, Christina; Hartmann, Anton: Spatial Heterogeneity of Autoinducer Regulation Systems. Sensors 12 (4), 2012, 4156-4171 more… BibTeX
  • Hilton, W. M.; Padalecki, S. S.; Ankerst, D. P.; Leach, R. J.; Thompson, I. M.: Temporal changes in the clinical approach to diagnosing prostate cancer. Journal of the National Cancer Institute Monographs (45), 2012, 162--168 more… BibTeX
  • Jourdan, C.; Petersen, A. K.; Gieger, C.; Döring, A.; Illig, T.; Wang-Sattler, R.; Meisinger, C.; Peters, A.; Adamski, J.; Prehn, C.; Suhre, K.; Altmaier, E.; Kastenmüller, G.; Römisch-Margl, W.; Theis, F. J.; Krumsiek, J.; Wichmann, H. E.; Linseisen, J.: Body fat free mass is associated with the serum metabolite profile in a population-based study. PLoS One 7 (6), 2012 more… BibTeX
  • Konrad, M.; Vyleta, M. L.; Theis, F. J.; Stock, M.; Tragust, S.; Klatt, M.; Drescher, V.; Marr, C.; Ugelvig, L. V.; Cremer, S.: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biol. 10 (4), 2012 more… BibTeX
  • Krug, S.; Kastenmüller, G.; Stückler, F.; Rist, M. J.; Skurk, T.; Sailer, M.; Raffler, J.; Römisch-Margl, W.; Adamski, J.; Prehn, C.; Frank, T.; Engel, K. H.; Hofmann, T.; Luy, B.; Zimmermann, R.; Moritz, F.; Schmitt-Kopplin, P.; Krumsiek, J.; Kremer, W.; Huber, F.; Oeh, U.; Theis, F. J.; Szymczak, W.; Hauner, H.; Suhre, K.; Daniel, H.: The dynamic range of the human metabolome revealed by challenges. Faseb J. 26 (6), 2012, 2607-2619 more… BibTeX
  • Krumsiek, J.; Suhre, K.; Evans, A. M.; Mitchell, M. W.; Mohney, R. P.; Milburn, M. V.; Wägele, B.; Römisch-Margl, W.; Illig, T.; Adamski, J.; Gieger, C.; Theis, F. J.; Kastenmüller, G.: Mining the unknown: A systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet. 8 (10), 2012 more… BibTeX
  • Krumsiek, J.; Suhre, K.; Illig, T.; Adamski, J.; Theis, F. J.: Bayesian independent component analysis recovers pathway signatures from blood metabolomics data. J. Proteome Res. 11 (8), 2012, 4120-4131 more… BibTeX
  • Marr, C.; Strasser, M.; Schwarzfischer, M.; Schroeder, T.; Theis, F. J.: Multi-scale modeling of GMP differentiation based on single-cell genealogies. FEBS J. 279 (18), 2012, 3488-3500 more… BibTeX
  • Meyer, Andrea; Megerle, Judith A; Kuttler, Christina; Müller, Johannes; Aguilar, Claudio; Eberl, Leo; Hense, Burkhard A; Rädler, Joachim O: Dynamics of AHL mediated quorum sensing under flow and non-flow conditions. Physical Biology 9 (2), 2012, 026007 more… BibTeX
  • Peng, C.; Li, N.; Ng, Y. K.; Zhang, J.; Meier, F.; Theis, F. J.; Merkenschlager, M.; Chen, W.; Wurst, W.; Prakash, N.: A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation. J. Neurosci. 32 (38), 2012, 13292-13308 more… BibTeX
  • Petersen, A. K.; Krumsiek, J.; Wägele, B.; Theis, F. J.; Wichmann, H. E.; Gieger, C.; Suhre, K.: On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. BMC Bioinformatics 13, 2012 more… BibTeX
  • Plant, C. C.; Mai Thai, S.; Shao, J.; Theis, F. J.; Meyer-Bäse, A.; Böhm, C.: Measuring non-Gaussianity by phi-transformed and fuzzy histograms. Advances in Artificial Neural Systems 2012, 2012 more… BibTeX
  • Pérez-Velázquez, J.; Schlicht, R.; Dulla, G.; Hense, B.A.; Kuttler, C.; Lindow, S.E.: Stochastic modeling of Pseudomonas syringae growth in the phyllosphere. Mathematical Biosciences 239 (1), 2012, 106-116 more… BibTeX
  • Roobol, M. J.; Schroeder, F. H.; Hugosson, J.; Jones, J. S.; Kattan, M. W.; Klein, E. A.; Hamdy, F.; Neal, D.; Donovan, J.; Parekh, D. J.; Ankerst, D. P.; Bartsch, G.; Klocker, H.; Horninger, W.; Benchikh, A.; Salama, G.; Villers, A.; Freedland, S. J.; Moreira, D. M.; Vickers, A. J.; Lilja, H.; Steyerberg, E. W.: Importance of prostate volume in the European Randomised Study of Screening for Prostate Cancer (ERSPC) risk calculators: results from the prostate biopsy collaborative group. World Journal of Urology 30 (2), 2012, 149--155 more… BibTeX
  • Ruepp, A.; Kowarsch, A.; Theis, F. J.: PhenomiR: MicroRNAs in human diseases and biological processes. Methods Mol. Biol. 822, 2012, 249-260 more… BibTeX
  • Schleip, Christoph; Ankerst, Donna P.; Böck, Andreas; Estrella, Nicole; Menzel, Annette: Comprehensive methodological analysis of long-term changes in phenological extremes in Germany. Global Change Biology 18 (7), 2012, 2349-2364 more… BibTeX
  • Schmidl, D.; Hug, S.; Li, W. B.; Greiter, M. B.; Theis, F. J.: Bayesian model selection validates a biokinetic model for zirconium processing in humans. BMC Syst. Biol. 6, 2012 more… BibTeX
  • Sterz, K.; Scherer, G.; Krumsiek, J.; Theis, F. J.; Ecker, J.: Identification and quantification of 1-hydroxybutene-2-yl mercapturic acid in human urine by UPLC- HILIC-MS/MS as a novel biomarker for 1,3-butadiene exposure. Chem. Res. Toxicol. 25 (8), 2012, 1565-1567 more… BibTeX
  • Strasser, M.; Theis, F. J.; Marr, C.: Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression. Biophys. J. 102 (1), 2012, 19-29 more… BibTeX
  • Thompson, IM; Ankerst, DP: Commentary to "Management of a patient with a persistently elevated PSA and negative biopsy" by JC Presti, Jr. AUA Update Series 31 (Lesson 1), 2012, 6 - 7 more… BibTeX
  • Thompson, IM; Ankerst, DP: Editorial for special issue on epidemiology and prevention of prostate cancer. World Journal of Urology 30 (2), 2012, 129 - 130 more… BibTeX
  • Thompson, IM; Ankerst, DP: The benefits of risk assessment tools for prostate cancer. European Urology 61 (4), 2012, 662 - 663 more… BibTeX
  • Williams, S. B.; Salami, S.; Regan, M. M.; Ankerst, D. P.; Wei, J. T.; Rubin, M. A.; Thompson, I. M.; Sanda, M. G.: Selective detection of histologically aggressive prostate cancer: an early detection research network prediction model to reduce unnecessary prostate biopsies with validation in the Prostate Cancer Prevention Trial (PCPT)l. Cancer 118 (10), 2012, 2651--2658 more… BibTeX
  • Winkler, C.; Krumsiek, J.; Lempainen, J.; Achenbach, P.; Grallert, H.; Giannopoulou, E.; Bunk, M.; Theis, F. J.; Bonifacio, E.; Ziegler, A. G.: A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes. Genes Immun. 13 (7), 2012, 549-555 more… BibTeX
  • Ziello, Chiara; Böck, Andreas; Estrella, Nicole; Ankerst, Donna; Menzel, Annette: First flowering of wind-pollinated species with the greatest phenological advances in Europe. Ecography 35 (11), 2012, 1017-1023 more… BibTeX

2011

  • Ankerst, D. P.; Pollock, B. H.; Liang, Y.; Dizdarevic, N.; Kyrylenko, S.; Boeck, A.; Thompson, I. M.; Leach, R.: Trends and co-trends of prostate-specific antigen and body mass index in a screened population. Urology 78 (1), 2011, 10-16 more… BibTeX
  • Baskaran, T.; Blöchl, F.; Brück, T.; Theis, F. J.: The Heckscher-Ohlin model and the network structure of international trade. Int. Rev. Econom. Finance 20 (2), 2011, 135-145 more… BibTeX
  • Blöchl, F.; Theis, F. J.; Vega-Redondo, F.; Fisher, E.: Vertex centralities in input-output networks reveal the structure of modern economies. Phys. Rev. E 83 (4), 2011 more… BibTeX
  • Blöchl, F.; Wittmann, D. M.; Theis, F. J.: Effective parameters determining the information flow in hierarchical biological systems. Bull. Math. Biol. 73 (4), 2011, 706-725 more… BibTeX
  • Breindl, C.; Waldherr, S.; Wittmann, D. M.; Theis, F. J.; Allgoewer, F.: Steady-state robustness of qualitative gene regulation networks. Int. J. Robust Nonlin. 21 (15), 2011, 1742-1758 more… BibTeX
  • Giessen, C.; Stintzing, S.; Laubender, R. P.; Ankerst, D. P.; Schulz, C.; Moosmann, N.; Modest, D. P.; Schalhorn, A.; von Weikersthal, L. F.; Heinemann, V.: Analysis for prognostic factors of 60-day mortality: evaluation of an irinotecan-based phase III trial performed in the first-line treatment of metastatic colorectal cancer. Clinical Colorectal Cancer 10 (4), 2011, 317--324 more… BibTeX
  • Hattersley, J.G.; Pérez-Velázquez, J.; Chappell, M.J.; Bearup, D.; Roper, D.; Dowson, C.; Bugg, T.; Evans, N.D.: Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis. Computer Methods and Programs in Biomedicine 104 (2), 2011, 70-80 more… BibTeX
  • Hennig, H.; Fleischmann, R.; Fredebohm, A.; Hagmayer, Y.; Nagler, J.; Witt, A.; Theis, F. J.; Geisel, T.: The nature and perception of fluctuations in human musical rhythms. PLoS ONE 6 (10), 2011 more… BibTeX
  • Kowarsch, A.; Preusse, M.; Marr, C.; Theis, F. J.: miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA 17 (5), 2011, 809-819 more… BibTeX
  • Krumsiek, J.; Marr, C.; Schroeder, T.; Theis, F. J.: Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS One 6 (8), 2011 more… BibTeX
  • Krumsiek, J.; Suhre, K.; Illig, T.; Adamski, J.; Theis, F. J.: Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst. Biol. 5 (1), 2011 more… BibTeX
  • Laaser, I.; Theis, F. J.; Hrabé de Angelis, M.; Kolb, H. J.; Adamski, J.: Huge splicing frequency in human Y chromosomal UTY gene. OMICS 15 (3), 2011, 141-154 more… BibTeX
  • Li, Y.; Boeck, A.; Haseneyer, G.; Korzun, V.; Wilde, P.; Schoen, C. C.; Ankerst, D. P.; Bauer, E.: Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms. BMC Plant Biology 11, 2011, 146 more… BibTeX
  • Li, Y.; Haseneyer, G.; Schoen, C. C.; Ankerst, D. P.; Korzun, V.; Wilde, P.; Bauer, E.: High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response. BMC Plant Biology 11, 2011, 6 more… BibTeX
  • Liang, Y.; Ankerst, D. P.; Ketchum, N. S.; Ercole, B.; Shah, G.; Shaughnessy Jr., J. D.; Leach, R. J.; Thompson, I. M.: Prospective evaluation of operating characteristics of prostate cancer detection biomarkers. Journal of Urology 185 (1), 2011, 104--110 more… BibTeX
  • Mittelstrass, K.; Ried, J. S.; Yu, Z.; Krumsiek, J.; Gieger, C.; Prehn, C.; Roemisch-Margl, W.; Polonikov, A.; Peters, A.; Theis, F. J.; Meitinger, T.; Kronenberg, F.; Weidinger, S.; Wichmann, H. E.; Suhre, K.; Wang-Sattler, R.; Adamski, J.; Illig, T.: Discovery of sexual dimorphisms in metabolic and genetic biomarkers. PLoS Genet. 7 (8), 2011 more… BibTeX
  • Raia, V.; Schilling, M.; Böhm, M.; Hahn, B.; Kowarsch, A.; Raue, A.; Sticht, C.; Bohl, S.; Saile, M.; Möller, P.; Gretz, N.; Timmer, J.; Theis, F. J.; Lehmann, W. D.; Lichter, P.; Klingmüller, U.: Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-Cell lymphoma allows prediction of therapeutic targets. Cancer Res. 71 (3), 2011, 693-704 more… BibTeX
  • Sass, S.; Dietmann, S.; Burk, U. C.; Brabletz, S.; Lutter, D.; Kowarsch, A.; Mayer, K. F. X.; Brabletz, T.; Ruepp, A.; Theis, F. J.; Wang, Y.: MicroRNAs coordinately regulate protein complexes. BMC Syst. Biol. 5, 2011 more… BibTeX
  • Theis, F. J.; Bohl, S.; Klingmüller, U.: Theoretical analysis of time-to-peak responses in biological reaction networks. Bull. Math. Biol. 73, 2011, 978-1003 more… BibTeX
  • Theis, F. J.; Kawanabe, M.; Müller, K. R.: Uniqueness of non-Gaussianity-based dimension reduction. IEEE Trans. Signal Process. 59 (9), 2011, 4478 - 4482 more… BibTeX
  • Theis, F. J.; Latif, N.; Wong, P.; Frishman, D.: Complex principal component and correlation structure of 16 yeast genomic variables. Mol. Biol. Evol. 28 (9), 2011, 2501-2512 more… BibTeX
  • Thompson Jr., IM; Leach, RJ; Ankerst, DP: Prostate Cancer Detection: A View of the Future. European Urology 59 (2), 2011, 191 - 193 more… BibTeX
  • Vincent, E.; Araki, S.; Theis, F. J.; Nolte, G.; Bofill, P.; Sawada, H.; Ozerov, A.; Gowreesunker, V.; Lutter, D.; Duong, N. Q. K.: The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges. Signal Process. 92 (8), 2011, 1928-1936 more… BibTeX
  • Wittmann, D. M.; Theis, F. J.: Dynamic regimes of random fuzzy logic networks. New J. Phys. 13, 2011 more… BibTeX

2010

  • Ansorg, M.; Blöchl, F.; zu Castell, W.; Theis, F. J.; Wittmann, D. M.: Gene regulation at the Mid-Hindbrain Boundary: Study of a mathematical model in the stationary limit. Int. J. Biomath. Biostat. 1 (1), 2010, 9-21 more… BibTeX
  • Fekete, Agnes; Kuttler, Christina; Rothballer, Michael; Hense, Burkhard A.; Fischer, Doreen; Buddrus-Schiemann, Katharina; Lucio, Marianna; Müller, Johannes; Schmitt-Kopplin, Philippe; Hartmann, Anton: Dynamic regulation of N -acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF de Dynamic regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF. FEMS Microbiology Ecology 72 (1), 2010, 22-34 more… BibTeX
  • Franke, R.; Theis, F. J.; Klamt, S.: From binary to multivalued to continuous models: The lac operon as a case study. J. Integr. Bioinform. 7 (1), 2010 more… BibTeX
  • Frederick, M.; Kuttler, C.; Hense, B.A. ; Müller, J.; Eberl, H.J.: A mathematical model of quorum sensing in patchy biofilm communities with slow background flow. Canadian Applied Mathematics Quarterly 18 (3), 2010, 267-298 more… BibTeX
  • Hartsperger, M. L.; Blöchl, F.; Stümpflen, V.; Theis, F. J.: Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. BMC Bioinformatics 11, 2010 more… BibTeX
  • Horster, S.; Laubender, R. P.; Lehmeyer, L.; Ankerst, D. P.; Eberle, J.; Reinert, R.; Imoehl, M.; van der Linden, M.; Schweiger, B.; Bogner, J. R.: Influence of antiretroviral therapy on immunogenicity of simultaneous vaccinations against influenza, pneumococcal disease and hepatitis A and B in human immunodeficiency virus positive individuals. Journal of Infection 61 (6), 2010, 484--491 more… BibTeX
  • Konopka, W.; Kiryk, A.; Novak, M.; Herwerth, M.; Parkitna, J. R.; Wawrzyniak, M.; Kowarsch, A.; Michaluk, P.; Dzwonek, J.; Arnsperger, T.; Wilczynski, G.; Merkenschlager, M.; Theis, F. J.; Köhr, G.; Kaczmarek, L.; Schütz, G.: MicroRNA loss enhances learning and memory in mice. J. Neurosci. 30 (44), 2010, 14835-14842 more… BibTeX
  • Kowarsch, A.; Blöchl, F.; Bohl, S.; Saile, M.; Gretz, N.; Klingmüller, U.; Theis, F. J.: Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. BMC Bioinformatics 11, 2010 more… BibTeX
  • Kowarsch, A.; Marr, C.; Schmidl, D.; Ruepp, A.; Theis, F. J.: Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways. PLoS ONE 5 (6), 2010 more… BibTeX
  • Kreuzpointner, L.; Simon, P.; Theis, F. J.: The ad coefficient as a descriptive measure of the within-group agreement of ratings. Brit. J. Math. Stat. Psychol. 63 (2), 2010, 341-360 more… BibTeX
  • Krumsiek, J.; Pölsterl, S.; Wittmann, D. M.; Theis, F. J.: Odefy - from discrete to continuous models. BMC Bioinformatics 11, 2010, 1-10 more… BibTeX
  • Liang, Y.; Ankerst, D. P.; Sanchez, M.; Leach, R. J.; Thompson, I. M.: Body mass index adjusted prostate-specific antigen and its application for prostate cancer screening. Urology 76 (5), 2010, 1268.e1-1268.e6 more… BibTeX
  • Lutter, D.; Marr, C.; Krumsiek, J.; Lang, E. W.; Theis, F. J.: Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects. BMC Genomics 11, 2010 more… BibTeX
  • Marr, C.; Theis, F. J.; Liebovitch, L. S.; Hütt, M. T.: Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. PLoS Comput. Biol. 6 (7), 2010 more… BibTeX
  • Mewes, H. W.; Ruepp, A.; Theis, F. J.; Rattei, T.; Walter, M. C.; Frishman, D.; Suhre, K.; Spannagl, M.; Mayer, K. F. X.; Stümpflen, V.; Antonov, A.: MIPS: Curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39, 2010, D220-D224 more… BibTeX
  • Meyer-Bäse, A.; Theis, F. J.; Emmett, M. R.: Robust stability analysis and design under consideration of multiple feedback loops of the tryptophan regulatory network of Escherichia coli. Adv. Exp. Med. Biol. 680, 2010, 189-197 more… BibTeX
  • Ruepp, A.; Kowarsch, A.; Schmidl, D.; Buggenthin, F.; Brauner, B.; Dunger, I.; Fobo, G.; Frishman, G.; Montrone, C.; Theis, F. J.: PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 11 (1), 2010 more… BibTeX
  • Theis, F. J.: Colored subspace analysis: Dimension reduction based on a signal's autocorrelation structure. IEEE Trans. Circuits Syst. I-Regul. Pap. 57 (7), 2010, 1463-1474 more… BibTeX
  • Thiemann, C.; Theis, F. J.; Grady, D.; Brune, R.; Brockmann, D.: The structure of borders in a small world. PLoS ONE 5 (11), 2010 more… BibTeX
  • Thompson, IM; Ankerst, DP; Tangen, CM: Prostate-Specific Antigen, Risk Factors, and Prostate Cancer: Confounders Nestled in an Enigma. Journal of the National Cancer Institute 102 (17), 2010, 1299 - 1301 more… BibTeX
  • Vickers, A. J.; Cronin, A. M.; Roobol, M. J.; Hugosson, J.; Jones, J. S.; Kattan, M. W.; Klein, E.; Hamdy, F.; Neal, D.; Donovan, J.; Parekh, D. J.; Ankerst, D.; Bartsch, G.; Klocker, H.; Horninger, W.; Benchikh, A.; Salama, G.; Villers, A.; Freedland, S. J.; Moreira, D. M.; Schroeder, F. H.; Lilja, H.: The relationship between prostate-specific antigen and prostate cancer risk: the Prostate Biopsy Collaborative Group. Clinical Cancer Research 16 (17), 2010, 4374--4381 more… BibTeX
  • Wittmann, D. M.; Marr, C.; Theis, F. J.: Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks. J. Theor. Biol. 266 (3), 2010, 436-448 more… BibTeX

2009

  • Ankerst, D. P.; Miyamoto, R.; Nair, P. V.; Pollock, B. H.; Thompson, I. M.; Parekh, D. J.: Yearly prostate specific antigen and digital rectal examination fluctuations in a screened population. Journal of Urology 181 (5), 2009, 2071--2075 more… BibTeX
  • Ankerst, DP; Diepolder, H; Horster, S: Topical treatment of anogenital human papillomavirus infection in male patients. Future Virology 4 (6), 2009, 531-541 more… BibTeX
  • Brawley, O. W.; Ankerst, D. P.; Thompson, I. M.: Screening for prostate cancer. CA: A cancer journal for clinicians 59 (4), 2009, 264--273 more… BibTeX
  • Dieplinger, H.; Ankerst, D. P.; Burges, A.; Lenhard, M.; Lingenhel, A.; Fineder, L.; Buchner, H.; Stieber, P.: Afamin and apolipoprotein A-IV: novel protein markers for ovarian cancer. Cancer Epidemiology Biomarkers and Prevention 18 (4), 2009, 1127--1133 more… BibTeX
  • Efendiev, Messoud; Müller, Johannes: Classification of Existence and Non-Existence of Running Fronts in Case of Fast Diffusion. Journal of Advanced Mathematics and Applications 19, 2009, 285-293 more… BibTeX
  • Eyre, S. J.; Ankerst, D. P.; Wei, J. T.; Nair, P. V.; Regan, M. M.; Bueti, G.; Tang, J.; Rubin, M. A.; Kearney, M.; Thompson, I. M.; Sanda, M. G.: Validation in a multiple urology practice cohort of the Prostate Cancer Prevention Trial calculator for predicting prostate cancer detection. Journal of Urology 182 (6), 2009, 2653--2658 more… BibTeX
  • Gruber, P.; Meyer-Bäse, A.; Foo, S.; Theis, F. J.: ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data. Eng. Appl. Artif. Intel. 22 (4-5), 2009, 497-504 more… BibTeX
  • Jansson, A. F.; Mueller, T. H.; Gliera, L.; Ankerst, D. P.; Wintergerst, U.; Belohradsky, B. H.; Jansson, V.: Clinical score for nonbacterial osteitis in children and adults. Arthritis & Rheumatism 60 (4), 2009, 1152--1159 more… BibTeX
  • King, John; Pérez-Velázquez, Judith; Byrne, H.M.: Singular travelling waves in a model for tumour encapsulation. Discrete and Continuous Dynamical Systems 25 (1), 2009, 195-230 more… BibTeX
  • Klamt, S.; Haus, U. U.; Theis, F. J.: Hypergraphs and cellular networks. PLoS Comput. Biol. 5 (5), 2009 more… BibTeX
  • Müller, Johannes; Spandl, Christoph: A Curtis–Hedlund–Lyndon theorem for Besicovitch and Weyl spaces. Theoretical Computer Science 410 (38-40), 2009, 3606-3615 more… BibTeX
  • Müller, Johannes; Spandl, Christoph: Embeddings of dynamical systems into cellular automata. Ergodic Theory and Dynamical Systems 29 (1), 2009, 165-177 more… BibTeX
  • Neher, R. A.; Mitkovski, M.; Kirchhoff, F.; Neher, E.; Theis, F. J.; Zeug, A.: Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophys. J. 96 (9), 2009, 3791-3800 more… BibTeX
  • Pérez-Velázquez, J.; Hattersley, J.G.; Chappell, M.J.; Bearup, D.; Roper, D.; Dowson, C.; Bugg, T.; Evans, N.D.: Indistinguishability and identifiability of kinetic models for the Mur C reaction in peptidoglycan biosynthesis* *EPSRC funded project Indistinguishability analysis for model discrimination in Systems Biology: A Feasibility Study applied to Bacterial Peptidoglycan Biosynthesis (EP/E057535/1). IFAC Proceedings Volumes 42 (12), 2009, 103-108 more… BibTeX
  • Sánchez-Garduño, Faustino; Maini, Philip K.; Pérez-Velázquez, Judith: A non-linear degenerate equation for direct aggregation and traveling wave dynamics. DCDS-B 13 (2), 2009, 455-487 more… BibTeX
  • Webb, K. J.; Norton, W. H. J.; Trümbach, D.; Meijer, A. H.; Ninkovic, J.; Topp, S.; Heck, D.; Marr, C.; Wurst, W.; Theis, F. J.; Spaink, H. P.; Bally-Cuif, L.: Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol. 10 (7), 2009 more… BibTeX
  • Wittmann, D. M.; Blöchl, F.; Trümbach, D.; Wurst, W.; Prakash, N.; Theis, F. J.: Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary. PLoS Comput. Biol. 5 (11), 2009 more… BibTeX
  • Wittmann, D. M.; Krumsiek, J.; Saez-Rodriguez, J.; Lauffenburg, D. A.; Klam, S.; Theis, F. J.: Transforming Boolean models to continuous models: Methodology and application to T-cell receptor signaling. BMC Syst. Biol. 3, 2009 more… BibTeX
  • Wittmann, D. M.; Schmidl, D.; Blöchl, F.; Theis, F. J.: Reconstruction of graphs based on random walks. Theor. Comput. Sci. 410 (38-40), 2009, 3826-3838 more… BibTeX
  • Zeiser, Stefan; Franz, Uwe; Müller, Johannes ; Liebscher, Volkmar: Hybrid Modeling of Noise Reduction by a Negatively Autoregulated System. Bulletin of Mathematical Biology 71 (4), 2009, 1006-1024 more… BibTeX

2008

  • Ankerst, D. P.; Groskopf, J.; Day, J. R.; Blase, A.; Rittenhouse, H.; Pollock, B. H.; Tangen, C.; Parekh, D.; Leach, R. J.; Thompson, I.: Predicting prostate cancer risk through incorporation of prostate cancer gene 3. Journal of Urology 180 (4), 2008, 1303--1308 more… BibTeX
  • Blankenburg, F.; Hatz, R.; Nagel, D.; Ankerst, D.; Reinmiedl, J.; Gruber, C.; Seidel, D.; Stieber, P.: Preoperative CYFRA 21-1 and CEA as prognostic factors in patients with stage I non-small cell lung cancer: external validation of a prognostic score. Tumor Biology 29 (4), 2008, 272--277 more… BibTeX
  • Brockmann, D.; Theis, F. J.: Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns. IEEE Pervasive Comput. 7 (4), 2008, 28-35 more… BibTeX
  • Heid, I. M.; Vollmert, C.; Kronenberg, F.; Huth, C.; Ankerst, D. P.; Luchner, A.; Hinney, A.; Broenner, G.; Wichmann, H. E.; Illig, T.; Doering, A.; Hebebrand, J.: Association of the MC4R V103I polymorphism with the metabolic syndrome: the KORA Study. Obesity 16 (2), 2008, 369--376 more… BibTeX
  • Hense, B. A.; Kuttler, C.; Müller, J.; Rothballer, M.; Hartmann, A.; Kreft, J. U.: Efficiency sensing - was messen Autoinduktoren wirklich? BIOspektrum 1, 2008, 18-21 more… BibTeX
  • Miyamoto, RK; Chabi, A; Johnson, DA; Ankerst, DP; Thompson, IM; Rozanski, TA: Complicated cataract surgery in patients receiving alpha blockers for benign prostatic hyperplasia. UroToday International Journal 1, 2008 more… BibTeX
  • Müller, Johannes; Brandt, Stefan; Mayerhofer, Katrin; Tjardes, Thorsten; Maegele, Marc: Tolerance and threshold in the extrinsic coagulation system. Mathematical Biosciences 211 (2), 2008, 226-254 more… BibTeX
  • Müller, Johannes; Kuttler, Christina; Hense, Burkhard A.: Sensitivity of the quorum sensing system is achieved by low pass filtering. Biosystems 92 (1), 2008, 76-81 more… BibTeX
  • Müller, Johannes; Kuttler, Christina; Hense, Burkhard A.; Zeiser, Stefan; Liebscher, Volkmar: Transcription, intercellular variability and correlated random walk. Mathematical Biosciences 216 (1), 2008, 30-39 more… BibTeX
  • Parekh, A. D.; Thomas, J. C.; Trusler, L.; Ankerst, D. P.; Deshpande, J. K.; Adams, M. C.; Pope 4th, J. C.; Brock 3rd, J. W.: Prospective evaluation of health related quality of life for pediatric patients with ureteropelvic junction obstruction. Journal of Urology 180 (5), 2008, 2171--2175 more… BibTeX
  • Proust-Lima, C.; Taylor, J. M.; Williams, S. G.; Ankerst, D. P.; Liu, N.; Kestin, L. L.; Bae, K.; Sandler, H. M.: Determinants of change in prostate-specific antigen over time and its association with recurrence after external beam radiation therapy for prostate cancer in five large cohorts. International Journal of Radiation Oncology, Biology, Physics 72 (3), 2008, 782--791 more… BibTeX
  • Pérez-Velázquez, J.; Evans, N.D.; Chappell, M.J.; Errington, R.J.; Smith, P.J.; Khan, I.: A Mathematical Model of Cyclin B1 Dynamics at the Single Cell Level in Osteosarcoma Cells. IFAC Proceedings Volumes 41 (2), 2008, 9057-9062 more… BibTeX
  • Reed, A. B.; Ankerst, D. P.; Leach, R. J.; Vipraio, G.; Thompson, I. M.; Parekh, D. J.: Total prostate specific antigen stability confirmed after long-term storage of serum at -80C. Journal of Urology 180 (2), 2008, 534--537 more… BibTeX
  • Rhodes, E. C.; Johnson-Pais, T. L.; Singer, F. R.; Ankerst, D. P.; Bruder, J. M.; Wisdom, J.; Hoon, D. S. B.; Lin, E.; Bone, H. G.; Simcic, K. J.; Leach, R. J.: Sequestosome 1 (SQSTM1) mutations in Paget's disease of bone from the United States. Calcified Tissue International 82 (4), 2008, 271--277 more… BibTeX
  • Schachtner, R.; Lutter, D.; Knollmüller, P.; Tomé, A. M.; Theis, F. J.; Schmitz, G.; Stetter, M.; Vilda, P. G.; Lang, E. W.: Knowledge-based gene expression classification via matrix factorization. Bioinformatics 24 (15), 2008, 1688-1697 more… BibTeX
  • Shepherd, B. E.; Redman, M. W.; Ankerst, D. P.: Does Finasteride Affect the Severity of Prostate Cancer? A Causal Sensitivity Analysis. Journal of the American Statistical Association 103 (484), 2008, 1392--1404 more… BibTeX
  • Stolte, Thomas; Hösel, Volker; Müller, Johannes; Speicher, Michael: Modeling Clonal Expansion from M-FISH Experiments. Journal of Computational Biology 15 (2), 2008, 221-230 more… BibTeX
  • Taylor, J. M. G.; Ankerst, D. P.; Andridge, R. R.: Validation of biomarker-based risk prediction models. Clinical Cancer Research 14 (19), 2008, 5977--5983 more… BibTeX
  • Thompson, I. M.; Ankerst, D. P.; Etzioni, R.; Wang, T.: It's time to abandon an upper limit of normal for prostate specific antigen: assessing the risk of prostate cancer. Journal of Urology 180 (4), 2008, 1219--1222 more… BibTeX
  • Thompson, I. M.; Tangen, C. M.; Ankerst, D. P.; Chi, C.; Lucia, M. S.; Goodman, P.; Parnes, H.; Coltman Jr., C. A.: The performance of prostate specific antigen for predicting prostate cancer is maintained after a prior negative prostate biopsy. Journal of Urology 180 (2), 2008, 544--547 more… BibTeX
  • Wong, P.; Althammer, S.; Hildebrand, A.; Kirschner, A.; Pagel, P.; Geissler, B.; Smialowski, P.; Blöchl, F.; Oesterheld, M.; Schmidt, T.; Strack, N.; Theis, F. J.; Ruepp, A.; Frishman, D.: An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics 9, 2008 more… BibTeX
  • Yildiz, A.; Guleryuz, S.; Ankerst, D. P.; Ongur, D.; Renshaw, P. F.: Protein kinase C inhibition in the treatment of mania: a double-blind, placebo-controlled trial of tamoxifen. Archives of General Psychiatry 65 (3), 2008, 255--263 more… BibTeX

2007

  • Boeck, S.; Ankerst, D. P.; Heinemann, V.: The role of adjuvant chemotherapy for patients with resected pancreatic cancer: systematic review of randomized controlled trials and meta-analysis. Oncology 72, 2007, 314--321 more… BibTeX
  • Bowen, D. J.; Fann, J. R.; Andersen, M. R.; Rhew, I. C.; Gralow, J. R.; Lewis, F. M.; Hunt, J. R.; Palomares, M.; Moinpour, C. M.; Ankerst, D. P.: Recruiting patients with breast cancer and their families to behavioral research in the post-HIPAA period. Oncology Nursing Forum 34 (5), 2007, 1049--1054 more… BibTeX
  • Canby-Hagino, E.; Hernandez, J.; Brand, T. C.; Troyer, D. A.; Higgins, B.; Ankerst, D. P.; Thompson, I. M.; Leach, R. J.; Parekh, D. J.: Prostate cancer risk with positive family history, normal prostate examination findings, and PSA less than 4.0 ng/mL. Urology 70 (4), 2007, 748--752 more… BibTeX
  • Etzioni, R. D.; Ankerst, D. P.; Weiss, N. S.; Inoue, L. Y.; Thompson, I. M.: Is prostate-specific antigen velocity useful in early detection of prostate cancer? A critical appraisal of the evidence. Journal of the National Cancer Institute 99 (20), 2007, 1510--1515 more… BibTeX
  • Etzioni, RD; Ankerst, DP; Thompson, IM: Re: Detection of Life-Threatening Prostate Cancer with Prostate-Specific Antigen Velocity During a Window of Curability. Journal of the National Cancer Institute 99 (6), 2007, 489 - 490 more… BibTeX
  • Fliser, D.; Kollerits, B.; Neyer, U.; Ankerst, D. P.; Lhotta, K.; Lingenhel, A.; Ritz, E.; Kronenberg, F.; Kuen, E.; Konig, P.; Kraatz, G.; Mann, J. F.; Muller, G. A.; Kohler, H.; Riegler, P.: Fibroblast growth factor 23 (FGF23) predicts progression of chronic kidney disease: the Mild to Moderate Kidney Disease (MMKD) Study. Journal of the American Society of Nephrology 18 (9), 2007, 2600--2608 more… BibTeX
  • Hadeler, K.P.; Müller, J.: Optimal harvesting and optimal vaccination. Mathematical Biosciences 206 (2), 2007, 249-272 more… BibTeX
  • Hense, B. A.; Kuttler, C.; Müller, J.; Rothballer, M.; Hartmann, A.; Kreft, J. U.: Does efficiency sensing unify diffusion and quorum sensing? Nature Reviews Microbiology 5 (3), 2007, 230-239 more… BibTeX
  • Markland, A. D.; Thompson, I. M.; Ankerst, D. P.; Higgins, B.; Kraus, S. R.: Lack of disparity in lower urinary tract symptom severity between community-dwelling non-Hispanic white, Mexican-American, and African-American men. Urology 69 (4), 2007, 697--702 more… BibTeX
  • Moinpour, C. M.; Darke, A. K.; Donaldson, G. W.; Thompson, I. M.; Langley, C.; Ankerst, D. P.; Patrick, D. L.; Ware, J. E.; Ganz, P. A.; Shumaker, S. A.; Lippman, S. M.; Coltman Jr., C. A.: Longitudinal analysis of sexual function reported by men in the Prostate Cancer Prevention Trial. Journal of the National Cancer Institute 99 (13), 2007, 1025--1035 more… BibTeX
  • Müller, Johannes; Hösel, Volker: Estimating the Tracing Probability from Contact History at the Onset of an Epidemic. Mathematical Population Studies 14, 2007, 211-236 more… BibTeX
  • Parekh, D. J.; Ankerst, D. P.; Baillargeon, J.; Higgins, B.; Platz, E. A.; Troyer, D.; Hernandez, J.; Leach, R. J.; Lokshin, A.; Thompson, I. M.: Assessment of 54 biomarkers for biopsy-detectable prostate cancer. Cancer, Epidemiology, Biomarkers and Prevention 16 (10), 2007, 1966--1972 more… BibTeX
  • Parekh, D. J.; Ankerst, D. P.; Troyer, D.; Srivastava, S.; Thompson, I. M.: Biomarkers for prostate cancer detection. Journal of Urology 178 (6), 2007, 2252--2259 more… BibTeX
  • Parekh, DJ; Ankerst, DP; Thompson, IM.: Prostate-Specific Antigen Levels, Prostate-Specific Antigen Kinetics, and Prostate Cancer Prognosis: A Tocsin Calling for Prospective Studies. Journal of the National Cancer Institute 99 (7), 2007, 496 - 497 more… BibTeX
  • Reed, A.; Ankerst, D. P.; Pollock, B. H.; Thompson, I. M.; Parekh, D. J.: Current age and race adjusted prostate specific antigen threshold values delay diagnosis of high grade prostate cancer. Journal of Urology 178 (5), 2007, 1929--1932 more… BibTeX
  • Thompson, I. M.; Ankerst, D. P.: Prostate-specific antigen in the early detection of prostate cancer. Canadian Medical Association Journal 176 (13), 2007, 1853--1858 more… BibTeX
  • Thompson, I. M.; Pauler Ankerst, D.; Chi, C.; Goodman, P. J.; Tangen, C. M.; Lippman, S. M.; Lucia, M. S.; Parnes, H. L.; Coltman Jr., C. A.: Prediction of prostate cancer for patients receiving finasteride: results from the Prostate Cancer Prevention Trial. Journal of Clinical Oncology 25 (21), 2007, 3076--3081 more… BibTeX
  • Zeiser, Stefan; Müller, Johannes; Liebscher, Volkmar: Modeling the Hes1 Oscillator. Journal of Computational Biology 14 (7), 2007, 984-1000 more… BibTeX

2006

  • Ankerst, D. P.; Engel, J.: Status of quality of life in breast cancer research before, during and beyond treatment. Expert Review Pharmacoeconomics & Outcomes Research 6 (2), 2006, 207--214 more… BibTeX
  • Ankerst, D. P.; Thompson, I. M.: Sensitivity and specificity of prostate-specific antigen for prostate cancer detection with high rates of biopsy verification. Archivio Italiano di Urologia e Andrologia 78 (4), 2006, 125--129 more… BibTeX
  • Ankerst, D. P.; Thompson, I. M.: Merging digital rectal exam, family history, age and prostate-specific antigen to create a decision-making tool. Archivio Italiano di Urologia e Andrologia 78 (4), 2006, 143--146 more… BibTeX
  • Ankerst, D. P.; Thompson, I. M.: New answers from the Prostate Cancer Prevention Trial on the chemoprevention of prostate cancer. Archivio Italiano di Urologia e Andrologia 78 (4), 2006, 154--156 more… BibTeX
  • Baillargeon, J.; Platz, E. A.; Rose, D. P.; Pollock, B. H.; Ankerst, D. P.; Haffner, S.; Higgins, B.; Lokshin, A.; Troyer, D.; Hernandez, J.; Lynch, S.; Leach, R. J.; Thompson, I. M.: Obesity, adipokines, and prostate cancer in a prospective population-based study. Cancer Epidemiology, Biomarkers and Prevention 15 (7), 2006, 1331--1335 more… BibTeX
  • Berry, D. L.; Moinpour, C. M.; Jiang, C. S.; Ankerst, D. P.; Petrylak, D. P.; Vinson, L. V.; Lara, P. N.; Jones, S.; Taplin, M. E.; Burch, P. A.; Hussain, M. H.; Crawford, E. D.: Quality of life and pain in advanced stage prostate cancer: results of a Southwest Oncology Group randomized trial comparing docetaxel and estramustine to mitoxantrone and prednisone. Journal of Clinical Oncology 24 (18), 2006, 2828--2835 more… BibTeX
  • Müller, J.; Kuttler, C.; Hense, B. A.; Rothballer, M.; Hartmann, A.: Cell-cell communication by quorum sensing and dimension-reduction. Journal of Mathematical Biology 53 (4), 2006, 672-702 more… BibTeX
  • Parekh, D. J.; Ankerst, D. P.; Higgins, B. A.; Hernandez, J.; Canby-Hagino, E.; Brand, T.; Troyer, D. A.; Leach, R. J.; Thompson, I. M.: External validation of the Prostate Cancer Prevention Trial risk calculator in a screened population. Urology 68 (6), 2006, 1152--1155 more… BibTeX
  • Petrylak, D. P.; Ankerst, D. P.; Jiang, C. S.; Tangen, C. M.; Hussain, M. H. A.; Lara Jr., P. N.; Jones, J. A.; Taplin, M. E.; Burch, P. A.; Kohli, M.; Benson, M. C.; Small, E. J.; Raghavan, D.; Crawford, E. D.: Evaluation of prostate-specific antigen declines for surrogacy in patients treated on SWOG 99-16. Journal of the National Cancer Institute 98 (8), 2006, 516--521 more… BibTeX
  • Thompson, I. M.; Ankerst, D. P.; Chi, C.; Goodman, P. J.; Tangen, C. M.; Lucia, M. S.; Feng, Z.; Parnes, H. L.; Coltman Jr., C. A.: Assessing prostate cancer risk: results from the Prostate Cancer Prevention Trial. Journal of the National Cancer Institute 98 (8), 2006, 529--534 more… BibTeX
  • Thompson, I. M.; Chi, C.; Ankerst, D. P.; Goodman, P. J.; Tangen, C. M.; Lippman, S. M.; Lucia, M. S.; Parnes, H. L.; Coltman, C. A.: Effect of finasteride on the sensitivity of PSA for detecting prostate cancer. Journal of the National Cancer Institute 98 (16), 2006, 1128--1133 more… BibTeX
  • Wilson, C. S.; Davidson, G. S.; Martin, S. B.; Andries, E.; Potter, J.; Harvey, R.; Ar, K.; Xu, Y.; Kopecky, K. J.; Ankerst, D. P.; Gundacker, H.; Slovak, M. L.; Mosquera-Caro, M.; Chen, I. M.; Stirewalt, D. L.; Murphy, M.; Schultz, F. A.; Kang, H.; Wang, X.; Radich, J. P.; Appelbaum, F. R.; Atlas, S. R.; Godwin, J.; Willman, C. L.: Gene expression profiling of adult acute myeloid leukemia identifies novel biologic clusters for risk classification and outcome prediction. Blood 108 (2), 2006, 685--696 more… BibTeX
  • Yildiz-Yesiloglu, A.; Ankerst, D. P.: Neurochemical alterations of the brain in bipolar disorder and their implications for pathophysiology: a systematic review of the in vivo proton magnetic resonance spectroscopy findings. Progress in Neuro-Psychopharmacology & Biological Psychiatry 30 (6), 2006, 969--995 more… BibTeX
  • Yildiz-Yesiloglu, A.; Ankerst, D. P.: Review of 1H magnetic resonance spectroscopy findings in major depressive disorder: a meta-analysis. Psychiatry Research 147 (1), 2006, 1--25 more… BibTeX

2005

  • Etzioni, R. D.; Howlader, N.; Shaw, P. A.; Ankerst, D. P.; Penson, D. F.; Goodman, P. J.; Thompson, I. M.: Long-term effects of finasteride on prostate specific antigen levels: results from the prostate cancer prevention trial. Journal of Urology 174 (3), 2005, 877--881 more… BibTeX
  • Hansen, LK; Feigl, P; Modiano, MR; Lopez, JA; Escobedo Sluder, S; Moinpour, CM; Pauler, DK; Meyskens, FL: And educational program to increase cervical and breast cancer screening in Hispanic women: A Southwest Oncology Group Study. Cancer Nursing 28 (1), 2005, 47-53 more… BibTeX
  • Hayden, D; Pauler, DK; Schoenfeld, D: An estimator for treatment comparisons among survivors in randomized trials. Biometrics 61, 2005, 305-310 more… BibTeX
  • Maecker, H. T.; Moon, J.; Bhatia, S.; Ghanekar, S. A.; Maino, V. C.; Payne, J. K.; Kuus-Reichel, K.; Chang, J. C.; Summers, A.; Clay, T. M.; Morse, M. A.; Lyerly, H. K.; DeLaRosa, C.; Ankerst, D. P.; Disis, M. L.: Impact of cryopreservation on tetramer, cytokine flow cytometry, and ELISPOT. BMC Immunology 6 (1), 2005, 17 more… BibTeX
  • Thompson, IM; Ankerst, DP; Chi, C; Lucia, MS; Goodman, P; Crowley, JJ; Parnes, HL; Coltman Jr., CA: The operating characteristics of prostate-specific antigen in a population with initial PSA of 3.0 ng/ml or lower. Journal of the American Medical Association 294 (1), 2005, 66-70 more… BibTeX

2004

  • Green, S; Pauler, DK: Statistics in clinical trials. Current Oncology Reports 6 (1), 2004, 36-41 more… BibTeX
  • McGregor, BA; Bowen, DJ; Ankerst, DP; Andersen, MR; Yasui, Y; McTiernan, A: Optimism, perceived risk of breast cancer, and cancer worry among a community-based sample of women. Health Psychology 23 (4), 2004, 339-344 more… BibTeX
  • Müller, J.; Hadeler, K.P.; Müller, V.; Waldmann, J.; Landstorfer, F.M.; Wisniewski, R.; Kantz, J.; Lang, F.: Influence of low power cm-/mm-microwaves on cardiovascular function. International Journal of Environmental Health Research 14 (5), 2004, 331-341 more… BibTeX
  • Müller, Johannes: Contact tracing and stochastic trees. Oberwolfach Reports, 2004 more… BibTeX
  • Thompson, IM; Pauler, DK; Goodman, PJ; Tangen, CM; Lucia, SM; Parnes, HL; Minasian, LM; Ford, LG; Lippman, SM; Crawford, ED; Crowley, JJ; Coltman Jr., CA: Prevalence of prostate cancer among men with a prostate-specific antigen level = or < 4.0 ng per milliliter. New England Journal of Medicine 350 (22), 2004, 2239-2246 more… BibTeX
  • Yildiz, A; Pauler, DK; Sachs, GS: Rates of study completion with single versus split daily dosing of antidepressants. Journal of Affective Disorders 78, 2004, 157-162 more… BibTeX

2003

  • Ganz, PA; Moinpour, CM; Pauler, DK; Kornblith, AB; Gaynor, ER; Balcerzak, SP; Gatti, GS; Erba, HP; McCoy, S; Press, OW; Fisher, RI: Health status and quality of life in patients with early stage Hodgkin's disease treated on Southwest Oncology Group Study 9133. Journal of Clinical Oncology 21 (18), 2003, 3512-3519 more… BibTeX
  • Mertz, A.; Guttenberger, M.; Müller, J.; Schönfisch, B.; Hampp, R.: Isozyme Variability in Brazilian Populations of Araucaria angustifolia. Biociencias 11 (1), 2003, 3-8 more… BibTeX
  • Müller, Johannes; Möhle, Martin: Family trees of continuous-time birth-and-death processes. Journal of Applied Probability 40 (4), 2003, 980-994 more… BibTeX
  • Müller, Johannes; Tjardes, Thorsten: Modeling the Cytokine Network In Vitro and In Vivo. Journal of Theoretical Medicine 5 (2), 2003, 93-110 more… BibTeX
  • Pauler, DK; McCoy, S; Moinpour, C: Pattern mixture models for longitudinals quality of life studies in advanced-stage disease. Statistics in Medicine 22, 2003, 795-809 more… BibTeX

2002

  • Pauler, DK; Finkelstein, DM: Predicting time to prostate cancer recurrence based on joint models for non-linear longitudinal biomarkers and event time outcomes. Statistics in Medicine 21, 2002, 3897-3911 more… BibTeX
  • Pauler, DK; Gower, KB; Goodman, PJ; Crowley, JJ; Thompson, IM: Biomarker-based methods for determining noncompliance in a prevention trial. Controlled Clinical Trials 23, 2002, 675-685 more… BibTeX
  • Pauler, DK; Laird, NM: Non-linear hierarchical models for monitoring compliance. Statistics in Medicine 21 (2), 2002, 219-229 more… BibTeX

2001

  • Pauler, DK; Menon, U; McIntosh, M; Symecko, HL; Skates, SJ; Jacobs, IJ: Factors influencing serum CA125II levels in healthy postmenopausal women. Cancer Epidemiology, Biomarkers and Prevention 10 (5), 2001, 489-493 more… BibTeX
  • Schneider, G.; Müller, J.: Bifurcation analysis for a spatially extended random walk system in mathematical biology. Communications in Applied Analysis 5, 2001, 247-264 more… BibTeX
  • Skates, SJ; Pauler, DK; Jacobs, IJ: Screening based on the risk of cancer calculation from Bayesian hierarchical change-point models of longitudinal markers. Journal of the American Statistical Association 96, 2001, 429-439 more… BibTeX
  • Toes, R.E.; Nussbaum, A.K.; Degermann, S.; Schirle, M.; Emmerich, N.P.; Kraft, M.; Laplace, C.; Zwinderman, A.; Dick, T.P.; Müller, J.; Schönfisch, B.; Schmid, C.; Fehling, H.J.; Stevanovic, S.; Rammensee, H.G.; Schild, H.: Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. Journal of Experimental Medicine 194 (1), 2001, 1-12 more… BibTeX
  • Welt, CK; Smith, ZA; Pauler, DK; Hall, JE: Differential regulation of inhibin A and inhibin B by luteinizing hormone, follicle-stimulating hormone, and stage of follicle development. Journal of Clinical Endocrinology and Metabolism 86 (6), 2001, 2531-2537 more… BibTeX

2000

  • Müller, J. ; Hadeler, K. P.: Monotonicity of the Number of Passages in Linear Chains and of the Basic Reproduction Number in Epidemic Models. Zeitschrift für Analysis und ihre Anwendungen 19 (1), 2000, 61-75 more… BibTeX
  • Müller, J., Kretzschmar, M., Dietz, K.: Contact tracing in stochastic and deterministic epidemic models. Mathematical Biosciences 164 (1), 2000, 39-64 more… BibTeX
  • Müller, Johannes: Optimal vaccination patterns in age-structured populations: Endemic case. Mathematical and Computer Modelling 31 (4-5), 2000, 149-160 more… BibTeX
  • Müller, Johannes; Schönfisch, Birgitt; Kirkilionis, Markus: Ring vaccination. Journal of Mathematical Biology 41 (2), 2000, 143-171 more… BibTeX
  • Pauler, D. K.; Laird, N. M.: A mixture model for longitudinal data with application to assessment of noncompliance. Biometrics 56 (2), 2000, 464--472 more… BibTeX
  • Pinzone, J. J.; Katznelson, L.; Danila, D. C.; Pauler, D. K.; Miller, C. S.; Klibanski, A.: Primary medical therapy of micro- and macroprolactinomas in men. Journal of Clinical Endocrinology and Metabolism 85 (9), 2000, 3053--3057 more… BibTeX

1999

  • Laird, Nan M.; Pauler, Donna K.: Discussion of "Adjusting for nonignorable drop-out using semiparametric nonresponse models" by DO Scharfstein, A Rotnitzky and JM Robins. Journal of the American Statistical Association 94 (448), 1999, 1133-1135 more… BibTeX
  • Müller, Johannes: Scaling Methods and Approximative Equations for Homogeneous Reaction—Diffusion Systems and Applications to Epidemics. Journal of Nonlinear Science 9 (2), 1999, 149-168 more… BibTeX
  • Müller, Johannes: Optimal vaccination patterns in age-structured populations. SIAM Journal on Applied Mathematics 59 (1), 1999, 222-241 more… BibTeX
  • Pauler, Donna K.; Wakefield, Jonathan C.; Kass, Robert E.: Bayes Factors and Approximations for Variance Component Models. Journal of the American Statistical Association 94 (448), 1999, 1242-1253 more… BibTeX

1998

  • Müller, Johannes; Hillen, Thomas: Modulation equations and parabolic limits of reaction random-walk systems. Mathematical Methods in the Applied Sciences 21 (13), 1998, 1207-1226 more… BibTeX
  • Pauler, DK: The Schwarz criterion and related methods for normal linear models. Biometrika 85, 1998, 13-27 more… BibTeX

1997

  • Müller, Johannes: Optimal vaccination strategies — for whom? Mathematical Biosciences 139 (2), 1997, 133-154 more… BibTeX

1996

  • Arango, V.; Underwood, M. D.; Pauler, D. K.; Kass, R. E.; Mann, J. J.: Differential age-related loss of pigmented locus coeruleus neurons in suicides, alcoholics, and alcoholic suicides. Alcoholism: Clinical and Experimental Research 20 (7), 1996, 1141--1147 more… BibTeX
  • Pauler, D. K.; Escobar, M. D.; Sweeney, J. A.; Greenhouse, J.: Mixture models for eye-tracking data: a case study. Statistics in Medicine 15 (13), 1996, 1365--1376 more… BibTeX

1993

  • Sweeney, J. A.; Clementz, B. A.; Escobar, M. D.; Li, S.; Pauler, D. K.; Haas, G. L.: Mixture analysis of pursuit eye-tracking dysfunction in schizophrenia. Biological Psychiatry 34 (5), 1993, 331--340 more… BibTeX

1992

  • Harris, Ian R.; Pauler, Donna K.: Locally quadratic log likelihood and data-based transformations. Communications in Statistics - Theory and Methods 21 (3), 1992, 637-646 more… BibTeX