Publications

*Authors highlighted in bold are members of the LiSyM network

An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action

Authors:
Anzt, H., Bach, F., Druskat, S., Löffler, F., Loewe, A., Renard, B. Y., Seemann, G., Struck, A., Achhammer, E., Aggarwal, P., Appel, F., Bader, M., Brusch, L., Busse, C., Chourdakis, G., Dabrowski, P. W., Ebert, P., Flemisch, B., Friedl, S., Fritzsch, B., Funk, M. D., Gast, V., Goth, F., Grad, J., Hermann, S., Hohmann, F., Janosch, S., Kutra, D., Linxweiler, J., Muth, T., Peters-Kottig, W., Rack, F., Raters, F. H., Rave, S., Reina, G., Reißig, M., Ropinski, T., Schaarschmidt, J., Seibold, H., Thiele, J. P., Uekermann, B., Unger, S., Weeber, R.
Journal:
F1000Res
Date Published:
2020-01-01
doi:
10.12688/f1000research.23224.1

Functional consequences of metabolic zonation in murine livers: New insights for an old story.

Authors:
Berndt, N., Kolbe, E., Gajowski, R., Eckstein, J., Ott, F., Meierhofer, D., Holzhutter, H. G., Matz-Soja, M.
Journal:
Hepatology
Date Published:
2020-04-14
PubMed ID:
32286709
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32286709

TGF-β2 silencing to target biliary-derived liver diseases

Authors:
Dropmann, A., Dooley, S., Dewidar, B., Hammad, S., Dediulia, T., Werle, J., Hartwig, V., Ghafoory, S., Woelfl, S., Korhonen, H., Janicot, M., Wosikowski, K., Itzel, T., Teufel, A., Schuppan, D., Stojanovic, A., Cerwenka, A., Nittka, S., Piiper, A., Gaiser, T., Beraza, N., Milkiewicz, M., Milkiewicz, P., Brain, J. G., Jones, D. E. J., Weiss, T. S., Zanger, U. M., Ebert, M., Meindl-Beinker, N. M.
Journal:
Gut
Date Published:
2020-01-28
doi:
10.1136/gutjnl-2019-319091

Magnetic resonance elastography quantification of the solid-to-fluid transition of liver tissue due to decellularization.

Authors:
Everwien, H., Ariza de Schellenberger, A., Haep, N., Tzschatzsch, H., Pratschke, J., Sauer, I. M., Braun, J., Hillebrandt, K. H., Sack, I.
Journal:
J Mech Behav Biomed Mater
Date Published:
2020-03-17
PubMed ID:
32174398
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32174398

Guided interactive image segmentation using machine learning and color based data set clustering

Authors:
Friebel, A., Johann, T., Drasdo, D., Hoehme, S.
Journal:
Preprint arXiv 2005.07662
Date Published:
2020-05-18

Geospatial precision simulations of community confined human interactions during SARS-CoV-2 transmission reveals bimodal intervention outcomes

Authors:
Goldenbogen, B., Adler, S. O., Bodeit, O., Wodke, J. A., Korman, A., Bonn, L., de Escalera, X. M. L., Haffner, J. E. L., Krantz, M., Karnetzki, M., Maintz, I., Mallis, L., Torres, R. U. M., Prawitz, H., Segelitz, P., Seeger, M., Linding, R., Klipp, E.
Date Published:
2020-05-06
doi:
10.1101/2020.05.03.20089235

Model predicts fundamental role of biomechanical control of cell cycle progression during liver regeneration after partial hepatectomy

Authors:
Hoehme, S., Gebhardt, R., Hengstler, J., Drasdo, D.
Journal:
Preprint arXiv 2005.09151
Date Published:
2020-05-18

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Authors:
Holland, C. H., Tanevski, J., Perales-Patón, J., Gleixner, J., Kumar, M. P., Mereu, E., Joughin, B. A., Stegle, O., Lauffenburger, D. A., Heyn, H., Szalai, B., Saez-Rodriguez, J.
Journal:
Genome Biol
Date Published:
2020-12-01
doi:
10.1186/s13059-020-1949-z

Mathematical Modeling of Free Fatty Acid-Induced Non-Alcoholic Fatty Liver Disease (NAFLD)

Authors:
Holzhütter, H., Berndt, N.
Date Published:
doi:
10.1101/2020.05.28.120626

A novel variant of the (13)C-methacetin liver function breath test that eliminates the confounding effect of individual differences in systemic CO2 kinetics.

Authors:
Holzhutter, H. G., Wuensch, T., Gajowski, R., Berndt, N., Bulik, S., Meierhofer, D., Stockmann, M.
Journal:
Arch Toxicol
Date Published:
2020-02-06
PubMed ID:
32020249
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32020249

Resilience of three-dimensional sinusoidal networks in liver tissue.

Authors:
Karschau, J., Scholich, A., Wise, J., Morales-Navarrete, H., Kalaidzidis, Y., Zerial, M., Friedrich, B. M.
Journal:
PLoS Comput Biol
Date Published:
2020-07-01
PubMed ID:
32598356
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32598356

SBML Level 3: an extensible format for the exchange and reuse of biological models

Authors:
Keating, S., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F., Finney, A., Gillespie, C., Helikar, T., Hoops, S., Malik-Sheriff, R., Moodie, S., Moraru, I., Myers, C., Naldi, A., Olivier, B., Sahle, S., Schaff, J., Smith, L., Swat, M., DT, , Watanabe, L., Wilkinson, D., Blinov, M., Begley, K., Faeder, J., Gómez, H., Hamm, T., Inagaki, Y., Liebermeister, W., Lister, A., Lucio, D., Mjolsness, E., Proctor, C., Raman, K., Rodriguez, N., Shaffer, C., Shapiro, B., Stelling, J., Swainston, N., Tanimura, N., Wagner, J., Meier-Schellersheim, M., Sauro, H., Palsson, B., Bolouri, H., Kitano, H., Funahashi, A., Hermjakob, H., Doyle, J., Hucka, M., members, S. C.
Journal:
Mol Syst Biol.
Date Published:
2020-07-01
doi:
10.15252/msb.20199110

Protein modification with ISG15 blocks coxsackievirus pathology by antiviral and metabolic reprogramming.

Authors:
Kespohl, M., Bredow, C., Klingel, K., Voss, M., Paeschke, A., Zickler, M., Poller, W., Kaya, Z., Eckstein, J., Fechner, H., Spranger, J., Fahling, M., Wirth, E. K., Radoshevich, L., Thery, F., Impens, F., Berndt, N., Knobeloch, K. P., Beling, A.
Journal:
Sci Adv
Date Published:
2020-03-21
PubMed ID:
32195343
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32195343

Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction.

Authors:
Kok, F., Rosenblatt, M., Teusel, M., Nizharadze, T., Goncalves Magalhaes, V., Dachert, C., Maiwald, T., Vlasov, A., Wasch, M., Tyufekchieva, S., Hoffmann, K., Damm, G., Seehofer, D., Boettler, T., Binder, M., Timmer, J., Schilling, M., Klingmuller, U.
Journal:
Mol Syst Biol
Date Published:
2020-07-23
PubMed ID:
32696599
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32696599

matthiaskoenig/sbmlsim: sbmlsim-v0.1.3: SBML simulation made easy

Authors:
König, M.
Date Published:
2020-07-01
doi:
10.5281/zenodo.3960592

matthiaskoenig/pkdb: PKDB-v0.8.0 - pharmacokinetics database

Authors:
König, M., Grzegorzewski, J.
Date Published:
2020-06-01
doi:
10.5281/zenodo.3911936

matthiaskoenig/sbmlutils: sbmlutils-v0.3.9: python utilities for SBML

Authors:
König, M.
Date Published:
2020-03-01
doi:
10.5281/zenodo.3728262

Executable Simulation Model of the Liver

Authors:
König, M.
Date Published:
2020-01-06
doi:
10.1101/2020.01.04.894873

matthiaskoenig/exsimo: exsimo-v0.3.2 - EXecutable SImulation MOdels

Authors:
König, M.
Date Published:
2020-01-01
doi:
10.5281/zenodo.3596897

A quantitative high-resolution computational mechanics cell model for growing and regenerating tissues

Authors:
van Liedekerke, P., Neitsch, J., Johann, T., Warmt, E., Gonzàlez-Valverde, I., Hoehme, S., Grosser, S., Kaes, J., Drasdo, D.
Journal:
Biomechanics and Modeling in Mechanobiology
Date Published:
2020-02-01
doi:
10.1007/s10237-019-01204-7

MEMOTE for standardized genome-scale metabolic model testing.

Authors:
Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Drager, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., Garcia-Jimenez, B., Hatzimanikatis, V., van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgard, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., Konig, M., Lakshmanan, M., Lee, D. Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sanchez, B. J., Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaca, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M., Zhang, C.
Journal:
Nat Biotechnol
Date Published:
2020-03-04
PubMed ID:
32123384
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32123384

Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration.

Authors:
Meyer, K., Morales-Navarrete, H., Seifert, S., Wilsch-Braeuninger, M., Dahmen, U., Tanaka, E. M., Brusch, L., Kalaidzidis, Y., Zerial, M.
Journal:
Mol Syst Biol
Date Published:
2020-02-25
PubMed ID:
32090478
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32090478

Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration

Authors:
Meyer, K., Morales‐Navarrete, H., Seifert, S., Wilsch‐Braeuninger, M., Dahmen, U., Tanaka, E. M., Brusch, L., Kalaidzidis, Y., Zerial, M.
Journal:
Mol Syst Biol
Date Published:
2020-02-24
doi:
10.15252/msb.20198985

Open modeling and exchange (OMEX) metadata specification version 1.0

Authors:
Neal, M. L., Gennari, J. H., Waltemath, D., Nickerson, D. P., König, M.
Journal:
Journal of Integrative Bioinformatics
Date Published:
2020-06-25
doi:
10.1515/jib-2020-0020

Severe metabolic alterations in liver cancer lead to ERK pathway activation and drug resistance.

Authors:
Nwosu, Z. C., Pioronska, W., Battello, N., Zimmer, A. D., Dewidar, B., Han, M., Pereira, S., Blagojevic, B., Castven, D., Charlestin, V., Holenya, P., Lochead, J., De La Torre, C., Gretz, N., Sajjakulnukit, P., Zhang, L., Ward, M. H., Marquardt, J. U., di Magliano, M. P., Lyssiotis, C. A., Sleeman, J., Wolfl, S., Ebert, M. P., Meyer, C., Hofmann, U., Dooley, S.
Journal:
EBioMedicine
Date Published:
2020-04-25
PubMed ID:
32330875
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32330875

Quantification of Nematic Cell Polarity in Three-dimensional Tissues

Authors:
Scholich, A., Syga, S., Morales-Navarrete, H., Miranda, F. S., Nonaka, H., Meyer, K., de Back, W., Brusch, L., Kalaidzidis, Y., Zerial, M., Julicher, F., Friedrich, B. M.
Journal:
Preprint
Date Published:
2020-04-22

Specifications of standards in systems and synthetic biology: status and developments in 2020

Authors:
Schreiber, F., Sommer, B., Czauderna, T., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., Waltemath, D.
Journal:
Journal of Integrative Bioinformatics
Date Published:
2020-06-29
doi:
10.1515/jib-2020-0022

Loss of hepatic Mboat7 leads to liver fibrosis.

Authors:
Thangapandi, V. R., Knittelfelder, O., Brosch, M., Patsenker, E., Vvedenskaya, O., Buch, S., Hinz, S., Hendricks, A., Nati, M., Herrmann, A., Rekhade, D. R., Berg, T., Matz-Soja, M., Huse, K., Klipp, E., Pauling, J. K., Wodke, J. A., Miranda Ackerman, J., Bonin, M. V., Aigner, E., Datz, C., von Schonfels, W., Nehring, S., Zeissig, S., Rocken, C., Dahl, A., Chavakis, T., Stickel, F., Shevchenko, A., Schafmayer, C., Hampe, J., Subramanian, P.
Journal:
Gut
Date Published:
2020-06-26
PubMed ID:
32591434
Link:
https://www.ncbi.nlm.nih.gov/pubmed/32591434

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Authors:
Waltemath, D., Golebiewski, M., Blinov, M. L., Gleeson, P., Hermjakob, H., Hucka, M., Inau, E. T., Keating, S. M., König, M., Krebs, O., Malik-Sheriff, R. S., Nickerson, D., Oberortner, E., Sauro, H. M., Schreiber, F., Smith, L., Stefan, M. I., Wittig, U., Myers, C. J.
Journal:
Journal of Integrative Bioinformatics
Date Published:
2020-06-29
doi:
10.1515/jib-2020-0005

Lipid-encapsulated siRNA for hepatocyte-directed treatment of advanced liver disease

Authors:
Woitok, M. M., Zoubek, M. E., Doleschel, D., Bartneck, M., Mohamed, M. R., Kießling, F., Lederle, W., Trautwein, C., Cubero, F. J.
Journal:
Cell Death & Disease
Date Published:
2020-05-01
doi:
10.1038/s41419-020-2571-4

Characterization of Lipid and Lipid Droplet Metabolism in Human HCC.

Authors:
Berndt, N., Eckstein, J., Heucke, N., Gajowski, R., Stockmann, M., Meierhofer, D., Holzhutter, H. G.
Journal:
Cells
Date Published:
2019-05-27
PubMed ID:
31137921
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31137921

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer

Authors:
Berndt, N., Egners, A., Mastrobuoni, G., Vvedenskaya, O., Fragoulis, A., Dugourd, A., Bulik, S., Pietzke, M., Bielow, C., van Gassel, R., Damink, S. W. O., Erdem, M., Saez-Rodriguez, J., Holzhütter, H., Kempa, S., Cramer, T.
Journal:
Br J Cancer
Date Published:
2019-12-10
doi:
10.1038/s41416-019-0659-3

Metabolic modelling of kidney diseases: Lessons learned from the liver

Authors:
Berndt, N., Patzak, A., Holzhütter, H.
Journal:
Acta Physiol
Date Published:
2019-08-09
doi:
10.1111/apha.13350

Dynamic liver function is an independent predictor of recurrence-free survival after curative liver resection for HCC - A retrospective cohort study.

Authors:
Bluthner, E., Bednarsch, J., Malinowski, M., Binder, P., Pratschke, J., Stockmann, M., Kaffarnik, M.
Journal:
Int J Surg
Date Published:
2019-09-09
PubMed ID:
31494333
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31494333

Advanced liver function assessment in patients with intestinal failure on long-term parenteral nutrition.

Authors:
Bluthner, E., Bednarsch, J., Pape, U. F., Karber, M., Maasberg, S., Gerlach, U. A., Pascher, A., Wiedenmann, B., Pratschke, J., Stockmann, M.
Journal:
Clin Nutr
Date Published:
2019-03-20
PubMed ID:
30885502
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30885502

The predictive value of future liver remnant function after liver resection for HCC in noncirrhotic and cirrhotic patients.

Authors:
Bluthner, E., Jara, M., Shrestha, R., Faber, W., Pratschke, J., Stockmann, M., Malinowski, M.
Journal:
HPB (Oxford)
Date Published:
2019-02-09
PubMed ID:
30733048
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30733048

Simultaneous isolation of parenchymal and non-parenchymal cells from healthy and diseased mice liver

Authors:
Dewidar, B., Dropmann, A., Gould, K., Hartwig, V., Dormann, C., Dooley, S., Hammad, S.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677066

Jagged-1 upregulation in stressed hepatocytes is crucial for liver regeneration

Authors:
Dewidar, B., Hammad, S., Ebert, M., Hengstler, J., Dooley, S.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677067

TGF-beta in Hepatic Stellate Cell Activation and Liver Fibrogenesis-Updated 2019.

Authors:
Dewidar, B., Meyer, C., Dooley, S., Meindl-Beinker, A. N.
Journal:
Cells
Date Published:
2019-11-11
PubMed ID:
31718044
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31718044

ECM1 is a gatekeeper that restrains TGF-β activation to maintain liver homeostasis and prevent fibrogenesis

Authors:
Dooley, S., Fan, W., Hammad, S., Gould, K., Longerich, T., Liu, T., Chen, W., Liu, C., Hou, J., Jia, J., Sun, B.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677068

Cooperative and distinct functions of MK2 and MK3 in the regulation of the macrophage transcriptional response to lipopolysaccharide.

Authors:
Ehlting, C., Rex, J., Albrecht, U., Deenen, R., Tiedje, C., Kohrer, K., Sawodny, O., Gaestel, M., Haussinger, D., Bode, J. G.
Journal:
Sci Rep
Date Published:
2019-07-30
PubMed ID:
31363109
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31363109

ECM1 Prevents Activation of Transforming Growth Factor beta, Hepatic Stellate Cells, and Fibrogenesis in Mice.

Authors:
Fan, W., Liu, T., Chen, W., Hammad, S., Longerich, T., Fu, Y., Li, N., He, Y., Liu, C., Zhang, Y., Lian, Q., Zhao, X., Yan, C., Li, L., Yi, C., Ling, Z., Ma, L., Zhao, X., Xu, H., Wang, P., Cong, M., You, H., Liu, Z., Wang, Y., Chen, J., Li, D., Hui, L., Dooley, S., Hou, J., Jia, J., Sun, B.
Journal:
Gastroenterology
Date Published:
2019-07-27
PubMed ID:
31362006
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31362006

Correlative SMLM and electron tomography reveals endosome nanoscale domains.

Authors:
Franke, C., Repnik, U., Segeletz, S., Brouilly, N., Kalaidzidis, Y., Verbavatz, J. M., Zerial, M.
Journal:
Traffic
Date Published:
2019-06-17
PubMed ID:
31206952
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31206952

Benchmark and integration of resources for the estimation of human transcription factor activities

Authors:
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D., Saez-Rodriguez, J.
Journal:
Genome Res.
Date Published:
2019-08-01
doi:
10.1101/gr.240663.118

Influence of Liver Fibrosis on Lobular Zonation

Authors:
Ghallab, A., Myllys, M., Holland, C., Zaza, A., Murad, W., Hassan, R., Ahmed, Y. A., Abbas, T., Abdelrahim, E., Schneider, K. M., Matz-Soja, M., Reinders, J., Gebhardt, R., Wirtz, T. H., Hatting, M., Drasdo, D., Saez-Rodriguez, J., Trautwein, C., Hengstler, J.
Journal:
Cells
Date Published:
2019-12-01
doi:
10.3390/cells8121556

Data Formats for Systems Biology and Quantitative Modeling

Authors:
Golebiewski, M.
Journal:
Encyclopedia of Bioinformatics and Computational Biology
Date Published:
2019-01-01
doi:
10.1016/B978-0-12-809633-8.20471-8

PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling

Authors:
Grzegorzewski, J., Brandhorst, J., Eleftheriadou, D., Green, K., König, M.
Date Published:
2019-09-09
doi:
10.1101/760884

Liver Fibrosis and Metabolic Alterations in Adults With alpha-1-antitrypsin Deficiency Caused by the Pi*ZZ Mutation.

Authors:
Hamesch, K., Mandorfer, M., Pereira, V. M., Moeller, L. S., Pons, M., Dolman, G. E., Reichert, M. C., Schneider, C. V., Woditsch, V., Voss, J., Lindhauer, C., Fromme, M., Spivak, I., Guldiken, N., Zhou, B., Arslanow, A., Schaefer, B., Zoller, H., Aigner, E., Reiberger, T., Wetzel, M., Siegmund, B., Simoes, C., Gaspar, R., Maia, L., Costa, D., Bento-Miranda, M., van Helden, J., Yagmur, E., Bzdok, D., Stolk, J., Gleiber, W., Knipel, V., Windisch, W., Mahadeva, R., Bals, R., Koczulla, R., Barrecheguren, M., Miravitlles, M., Janciauskiene, S., Stickel, F., Lammert, F., Liberal, R., Genesca, J., Griffiths, W. J., Trauner, M., Krag, A., Trautwein, C., Strnad, P.
Journal:
Gastroenterology
Date Published:
2019-05-24
PubMed ID:
31121167
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31121167

Second exposure to acetaminophen overdose is associated with liver fibrosis in mice

Authors:
Hammad, M. A. A. O. L. H. A. T. J. L. S. H. A. A. F. E. Z. M. R. H. T. A. S. D. S.
Journal:
EXCLI
Date Published:
2019-02-06
doi:
10.17179/excli2018-1920
PubMed ID:
30956639
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30956639

Cellular and nuclear hepatocyte ploidy represent a repository in regenerating livers

Authors:
Hammad, S., Dahmen, U., Othman, A., Recklinghausen, I., Hengstler, J., Klingmüller, U., Dooley, S.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677076

ECM1 stabilizes matrix deposited latent TGF-β to maintain liver homeostasis and prevent fibrogenesis

Authors:
Hammad, S., Fan, W., Liu, T., Chen, W., Gould, K., Longerich, T., Haußer-Siller, I., Hou, J., Jia, J., Sun, B., Dooely, S.
Date Published:
2019-01-01
doi:
10.1055/s-0039-1695261

Aged Abcb4-/- mice upon acute sublethal chemical insult recapitulate features of acute-on-chronic liver failure in patients

Authors:
Hammad, S., Hengstler, J., Dooley, S.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677077

CYP2E1 recovery is associated with a pericentral fibrosis pattern after repeated CCl4 insults

Authors:
Hammad, S., Zhao, J., Yin, Y., Zaza, A., Drasdo, D., Hengstler, J., Dooley, S.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677078

Liver cell type specific discrimination of TGF-beta signaling and outcome in vitro and in vivo

Authors:
Han, M., Nwosu, Z., Ebert, M., Hammad, S., Dooley, S., Meyer, C.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677079

Non-invasive structure-function assessment of the liver by 2D time-harmonic elastography and the dynamic Liver MAximum capacity (LiMAx) test.

Authors:
Heucke, N., Wuensch, T., Mohr, J., Kaffarnik, M., Arsenic, R., Sinn, B., Muller, T., Pratschke, J., Stockmann, M., Sack, I., Tzschatzsch, H.
Journal:
J Gastroenterol Hepatol
Date Published:
2019-02-13
PubMed ID:
30756433
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30756433

Transfer of regulatory knowledge from human to mouse for functional genomics analysis

Authors:
Holland, C. H., Szalai, B., Saez-Rodriguez, J.
Journal:
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Date Published:
2019-09-01
doi:
10.1016/j.bbagrm.2019.194431

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Authors:
Hucka, M., Bergmann, F. T., Chaouiya, C., Drager, A., Hoops, S., Keating, S. M., Konig, M., Novere, N. L., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J., Zhang, F.
Journal:
J Integr Bioinform
Date Published:
2019-06-20
PubMed ID:
31219795
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31219795

Tomoelastography for the Evaluation of Pediatric Nonalcoholic Fatty Liver Disease

Authors:
Hudert, C. A., Tzschätzsch, H., Rudolph, B., Bläker, H., Loddenkemper, C., Müller, H., Henning, S., Bufler, P., Hamm, B., Braun, J., Holzhütter, H., Wiegand, S., Sack, I., Guo, J.
Journal:
Investigative Radiology
Date Published:
2019-04-01
doi:
10.1097/RLI.0000000000000529

Editorial: Systems Biology and Bioinformatics in Gastroenterology and Hepatology

Authors:
Jansen, P. L. M., Breuhahn, K., Teufel, A., Dooley, S.
Journal:
Front. Physiol.
Date Published:
2019-11-22
doi:
10.3389/fphys.2019.01438

Effect of alcohol on the interleukin 6-mediated inflammatory response in a new mouse model of acute-on-chronic liver injury

Authors:
Karatayli, E., Hall, R. A., Weber, S. N., Dooley, S., Lammert, F.
Journal:
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
Date Published:
2019-02-01
doi:
10.1016/j.bbadis.2018.11.008

Quantitative MRI for Assessment of Treatment Outcomes in a Rabbit VX2 Hepatic Tumor Model.

Authors:
Keller, S., Chapiro, J., Brangsch, J., Reimann, C., Collettini, F., Sack, I., Savic, L. J., Hamm, B., Goldberg, S. N., Makowski, M.
Journal:
J Magn Reson Imaging
Date Published:
2019-11-12
PubMed ID:
31713973
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31713973

Quantitative MRI for Assessment of Treatment Outcomes in a Rabbit VX2 Hepatic Tumor Model

Authors:
Keller, S., Chapiro, J., Brangsch, J., Reimann, C., Collettini, F., Sack, I., Savic, L. J., Hamm, B., Goldberg, S. N., Makowski, M.
Journal:
J Magn Reson Imaging
Date Published:
2019-11-12
doi:
10.1002/jmri.26968

Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human

Authors:
Kolbe, E., Aleithe, S., Rennert, C., Spormann, L., Ott, F., Meierhofer, D., Gajowski, R., Stöpel, C., Hoehme, S., Kücken, M., Brusch, L., Seifert, M., von Schoenfels, W., Schafmayer, C., Brosch, M., Hofmann, U., Damm, G., Seehofer, D., Hampe, J., Gebhardt, R., Matz-Soja, M.
Journal:
Cell Reports
Date Published:
2019-12-01
doi:
10.1016/j.celrep.2019.11.104

Model Order Reduction (MOR) of Function‐Perfusion‐Growth Simulation in the Human Fatty Liver via Artificial Neural Network (ANN)

Authors:
Lambers, L., Ricken, T., König, M.
Journal:
PAMM
Date Published:
2019-11-01
doi:
10.1002/pamm.201900429

Multiparametric Quantitative MRI for the Detection of IgA Nephropathy Using Tomoelastography, DWI, and BOLD Imaging.

Authors:
Lang, S. T., Guo, J., Bruns, A., Durr, M., Braun, J., Hamm, B., Sack, I., Marticorena Garcia, S. R.
Journal:
Invest Radiol
Date Published:
2019-07-02
PubMed ID:
31261295
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31261295

Adenovirusmediated overexpression of bone morphogenetic protein9 promotes methionine choline deficiencyinduced nonalcoholic steatohepatitis in nonobese mice.

Authors:
Li, Q., Liu, B., Breitkopf-Heinlein, K., Weng, H., Jiang, Q., Dong, P., Dooley, S., Xu, K., Ding, H.
Journal:
Mol Med Rep
Date Published:
2019-07-20
PubMed ID:
31322255
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31322255

Mapping connections in signaling networks with ambiguous modularity.

Authors:
Lill, D., Rukhlenko, O. S., Mc Elwee, A. J., Kashdan, E., Timmer, J., Kholodenko, B. N.
Journal:
NPJ Syst Biol Appl
Date Published:
2019-06-01
PubMed ID:
31149348
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31149348

Local Riemannian geometry of model manifolds and its implications for practical parameter identifiability

Authors:
Lill, D., Timmer, J., Kaschek, D.
Journal:
PLoS ONE
Date Published:
2019-06-03
doi:
10.1371/journal.pone.0217837

Transcription factor TRIM33 controls liver progenitor cell towards hepatocyte differentiation through synergizing with phosphorylated Smad2/3 in liver cirrhosis

Authors:
Lin, T., Wang, S., Shao, C., Yuan, X., Wandrer, F., Bantel, H., Ebert, M., Ding, H., Dooley, S., Weng, H.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677086

Tick-tock hedgehog-mutual crosstalk with liver circadian clock promotes liver steatosis.

Authors:
Marbach-Breitruck, E., Matz-Soja, M., Abraham, U., Schmidt-Heck, W., Sales, S., Rennert, C., Kern, M., Aleithe, S., Spormann, L., Thiel, C., Gerlini, R., Arnold, K., Kloting, N., Guthke, R., Rozman, D., Teperino, R., Shevchenko, A., Kramer, A., Gebhardt, R.
Journal:
J Hepatol
Date Published:
2019-02-04
PubMed ID:
30711403
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30711403

Tomoelastography for non-invasive detection and treatment monitoring in acute appendicitis.

Authors:
Marticorena Garcia, S. R., Hamm, B., Sack, I.
Journal:
BMJ Case Rep
Date Published:
2019-08-26
PubMed ID:
31451472
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31451472

beta-Catenin and Yes-Associated Protein 1 Cooperate in Hepatoblastoma Pathogenesis.

Authors:
Min, Q., Molina, L., Li, J., Adebayo Michael, A. O., Russell, J. O., Preziosi, M. E., Singh, S., Poddar, M., Matz-Soja, M., Ranganathan, S., Bell, A. W., Gebhardt, R., Gaunitz, F., Yu, J., Tao, J., Monga, S. P.
Journal:
Am J Pathol
Date Published:
2019-02-23
PubMed ID:
30794807
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30794807

Liquid-crystal organization of liver tissue.

Authors:
Morales-Navarrete, H., Nonaka, H., Scholich, A., Segovia-Miranda, F., de Back, W., Meyer, K., Bogorad, R. L., Koteliansky, V., Brusch, L., Kalaidzidis, Y., Julicher, F., Friedrich, B. M., Zerial, M.
Journal:
Elife
Date Published:
2019-06-17
PubMed ID:
31204997
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31204997

Wet-tip versus dry-tip regimes of osmotically driven fluid flow

Authors:
Ostrenko, O., Hampe, J., Brusch, L.
Journal:
Sci Rep
Date Published:
2019-12-01
doi:
10.1038/s41598-019-40853-7

Common NOD2 Risk Variants as Major Susceptibility Factors for Bacterial Infections in Compensated Cirrhosis.

Authors:
Reichert, M. C., Ripoll, C., Casper, M., Greinert, R., Vandieken, E., Grunhage, F., Appenrodt, B., Zipprich, A., Lammert, F.
Journal:
Clin Transl Gastroenterol
Date Published:
2019-02-01
PubMed ID:
30702490
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30702490

Diagnostic performance of tomoelastography of the liver and spleen for staging hepatic fibrosis

Authors:
Reiter, R., Tzschätzsch, H., Schwahofer, F., Haas, M., Bayerl, C., Muche, M., Klatt, D., Majumdar, S., Uyanik, M., Hamm, B., Braun, J., Sack, I., Asbach, P.
Journal:
Eur Radiol
Date Published:
2019-11-11
doi:
10.1007/s00330-019-06471-7

Assessment of Chemotherapy-Induced Organ Damage with Ga-68 Labeled Duramycin.

Authors:
Rix, A., Drude, N. I., Mrugalla, A., Baskaya, F., Pak, K. Y., Gray, B., Kaiser, H. J., Tolba, R. H., Fiegle, E., Lederle, W., Mottaghy, F. M., Kiessling, F.
Journal:
Mol Imaging Biol
Date Published:
2019-08-08
PubMed ID:
31396770
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31396770

Sensitivity of multifrequency magnetic resonance elastography and diffusion-weighted imaging to cellular and stromal integrity of liver tissue.

Authors:
de Schellenberger, A. A., Tzschatzsch, H., Polchlopek, B., Bertalan, G., Schrank, F., Garczynska, K., Janmey, P. A., Braun, J., Sack, I.
Journal:
J Biomech
Date Published:
2019-05-09
PubMed ID:
30961968
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30961968

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Authors:
Schreiber, F., Sommer, B., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., Waltemath, D.
Date Published:
2019-06-26
doi:
10.1515/jib-2019-0035

Resection of hepatic and pulmonary metastasis from metastatic esophageal and gastric cancer: a nationwide study.

Authors:
Seesing, M. F. J., van der Veen, A., Brenkman, H. J. F., Stockmann, H. B. A. C., Nieuwenhuijzen, G. A. P., Rosman, C., van den Wildenberg, F. J. H., van Berge Henegouwen, M. I., van Duijvendijk, P., Wijnhoven, B. P. L., Stoot, J. H. M. B., Lacle, M., Ruurda, J. P., van Hillegersberg, R.
Journal:
Dis Esophagus
Date Published:
2019-12-31
PubMed ID:
31220859
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31220859

Three-dimensional spatially resolved geometrical and functional models of human liver tissue reveal new aspects of NAFLD progression.

Authors:
Segovia-Miranda, F., Morales-Navarrete, H., Kucken, M., Moser, V., Seifert, S., Repnik, U., Rost, F., Brosch, M., Hendricks, A., Hinz, S., Rocken, C., Lutjohann, D., Kalaidzidis, Y., Schafmayer, C., Brusch, L., Hampe, J., Zerial, M.
Journal:
Nat Med
Date Published:
2019-12-02
PubMed ID:
31792455
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31792455

Transient elastography for screening of liver fibrosis: Cost-effectiveness analysis from six prospective cohorts in Europe and Asia.

Authors:
Serra-Burriel, M., Graupera, I., Toran, P., Thiele, M., Roulot, D., Wai-Sun Wong, V., Neil Guha, I., Fabrellas, N., Arslanow, A., Exposito, C., Hernandez, R., Lai-Hung Wong, G., Harman, D., Darwish Murad, S., Krag, A., Pera, G., Angeli, P., Galle, P., Aithal, G. P., Caballeria, L., Castera, L., Gines, P., Lammert, F.
Journal:
J Hepatol
Date Published:
2019-08-31
PubMed ID:
31470067
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31470067

Tomoelastography Distinguishes Noninvasively between Benign and Malignant Liver Lesions.

Authors:
Shahryari, M., Tzschatzsch, H., Guo, J., Marticorena Garcia, S. R., Boning, G., Fehrenbach, U., Stencel, L., Asbach, P., Hamm, B., Kas, J. A., Braun, J., Denecke, T., Sack, I.
Journal:
Cancer Res
Date Published:
2019-11-15
PubMed ID:
31551364
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31551364

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Authors:
Stanford, N. J., Scharm, M., Dobson, P. D., Golebiewski, M., Hucka, M., Kothamachu, V. B., Nickerson, D., Owen, S., Pahle, J., Wittig, U., Waltemath, D., Goble, C., Mendes, P., Snoep, J.
Journal:
Methods Mol Biol
Date Published:
2019-10-12
PubMed ID:
31602618
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31602618

Glial cell line-derived neurotrophic factor (GDNF) mediates hepatic stellate cell activation via ALK5/Smad signalling.

Authors:
Tao, L., Ma, W., Wu, L., Xu, M., Yang, Y., Zhang, W., Sha, W., Li, H., Xu, J., Feng, R., Xue, D., Zhang, J., Dooley, S., Seki, E., Liu, P., Liu, C.
Journal:
Gut
Date Published:
2019-06-06
PubMed ID:
31171625
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31171625

Predicting liver failure after extended right hepatectomy following right portal vein embolization with gadoxetic acid-enhanced MRI.

Authors:
Theilig, D., Steffen, I., Malinowski, M., Stockmann, M., Seehofer, D., Pratschke, J., Hamm, B., Denecke, T., Geisel, D.
Journal:
Eur Radiol
Date Published:
2019-03-23
PubMed ID:
30899977
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30899977

Intravital dynamic and correlative imaging reveals diffusion-dominated canalicular and flow-augmented ductular bile flux

Authors:
Vartak, N., Guenther, G., Joly, F., Damle-Vartak, A., Wibbelt, G., Fickel, J., Jörs, S., Begher-Tibbe, B., Friebel, A., Wansing, K., Ghallab, A., Rosselin, M., Boissier, N., Vignon-Clementel, I., Hedberg, C., Geisler, F., Hofer, H., Jansen, P., Hoehme, S., Drasdo, D., Hengstler, J. G.
Date Published:
2019-09-26
doi:
10.1101/778803

Maintenance of functional hepatocellular polarity determines recovery in acute-on-chronic liver failure

Authors:
Wang, S., Feng, R., Yuan, X., Wandrer, F., Ebert, M., Bantel, H., Li, H., Dooley, S., Weng, H.
Date Published:
2019-01-01
doi:
10.1055/s-0038-1677156

Genetic Variants in the Promoter Region of the Macrophage Migration Inhibitory Factor are Associated with the Severity of Hepatitis C Virus-Induced Liver Fibrosis.

Authors:
Wirtz, T. H., Fischer, P., Backhaus, C., Bergmann, I., Brandt, E. F., Heinrichs, D., Koenen, M. T., Schneider, K. M., Eggermann, T., Kurth, I., Stoppe, C., Bernhagen, J., Bruns, T., Fischer, J., Berg, T., Trautwein, C., Berres, M. L.
Journal:
Int J Mol Sci
Date Published:
2019-07-31
PubMed ID:
31370326
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31370326

Hepatic CYP1A2 activity in liver tumors and the implications for preoperative volume-function analysis.

Authors:
Wuensch, T., Heucke, N., Wizenty, J., Quint, J., Sinn, B., Arsenic, R., Jara, M., Kaffarnik, M., Pratschke, J., Stockmann, M.
Journal:
Am J Physiol Gastrointest Liver Physiol
Date Published:
2019-03-14
PubMed ID:
30869529
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30869529

Identification of serological markers for pre- and postoperative fasting periods.

Authors:
Wuensch, T., Quint, J., Mueller, V., Mueller, A., Wizenty, J., Kaffarnik, M., Kern, B., Stockmann, M., Biebl, M., Pratschke, J., Aigner, F.
Journal:
Clin Nutr ESPEN
Date Published:
2019-03-25
PubMed ID:
30904213
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30904213

Expression Analysis of Fibronectin Type III Domain-Containing (FNDC) Genes in Inflammatory Bowel Disease and Colorectal Cancer.

Authors:
Wuensch, T., Wizenty, J., Quint, J., Spitz, W., Bosma, M., Becker, O., Adler, A., Veltzke-Schlieker, W., Stockmann, M., Weiss, S., Biebl, M., Pratschke, J., Aigner, F.
Journal:
Gastroenterol Res Pract
Date Published:
2019-05-17
PubMed ID:
31093274
Link:
https://www.ncbi.nlm.nih.gov/pubmed/31093274

Liver-specific Repin1 deficiency impairs transient hepatic steatosis in liver regeneration.

Authors:
Abshagen, K., Degenhardt, B., Liebig, M., Wendt, A., Genz, B., Schaeper, U., Stumvoll, M., Hofmann, U., Frank, M., Vollmar, B., Kloting, N.
Journal:
Sci Rep
Date Published:
2018-01-18
PubMed ID:
30442920
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30442920

Whither systems medicine?

Authors:
Apweiler, R., Beissbarth, T., Berthold, M. R., Bluthgen, N., Burmeister, Y., Dammann, O., Deutsch, A., Feuerhake, F., Franke, A., Hasenauer, J., Hoffmann, S., Hofer, T., Jansen, P. L., Kaderali, L., Klingmuller, U., Koch, I., Kohlbacher, O., Kuepfer, L., Lammert, F., Maier, D., Pfeifer, N., Radde, N., Rehm, M., Roeder, I., Saez-Rodriguez, J., Sax, U., Schmeck, B., Schuppert, A., Seilheimer, B., Theis, F. J., Vera, J., Wolkenhauer, O.
Journal:
Exp Mol Med
Date Published:
2018-03-03
PubMed ID:
29497170
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29497170

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

Authors:
Bergmann, F. T., Cooper, J., Konig, M., Moraru, I., Nickerson, D., Le Novere, N., Olivier, B. G., Sahle, S., Smith, L., Waltemath, D.
Journal:
J Integr Bioinform
Date Published:
2018-03-20
PubMed ID:
29550789
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29550789

HEPATOKIN1 is a biochemistry-based model of liver metabolism for applications in medicine and pharmacology.

Authors:
Berndt, N., Bulik, S., Wallach, I., Wunsch, T., Konig, M., Stockmann, M., Meierhofer, D., Holzhutter, H. G.
Journal:
Nat Commun
Date Published:
2018-06-21
PubMed ID:
29921957
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29921957

A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism.

Authors:
Berndt, N., Horger, M. S., Bulik, S., Holzhutter, H. G.
Journal:
PLoS Comput Biol
Date Published:
2018-02-16
PubMed ID:
29447152
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29447152

Possible neurotoxicity of the anesthetic propofol: evidence for the inhibition of complex II of the respiratory chain in area CA3 of rat hippocampal slices.

Authors:
Berndt, N., Rosner, J., Haq, R. U., Kann, O., Kovacs, R., Holzhutter, H. G., Spies, C., Liotta, A.
Journal:
Arch Toxicol
Date Published:
2018-08-26
PubMed ID:
30143847
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30143847

Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control

Authors:
Brosch, M., Kattler, K., Herrmann, A., von Schönfels, W., Nordström, K., Seehofer, D., Damm, G., Becker, T., Zeissig, S., Nehring, S., Reichel, F., Moser, V., Thangapandi, R. V., Stickel, F., Baretton, G., Röcken, C., Muders, M., Matz-Soja, M., Krawczak, M., Gasparoni, G., Hartmann, H., Dahl, A., Schafmayer, C., Walter, J., Hampe, J.
Journal:
Nat Commun
Date Published:
2018-12-01
doi:
10.1038/s41467-018-06611-5

Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control

Authors:
Brosch, M., Kattler, K., Herrmann, A., von Schönfels, W., Nordström, K., Seehofer, D., Damm, G., Becker, T., Zeissig, S., Nehring, S., Reichel, F., Moser, V., Thangapandi, R. V., Stickel, F., Baretton, G., Röcken, C., Muders, M., Matz-Soja, M., Krawczak, M., Gasparoni, G., Hartmann, H., Dahl, A., Schafmayer, C., Walter, J., Hampe, J.
Journal:
Nat Commun
Date Published:
2018-12-01
doi:
10.1038/s41467-018-06611-5

Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

Authors:
Choi, K., Medley, J. K., Konig, M., Stocking, K., Smith, L., Gu, S., Sauro, H. M.
Journal:
Biosystems
Date Published:
2018-07-28
PubMed ID:
30053414
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30053414

3D visualization of the biliary tree by X-ray phase-contrast computed tomography

Authors:
Damle-Vartak, A.
Journal:
Arch Toxicol
Date Published:
2018-12-01
doi:
10.1007/s00204-018-2346-1

The importance of membrane microdomains for bile salt-dependent biliary lipid secretion.

Authors:
Eckstein, J., Holzhutter, H. G., Berndt, N.
Journal:
J Cell Sci
Date Published:
2018-03-01
PubMed ID:
29420298
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29420298

Clinical and Functional Relevance of the Monocarboxylate Transporter Family in Disease Pathophysiology and Drug Therapy.

Authors:
Fisel, P., Schaeffeler, E., Schwab, M.
Journal:
Clin Transl Sci
Date Published:
2018-04-17
PubMed ID:
29660777
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29660777

Systemic regulation of bilirubin homeostasis: Potential benefits of hyperbilirubinemia

Authors:
Fujiwara, R., Haag, M., Schaeffeler, E., Nies, A. T., Zanger, U. M., Schwab, M.
Journal:
Hepatology
Date Published:
2018-04-01
doi:
10.1002/hep.29599

Ethanol sensitizes hepatocytes for TGF-beta-triggered apoptosis.

Authors:
Gaitantzi, H., Meyer, C., Rakoczy, P., Thomas, M., Wahl, K., Wandrer, F., Bantel, H., Alborzinia, H., Wolfl, S., Ehnert, S., Nussler, A., Bergheim, I., Ciuclan, L., Ebert, M., Breitkopf-Heinlein, K., Dooley, S.
Journal:
Cell Death Dis
Date Published:
2018-01-21
doi:
10.1038/s41419-017-0071-y
PubMed ID:
29352207
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29352207

Ethanol sensitizes hepatocytes for TGF-β-triggered apoptosis

Authors:
Gaitantzi, H., Meyer, C., Rakoczy, P., Thomas, M., Wahl, K., Wandrer, F., Bantel, H., Alborzinia, H., Wölfl, S., Ehnert, S., Nüssler, A., Bergheim, I., Ciuclan, L., Ebert, M., Breitkopf-Heinlein, K., Dooley, S.
Journal:
Cell Death Dis
Date Published:
2018-02-01
doi:
10.1038/s41419-017-0071-y

Bile micro-infarcts in cholestasis are initiated by rupture of the apical hepatocyte membrane and cause shunting of bile to sinusoidal blood

Authors:
Ghallab, A., Hofmann, U., Sezgin, S., Vartak, N., Hassan, R., Zaza, A., Godoy, P., Schneider, K. M., Guenther, G., Ahmed, Y. A., Abbas, A. A., Keitel, V., Kuepfer, L., Dooley, S., Lammert, F., Trautwein, C., Spiteller, M., Drasdo, D., Hofmann, A. F., Jansen, P. L. M., Hengstler, J. G., Reif, R.
Journal:
HEP
Date Published:
2018-08-13
doi:
10.1002/hep.30213

Galunisertib modifies the liver fibrotic composition in the Abcb4Ko mouse model

Authors:
Hammad, S., Cavalcanti, E., Werle, J., Caruso, M. L., Dropmann, A., Ignazzi, A., Ebert, M. P., Dooley, S., Giannelli, G.
Journal:
Arch Toxicol
Date Published:
2018-05-28
doi:
10.1007/s00204-018-2231-y

Confounding influence of tamoxifen in mouse models of Cre recombinase-induced gene activity or modulation

Authors:
Hammad, S., Othman, A., Meyer, C., Telfah, A., Lambert, J., Dewidar, B., Werle, J., Nwosu, Z. C., Mahli, A., Dormann, C., Gao, Y., Gould, K., Han, M., Yuan, X., Gogiashvili, M., Hergenröder, R., Hellerbrand, C., Thomas, M., Ebert, M. P., Amasheh, S., Hengstler, J. G., Dooley, S.
Journal:
Arch Toxicol
Date Published:
2018-07-04
doi:
10.1007/s00204-018-2254-4

Evolutionary Distance Predicts Recurrence After Liver Transplantation in Multifocal Hepatocellular Carcinoma.

Authors:
Heits, N., Brosch, M., Herrmann, A., Behrens, R., Rocken, C., Schrem, H., Kaltenborn, A., Klempnauer, J., Kreipe, H. H., Reichert, B., Lenschow, C., Wilms, C., Vogel, T., Wolters, H., Wardelmann, E., Seehofer, D., Buch, S., Zeissig, S., Pannach, S., Raschzok, N., Dietel, M., von Schoenfels, W., Hinz, S., Teufel, A., Evert, M., Franke, A., Becker, T., Braun, F., Hampe, J., Schafmayer, C.
Journal:
Transplantation
Date Published:
2018-07-12
PubMed ID:
29994984
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29994984

Focused scores enable reliable discrimination of small differences in steatosis.

Authors:
Homeyer, A., Hammad, S., Schwen, L. O., Dahmen, U., Hofener, H., Gao, Y., Dooley, S., Schenk, A.
Journal:
Diagn Pathol
Date Published:
2018-09-20
PubMed ID:
30231920
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30231920

Genetic determinants of steatosis and fibrosis progression in pediatric non-alcoholic fatty liver disease.

Authors:
Hudert, C. A., Selinski, S., Rudolph, B., Blaker, H., Loddenkemper, C., Thielhorn, R., Berndt, N., Golka, K., Cadenas, C., Reinders, J., Henning, S., Bufler, P., Jansen, P. L. M., Holzhutter, H. G., Meierhofer, D., Hengstler, J. G., Wiegand, S.
Journal:
Liver Int
Date Published:
2018-01-18
PubMed ID:
30444569
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30444569

US Time-Harmonic Elastography: Detection of Liver Fibrosis in Adolescents with Extreme Obesity with Nonalcoholic Fatty Liver Disease

Authors:
Hudert, C. A., Tzschätzsch, H., Guo, J., Rudolph, B., Bläker, H., Loddenkemper, C., Luck, W., Müller, H., Baumgart, D. C., Hamm, B., Braun, J., Holzhütter, H., Wiegand, S., Sack, I.
Journal:
Radiology
Date Published:
2018-07-01
doi:
10.1148/radiol.2018172928

Effects of Gene Variants Controlling Vitamin D Metabolism and Serum Levels on Hepatic Steatosis.

Authors:
Jamka, M., Arslanow, A., Bohner, A., Krawczyk, M., Weber, S. N., Grunhage, F., Lammert, F., Stokes, C. S.
Journal:
Digestion
Date Published:
2018-03-08
doi:
10.1159/000485180
PubMed ID:
29514138
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29514138

Effects of Gene Variants Controlling Vitamin D Metabolism and Serum Levels on Hepatic Steatosis

Authors:
Jamka, M., Arslanow, A., Bohner, A., Krawczyk, M., Weber, S. N., Grünhage, F., Lammert, F., Stokes, C. S.
Journal:
Digestion
Date Published:
2018-02-07
doi:
10.1159/000485180

Prospective Assessment of Liver Function by an Enzymatic Liver Function Test to Estimate Short-Term Survival in Patients with Liver Cirrhosis.

Authors:
Jara, M., Dziodzio, T., Malinowski, M., Luttgert, K., Nikolov, R., Ritschl, P. V., Ollinger, R., Pratschke, J., Stockmann, M.
Journal:
Dig Dis Sci
Date Published:
2018-11-09
PubMed ID:
30406480
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30406480

Effect of alcohol on the interleukin 6-mediated inflammatory response in a new mouse model of acute-on-chronic liver injury.

Authors:
Karatayli, E., Hall, R. A., Weber, S. N., Dooley, S., Lammert, F.
Journal:
Biochim Biophys Acta Mol Basis Dis
Date Published:
2018-11-15
doi:
10.1016/j.bbadis.2018.11.008
PubMed ID:
30447270
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30447270

Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues.

Authors:
Knittelfelder, O., Traikov, S., Vvedenskaya, O., Schuhmann, A., Segeletz, S., Shevchenko, A., Shevchenko, A.
Journal:
Anal Chem
Date Published:
2018-07-30
PubMed ID:
30004672
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30004672

Could inherited predisposition drive non-obese fatty liver disease? Results from German tertiary referral centers.

Authors:
Krawczyk, M., Bantel, H., Rau, M., Schattenberg, J. M., Grunhage, F., Pathil, A., Demir, M., Kluwe, J., Boettler, T., Weber, S. N., Geier, A., Lammert, F.
Journal:
J Hum Genet
Date Published:
2018-02-28
PubMed ID:
29483677
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29483677

Hepatic Smad7 overexpression causes severe iron overload in mice

Authors:
Lai, D., Teng, F., Hammad, S., Werle, J., Maas, T., Teufel, A., Muckenthaler, M. U., Dooley, S., Spasić, M. V.
Journal:
Blood
Date Published:
2018-02-01
doi:
10.1182/blood-2017-07-796797

Single cell polarity in liquid phase facilitates tumour metastasis.

Authors:
Lorentzen, A., Becker, P. F., Kosla, J., Saini, M., Weidele, K., Ronchi, P., Klein, C., Wolf, M. J., Geist, F., Seubert, B., Ringelhan, M., Mihic-Probst, D., Esser, K., Roblek, M., Kuehne, F., Bianco, G., O'Connor, T., Muller, Q., Schuck, K., Lange, S., Hartmann, D., Spaich, S., Gross, O., Utikal, J., Haferkamp, S., Sprick, M. R., Damle-Vartak, A., Hapfelmeier, A., Huser, N., Protzer, U., Trumpp, A., Saur, D., Vartak, N., Klein, C. A., Polzer, B., Borsig, L., Heikenwalder, M.
Journal:
Nat Commun
Date Published:
2018-03-02
PubMed ID:
29491397
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29491397

Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression.

Authors:
Lucarelli, P., Schilling, M., Kreutz, C., Vlasov, A., Boehm, M. E., Iwamoto, N., Steiert, B., Lattermann, S., Wasch, M., Stepath, M., Matter, M. S., Heikenwalder, M., Hoffmann, K., Deharde, D., Damm, G., Seehofer, D., Muciek, M., Gretz, N., Lehmann, W. D., Timmer, J., Klingmuller, U.
Journal:
Cell Syst
Date Published:
2018-02-19
PubMed ID:
29248373
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29248373

Full-Field-of-View Time-Harmonic Elastography of the Native Kidney.

Authors:
Marticorena Garcia, S. R., Grossmann, M., Lang, S. T., Nguyen Trong, M., Schultz, M., Guo, J., Hamm, B., Braun, J., Sack, I., Tzschatzsch, H.
Journal:
Ultrasound Med Biol
Date Published:
2018-02-27
PubMed ID:
29478787
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29478787

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Authors:
Medley, J. K., Choi, K., Konig, M., Smith, L., Gu, S., Hellerstein, J., Sealfon, S. C., Sauro, H. M.
Journal:
PLoS Comput Biol
Date Published:
2018-06-16
PubMed ID:
29906293
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29906293

Liquid-crystal organization of liver tissue

Authors:
Morales-Navarrete, H., Nonaka, H., Scholich, A., Segovia-Miranda, F., de Back, W., Meyer, K., Bogorad, R. L., Koteliansky, V., Brusch, L., Kalaidzidis, Y., Julicher, F., Friedrich, B. M., Zerial, M.
Date Published:
2018-12-13
doi:
10.1101/495952

Macrophage Transactivation for Chemokine Production Identified as a Negative Regulator of Granulomatous Inflammation Using Agent-Based Modeling

Authors:
Moyo, D., Beattie, L., Andrews, P. S., Moore, J. W. J., Timmis, J., Sawtell, A., Hoehme, S., Sampson, A. T., Kaye, P. M.
Journal:
Frontiers in Immunology
Date Published:
2018-03-27
doi:
10.3389/fimmu.2018.00637

Harmonizing semantic annotations for computational models in biology.

Authors:
Neal, M. L., Konig, M., Nickerson, D., Misirli, G., Kalbasi, R., Drager, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., Crook, S., de Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., Myers, C., Olivier, B. G., Sauro, H. M., Scharm, M., Snoep, J. L., Toure, V., Wipat, A., Wolkenhauer, O., Waltemath, D.
Journal:
Brief Bioinform
Date Published:
2018-01-22
PubMed ID:
30462164
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30462164

Liver cancer cell lines distinctly mimic the metabolic gene expression pattern of the corresponding human tumours.

Authors:
Nwosu, Z. C., Battello, N., Rothley, M., Pioronska, W., Sitek, B., Ebert, M. P., Hofmann, U., Sleeman, J., Wolfl, S., Meyer, C., Megger, D. A., Dooley, S.
Journal:
J Exp Clin Cancer Res
Date Published:
2018-09-05
PubMed ID:
30176945
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30176945

Model-based identification of TNFalpha-induced IKKbeta-mediated and IkappaBalpha-mediated regulation of NFkappaB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds.

Authors:
Oppelt, A., Kaschek, D., Huppelschoten, S., Sison-Young, R., Zhang, F., Buck-Wiese, M., Herrmann, F., Malkusch, S., Kruger, C. L., Meub, M., Merkt, B., Zimmermann, L., Schofield, A., Jones, R. P., Malik, H., Schilling, M., Heilemann, M., van de Water, B., Goldring, C. E., Park, B. K., Timmer, J., Klingmuller, U.
Journal:
NPJ Syst Biol Appl
Date Published:
2018-06-15
PubMed ID:
29900006
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29900006

ABCB4 Gene Aberrations in Human Liver Disease: An Evolving Spectrum

Authors:
Reichert, M., Lammert, F.
Journal:
Semin Liver Dis
Date Published:
2018-10-24
doi:
10.1055/s-0038-1667299

The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism – A Systems Biology Analysis Using Self-Organizing Maps

Authors:
Rennert, C., Vlaic, S., Marbach-Breitrück, E., Thiel, C., Sales, S., Shevchenko, A., Gebhardt, R., Matz-Soja, M.
Journal:
Front. Physiol.
Date Published:
2018-09-10
doi:
10.3389/fphys.2018.01180

Histologic improvement of NAFLD in patients with obesity after bariatric surgery based on standardized NAS (NAFLD activity score).

Authors:
von Schonfels, W., Beckmann, J. H., Ahrens, M., Hendricks, A., Rocken, C., Szymczak, S., Hampe, J., Schafmayer, C.
Journal:
Surg Obes Relat Dis
Date Published:
2018-08-28
PubMed ID:
30146425
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30146425

Electrosurgical liver resection has a superior regeneration outcome as compared to en-bloc ligation in a novel model of partial hepatectomy in mice

Authors:
von Schonfels, W., Schafmayer, C., Hampe, J.
Journal:
prepublication
Date Published:
2018-01-27
doi:
10.1055/s-0037-1612784

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

Authors:
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., Novere, N. L., Myers, C., Nickerson, D., Sommer, B., Waltemath, D.
Journal:
J Integr Bioinform
Date Published:
2018-03-30
PubMed ID:
29596055
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29596055

Spatio-temporal visualization of the distribution of acetaminophen as well as its metabolites and adducts in mouse livers by MALDI MSI

Authors:
Sezgin, S., Hassan, R., Zühlke, S., Kuepfer, L., Hengstler, J. G., Spiteller, M., Ghallab, A.
Journal:
Arch Toxicol
Date Published:
2018-07-23
doi:
10.1007/s00204-018-2271-3

Genetic variants in PNPLA3 and TM6SF2 predispose to the development of hepatocellular carcinoma in individuals with alcohol-related cirrhosis

Authors:
Stickel, F., Buch, S., Nischalke, H. D., Weiss, K. H., Gotthardt, D., Fischer, J., Rosendahl, J., Marot, A., Elamly, M., Casper, M., Lammert, F., McQuillin, A., Zopf, S., Spengler, U., Marhenke, S., Kirstein, M. M., Vogel, A., Eyer, F., von Felden, J., Wege, H., Buch, T., Schafmayer, C., Braun, F., Deltenre, P., Berg, T., Morgan, M. Y., Hampe, J.
Journal:
Am J Gastroenterol
Date Published:
2018-10-01
doi:
10.1038/s41395-018-0041-8

MicroRNA-942 mediates hepatic stellate cell activation by regulating BAMBI expression in human liver fibrosis.

Authors:
Tao, L., Xue, D., Shen, D., Ma, W., Zhang, J., Wang, X., Zhang, W., Wu, L., Pan, K., Yang, Y., Nwosu, Z. C., Dooley, S., Seki, E., Liu, C.
Journal:
Arch Toxicol
Date Published:
2018-08-12
PubMed ID:
30097701
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30097701

Analytical challenges in human plasma lipidomics: A winding path towards the truth

Authors:
Vvedenskaya, O., Wang, Y., Ackerman, J. M., Knittelfelder, O., Shevchenko, A.
Journal:
TrAC Trends in Analytical Chemistry
Date Published:
2018-10-20
doi:
10.1016/j.trac.2018.10.013

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

Authors:
Waltemath, D., Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., Le Novere, N., Mi, H., Moraru, I. I., Myers, C. J., Nickerson, D., Olivier, B. G., Rodriguez, N., Schreiber, F., Smith, L., Zhang, F., Bonnet, E.
Journal:
Stand Genomic Sci
Date Published:
2018-08-09
PubMed ID:
30117501
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30117501

The fruit fly Drosophila melanogaster as an innovative preclinical ADME model for solute carrier membrane transporters, with consequences for pharmacology and drug therapy.

Authors:
Wang, Y., Moussian, B., Schaeffeler, E., Schwab, M., Nies, A. T.
Journal:
Drug Discov Today
Date Published:
2018-06-12
PubMed ID:
29890226
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29890226

Inverse agonist of ERRgamma reduces cannabinoid receptor type 1-mediated induction of fibrinogen synthesis in mice with a high-fat diet-intoxicated liver.

Authors:
Zhang, Y., Kim, D. K., Jung, Y. S., Kim, Y. H., Lee, Y. S., Kim, J., Jeong, W. I., Lee, I. K., Cho, S. J., Dooley, S., Lee, C. H., Choi, H. S.
Journal:
Arch Toxicol
Date Published:
2018-07-19
PubMed ID:
30019168
Link:
https://www.ncbi.nlm.nih.gov/pubmed/30019168

Quantitative and integrative analysis of paracrine hepatocyte activation by nonparenchymal cells upon lipopolysaccharide induction

Authors:
Beuke, K., Schildberg, F. A., Pinna, F., Albrecht, U., Liebe, R., Bissinger, M., Schirmacher, P., Dooley, S., Bode, J. G., Knolle, P. A., Kummer, U., Breuhahn, K., Sahle, S.
Journal:
FEBS J
Date Published:
2017-03-01
doi:
10.1111/febs.14022

A compact 0.5 T MR elastography device and its application for studying viscoelasticity changes in biological tissues during progressive formalin fixation.

Authors:
Braun, J., Tzschatzsch, H., Korting, C., Ariza de Schellenberger, A., Jenderka, M., Driessle, T., Ledwig, M., Sack, I.
Journal:
Magn Reson Med
Date Published:
2017-03-20
PubMed ID:
28321914
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28321914

BMP-9 interferes with liver regeneration and promotes liver fibrosis.

Authors:
Breitkopf-Heinlein, K., Meyer, C., Konig, C., Gaitantzi, H., Addante, A., Thomas, M., Wiercinska, E., Cai, C., Li, Q., Wan, F., Hellerbrand, C., Valous, N. A., Hahnel, M., Ehlting, C., Bode, J. G., Muller-Bohl, S., Klingmuller, U., Altenoder, J., Ilkavets, I., Goumans, M. J., Hawinkels, L. J., Lee, S. J., Wieland, M., Mogler, C., Ebert, M. P., Herrera, B., Augustin, H., Sanchez, A., Dooley, S., Ten Dijke, P.
Journal:
Gut
Date Published:
2017-03-25
doi:
10.1136/gutjnl-2016-313314
PubMed ID:
28336518
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28336518

BMP-9 interferes with liver regeneration and promotes liver fibrosis.

Authors:
Breitkopf-Heinlein, K., Meyer, C., Konig, C., Gaitantzi, H., Addante, A., Thomas, M., Wiercinska, E., Cai, C., Li, Q., Wan, F., Hellerbrand, C., Valous, N. A., Hahnel, M., Ehlting, C., Bode, J. G., Muller-Bohl, S., Klingmuller, U., Altenoder, J., Ilkavets, I., Goumans, M. J., Hawinkels, L. J., Lee, S. J., Wieland, M., Mogler, C., Ebert, M. P., Herrera, B., Augustin, H., Sanchez, A., Dooley, S., Ten Dijke, P.
Journal:
Gut
Date Published:
2017-03-23
doi:
10.1136/gutjnl-2016-313314
PubMed ID:
28336518
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28336518

Computational Modeling in Liver Surgery

Authors:
Christ, B., Dahmen, U., Herrmann, K., König, M., Reichenbach, J. R., Ricken, T., Schleicher, J., Schwen, L. O., Vlaic, S., Waschinsky, N.
Journal:
Front. Physiol.
Date Published:
2017-11-14
doi:
10.3389/fphys.2017.00906

Large-scale computational models of liver metabolism: How far from the clinics?

Authors:
Cvitanovic, T., Reichert, M. C., Moskon, M., Mraz, M., Lammert, F., Rozman, D.
Journal:
Hepatology
Date Published:
2017-05-19
PubMed ID:
28520105
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28520105

Tomoelastography of the prostate using multifrequency MR elastography and externally placed pressurized-air drivers.

Authors:
Dittmann, F., Reiter, R., Guo, J., Haas, M., Asbach, P., Fischer, T., Braun, J., Sack, I.
Journal:
Magn Reson Med
Date Published:
2017-06-06
PubMed ID:
28585229
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28585229

Hepatocyte-specific Smad7 deletion accelerates DEN-induced HCC via activation of STAT3 signaling in mice

Authors:
Feng, T., Dzieran, J., Yuan, X., Dropmann, A., Maass, T., Teufel, A., Marhenke, S., Gaiser, T., Rückert, F., Kleiter, I., Kanzler, S., Ebert, M. P., Vogel, A., ten Dijke, P., Dooley, S., Meindl-Beinker, N. M.
Journal:
Oncogenesis
Date Published:
2017-01-01
doi:
10.1038/oncsis.2016.85

The importance of drug transporter characterization to precision medicine.

Authors:
Fisel, P., Nies, A. T., Schaeffeler, E., Schwab, M.
Journal:
Expert Opin Drug Metab Toxicol
Date Published:
2017-02-01
PubMed ID:
28140687
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28140687

Quantification of substrate and cellular strains in stretchable 3D cell cultures: an experimental and computational framework

Authors:
GONZÁLEZ-AVALOS, P., MÜRNSEER, M., DEEG, J., BACHMANN, A., SPATZ, J., DOOLEY, S., EILS, R., GLADILIN, E.
Journal:
Journal of Microscopy
Date Published:
2017-05-01
doi:
10.1111/jmi.12520

A frequent misinterpretation in current research on liver fibrosis: the vessel in the center of CCl4-induced pseudolobules is a portal vein.

Authors:
Hammad, S., Braeuning, A., Meyer, C., Mohamed, F. E. Z. A., Hengstler, J. G., Dooley, S.
Journal:
Arch Toxicol
Date Published:
2017-08-22
PubMed ID:
28825120
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28825120

Model prediction and validation of an order mechanism controlling the spatio-temporal phenotype of early hepatocellular carcinoma

Authors:
Hoehme, S., Bertaux, F., Weens, W., Grasl-Kraupp, B., Hengstler, J. G., Drasdo, D.
Journal:
Bulletin of Mathematical Biology
Date Published:
2017-12-28

Physiologic Reduction of Hepatic Venous Blood Flow by the Valsalva Maneuver Decreases Liver Stiffness.

Authors:
Ipek-Ugay, S., Tzschatzsch, H., Braun, J., Fischer, T., Sack, I.
Journal:
J Ultrasound Med
Date Published:
2017-03-20
PubMed ID:
28319252
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28319252

The ascending pathophysiology of cholestatic liver disease.

Authors:
Jansen, P. L., Ghallab, A., Vartak, N., Reif, R., Schaap, F. G., Hampe, J., Hengstler, J. G.
Journal:
Hepatology
Date Published:
2017-02-17
doi:
10.1002/hep.28965
PubMed ID:
27981592
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27981592

The ascending pathophysiology of cholestatic liver disease

Authors:
Jansen, P. L., Ghallab, A., Vartak, N., Reif, R., Schaap, F. G., Hampe, J., Hengstler, J. G.
Journal:
Hepatology
Date Published:
2017-02-01
doi:
10.1002/hep.28965

Ligand-dependent and -independent regulation of human hepatic sphingomyelin phosphodiesterase acid-like 3A expression by pregnane X receptor and crosstalk with liver X receptor.

Authors:
Jeske, J., Bitter, A., Thasler, W. E., Weiss, T. S., Schwab, M., Burk, O.
Journal:
Biochem Pharmacol
Date Published:
2017-04-18
PubMed ID:
28414139
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28414139

The formation of estrogen-like tamoxifen metabolites and their influence on enzyme activity and gene expression of ADME genes.

Authors:
Johanning, J., Kroner, P., Thomas, M., Zanger, U. M., Norenberg, A., Eichelbaum, M., Schwab, M., Brauch, H., Schroth, W., Murdter, T. E.
Journal:
Arch Toxicol
Date Published:
2017-12-28
PubMed ID:
29285606
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29285606

Translational learning from clinical studies predicts drug pharmacokinetics across patient populations

Authors:
Krauss, M., Hofmann, U., Schafmayer, C., Igel, S., Schlender, J., Mueller, C., Brosch, M., von Schoenfels, W., Erhart, W., Schuppert, A., Block, M., Schaeffeler, E., Boehmer, G., Goerlitz, L., Hoecker, J., Lippert, J., Kerb, R., Hampe, J., Kuepfer, L., Schwab, M.
Journal:
npj Syst Biol Appl
Date Published:
2017-12-01
doi:
10.1038/s41540-017-0012-5

Translational learning from clinical studies predicts drug pharmacokinetics across patient populations.

Authors:
Krauss, M., Hofmann, U., Schafmayer, C., Igel, S., Schlender, J., Mueller, C., Brosch, M., von Schoenfels, W., Erhart, W., Schuppert, A., Block, M., Schaeffeler, E., Boehmer, G., Goerlitz, L., Hoecker, J., Lippert, J., Kerb, R., Hampe, J., Kuepfer, L., Schwab, M.
Journal:
NPJ Syst Biol Appl
Date Published:
2017-06-27
doi:
10.1038/s41540-017-0012-5
PubMed ID:
28649438
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28649438

Panel of three novel serum markers predicts liver stiffness and fibrosis stages in patients with chronic liver disease.

Authors:
Krawczyk, M., Zimmermann, S., Hess, G., Holz, R., Dauer, M., Raedle, J., Lammert, F., Grunhage, F.
Journal:
PLoS One
Date Published:
2017-03-17
PubMed ID:
28301573
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28301573

Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione.

Authors:
Kurschner, G., Zhang, Q., Clima, R., Xiao, Y., Busch, J. F., Kilic, E., Jung, K., Berndt, N., Bulik, S., Holzhutter, H. G., Gasparre, G., Attimonelli, M., Babu, M., Meierhofer, D.
Journal:
Oncotarget
Date Published:
2017-12-01
PubMed ID:
29285300
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29285300

Hepatic Smad7-overexpression causes severe iron overload in the mouse.

Authors:
Lai, D., Teng, F., Hammad, S., Werle, J., Maas, T., Teufel, A., Muckenthaler, M. U., Dooley, S., Vujic Spasic, M.
Journal:
Blood
Date Published:
2017-12-13
doi:
10.1182/blood-2017-07-796797
PubMed ID:
29237592
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29237592

Adverse outcome pathways: opportunities, limitations and open questions.

Authors:
Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., Drasdo, D., Hohme, S., Schwarz, M., Hartung, T., Braunbeck, T., Beltman, J., Vrieling, H., Sanz, F., Forsby, A., Gadaleta, D., Fisher, C., Kelm, J., Fluri, D., Ecker, G., Zdrazil, B., Terron, A., Jennings, P., van der Burg, B., Dooley, S., Meijer, A. H., Willighagen, E., Martens, M., Evelo, C., Mombelli, E., Taboureau, O., Mantovani, A., Hardy, B., Koch, B., Escher, S., van Thriel, C., Cadenas, C., Kroese, D., van de Water, B., Hengstler, J. G.
Journal:
Arch Toxicol
Date Published:
2017-10-19
PubMed ID:
29051992
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29051992

Tomoelastography of the native kidney: Regional variation and physiological effects on in vivo renal stiffness.

Authors:
Marticorena Garcia, S. R., Grossmann, M., Lang, S. T., Tzschatzsch, H., Dittmann, F., Hamm, B., Braun, J., Guo, J., Sack, I.
Journal:
Magn Reson Med
Date Published:
2017-08-30
PubMed ID:
28856718
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28856718

Computational modelling of Hedgehog signalling in liver regeneration

Authors:
Matz-Soja, M.
Journal:
Drug Discovery Today: Disease Models
Date Published:
2017-07-01
doi:
10.1016/j.ddmod.2017.06.001

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule

Authors:
Meyer, K., Ostrenko, O., Bourantas, G., Morales-Navarrete, H., Porat-Shliom, N., Segovia-Miranda, F., Nonaka, H., Ghaemi, A., Verbavatz, J., Brusch, L., Sbalzarini, I., Kalaidzidis, Y., Weigert, R., Zerial, M.
Journal:
Cell Systems
Date Published:
2017-03-01
doi:
10.1016/j.cels.2017.02.008

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

Authors:
Meyer, K., Ostrenko, O., Bourantas, G., Morales-Navarrete, H., Porat-Shliom, N., Segovia-Miranda, F., Nonaka, H., Ghaemi, A., Verbavatz, J. M., Brusch, L., Sbalzarini, I., Kalaidzidis, Y., Weigert, R., Zerial, M.
Journal:
Cell Syst
Date Published:
2017-03-18
doi:
10.1016/j.cels.2017.02.008
PubMed ID:
28330614
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28330614

The level of caveolin-1 expression determines response to TGF-β as a tumour suppressor in hepatocellular carcinoma cells

Authors:
Moreno-Càceres, J., Caballero-Díaz, D., Nwosu, Z. C., Meyer, C., López-Luque, J., Malfettone, A., Lastra, R., Serrano, T., Ramos, E., Dooley, S., Fabregat, I.
Journal:
Cell Death Dis
Date Published:
2017-10-12
doi:
10.1038/cddis.2017.469

SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten

Authors:
Müller, W., Bittkowski, M., Golebiewski, M., Kania, R., Rey, M., Weidemann, A., Wittig, U.
Journal:
Datenbank Spektrum
Date Published:
2017-03-01
doi:
10.1007/s13222-016-0243-4

A brief history of COMBINE

Authors:
Myers, C. J., Bader, G., Gleeson, P., Golebiewski, M., Hucka, M., le Novere, N., Nickerson, D. P., Schreiber, F., Waltemath, D.
Journal:
2017 Winter Simulation Conference (WSC)
Date Published:
2017-12-01
doi:
10.1109/WSC.2017.8247840

Identification of the Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma

Authors:
Nwosu, Z. C., Megger, D. A., Hammad, S., Sitek, B., Roessler, S., Ebert, M. P., Meyer, C., Dooley, S.
Journal:
Cellular and Molecular Gastroenterology and Hepatology
Date Published:
2017-09-01
doi:
10.1016/j.jcmgh.2017.05.004

pSSAlib: The partial-propensity stochastic chemical network simulator

Authors:
Ostrenko, O., Incardona, P., Ramaswamy, R., Brusch, L., Sbalzarini, I. F.
Journal:
PLoS Comput Biol
Date Published:
2017-12-04
doi:
10.1371/journal.pcbi.1005865

4-O'-methylhonokiol protects from alcohol/carbon tetrachloride-induced liver injury in mice.

Authors:
Patsenker, E., Chicca, A., Petrucci, V., Moghadamrad, S., de Gottardi, A., Hampe, J., Gertsch, J., Semmo, N., Stickel, F.
Journal:
J Mol Med (Berl)
Date Published:
2017-07-08
PubMed ID:
28689299
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28689299

Quantitative analysis of hepatic macro- and microvascular alterations during cirrhogenesis in the rat.

Authors:
Peeters, G., Debbaut, C., Friebel, A., Cornillie, P., De Vos, W. H., Favere, K., Vander Elst, I., Vandecasteele, T., Johann, T., Van Hoorebeke, L., Monbaliu, D., Drasdo, D., Hoehme, S., Laleman, W., Segers, P.
Journal:
J Anat
Date Published:
2017-12-04
PubMed ID:
29205328
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29205328

Pharmacokinetics and pharmacodynamics of thiopurines in an in vitro model of human hepatocytes: Insights from an innovative mass spectrometry assay.

Authors:
Pelin, M., Genova, E., Fusco, L., Marisat, M., Hofmann, U., Favretto, D., Lucafo, M., Taddio, A., Martelossi, S., Ventura, A., Stocco, G., Schwab, M., Decorti, G.
Journal:
Chem Biol Interact
Date Published:
2017-08-12
PubMed ID:
28811125
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28811125

In vivo imaging of systemic transport and elimination of xenobiotics and endogenous molecules in mice

Authors:
Reif, R., Ghallab, A., Beattie, L., Günther, G., Kuepfer, L., Kaye, P. M., Hengstler, J. G.
Journal:
Arch Toxicol
Date Published:
2017-03-01
doi:
10.1007/s00204-016-1906-5

Conditional loss of hepatocellular Hedgehog signaling in female mice leads to the persistence of hepatic steroidogenesis, androgenization and infertility

Authors:
Rennert, C., Eplinius, F., Hofmann, U., Johänning, J., Rolfs, F., Schmidt-Heck, W., Guthke, R., Gebhardt, R., Ricken, A. M., Matz-Soja, M.
Journal:
Arch Toxicol
Date Published:
2017-05-30
doi:
10.1007/s00204-017-1999-5

Bio-degradable highly fluorescent conjugated polymer nanoparticles for bio-medical imaging applications

Authors:
Repenko, T., Rix, A., Ludwanowski, S., Go, D., Kiessling, F., Lederle, W., Kuehne, A. J. C.
Journal:
Nat Commun
Date Published:
2017-12-01
doi:
10.1038/s41467-017-00545-0

Robust detection and segmentation of cell nuclei in biomedical images based on a computational topology framework

Authors:
Rojas-Moraleda, R., Xiong, W., Halama, N., Breitkopf-Heinlein, K., Dooley, S., Salinas, L., Heermann, D. W., Valous, N. A.
Journal:
Medical Image Analysis
Date Published:
2017-05-01
doi:
10.1016/j.media.2017.02.009

Lipidomics of Human Blood Plasma by High-Resolution Shotgun Mass Spectrometry.

Authors:
Sales, S., Knittelfelder, O., Shevchenko, A.
Journal:
Methods Mol Biol
Date Published:
2017-07-04
PubMed ID:
28674888
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28674888

Physiologically-based modelling in mice suggests an aggravated loss of clearance capacity after toxic liver damage

Authors:
Schenk, A., Ghallab, A., Hofmann, U., Hassan, R., Schwarz, M., Schuppert, A., Schwen, L. O., Braeuning, A., Teutonico, D., Hengstler, J. G., Kuepfer, L.
Journal:
Sci Rep
Date Published:
2017-12-01
doi:
10.1038/s41598-017-04574-z

Physiologically-based modelling in mice suggests an aggravated loss of clearance capacity after toxic liver damage

Authors:
Schenk, A., Ghallab, A., Hofmann, U., Hassan, R., Schwarz, M., Schuppert, A., Schwen, L. O., Braeuning, A., Teutonico, D., Hengstler, J. G., Kuepfer, L.
Journal:
Sci Rep
Date Published:
2017-12-01
doi:
10.1038/s41598-017-04574-z

Global Transcriptional Response of Human Liver Cells to Ethanol Stress of Different Strength Reveals Hormetic Behavior.

Authors:
Schmidt-Heck, W., Wonne, E. C., Hiller, T., Menzel, U., Koczan, D., Damm, G., Seehofer, D., Knospel, F., Freyer, N., Guthke, R., Dooley, S., Zeilinger, K.
Journal:
Alcohol Clin Exp Res
Date Published:
2017-02-23
doi:
10.1111/acer.13361
PubMed ID:
28226195
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28226195

Global Transcriptional Response of Human Liver Cells to Ethanol Stress of Different Strength Reveals Hormetic Behavior

Authors:
Schmidt-Heck, W., Wönne, E. C., Hiller, T., Menzel, U., Koczan, D., Damm, G., Seehofer, D., Knöspel, F., Freyer, N., Guthke, R., Dooley, S., Zeilinger, K.
Journal:
Alcohol Clin Exp Res
Date Published:
2017-05-01
doi:
10.1111/acer.13361

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Authors:
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Le Novere, N., Myers, C., Nickerson, D., Sommer, B., Walthemath, D.
Journal:
J Integr Bioinform
Date Published:
2017-02-12
PubMed ID:
28187405
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28187405

Monitoring Membrane Lipidome Turnover by Metabolic (15)N Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry.

Authors:
Schuhmann, K., Srzentic, K., Nagornov, K. O., Thomas, H., Gutmann, T., Coskun, U., Tsybin, Y. O., Shevchenko, A.
Journal:
Anal Chem
Date Published:
2017-12-05
PubMed ID:
29111682
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29111682

Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics.

Authors:
Schuhmann, K., Thomas, H., Ackerman, J. M., Nagornov, K. O., Tsybin, Y. O., Shevchenko, A.
Journal:
Anal Chem
Date Published:
2017-06-15
PubMed ID:
28570056
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28570056

Modeling approaches for hepatic spatial heterogeneity in pharmacokinetic simulations

Authors:
Schwen, L. O., Kuepfer, L., Preusser, T.
Journal:
Drug Discovery Today: Disease Models
Date Published:
2017-11-29
doi:
10.1016/j.ddmod.2017.09.002

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib.

Authors:
Sobotta, S., Raue, A., Huang, X., Vanlier, J., Junger, A., Bohl, S., Albrecht, U., Hahnel, M. J., Wolf, S., Mueller, N. S., D'Alessandro, L. A., Mueller-Bohl, S., Boehm, M. E., Lucarelli, P., Bonefas, S., Damm, G., Seehofer, D., Lehmann, W. D., Rose-John, S., van der Hoeven, F., Gretz, N., Theis, F. J., Ehlting, C., Bode, J. G., Timmer, J., Schilling, M., Klingmuller, U.
Journal:
Front Physiol
Date Published:
2017-10-09
PubMed ID:
29062282
Link:
https://www.ncbi.nlm.nih.gov/pubmed/29062282

Serum metabolic signatures in patients with overt hepatic encephalopathy.

Authors:
Stengel, S., Stallmach, A., Richter, K., Landrock, A., Hampe, J., Bruns, T.
Journal:
J Hepatol
Date Published:
2017-07-06
PubMed ID:
28690175
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28690175

Pathophysiology and Management of Alcoholic Liver Disease: Update 2016.

Authors:
Stickel, F., Datz, C., Hampe, J., Bataller, R.
Journal:
Gut Liver
Date Published:
2017-03-15
PubMed ID:
28274107
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28274107

Towards knowledge-driven cross-species extrapolation

Authors:
Thiel, C., Hofmann, U., Ghallab, A., Gebhardt, R., Hengstler, J. G., Kuepfer, L.
Journal:
Drug Discovery Today: Disease Models
Date Published:
2017-04-01
doi:
10.1016/j.ddmod.2017.02.008

A unifying mathematical model of lipid droplet metabolism reveals key molecular players in the development of hepatic steatosis.

Authors:
Wallstab, C., Eleftheriadou, D., Schulz, T., Damm, G., Seehofer, D., Borlak, J., Holzhutter, H. G., Berndt, N.
Journal:
FEBS J
Date Published:
2017-08-02
PubMed ID:
28763157
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28763157

Orphan nuclear receptor ERRγ is a key regulator of human fibrinogen gene expression

Authors:
Zhang, Y., Kim, D., Lu, Y., Jung, Y. S., Lee, J., Kim, Y., Lee, Y. S., Kim, J., Dewidar, B., Jeong, W., Lee, I., Cho, S. J., Dooley, S., Lee, C., Li, X., Choi, H.
Journal:
PLoS ONE
Date Published:
2017-07-27
doi:
10.1371/journal.pone.0182141

The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

Authors:
Bulik, S., Holzhutter, H. G., Berndt, N.
Journal:
BMC Biol
Date Published:
2016-03-02
PubMed ID:
26935066
Link:
https://www.ncbi.nlm.nih.gov/pubmed/26935066

Transforming Growth Factor β1 (TGF-β1) Activates Hepcidin mRNA Expression in Hepatocytes

Authors:
Chen, S., Feng, T., Spasić, M. V., Altamura, S., Breitkopf-Heinlein, K., Altenöder, J., Weiss, T. S., Dooley, S., Muckenthaler, M. U.
Journal:
J. Biol. Chem.
Date Published:
2016-06-17
doi:
10.1074/jbc.M115.691543

Tomoelastography of the abdomen: Tissue mechanical properties of the liver, spleen, kidney, and pancreas from single MR elastography scans at different hydration states.

Authors:
Dittmann, F., Tzschatzsch, H., Hirsch, S., Barnhill, E., Braun, J., Sack, I., Guo, J.
Journal:
Magn Reson Med
Date Published:
2016-10-03
PubMed ID:
27699875
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27699875

TGF-β1 and TGF-β2 abundance in liver diseases of mice and men

Authors:
Dropmann, A., Dediulia, T., Breitkopf-Heinlein, K., Korhonen, H., Janicot, M., Weber, S. N., Thomas, M., Piiper, A., Bertran, E., Fabregat, I., Abshagen, K., Hess, J., Angel, P., Coulouarn, C., Dooley, S., Meindl-Beinker, N. M.
Journal:
Oncotarget
Date Published:
2016-04-12
doi:
10.18632/oncotarget.6967

DNA Methylation of ADME Genes.

Authors:
Fisel, P., Schaeffeler, E., Schwab, M.
Journal:
Clin Pharmacol Ther
Date Published:
2016-04-12
PubMed ID:
27061006
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27061006

Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases

Authors:
Ghallab, A., Cellière, G., Henkel, S. G., Driesch, D., Hoehme, S., Hofmann, U., Zellmer, S., Godoy, P., Sachinidis, A., Blaszkewicz, M., Reif, R., Marchan, R., Kuepfer, L., Häussinger, D., Drasdo, D., Gebhardt, R., Hengstler, J. G.
Journal:
Journal of Hepatology
Date Published:
2016-04-01
doi:
10.1016/j.jhep.2015.11.018

Creation of Three-Dimensional Liver Tissue Models from Experimental Images for Systems Medicine.

Authors:
Hoehme, S., Friebel, A., Hammad, S., Drasdo, D., Hengstler, J. G.
Journal:
Methods Mol Biol
Date Published:
2016-11-11
PubMed ID:
27830563
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27830563

Orphan nuclear receptor SHP regulates iron metabolism through inhibition of BMP6-mediated hepcidin expression.

Authors:
Kim, D. K., Kim, Y. H., Jung, Y. S., Kim, K. S., Jeong, J. H., Lee, Y. S., Yuk, J. M., Oh, B. C., Choy, H. E., Dooley, S., Muckenthaler, M. U., Lee, C. H., Choi, H. S.
Journal:
Sci Rep
Date Published:
2016-10-01
PubMed ID:
27688041
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27688041

Driving the Model to Its Limit: Profile Likelihood Based Model Reduction.

Authors:
Maiwald, T., Hass, H., Steiert, B., Vanlier, J., Engesser, R., Raue, A., Kipkeew, F., Bock, H. H., Kaschek, D., Kreutz, C., Timmer, J.
Journal:
PLoS One
Date Published:
2016-09-03
PubMed ID:
27588423
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27588423

Hedgehog signaling is a potent regulator of liver lipid metabolism and reveals a GLI-code associated with steatosis.

Authors:
Matz-Soja, M., Rennert, C., Schonefeld, K., Aleithe, S., Boettger, J., Schmidt-Heck, W., Weiss, T. S., Hovhannisyan, A., Zellmer, S., Kloting, N., Schulz, A., Kratzsch, J., Guthke, R., Gebhardt, R.
Journal:
Elife
Date Published:
2016-05-17
PubMed ID:
27185526
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27185526

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.

Authors:
Merkle, R., Steiert, B., Salopiata, F., Depner, S., Raue, A., Iwamoto, N., Schelker, M., Hass, H., Wasch, M., Bohm, M. E., Mucke, O., Lipka, D. B., Plass, C., Lehmann, W. D., Kreutz, C., Timmer, J., Schilling, M., Klingmuller, U.
Journal:
PLoS Comput Biol
Date Published:
2016-08-06
PubMed ID:
27494133
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27494133

NAFLD is associated with methylation shifts with relevance for the expression of genes involved in lipoprotein particle composition.

Authors:
Mwinyi, J., Bostrom, A. E., Pisanu, C., Murphy, S. K., Erhart, W., Schafmayer, C., Hampe, J., Moylan, C., Schioth, H. B.
Journal:
Biochim Biophys Acta
Date Published:
2016-12-18
PubMed ID:
27993651
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27993651

Impact of Membrane Drug Transporters on Resistance to Small-Molecule Tyrosine Kinase Inhibitors.

Authors:
Neul, C., Schaeffeler, E., Sparreboom, A., Laufer, S., Schwab, M., Nies, A. T.
Journal:
Trends Pharmacol Sci
Date Published:
2016-10-25
PubMed ID:
27659854
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27659854

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

Authors:
Nickerson, D., Atalag, K., de Bono, B., Geiger, J., Goble, C., Hollmann, S., Lonien, J., Muller, W., Regierer, B., Stanford, N. J., Golebiewski, M., Hunter, P.
Journal:
Interface Focus
Date Published:
2016-04-07
PubMed ID:
27051515
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27051515

Evolving Insights on Metabolism, Autophagy, and Epigenetics in Liver Myofibroblasts.

Authors:
Nwosu, Z. C., Alborzinia, H., Wolfl, S., Dooley, S., Liu, Y.
Journal:
Front Physiol
Date Published:
2016-06-18
PubMed ID:
27313533
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27313533

Caveolin-1 in the regulation of cell metabolism: a cancer perspective.

Authors:
Nwosu, Z. C., Ebert, M. P., Dooley, S., Meyer, C.
Journal:
Mol Cancer
Date Published:
2016-11-18
PubMed ID:
27852311
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27852311

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

Authors:
Pauling, J., Klipp, E.
Journal:
J Integr Bioinform
Date Published:
2016-12-22
PubMed ID:
28187425
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28187425

A multilevel framework to reconstruct anatomical 3D models of the hepatic vasculature in rat livers

Authors:
Peeters, G., Debbaut, C., Laleman, W., Friebel, A., Monbaliu, D., Elst, I. V., Detrez, J. R., Vandecasteele, T., Johann, T., de Schryver, T., van Hoorebeke, L., Favere, K., Verbeke, J., Drasdo, D., Hoehme, S., Segers, P., Cornillie, P., de Vos, W. H.
Journal:
Journal of anatomy
Date Published:
2016-12-28
PubMed ID:
27995631
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27995631

Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome.

Authors:
Sales, S., Graessler, J., Ciucci, S., Al-Atrib, R., Vihervaara, T., Schuhmann, K., Kauhanen, D., Sysi-Aho, M., Bornstein, S. R., Bickle, M., Cannistraci, C. V., Ekroos, K., Shevchenko, A.
Journal:
Sci Rep
Date Published:
2016-06-14
PubMed ID:
27295977
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27295977

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease.

Authors:
Schioth, H. B., Bostrom, A., Murphy, S. K., Erhart, W., Hampe, J., Moylan, C., Mwinyi, J.
Journal:
BMC Genomics
Date Published:
2016-06-14
PubMed ID:
27301979
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27301979

Computational Modeling of Lipid Metabolism in Yeast.

Authors:
Schutzhold, V., Hahn, J., Tummler, K., Klipp, E.
Journal:
Front Mol Biosci
Date Published:
2016-09-27
PubMed ID:
27730126
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27730126

Delta-Like Ligand 4 Modulates Liver Damage by Down-Regulating Chemokine Expression

Authors:
Shen, Z., Liu, Y., Dewidar, B., Hu, J., Park, O., Feng, T., Xu, C., Yu, C., Li, Q., Meyer, C., Ilkavets, I., Müller, A., Stump-Guthier, C., Munker, S., Liebe, R., Zimmer, V., Lammert, F., Mertens, P. R., Li, H., ten Dijke, P., Augustin, H. G., Li, J., Gao, B., Ebert, M. P., Dooley, S., Li, Y., Weng, H.
Journal:
The American Journal of Pathology
Date Published:
2016-07-01
doi:
10.1016/j.ajpath.2016.03.010

L1 regularization facilitates detection of cell type-specific parameters in dynamical systems.

Authors:
Steiert, B., Timmer, J., Kreutz, C.
Journal:
Bioinformatics
Date Published:
2016-09-03
PubMed ID:
27587694
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27587694

The genetics of alcohol dependence and alcohol-related liver disease.

Authors:
Stickel, F., Moreno, C., Hampe, J., Morgan, M. Y.
Journal:
J Hepatol
Date Published:
2016-08-27
PubMed ID:
27575312
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27575312

Polymorphic variation in TPMT is the principal determinant of TPMT phenotype: A meta-analysis of three genome-wide association studies.

Authors:
Tamm, R., Magi, R., Tremmel, R., Winter, S., Mihailov, E., Smid, A., Moricke, A., Klein, K., Schrappe, M., Stanulla, M., Houlston, R., Weinshilboum, R., Mlinaric Rascan, I., Metspalu, A., Milani, L., Schwab, M., Schaeffeler, E.
Journal:
Clin Pharmacol Ther
Date Published:
2016-10-23
PubMed ID:
27770449
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27770449

Comparison of Gene Expression Patterns Between Mouse Models of Nonalcoholic Fatty Liver Disease and Liver Tissues From Patients.

Authors:
Teufel, A., Itzel, T., Erhart, W., Brosch, M., Wang, X. Y., Kim, Y. O., von Schonfels, W., Herrmann, A., Bruckner, S., Stickel, F., Dufour, J. F., Chavakis, T., Hellerbrand, C., Spang, R., Maass, T., Becker, T., Schreiber, S., Schafmayer, C., Schuppan, D., Hampe, J.
Journal:
Gastroenterology
Date Published:
2016-06-19
PubMed ID:
27318147
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27318147

Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.

Authors:
Wahl, S., Drong, A., Lehne, B., Loh, M., Scott, W. R., Kunze, S., Tsai, P. C., Ried, J. S., Zhang, W., Yang, Y., Tan, S., Fiorito, G., Franke, L., Guarrera, S., Kasela, S., Kriebel, J., Richmond, R. C., Adamo, M., Afzal, U., Ala-Korpela, M., Albetti, B., Ammerpohl, O., Apperley, J. F., Beekman, M., Bertazzi, P. A., Black, S. L., Blancher, C., Bonder, M. J., Brosch, M., Carstensen-Kirberg, M., de Craen, A. J., de Lusignan, S., Dehghan, A., Elkalaawy, M., Fischer, K., Franco, O. H., Gaunt, T. R., Hampe, J., Hashemi, M., Isaacs, A., Jenkinson, A., Jha, S., Kato, N., Krogh, V., Laffan, M., Meisinger, C., Meitinger, T., Mok, Z. Y., Motta, V., Ng, H. K., Nikolakopoulou, Z., Nteliopoulos, G., Panico, S., Pervjakova, N., Prokisch, H., Rathmann, W., Roden, M., Rota, F., Rozario, M. A., Sandling, J. K., Schafmayer, C., Schramm, K., Siebert, R., Slagboom, P. E., Soininen, P., Stolk, L., Strauch, K., Tai, E. S., Tarantini, L., Thorand, B., Tigchelaar, E. F., Tumino, R., Uitterlinden, A. G., van Duijn, C., van Meurs, J. B., Vineis, P., Wickremasinghe, A. R., Wijmenga, C., Yang, T. P., Yuan, W., Zhernakova, A., Batterham, R. L., Smith, G. D., Deloukas, P., Heijmans, B. T., Herder, C., Hofman, A., Lindgren, C. M., Milani, L., van der Harst, P., Peters, A., Illig, T., Relton, C. L., Waldenberger, M., Jarvelin, M. R., Bollati, V., Soong, R., Spector, T. D., Scott, J., McCarthy, M. I., Elliott, P., Bell, J. T., Matullo, G., Gieger, C., Kooner, J. S., Grallert, H., Chambers, J. C.
Journal:
Nature
Date Published:
2016-12-21
PubMed ID:
28002404
Link:
https://www.ncbi.nlm.nih.gov/pubmed/28002404

Toward Community Standards and Software for Whole-Cell Modeling.

Authors:
Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., Czauderna, T., Goldberg, A. P., Gomez, H. F., Hahn, J., Hameri, T., Gardiol, D. F., Kazakiewicz, D., Kiselev, I., Knight-Schrijver, V., Knupfer, C., Konig, M., Lee, D., Lloret-Villas, A., Mandrik, N., Medley, J. K., Moreau, B., Naderi-Meshkin, H., Palaniappan, S. K., Priego-Espinosa, D., Scharm, M., Sharma, M., Smallbone, K., Stanford, N. J., Song, J. H., Theile, T., Tokic, M., Tomar, N., Toure, V., Uhlendorf, J., Varusai, T. M., Watanabe, L. H., Wendland, F., Wolfien, M., Yurkovich, J. T., Zhu, Y., Zardilis, A., Zhukova, A., Schreiber, F.
Journal:
IEEE Trans Biomed Eng
Date Published:
2016-06-10
PubMed ID:
27305665
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27305665

Longitudinal micro-computed tomography monitoring of progressive liver regeneration in a mouse model of partial hepatectomy.

Authors:
Will, O. M., Damm, T., Campbell, G. M., von Schonfells, W., Acil, Y., Will, M., Chalaris-Rissmann, A., Ayna, M., Drucker, C., Gluer, C. C.
Journal:
Lab Anim
Date Published:
2016-12-08
PubMed ID:
27932685
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27932685

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Authors:
Wolstencroft, K., Krebs, O., Snoep, J. L., Stanford, N. J., Bacall, F., Golebiewski, M., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland-Reyes, S., Straszewski, J., van Niekerk, D. D., Williams, A. R., Malmstrom, L., Rinn, B., Muller, W., Goble, C.
Journal:
Nucleic Acids Res
Date Published:
2016-12-03
PubMed ID:
27899646
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27899646

Functional properties of hepatocytes in vitro are correlated with cell polarity maintenance.

Authors:
Zeigerer, A., Wuttke, A., Marsico, G., Seifert, S., Kalaidzidis, Y., Zerial, M.
Journal:
Exp Cell Res
Date Published:
2016-12-01
PubMed ID:
27916608
Link:
https://www.ncbi.nlm.nih.gov/pubmed/27916608

Cholestasis-induced adaptive remodeling of interlobular bile ducts.

Authors:
Vartak, N., Damle-Vartak, A., Richter, B., Dirsch, O., Dahmen, U., Hammad, S., Hengstler, J. G.
Journal:
Hepatology
Date Published:
2015-11-27
PubMed ID:
26610202
Link:
https://www.ncbi.nlm.nih.gov/pubmed/26610202