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List of works by Frank Bergmann

15-lipoxygenase-1 production is lost in pancreatic cancer and overexpression of the gene inhibits tumor cell growth

scientific article

A Portable Structural Analysis Library for Reaction Networks

A Profile of Today's SBML-Compatible Software

scholarly article published December 2011

A novel animal model of severe pancreatitis in mice and its differences to the rat.

scientific article published on 22 July 2008

Acinar cell carcinoma of the pancreas: is resection justified even in limited metastatic disease?

scientific article published on 27 March 2011

Anaplastic pancreatic cancer: Presentation, surgical management, and outcome

scientific article published on 9 June 2010

Antimony: a modular model definition language

scientific article

Autoimmune pancreatocholangitis, non-autoimmune pancreatitis and primary sclerosing cholangitis: a comparative morphological and immunological analysis

scientific article

Bifurcation discovery tool

scientific article published on 4 August 2005

COMBINE Archive Specification Version 1.

scientific article published on 4 September 2015

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

scientific article

CXCL14 expression and potential function in pancreatic cancer

scientific article published on 28 November 2007

Cannabinoids in pancreatic cancer: correlation with survival and pain

scientific article

Cannabinoids reduce markers of inflammation and fibrosis in pancreatic stellate cells

scientific article

Clinical significance and regulation of the costimulatory molecule B7-H1 in pancreatic cancer

scientific article

Clinicopathologic characteristics of patients with resected multifocal intraductal papillary mucinous neoplasm of the pancreas

scientific article

Comparing simulation results of SBML capable simulators

scientific article published on 25 June 2008

Computational Tools for Modeling Protein Networks

Enucleation: A treatment alternative for branch duct intraductal papillary mucinous neoplasms

scientific article published on 21 November 2016

EnzymeML: seamless data flow and modeling of enzymatic data

scientific article published on 9 February 2023

Identification of a tumor-reactive T-cell repertoire in the immune infiltrate of patients with resectable pancreatic ductal adenocarcinoma

scientific article

Large-cell neuroendocrine carcinoma of the major duodenal papilla: case report

scientific article published on 01 November 2004

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Main-duct Intraductal Papillary Mucinous Neoplasm: High Cancer Risk in Duct Diameter of 5 to 9 mm

scientific article published on November 2015

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

article by Dagmar Waltemath et al published 15 March 2014 in Standards in genomic sciences

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metastasis of rectal adenocarcinoma to the pancreas. Two case reports and a review of the literature

scientific article published on 10 March 2007

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Mononuclear cells modulate the activity of pancreatic stellate cells which in turn promote fibrosis and inflammation in chronic pancreatitis

scientific article

Most Pancreatic Cancer Resections are R1 Resections

Neural fractalkine expression is closely linked to pain and pancreatic neuritis in human chronic pancreatitis

scientific article published on 19 January 2009

Oligoclonal T-cell populations in an inflammatory pseudotumor of the pancreas possibly related to autoimmune pancreatitis: an immunohistochemical and molecular analysis.

scientific article

Pain sensation in pancreatic diseases is not uniform: the different facets of pancreatic pain

scientific article published on July 2014

Pancreatic Cancer Surgery: The New R-status Counts

scientific article

Pancreatic cancer surgery in the new millennium: better prediction of outcome

scientific article

Pancreatic main-duct involvement in branch-duct IPMNs: an underestimated risk

scientific article published in November 2014

Pancreatic metastasis from gastric carcinoma: a case report

scientific article

Pancreatic metastasis of Merkel cell carcinoma and concomitant insulinoma: case report and literature review

scientific article

Pancreatic neuropathy and neuropathic pain--a comprehensive pathomorphological study of 546 cases

scientific article

Pancreatic neuropathy results in "neural remodeling" and altered pancreatic innervation in chronic pancreatitis and pancreatic cancer.

scientific article published on 30 June 2009

Piecewise parameter estimation for stochastic models in COPASI.

scientific article published on 18 January 2016

Preoperative Serum Thymidine Kinase Activity as Novel Monitoring, Prognostic, and Predictive Biomarker in Pancreatic Cancer

scientific article published on 16 November 2017

Prognostic significance of erythropoietin in pancreatic adenocarcinoma

scientific article

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

scientific article (publication date: 2015)

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

RIP3 attenuates the pancreatic damage induced by deletion of ATG7.

scientific article

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

scientific article

SBML Level 3 Package Proposal: Annotation

SBML Level 3 Package: Flux Balance Constraints version 2

scientific article published on 09 March 2018

SBML Level 3 package: Render, Version 1, Release 1

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

scientific article published on 01 August 2020

SBML2TikZ: supporting the SBML render extension in LaTeX.

scientific article

SBW - A Modular Framework for Systems Biology

SBtab: a flexible table format for data exchange in systems biology

scientific article

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML: Nested Simulation Proposal

Selective inhibition of the p38 alternative activation pathway in infiltrating T cells inhibits pancreatic cancer progression.

scientific article

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

scientific article published on 04 September 2015

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

scientific article published on 19 March 2018

Small (Sendai negative) branch-duct IPMNs: not harmless

scientific article published in August 2012

Software Tools for Systems Biology

scholarly article published 2010

Software support for SBGN maps: SBGN-ML and LibSBGN.

scientific article

Solid type clear cell carcinoma of the pancreas: differential diagnosis of an unusual case and review of the literature

scientific article published on 24 April 2007

Standards and ontologies in computational systems biology

scientific article

Supporting the SBML layout extension

scientific article published on 11 October 2006

Survival data justifies resection for pancreatic metastases

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

scientific article published on 04 August 2020

Systems biology graphical notation markup language (SBGNML) version 0.3.

scientific article published on 22 June 2020

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

scientific article published on 04 September 2015

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core

scientific article published on 04 September 2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

scientific article

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

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

scientific article published on 20 June 2019

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

scientific article published on 9 March 2018

The bile acid receptor FXR attenuates acinar cell autophagy in chronic pancreatitis

scientific article

The impact of MFG-E8 in chronic pancreatitis: potential for future immunotherapy? ⬇️

scientific article published on January 16, 2013

The neurotrophic factor artemin influences the extent of neural damage and growth in chronic pancreatitis

scientific article published on 17 October 2006

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

scientific article published in March 2024

TinkerCell: modular CAD tool for synthetic biology

scientific article published on 29 October 2009

Total pancreatectomy for primary pancreatic neoplasms: renaissance of an unpopular operation

scientific article

Toward Community Standards and Software for Whole-Cell Modeling

scientific article

libSBML New conversion API

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